@article {pmid38502495, year = {2024}, author = {Maréchal, E}, title = {How Did Thylakoids Emerge in Cyanobacteria, and How Were the Primary Chloroplast and Chromatophore Acquired?.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2776}, number = {}, pages = {3-20}, pmid = {38502495}, issn = {1940-6029}, abstract = {The emergence of thylakoid membranes in cyanobacteria is a key event in the evolution of all oxygenic photosynthetic cells, from prokaryotes to eukaryotes. Recent analyses show that they could originate from a unique lipid phase transition rather than from a supposed vesicular budding mechanism. Emergence of thylakoids coincided with the great oxygenation event, more than two billion years ago. The acquisition of semi-autonomous organelles, such as the mitochondrion, the chloroplast, and, more recently, the chromatophore, is a critical step in the evolution of eukaryotes. They resulted from primary endosymbiotic events that seem to share general features, i.e., an acquisition of a bacterium/cyanobacteria likely via a phagocytic membrane, a genome reduction coinciding with an escape of genes from the organelle to the nucleus, and, finally, the appearance of an active system translocating nuclear-encoded proteins back to the organelles. An intense mobilization of foreign genes of bacterial origin, via horizontal gene transfers, plays a critical role. Some third partners, like Chlamydia, might have facilitated the transition from cyanobacteria to the early chloroplast. This chapter further details our current understanding of primary endosymbiosis, focusing on primary chloroplasts, thought to have appeared over a billion years ago, and the chromatophore, which appeared around a hundred years ago.}, } @article {pmid38498818, year = {2024}, author = {Bozdag, GO and Szeinbaum, N and Conlin, PL and Chen, K and Fos, SM and Garcia, A and Penev, PI and Schaible, GA and Trubl, G}, title = {Chapter 5: Major Biological Innovations in the History of Life on Earth.}, journal = {Astrobiology}, volume = {24}, number = {S1}, pages = {S107-S123}, doi = {10.1089/ast.2021.0119}, pmid = {38498818}, issn = {1557-8070}, abstract = {All organisms living on Earth descended from a single, common ancestral population of cells, known as LUCA-the last universal common ancestor. Since its emergence, the diversity and complexity of life have increased dramatically. This chapter focuses on four key biological innovations throughout Earth's history that had a significant impact on the expansion of phylogenetic diversity, organismal complexity, and ecospace habitation. First is the emergence of the last universal common ancestor, LUCA, which laid the foundation for all life-forms on Earth. Second is the evolution of oxygenic photosynthesis, which resulted in global geochemical and biological transformations. Third is the appearance of a new type of cell-the eukaryotic cell-which led to the origin of a new domain of life and the basis for complex multicellularity. Fourth is the multiple independent origins of multicellularity, resulting in the emergence of a new level of complex individuality. A discussion of these four key events will improve our understanding of the intertwined history of our planet and its inhabitants and better inform the extent to which we can expect life at different degrees of diversity and complexity elsewhere.}, } @article {pmid38472392, year = {2024}, author = {Tran, LT and Akıl, C and Senju, Y and Robinson, RC}, title = {The eukaryotic-like characteristics of small GTPase, roadblock and TRAPPC3 proteins from Asgard archaea.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {273}, pmid = {38472392}, issn = {2399-3642}, support = {JPMJCR19S5//MEXT | JST | Core Research for Evolutional Science and Technology (CREST)/ ; JP20H00476//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP19K23727//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP23K05718//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP23H04423//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; GBMF9743//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; GBMF9743//Simons Foundation/ ; }, abstract = {Membrane-enclosed organelles are defining features of eukaryotes in distinguishing these organisms from prokaryotes. Specification of distinct membranes is critical to assemble and maintain discrete compartments. Small GTPases and their regulators are the signaling molecules that drive membrane-modifying machineries to the desired location. These signaling molecules include Rab and Rag GTPases, roadblock and longin domain proteins, and TRAPPC3-like proteins. Here, we take a structural approach to assess the relatedness of these eukaryotic-like proteins in Asgard archaea, the closest known prokaryotic relatives to eukaryotes. We find that the Asgard archaea GTPase core domains closely resemble eukaryotic Rabs and Rags. Asgard archaea roadblock, longin and TRAPPC3 domain-containing proteins form dimers similar to those found in the eukaryotic TRAPP and Ragulator complexes. We conclude that the emergence of these protein architectures predated eukaryogenesis, however further adaptations occurred in proto-eukaryotes to allow these proteins to regulate distinct internal membranes.}, } @article {pmid38449346, year = {2024}, author = {Speijer, D}, title = {How mitochondrial cristae illuminate the important role of oxygen during eukaryogenesis.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {}, number = {}, pages = {e2300193}, doi = {10.1002/bies.202300193}, pmid = {38449346}, issn = {1521-1878}, abstract = {Inner membranes of mitochondria are extensively folded, forming cristae. The observed overall correlation between efficient eukaryotic ATP generation and the area of internal mitochondrial inner membranes both in unicellular organisms and metazoan tissues seems to explain why they evolved. However, the crucial use of molecular oxygen (O2) as final acceptor of the electron transport chain is still not sufficiently appreciated. O2 was an essential prerequisite for cristae development during early eukaryogenesis and could be the factor allowing cristae retention upon loss of mitochondrial ATP generation. Here I analyze illuminating bacterial and unicellular eukaryotic examples. I also discuss formative influences of intracellular O2 consumption on the evolution of the last eukaryotic common ancestor (LECA). These considerations bring about an explanation for the many genes coming from other organisms than the archaeon and bacterium merging at the start of eukaryogenesis.}, } @article {pmid38436469, year = {2024}, author = {van der Gulik, PTS and Hoff, WD and Speijer, D}, title = {The contours of evolution: In defence of Darwin's tree of life paradigm.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {}, number = {}, pages = {e2400012}, doi = {10.1002/bies.202400012}, pmid = {38436469}, issn = {1521-1878}, abstract = {Both the concept of a Darwinian tree of life (TOL) and the possibility of its accurate reconstruction have been much criticized. Criticisms mostly revolve around the extensive occurrence of lateral gene transfer (LGT), instances of uptake of complete organisms to become organelles (with the associated subsequent gene transfer to the nucleus), as well as the implications of more subtle aspects of the biological species concept. Here we argue that none of these criticisms are sufficient to abandon the valuable TOL concept and the biological realities it captures. Especially important is the need to conceptually distinguish between organismal trees and gene trees, which necessitates incorporating insights into widely occurring LGT into modern evolutionary theory. We demonstrate that all criticisms, while based on important new findings, do not invalidate the TOL. After considering the implications of these new insights, we find that the contours of evolution are best represented by a TOL.}, } @article {pmid38391233, year = {2024}, author = {Charles-Orszag, A and Petek-Seoane, NA and Mullins, RD}, title = {Archaeal actins and the origin of a multi-functional cytoskeleton.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {e0034823}, doi = {10.1128/jb.00348-23}, pmid = {38391233}, issn = {1098-5530}, abstract = {Actin and actin-like proteins form filamentous polymers that carry out important cellular functions in all domains of life. In this review, we sketch a map of the function and regulation of actin-like proteins across bacteria, archaea, and eukarya, marking some of the terra incognita that remain in this landscape. We focus particular attention on archaea because mapping the structure and function of cytoskeletal systems across this domain promises to help us understand the evolutionary relationship between the (mostly) mono-functional actin-like filaments found in bacteria and the multi-functional actin cytoskeletons that characterize eukaryotic cells.}, } @article {pmid38335232, year = {2024}, author = {von der Dunk, SHA and Hogeweg, P and Snel, B}, title = {Intracellular signaling in proto-eukaryotes evolves to alleviate regulatory conflicts of endosymbiosis.}, journal = {PLoS computational biology}, volume = {20}, number = {2}, pages = {e1011860}, doi = {10.1371/journal.pcbi.1011860}, pmid = {38335232}, issn = {1553-7358}, abstract = {The complex eukaryotic cell resulted from a merger between simpler prokaryotic cells, yet the role of the mitochondrial endosymbiosis with respect to other eukaryotic innovations has remained under dispute. To investigate how the regulatory challenges associated with the endosymbiotic state impacted genome and network evolution during eukaryogenesis, we study a constructive computational model where two simple cells are forced into an obligate endosymbiosis. Across multiple in silico evolutionary replicates, we observe the emergence of different mechanisms for the coordination of host and symbiont cell cycles, stabilizing the endosymbiotic relationship. In most cases, coordination is implicit, without signaling between host and symbiont. Signaling only evolves when there is leakage of regulatory products between host and symbiont. In the fittest evolutionary replicate, the host has taken full control of the symbiont cell cycle through signaling, mimicking the regulatory dominance of the nucleus over the mitochondrion that evolved during eukaryogenesis.}, } @article {pmid38307786, year = {2024}, author = {Muñoz-Gómez, SA}, title = {The energetic costs of cellular complexity in evolution.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2024.01.003}, pmid = {38307786}, issn = {1878-4380}, abstract = {The evolutionary history of cells has been marked by drastic increases in complexity. Some hypothesize that such cellular complexification requires a massive energy flux as the origin of new features is hypothetically more energetically costly than their evolutionary maintenance. However, it remains unclear how increases in cellular complexity demand more energy. I propose that the early evolution of new genes with weak functions imposes higher energetic costs by overexpression before their functions are evolutionarily refined. In the long term, the accumulation of new genes deviates resources away from growth and reproduction. Accrued cellular complexity further requires additional infrastructure for its maintenance. Altogether, this suggests that larger and more complex cells are defined by increased survival but lower reproductive capacity.}, } @article {pmid38307322, year = {2024}, author = {Biran, A and Santos, TCB and Dingjan, T and Futerman, AH}, title = {The Sphinx and the egg: Evolutionary enigmas of the (glyco)sphingolipid biosynthetic pathway.}, journal = {Biochimica et biophysica acta. Molecular and cell biology of lipids}, volume = {}, number = {}, pages = {159462}, doi = {10.1016/j.bbalip.2024.159462}, pmid = {38307322}, issn = {1879-2618}, abstract = {In eukaryotes, the de novo synthesis of sphingolipids (SLs) consists of multiple sequential steps which are compartmentalized between the endoplasmic reticulum and the Golgi apparatus. Studies over many decades have identified the enzymes in the pathway, their localization, topology and an array of regulatory mechanisms. However, little is known about the evolutionary forces that underly the generation of this complex pathway or of its anteome, i.e., the metabolic pathways that converge on the SL biosynthetic pathway and are essential for its activity. After briefly describing the pathway, we discuss the mechanisms by which the enzymes of the SL biosynthetic pathway are targeted to their different subcellular locations, how the pathway per se may have evolved, including its compartmentalization, and the relationship of the pathway to eukaryogenesis. We discuss the circular interdependence of the evolution of the SL pathway, and comment on whether current Darwinian evolutionary models are able to provide genuine mechanistic insight into how the pathway came into being.}, } @article {pmid38228651, year = {2024}, author = {Krishnan, N and Csiszár, V and Móri, TF and Garay, J}, title = {Genesis of ectosymbiotic features based on commensalistic syntrophy.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {1366}, pmid = {38228651}, issn = {2045-2322}, support = {955708//Horizon 2020/ ; 125569//NKFIH/ ; }, mesh = {Humans ; Phylogeny ; *Symbiosis ; *Eukaryota ; Mitochondria ; Biological Evolution ; }, abstract = {The symbiogenetic origin of eukaryotes with mitochondria is considered a major evolutionary transition. The initial interactions and conditions of symbiosis, along with the phylogenetic affinity of the host, are widely debated. Here, we focus on a possible evolutionary path toward an association of individuals of two species based on unidirectional syntrophy. With the backing of a theoretical model, we hypothesize that the first step in the evolution of such symbiosis could be the appearance of a linking structure on the symbiont's membrane, using which it forms an ectocommensalism with its host. We consider a commensalistic model based on the syntrophy hypothesis in the framework of coevolutionary dynamics and mutant invasion into a monomorphic resident system (evolutionary substitution). We investigate the ecological and evolutionary stability of the consortium (or symbiotic merger), with vertical transmissions playing a crucial role. The impact of the 'effectiveness of vertical transmission' on the dynamics is also analyzed. We find that the transmission of symbionts and the additional costs incurred by the mutant determine the conditions of fixation of the consortia. Additionally, we observe that small and highly metabolically active symbionts are likely to form the consortia.}, } @article {pmid38225278, year = {2024}, author = {Lu, Z and Xia, R and Zhang, S and Pan, J and Liu, Y and Wolf, YI and Koonin, EV and Li, M}, title = {Evolution of optimal growth temperature in Asgard archaea inferred from the temperature dependence of GDP binding to EF-1A.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {515}, pmid = {38225278}, issn = {2041-1723}, mesh = {*Archaea/genetics/metabolism ; Temperature ; Phylogeny ; *Eukaryota ; }, abstract = {The archaeal ancestor of eukaryotes apparently belonged to the phylum Asgardarchaeota, but the ecology and evolution of Asgard archaea are poorly understood. The optimal GDP-binding temperature of a translation elongation factor (EF-1A or EF-Tu) has been previously shown to correlate with the optimal growth temperature of diverse prokaryotes. Here, we reconstruct ancestral EF-1A sequences and experimentally measure the optimal GDP-binding temperature of EF-1A from ancient and extant Asgard archaea, to infer the evolution of optimal growth temperatures in Asgardarchaeota. Our results suggest that the Asgard ancestor of eukaryotes was a moderate thermophile, with an optimal growth temperature around 53 °C. The origin of eukaryotes appears to coincide with a transition from thermophilic to mesophilic lifestyle during the evolution of Asgard archaea.}, } @article {pmid38219525, year = {2024}, author = {Romero, H and Aguilar, PS and Graña, M and Langleib, M and Gudiño, V and Podbilewicz, B}, title = {Membrane fusion and fission during eukaryogenesis.}, journal = {Current opinion in cell biology}, volume = {86}, number = {}, pages = {102321}, doi = {10.1016/j.ceb.2023.102321}, pmid = {38219525}, issn = {1879-0410}, abstract = {All eukaryotes can be traced back to a single shared ancestral lineage that emerged from interactions between different prokaryotic cells. Current models of eukaryogenesis describe various selective forces and evolutionary mechanisms that contributed to the formation of eukaryotic cells. Central to this process were significant changes in cellular structure, resulting in the configuration of a new cell type characterized by internal membrane compartments. Additionally, eukaryogenesis results in a life cycle that relies on cell-cell fusion. We discuss the potential roles of proteins involved in remodeling cellular membranes, highlighting two critical stages in the evolution of eukaryotes: the internalization of symbiotic partners and a scenario wherein the emergence of sexual reproduction is linked to a polyploid ancestor generated by cell-cell fusion.}, } @article {pmid38179456, year = {2023}, author = {Medina-Chávez, NO and Torres-Cerda, A and Chacón, JM and Harcombe, WR and De la Torre-Zavala, S and Travisano, M}, title = {Disentangling a metabolic cross-feeding in a halophilic archaea-bacteria consortium.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1276438}, pmid = {38179456}, issn = {1664-302X}, abstract = {Microbial syntrophy, a cooperative metabolic interaction among prokaryotes, serves a critical role in shaping communities, due to the auxotrophic nature of many microorganisms. Syntrophy played a key role in the evolution of life, including the hypothesized origin of eukaryotes. In a recent exploration of the microbial mats within the exceptional and uniquely extreme Cuatro Cienegas Basin (CCB), a halophilic isolate, designated as AD140, emerged as a standout due to its distinct growth pattern. Subsequent genome sequencing revealed AD140 to be a co-culture of a halophilic archaeon from the Halorubrum genus and a marine halophilic bacterium, Marinococcus luteus, both occupying the same ecological niche. This intriguing coexistence hints at an early-stage symbiotic relationship that thrives on adaptability. By delving into their metabolic interdependence through genomic analysis, this study aims to uncover shared characteristics that enhance their symbiotic association, offering insights into the evolution of halophilic microorganisms and their remarkable adaptations to high-salinity environments.}, } @article {pmid38113835, year = {2023}, author = {Whelan, TA and Fast, NM}, title = {Exploring the highly reduced spliceosome of Pseudoloma neurophilia.}, journal = {Current biology : CB}, volume = {33}, number = {24}, pages = {R1280-R1281}, doi = {10.1016/j.cub.2023.10.034}, pmid = {38113835}, issn = {1879-0445}, mesh = {*Spliceosomes/genetics/metabolism ; Introns/genetics ; RNA Splicing ; RNA, Small Nuclear/genetics/metabolism ; *Microsporidia/genetics/metabolism ; }, abstract = {Spliceosomal introns evolved early in eukaryogenesis, originating from self-splicing group II introns that invaded the proto-eukaryotic genome[1]. Elements of these ribozymes, now called snRNAs (U1, U2, U4, U5, U6), were co-opted to excise these invasive elements. Prior to eukaryotic diversification, the spliceosome is predicted to have accumulated hundreds of proteins[2]. This early complexification has obscured our understanding of spliceosomal evolution. Reduced systems with few introns and tiny spliceosomes give insights into the plasticity of the splicing reaction and provide an opportunity to study the evolution of the spliceosome[3][,][4]. Microsporidia are intracellular parasites possessing extremely reduced genomes that have lost many, and in some instances all, introns[5]. In the purportedly intron-lacking genome of the microsporidian Pseudoloma neurophilia[6], we identified two introns that are spliced at high levels. Furthermore, with only 14 predicted proteins, the P. neurophilia spliceosome could be the smallest known. Intriguingly, the few proteins retained are divergent compared to canonical orthologs. Even the central spliceosomal protein Prp8, which originated from the proteinaceous component of group II introns, is extremely divergent. This is unusual given that Prp8 is highly conserved across eukaryotes, including other microsporidia. All five P. neurophilia snRNAs are present, and all but U2 have diverged extensively, likely resulting from the loss of interacting proteins. Despite this divergence, U1 and U2 are predicted to pair with intron sequences more extensively than previously described. The P. neurophilia spliceosome is retained to splice a mere two introns and, with few proteins and reliance on RNA-RNA interactions, could function in a manner more reminiscent of presumed ancestral splicing.}, } @article {pmid38103995, year = {2023}, author = {Yu, Y and Li, YP and Ren, K and Hao, X and Fru, EC and Rønn, R and Rivera, WL and Becker, K and Feng, R and Yang, J and Rensing, C}, title = {A brief history of metal recruitment in protozoan predation.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2023.11.008}, pmid = {38103995}, issn = {1878-4380}, abstract = {Metals and metalloids are used as weapons for predatory feeding by unicellular eukaryotes on prokaryotes. This review emphasizes the role of metal(loid) bioavailability over the course of Earth's history, coupled with eukaryogenesis and the evolution of the mitochondrion to trace the emergence and use of the metal(loid) prey-killing phagosome as a feeding strategy. Members of the genera Acanthamoeba and Dictyostelium use metals such as zinc (Zn) and copper (Cu), and possibly metalloids, to kill their bacterial prey after phagocytosis. We provide a potential timeline on when these capacities first evolved and how they correlate with perceived changes in metal(loid) bioavailability through Earth's history. The origin of phagotrophic eukaryotes must have postdated the Great Oxidation Event (GOE) in agreement with redox-dependent modification of metal(loid) bioavailability for phagotrophic poisoning. However, this predatory mechanism is predicted to have evolved much later - closer to the origin of the multicellular metazoans and the evolutionary development of the immune systems.}, } @article {pmid38060007, year = {2023}, author = {Romei, M and Carpentier, M and Chomilier, J and Lecointre, G}, title = {Origins and Functional Significance of Eukaryotic Protein Folds.}, journal = {Journal of molecular evolution}, volume = {91}, number = {6}, pages = {854-864}, pmid = {38060007}, issn = {1432-1432}, support = {IPV program of Sorbonne University, PhD grant//Sorbonne Université/ ; }, mesh = {Animals ; Phylogeny ; *Bacteria/genetics ; *Archaea/genetics ; Proteins ; Eukaryota/genetics ; Biological Evolution ; }, abstract = {Folds are the architecture and topology of a protein domain. Categories of folds are very few compared to the astronomical number of sequences. Eukaryotes have more protein folds than Archaea and Bacteria. These folds are of two types: shared with Archaea and/or Bacteria on one hand and specific to eukaryotic clades on the other hand. The first kind of folds is inherited from the first endosymbiosis and confirms the mixed origin of eukaryotes. In a dataset of 1073 folds whose presence or absence has been evidenced among 210 species equally distributed in the three super-kingdoms, we have identified 28 eukaryotic folds unambiguously inherited from Bacteria and 40 eukaryotic folds unambiguously inherited from Archaea. Compared to previous studies, the repartition of informational function is higher than expected for folds originated from Bacteria and as high as expected for folds inherited from Archaea. The second type of folds is specifically eukaryotic and associated with an increase of new folds within eukaryotes distributed in particular clades. Reconstructed ancestral states coupled with dating of each node on the tree of life provided fold appearance rates. The rate is on average twice higher within Eukaryota than within Bacteria or Archaea. The highest rates are found in the origins of eukaryotes, holozoans, metazoans, metazoans stricto sensu, and vertebrates: the roots of these clades correspond to bursts of fold evolution. We could correlate the functions of some of the fold synapomorphies within eukaryotes with significant evolutionary events. Among them, we find evidence for the rise of multicellularity, adaptive immune system, or virus folds which could be linked to an ecological shift made by tetrapods.}, } @article {pmid38046947, year = {2023}, author = {Pollard, TD and Korn, ED}, title = {Discovery of the first unconventional myosin: Acanthamoeba myosin-I.}, journal = {Frontiers in physiology}, volume = {14}, number = {}, pages = {1324623}, pmid = {38046947}, issn = {1664-042X}, abstract = {Having characterized actin from Acanthamoeba castellanii (Weihing and Korn, Biochemistry, 1971, 10, 590-600) and knowing that myosin had been isolated from the slime mold Physarum (Hatano and Tazawa, Biochim. Biophys. Acta, 1968, 154, 507-519; Adelman and Taylor, Biochemistry, 1969, 8, 4976-4988), we set out in 1969 to find myosin in Acanthamoeba. We used K-EDTA-ATPase activity to assay myosin, because it is a unique feature of muscle myosins. After slightly less than 3 years, we purified a K-EDTA ATPase that interacted with actin. Actin filaments stimulated the Mg-ATPase activity of the crude enzyme, but this was lost with further purification. Recombining fractions from the column where this activity was lost revealed a "cofactor" that allowed actin filaments to stimulate the Mg-ATPase of the purified enzyme. The small size of the heavy chain and physical properties of the purified myosin were unprecedented, so many were skeptical, assuming that our myosin was a proteolytic fragment of a larger myosin similar to muscle or Physarum myosin. Subsequently our laboratories confirmed that Acanthamoeba myosin-I is a novel unconventional myosin that interacts with membrane lipids (Adams and Pollard, Nature, 1989, 340 (6234), 565-568) and that the cofactor is a myosin heavy chain kinase (Maruta and Korn, J. Biol. Chem., 1977, 252, 8329-8332). Phylogenetic analysis (Odronitz and Kollmar, Genome Biology, 2007, 8, R196) later established that class I myosin was the first myosin to appear during the evolution of eukaryotes.}, } @article {pmid38018971, year = {2023}, author = {Baum, B and Spang, A}, title = {On the origin of the nucleus: a hypothesis.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {87}, number = {4}, pages = {e0018621}, pmid = {38018971}, issn = {1098-5557}, support = {/WT_/Wellcome Trust/United Kingdom ; 222460/WT_/Wellcome Trust/United Kingdom ; 947317/ERC_/European Research Council/International ; }, mesh = {Phylogeny ; *Eukaryotic Cells ; *Genome, Archaeal ; Archaea/genetics ; Bacteria/genetics ; Biological Evolution ; }, abstract = {SUMMARYIn this hypothesis article, we explore the origin of the eukaryotic nucleus. In doing so, we first look afresh at the nature of this defining feature of the eukaryotic cell and its core functions-emphasizing the utility of seeing the eukaryotic nucleoplasm and cytoplasm as distinct regions of a common compartment. We then discuss recent progress in understanding the evolution of the eukaryotic cell from archaeal and bacterial ancestors, focusing on phylogenetic and experimental data which have revealed that many eukaryotic machines with nuclear activities have archaeal counterparts. In addition, we review the literature describing the cell biology of representatives of the TACK and Asgardarchaeaota - the closest known living archaeal relatives of eukaryotes. Finally, bringing these strands together, we propose a model for the archaeal origin of the nucleus that explains much of the current data, including predictions that can be used to put the model to the test.}, } @article {pmid37978174, year = {2023}, author = {Mahendrarajah, TA and Moody, ERR and Schrempf, D and Szánthó, LL and Dombrowski, N and Davín, AA and Pisani, D and Donoghue, PCJ and Szöllősi, GJ and Williams, TA and Spang, A}, title = {ATP synthase evolution on a cross-braced dated tree of life.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7456}, pmid = {37978174}, issn = {2041-1723}, mesh = {Phylogeny ; *Bacteria/genetics ; *Archaea/genetics ; Mitochondria/genetics ; Adenosine Triphosphate ; Evolution, Molecular ; Eukaryota/genetics ; Biological Evolution ; }, abstract = {The timing of early cellular evolution, from the divergence of Archaea and Bacteria to the origin of eukaryotes, is poorly constrained. The ATP synthase complex is thought to have originated prior to the Last Universal Common Ancestor (LUCA) and analyses of ATP synthase genes, together with ribosomes, have played a key role in inferring and rooting the tree of life. We reconstruct the evolutionary history of ATP synthases using an expanded taxon sampling set and develop a phylogenetic cross-bracing approach, constraining equivalent speciation nodes to be contemporaneous, based on the phylogenetic imprint of endosymbioses and ancient gene duplications. This approach results in a highly resolved, dated species tree and establishes an absolute timeline for ATP synthase evolution. Our analyses show that the divergence of ATP synthase into F- and A/V-type lineages was a very early event in cellular evolution dating back to more than 4 Ga, potentially predating the diversification of Archaea and Bacteria. Our cross-braced, dated tree of life also provides insight into more recent evolutionary transitions including eukaryogenesis, showing that the eukaryotic nuclear and mitochondrial lineages diverged from their closest archaeal (2.67-2.19 Ga) and bacterial (2.58-2.12 Ga) relatives at approximately the same time, with a slightly longer nuclear stem-lineage.}, } @article {pmid37939146, year = {2023}, author = {Garcia, PS and Barras, F and Gribaldo, S}, title = {Components of iron-Sulfur cluster assembly machineries are robust phylogenetic markers to trace the origin of mitochondria and plastids.}, journal = {PLoS biology}, volume = {21}, number = {11}, pages = {e3002374}, pmid = {37939146}, issn = {1545-7885}, mesh = {Phylogeny ; *Iron-Sulfur Proteins/genetics/metabolism ; Plastids/genetics/metabolism ; Mitochondria/genetics/metabolism ; Iron/metabolism ; Sulfur/metabolism ; }, abstract = {Establishing the origin of mitochondria and plastids is key to understand 2 founding events in the origin and early evolution of eukaryotes. Recent advances in the exploration of microbial diversity and in phylogenomics approaches have indicated a deep origin of mitochondria and plastids during the diversification of Alphaproteobacteria and Cyanobacteria, respectively. Here, we strongly support these placements by analyzing the machineries for assembly of iron-sulfur ([Fe-S]) clusters, an essential function in eukaryotic cells that is carried out in mitochondria by the ISC machinery and in plastids by the SUF machinery. We assessed the taxonomic distribution of ISC and SUF in representatives of major eukaryotic supergroups and analyzed the phylogenetic relationships with their prokaryotic homologues. Concatenation datasets of core ISC proteins show an early branching of mitochondria within Alphaproteobacteria, right after the emergence of Magnetococcales. Similar analyses with the SUF machinery place primary plastids as sister to Gloeomargarita within Cyanobacteria. Our results add to the growing evidence of an early emergence of primary organelles and show that the analysis of essential machineries of endosymbiotic origin provide a robust signal to resolve ancient and fundamental steps in eukaryotic evolution.}, } @article {pmid37840457, year = {2023}, author = {Câmara, AS and Kubalová, I and Schubert, V}, title = {Helical chromonema coiling is conserved in eukaryotes.}, journal = {The Plant journal : for cell and molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/tpj.16484}, pmid = {37840457}, issn = {1365-313X}, support = {Schu 762/11-1//Deutsche Forschungsgemeinschaft/ ; SO 2132/1-1//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Efficient chromatin condensation is required to transport chromosomes during mitosis and meiosis, forming daughter cells. While it is well accepted that these processes follow fundamental rules, there has been a controversial debate for more than 140 years on whether the higher-order chromatin organization in chromosomes is evolutionarily conserved. Here, we summarize historical and recent investigations based on classical and modern methods. In particular, classical light microscopy observations based on living, fixed, and treated chromosomes covering a wide range of plant and animal species, and even in single-cell eukaryotes suggest that the chromatids of large chromosomes are formed by a coiled chromatin thread, named the chromonema. More recently, these findings were confirmed by electron and super-resolution microscopy, oligo-FISH, molecular interaction data, and polymer simulation. Altogether, we describe common and divergent features of coiled chromonemata in different species. We hypothesize that chromonema coiling in large chromosomes is a fundamental feature established early during the evolution of eukaryotes to handle increasing genome sizes.}, } @article {pmid37803921, year = {2024}, author = {Weston, EJ and Eglit, Y and Simpson, AGB}, title = {Kaonashia insperata gen. et sp. nov., a eukaryotrophic flagellate, represents a novel major lineage of heterotrophic stramenopiles.}, journal = {The Journal of eukaryotic microbiology}, volume = {71}, number = {1}, pages = {e13003}, doi = {10.1111/jeu.13003}, pmid = {37803921}, issn = {1550-7408}, support = {298366-2019//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Phylogeny ; *Stramenopiles/genetics ; DNA, Ribosomal/genetics ; *Diatoms/genetics ; Cryptophyta/genetics ; }, abstract = {Eukaryotrophic protists are ecologically significant and possess characteristics key to understanding the evolution of eukaryotes; however, they remain poorly studied, due partly to the complexities of maintaining predator-prey cultures. Kaonashia insperata, gen. nov., et sp. nov., is a free-swimming biflagellated eukaryotroph with a conspicuous ventral groove, a trait observed in distantly related lineages across eukaryote diversity. Di-eukaryotic (predator-prey) cultures of K. insperata with three marine algae (Isochrysis galbana, Guillardia theta, and Phaeodactylum tricornutum) were established by single-cell isolation. Growth trials showed that the studied K. insperata clone grew particularly well on G. theta, reaching a peak abundance of 1.0 × 10[5] ± 4.0 × 10[4] cells ml[-1] . Small-subunit ribosomal DNA phylogenies infer that K. insperata is a stramenopile with moderate support; however, it does not fall within any well-defined phylogenetic group, including environmental sequence clades (e.g. MASTs), and its specific placement remains unresolved. Electron microscopy shows traits consistent with stramenopile affinity, including mastigonemes on the anterior flagellum and tubular mitochondrial cristae. Kaonashia insperata may represent a novel major lineage within stramenopiles, and be important for understanding the evolutionary history of the group. While heterotrophic stramenopile flagellates are considered to be predominantly bacterivorous, eukaryotrophy may be relatively widespread amongst this assemblage.}, } @article {pmid37765506, year = {2023}, author = {Wegner, L and Porth, ML and Ehlers, K}, title = {Multicellularity and the Need for Communication-A Systematic Overview on (Algal) Plasmodesmata and Other Types of Symplasmic Cell Connections.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {18}, pages = {}, pmid = {37765506}, issn = {2223-7747}, support = {EH 372/1-1//Deutsche Forschungsgemeinschaft/ ; }, abstract = {In the evolution of eukaryotes, the transition from unicellular to simple multicellular organisms has happened multiple times. For the development of complex multicellularity, characterized by sophisticated body plans and division of labor between specialized cells, symplasmic intercellular communication is supposed to be indispensable. We review the diversity of symplasmic connectivity among the eukaryotes and distinguish between distinct types of non-plasmodesmatal connections, plasmodesmata-like structures, and 'canonical' plasmodesmata on the basis of developmental, structural, and functional criteria. Focusing on the occurrence of plasmodesmata (-like) structures in extant taxa of fungi, brown algae (Phaeophyceae), green algae (Chlorophyta), and streptophyte algae, we present a detailed critical update on the available literature which is adapted to the present classification of these taxa and may serve as a tool for future work. From the data, we conclude that, actually, development of complex multicellularity correlates with symplasmic connectivity in many algal taxa, but there might be alternative routes. Furthermore, we deduce a four-step process towards the evolution of canonical plasmodesmata and demonstrate similarity of plasmodesmata in streptophyte algae and land plants with respect to the occurrence of an ER component. Finally, we discuss the urgent need for functional investigations and molecular work on cell connections in algal organisms.}, } @article {pmid37727796, year = {2023}, author = {Craig, JM and Kumar, S and Hedges, SB}, title = {The origin of eukaryotes and rise in complexity were synchronous with the rise in oxygen.}, journal = {Frontiers in bioinformatics}, volume = {3}, number = {}, pages = {1233281}, pmid = {37727796}, issn = {2673-7647}, support = {R01 GM126567/GM/NIGMS NIH HHS/United States ; R35 GM139540/GM/NIGMS NIH HHS/United States ; }, abstract = {The origin of eukaryotes was among the most important events in the history of life, spawning a new evolutionary lineage that led to all complex multicellular organisms. However, the timing of this event, crucial for understanding its environmental context, has been difficult to establish. The fossil and biomarker records are sparse and molecular clocks have thus far not reached a consensus, with dates spanning 2.1-0.91 billion years ago (Ga) for critical nodes. Notably, molecular time estimates for the last common ancestor of eukaryotes are typically hundreds of millions of years younger than the Great Oxidation Event (GOE, 2.43-2.22 Ga), leading researchers to question the presumptive link between eukaryotes and oxygen. We obtained a new time estimate for the origin of eukaryotes using genetic data of both archaeal and bacterial origin, the latter rarely used in past studies. We also avoided potential calibration biases that may have affected earlier studies. We obtained a conservative interval of 2.2-1.5 Ga, with an even narrower core interval of 2.0-1.8 Ga, for the origin of eukaryotes, a period closely aligned with the rise in oxygen. We further reconstructed the history of biological complexity across the tree of life using three universal measures: cell types, genes, and genome size. We found that the rise in complexity was temporally consistent with and followed a pattern similar to the rise in oxygen. This suggests a causal relationship stemming from the increased energy needs of complex life fulfilled by oxygen.}, } @article {pmid37713454, year = {2023}, author = {Porter, SM and Riedman, LA}, title = {Frameworks for Interpreting the Early Fossil Record of Eukaryotes.}, journal = {Annual review of microbiology}, volume = {77}, number = {}, pages = {173-191}, doi = {10.1146/annurev-micro-032421-113254}, pmid = {37713454}, issn = {1545-3251}, mesh = {*Eukaryota/genetics ; *Fossils ; Eukaryotic Cells ; Paleontology ; Ecology ; }, abstract = {The origin of modern eukaryotes is one of the key transitions in life's history, and also one of the least understood. Although the fossil record provides the most direct view of this process, interpreting the fossils of early eukaryotes and eukaryote-grade organisms is not straightforward. We present two end-member models for the evolution of modern (i.e., crown) eukaryotes-one in which modern eukaryotes evolved early, and another in which they evolved late-and interpret key fossils within these frameworks, including where they might fit in eukaryote phylogeny and what they may tell us about the evolution of eukaryotic cell biology and ecology. Each model has different implications for understanding the rise of complex life on Earth, including different roles of Earth surface oxygenation, and makes different predictions that future paleontological studies can test.}, } @article {pmid37699353, year = {2023}, author = {Donoghue, PCJ and Kay, C and Spang, A and Szöllősi, G and Nenarokova, A and Moody, ERR and Pisani, D and Williams, TA}, title = {Defining eukaryotes to dissect eukaryogenesis.}, journal = {Current biology : CB}, volume = {33}, number = {17}, pages = {R919-R929}, doi = {10.1016/j.cub.2023.07.048}, pmid = {37699353}, issn = {1879-0445}, support = {BB/T012773/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Eukaryota/genetics ; Phylogeny ; *Eukaryotic Cells ; Biological Evolution ; Dissent and Disputes ; }, abstract = {The origin of eukaryotes is among the most contentious debates in evolutionary biology, attracting multiple seemingly incompatible theories seeking to explain the sequence in which eukaryotic characteristics were acquired. Much of the controversy arises from differing views on the defining characteristics of eukaryotes. We argue that eukaryotes should be defined phylogenetically, and that doing so clarifies where competing hypotheses of eukaryogenesis agree and how we may test among aspects of disagreement. Some hypotheses make predictions about the phylogenetic origins of eukaryotic genes and are distinguishable on that basis. However, other hypotheses differ only in the order of key evolutionary steps, like mitochondrial endosymbiosis and nuclear assembly, which cannot currently be distinguished phylogenetically. Stages within eukaryogenesis may be made identifiable through the absolute dating of gene duplicates that map to eukaryotic traits, such as in genes of host or mitochondrial origin that duplicated and diverged functionally prior to emergence of the last eukaryotic common ancestor. In this way, it may finally be possible to distinguish heat from light in the debate over eukaryogenesis.}, } @article {pmid37666024, year = {2023}, author = {Field, MC}, title = {Deviating from the norm: Nuclear organisation in trypanosomes.}, journal = {Current opinion in cell biology}, volume = {85}, number = {}, pages = {102234}, doi = {10.1016/j.ceb.2023.102234}, pmid = {37666024}, issn = {1879-0410}, mesh = {*Nuclear Pore Complex Proteins ; Evolution, Molecular ; Nuclear Envelope/metabolism ; Nuclear Pore/metabolism ; *Trypanosoma/metabolism ; Lamins/metabolism ; Cell Nucleus/metabolism ; Nuclear Lamina/metabolism ; }, abstract = {At first glance the nucleus is a highly conserved organelle. Overall nuclear morphology, the octagonal nuclear pore complex, the presence of peripheral heterochromatin and the nuclear envelope appear near constant features right down to the ultrastructural level. New work is revealing significant compositional divergence within these nuclear structures and their associated functions, likely reflecting adaptations and distinct mechanisms between eukaryotic lineages and especially the trypanosomatids. While many examples of mechanistic divergence currently lack obvious functional interpretations, these studies underscore the malleability of nuclear architecture. I will discuss some recent findings highlighting these facets within trypanosomes, together with the underlying evolutionary framework and make a call for the exploration of nuclear function in non-canonical experimental organisms.}, } @article {pmid37632100, year = {2023}, author = {Gaïa, M and Forterre, P}, title = {From Mimivirus to Mirusvirus: The Quest for Hidden Giants.}, journal = {Viruses}, volume = {15}, number = {8}, pages = {}, pmid = {37632100}, issn = {1999-4915}, mesh = {*Mimiviridae/genetics ; Eukaryota ; *Giant Viruses/genetics ; }, abstract = {Our perception of viruses has been drastically evolving since the inception of the field of virology over a century ago. In particular, the discovery of giant viruses from the Nucleocytoviricota phylum marked a pivotal moment. Their previously concealed diversity and abundance unearthed an unprecedented complexity in the virus world, a complexity that called for new definitions and concepts. These giant viruses underscore the intricate interactions that unfold over time between viruses and their hosts, and are themselves suspected to have played a significant role as a driving force in the evolution of eukaryotes since the dawn of this cellular domain. Whether they possess exceptional relationships with their hosts or whether they unveil the actual depths of evolutionary connections between viruses and cells otherwise hidden in smaller viruses, the attraction giant viruses exert on the scientific community and beyond continues to grow. Yet, they still hold surprises. Indeed, the recent identification of mirusviruses connects giant viruses to herpesviruses, each belonging to distinct viral realms. This discovery substantially broadens the evolutionary landscape of Nucleocytoviricota. Undoubtedly, the years to come will reveal their share of surprises.}, } @article {pmid37606230, year = {2023}, author = {Yubuki, N and Torruella, G and Galindo, LJ and Heiss, AA and Ciobanu, MC and Shiratori, T and Ishida, KI and Blaz, J and Kim, E and Moreira, D and López-García, P and Eme, L}, title = {Molecular and morphological characterization of four new ancyromonad genera and proposal for an updated taxonomy of the Ancyromonadida.}, journal = {The Journal of eukaryotic microbiology}, volume = {70}, number = {6}, pages = {e12997}, doi = {10.1111/jeu.12997}, pmid = {37606230}, issn = {1550-7408}, mesh = {Phylogeny ; Sequence Analysis, DNA ; *Eukaryota ; RNA, Ribosomal, 18S/genetics ; Microscopy, Electron ; }, abstract = {Ancyromonads are small biflagellated protists with a bean-shaped morphology. They are cosmopolitan in marine, freshwater, and soil environments, where they attach to surfaces while feeding on bacteria. These poorly known grazers stand out by their uncertain phylogenetic position in the tree of eukaryotes, forming a deep-branching "orphan" lineage that is considered key to a better understanding of the early evolution of eukaryotes. Despite their ecological and evolutionary interest, only limited knowledge exists about their true diversity. Here, we aimed to characterize ancyromonads better by integrating environmental surveys with behavioral observation and description of cell morphology, for which sample isolation and culturing are indispensable. We studied 18 ancyromonad strains, including 14 new isolates and seven new species. We described three new and genetically divergent genera: Caraotamonas, Nyramonas, and Olneymonas, together encompassing four species. The remaining three new species belong to the already-known genera Fabomonas and Ancyromonas. We also raised Striomonas, formerly a subgenus of Nutomonas, to full genus status, on morphological and phylogenetic grounds. We studied the morphology of diverse ancyromonads under light and electron microscopy and carried out molecular phylogenetic analyses, also including 18S rRNA gene sequences from several environmental surveys. Based on these analyses, we have updated the taxonomy of Ancyromonadida.}, } @article {pmid37558594, year = {2023}, author = {van Hooff, JJE}, title = {Towards unraveling the origins of eukaryotic nuclear genome organization.}, journal = {Trends in cell biology}, volume = {33}, number = {10}, pages = {820-823}, doi = {10.1016/j.tcb.2023.07.008}, pmid = {37558594}, issn = {1879-3088}, mesh = {Humans ; *Eukaryota/genetics ; *Archaea/genetics ; Phylogeny ; Eukaryotic Cells/metabolism ; Prokaryotic Cells/metabolism ; }, abstract = {With 3D genome mapping maturing over the past decade, studies exposed the differences between eukaryotic and prokaryotic genome organization. This raises the question of how the complex eukaryotic genome organization originated. Here, I explore potential pathways to answering this question, guided by our changing understanding of the origins of eukaryotes.}, } @article {pmid37553111, year = {2023}, author = {Hernández, G and Vazquez-Pianzola, P}, title = {eIF4E as a molecular wildcard in metazoans RNA metabolism.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {98}, number = {6}, pages = {2284-2306}, doi = {10.1111/brv.13005}, pmid = {37553111}, issn = {1469-185X}, mesh = {Humans ; Animals ; *Drosophila melanogaster/genetics ; *Eukaryotic Initiation Factor-4E/genetics/chemistry/metabolism ; RNA, Messenger/genetics/metabolism ; RNA/metabolism ; }, abstract = {The evolutionary origin of eukaryotes spurred the transition from prokaryotic-like translation to a more sophisticated, eukaryotic translation. During this process, successive gene duplication of a single, primordial eIF4E gene encoding the mRNA cap-binding protein eukaryotic translation initiation factor 4E (eIF4E) gave rise to a plethora of paralog genes across eukaryotes that underwent further functional diversification in RNA metabolism. The ability to take different roles is due to eIF4E promiscuity in binding many partner proteins, rendering eIF4E a highly versatile and multifunctional player that functions as a molecular wildcard. Thus, in metazoans, eIF4E paralogs are involved in various processes, including messenger RNA (mRNA) processing, export, translation, storage, and decay. Moreover, some paralogs display differential expression in tissues and developmental stages and show variable biochemical properties. In this review, we discuss recent advances shedding light on the functional diversification of eIF4E in metazoans. We emphasise humans and two phylogenetically distant species which have become paradigms for studies on development, namely the fruit fly Drosophila melanogaster and the roundworm Caenorhabditis elegans.}, } @article {pmid37511529, year = {2023}, author = {Kordiš, D and Turk, V}, title = {Origin and Early Diversification of the Papain Family of Cysteine Peptidases.}, journal = {International journal of molecular sciences}, volume = {24}, number = {14}, pages = {}, pmid = {37511529}, issn = {1422-0067}, support = {P1-0207, P1-0140, J1-2473//Slovenian Research Agency/ ; }, mesh = {*Papain/genetics/metabolism ; Cysteine/metabolism ; Evolution, Molecular ; Phylogeny ; Eukaryota/genetics ; Archaea/genetics ; *Cysteine Proteases/metabolism ; Peptide Hydrolases/metabolism ; }, abstract = {Peptidases of the papain family play a key role in protein degradation, regulated proteolysis, and the host-pathogen arms race. Although the papain family has been the subject of many studies, knowledge about its diversity, origin, and evolution in Eukaryota, Bacteria, and Archaea is limited; thus, we aimed to address these long-standing knowledge gaps. We traced the origin and expansion of the papain family with a phylogenomic analysis, using sequence data from numerous prokaryotic and eukaryotic proteomes, transcriptomes, and genomes. We identified the full complement of the papain family in all prokaryotic and eukaryotic lineages. Analysis of the papain family provided strong evidence for its early diversification in the ancestor of eukaryotes. We found that the papain family has undergone complex and dynamic evolution through numerous gene duplications, which produced eight eukaryotic ancestral paralogous C1A lineages during eukaryogenesis. Different evolutionary forces operated on C1A peptidases, including gene duplication, horizontal gene transfer, and gene loss. This study challenges the current understanding of the origin and evolution of the papain family and provides valuable insights into their early diversification. The findings of this comprehensive study provide guidelines for future structural and functional studies of the papain family.}, } @article {pmid37507225, year = {2023}, author = {Esposti, MD}, title = {Eukaryotes inherited inositol lipids from bacteria: implications for the models of eukaryogenesis.}, journal = {FEBS letters}, volume = {597}, number = {19}, pages = {2484-2496}, doi = {10.1002/1873-3468.14708}, pmid = {37507225}, issn = {1873-3468}, abstract = {The merger of two very different microbes, an anaerobic archaeon and an aerobic bacterium, led to the birth of eukaryotic cells. Current models hypothesize that an archaeon engulfed bacteria through external protrusions that then fused together forming the membrane organelles of eukaryotic cells, including mitochondria. Images of cultivated Lokiarchaea sustain this concept, first proposed in the inside-out model which assumes that the membrane traffic system of archaea drove the merging with bacterial cells through membrane expansions containing inositol lipids, considered to have evolved first in archaea. This assumption has been evaluated here in detail. The data indicate that inositol lipids first emerged in bacteria, not in archaea. The implications of this finding for the models of eukaryogenesis are discussed.}, } @article {pmid37491455, year = {2023}, author = {von der Dunk, SHA and Hogeweg, P and Snel, B}, title = {Obligate endosymbiosis enables genome expansion during eukaryogenesis.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {777}, pmid = {37491455}, issn = {2399-3642}, mesh = {Phylogeny ; *Eukaryotic Cells/metabolism ; *Symbiosis/genetics ; Biological Evolution ; Mitochondria/genetics ; }, abstract = {The endosymbiosis of an alpha-proteobacterium that gave rise to mitochondria was one of the key events in eukaryogenesis. One striking outcome of eukaryogenesis was a much more complex cell with a large genome. Despite the existence of many alternative hypotheses for this and other patterns potentially related to endosymbiosis, a constructive evolutionary model in which these hypotheses can be studied is still lacking. Here, we present a theoretical approach in which we focus on the consequences rather than the causes of mitochondrial endosymbiosis. Using a constructive evolutionary model of cell-cycle regulation, we find that genome expansion and genome size asymmetry arise from emergent host-symbiont cell-cycle coordination. We also find that holobionts with large host and small symbiont genomes perform best on long timescales and mimic the outcome of eukaryogenesis. By designing and studying a constructive evolutionary model of obligate endosymbiosis, we uncovered some of the forces that may drive the patterns observed in nature. Our results provide a theoretical foundation for patterns related to mitochondrial endosymbiosis, such as genome size asymmetry, and reveal evolutionary outcomes that have not been considered so far, such as cell-cycle coordination without direct communication.}, } @article {pmid37442362, year = {2023}, author = {Gollo, G}, title = {On the emergence of eukaryotes and other enigmas.}, journal = {Bio Systems}, volume = {231}, number = {}, pages = {104958}, doi = {10.1016/j.biosystems.2023.104958}, pmid = {37442362}, issn = {1872-8324}, mesh = {Male ; Humans ; *Eukaryota ; *Semen ; Biological Evolution ; Cell Nucleus ; Mitosis ; }, abstract = {The origin of eukaryotes is one of the most fundamental problems in the entire history of life. How did eukaryotes arise? Previous attempts to solve the problem are very far from an answer, at best they propose a solution to one of the various innovations that ended up culminating in eukaryotes. Based on a hypothetical-deductive methodology, as usual in evolutionary issues, I propose that eukaryotes emerged from the endosymbiotic association between a flagellate parasite and its host, of which the sperm is the main vestige. The hypothesis unifies the solution to the vast array of acquisitions shared by eukaryotes that differentiate them from other beings, remarkably cell nucleus, mitosis, meiosis and sexual reproduction. The solution has a deep impact on understanding the origin and functioning of all complex life forms.}, } @article {pmid37316666, year = {2023}, author = {Eme, L and Tamarit, D and Caceres, EF and Stairs, CW and De Anda, V and Schön, ME and Seitz, KW and Dombrowski, N and Lewis, WH and Homa, F and Saw, JH and Lombard, J and Nunoura, T and Li, WJ and Hua, ZS and Chen, LX and Banfield, JF and John, ES and Reysenbach, AL and Stott, MB and Schramm, A and Kjeldsen, KU and Teske, AP and Baker, BJ and Ettema, TJG}, title = {Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes.}, journal = {Nature}, volume = {618}, number = {7967}, pages = {992-999}, pmid = {37316666}, issn = {1476-4687}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Archaea/classification/cytology/genetics ; *Eukaryota/classification/cytology/genetics ; Eukaryotic Cells/classification/cytology ; *Phylogeny ; Prokaryotic Cells/classification/cytology ; Datasets as Topic ; Gene Duplication ; Evolution, Molecular ; }, abstract = {In the ongoing debates about eukaryogenesis-the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors-members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes[1]. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved[2-4]. Here we analyse distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea and as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree and species tree reconciliation approaches, we show that analogous to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared with other archaea. Finally, we infer that the last common ancestor of Asgard archaea was probably a thermophilic chemolithotroph and that the lineage from which eukaryotes evolved adapted to mesophilic conditions and acquired the genetic potential to support a heterotrophic lifestyle. Our work provides key insights into the prokaryote-to-eukaryote transition and a platform for better understanding the emergence of cellular complexity in eukaryotic cells.}, } @article {pmid37276405, year = {2023}, author = {Kumar, P and Babu, KSD and Singh, AK and Singh, DK and Nalli, A and Mukul, SJ and Roy, A and Mazeed, M and Raman, B and Kruparani, SP and Siddiqi, I and Sankaranarayanan, R}, title = {Distinct localization of chiral proofreaders resolves organellar translation conflict in plants.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {24}, pages = {e2219292120}, pmid = {37276405}, issn = {1091-6490}, mesh = {*Organelles/metabolism ; Mitochondria/metabolism ; RNA, Transfer, Amino Acyl/metabolism ; Chloroplasts/metabolism ; RNA, Transfer/metabolism ; *Arabidopsis/genetics ; }, abstract = {Plants have two endosymbiotic organelles originated from two bacterial ancestors. The transition from an independent bacterium to a successful organelle would have required extensive rewiring of biochemical networks for its integration with archaeal host. Here, using Arabidopsis as a model system, we show that plant D-aminoacyl-tRNA deacylase 1 (DTD1), of bacterial origin, is detrimental to organellar protein synthesis owing to its changed tRNA recognition code. Plants survive this conflict by spatially restricting the conflicted DTD1 to the cytosol. In addition, plants have targeted archaeal DTD2 to both the organelles as it is compatible with their translation machinery due to its strict D-chiral specificity and lack of tRNA determinants. Intriguingly, plants have confined bacterial-derived DTD1 to work in archaeal-derived cytosolic compartment whereas archaeal DTD2 is targeted to bacterial-derived organelles. Overall, the study provides a remarkable example of the criticality of optimization of biochemical networks for survival and evolution of plant mitochondria and chloroplast.}, } @article {pmid37254790, year = {2023}, author = {López-García, P and Moreira, D}, title = {The symbiotic origin of the eukaryotic cell.}, journal = {Comptes rendus biologies}, volume = {346}, number = {}, pages = {55-73}, doi = {10.5802/crbiol.118}, pmid = {37254790}, issn = {1768-3238}, mesh = {*Eukaryotic Cells ; *Symbiosis ; Phylogeny ; Archaea/genetics ; Eukaryota/genetics ; Biological Evolution ; }, abstract = {Eukaryogenesis represented a major evolutionary transition that led to the emergence of complex cells from simpler ancestors. For several decades, the most accepted scenario involved the evolution of an independent lineage of proto-eukaryotes endowed with an endomembrane system, including a nuclear compartment, a developed cytoskeleton and phagocytosis, which engulfed the alphaproteobacterial ancestor of mitochondria. However, the recent discovery by metagenomic and cultural approaches of Asgard archaea, which harbour many genes in common with eukaryotes and are their closest relatives in phylogenomic trees, rather supports scenarios based on the symbiosis of one Asgard-like archaeon and one or more bacteria at the origin of the eukaryotic cell. Here, we review the recent discoveries that led to this conceptual shift, briefly evoking current models of eukaryogenesis and the challenges ahead to discriminate between them and to establish a detailed, plausible scenario that accounts for the evolution of eukaryotic traits from those of their prokaryotic ancestors.}, } @article {pmid37236370, year = {2023}, author = {Řezanka, T and Kyselová, L and Murphy, DJ}, title = {Archaeal lipids.}, journal = {Progress in lipid research}, volume = {91}, number = {}, pages = {101237}, doi = {10.1016/j.plipres.2023.101237}, pmid = {37236370}, issn = {1873-2194}, mesh = {*Archaea/chemistry/metabolism ; *Membrane Lipids/metabolism ; Bacteria/metabolism ; Terpenes/metabolism ; Ethers/chemistry/metabolism ; }, abstract = {The major archaeal membrane glycerolipids are distinguished from those of bacteria and eukaryotes by the contrasting stereochemistry of their glycerol backbones, and by the use of ether-linked isoprenoid-based alkyl chains rather than ester-linked fatty acyl chains for their hydrophobic moieties. These fascinating compounds play important roles in the extremophile lifestyles of many species, but are also present in the growing numbers of recently discovered mesophilic archaea. The past decade has witnessed significant advances in our understanding of archaea in general and their lipids in particular. Much of the new information has come from the ability to screen large microbial populations via environmental metagenomics, which has revolutionised our understanding of the extent of archaeal biodiversity that is coupled with a strict conservation of their membrane lipid compositions. Significant additional progress has come from new culturing and analytical techniques that are gradually enabling archaeal physiology and biochemistry to be studied in real time. These studies are beginning to shed light on the much-discussed and still-controversial process of eukaryogenesis, which probably involved both bacterial and archaeal progenitors. Puzzlingly, although eukaryotes retain many attributes of their putative archaeal ancestors, their lipid compositions only reflect their bacterial progenitors. Finally, elucidation of archaeal lipids and their metabolic pathways have revealed potentially interesting applications that have opened up new frontiers for biotechnological exploitation of these organisms. This review is concerned with the analysis, structure, function, evolution and biotechnology of archaeal lipids and their associated metabolic pathways.}, } @article {pmid37127702, year = {2023}, author = {Krupovic, M and Dolja, VV and Koonin, EV}, title = {The virome of the last eukaryotic common ancestor and eukaryogenesis.}, journal = {Nature microbiology}, volume = {8}, number = {6}, pages = {1008-1017}, pmid = {37127702}, issn = {2058-5276}, mesh = {*Eukaryota ; Eukaryotic Cells ; Virome ; Phylogeny ; Archaea/genetics ; Bacteria/genetics ; *Viruses/genetics ; }, abstract = {All extant eukaryotes descend from the last eukaryotic common ancestor (LECA), which is thought to have featured complex cellular organization. To gain insight into LECA biology and eukaryogenesis-the origin of the eukaryotic cell, which remains poorly understood-we reconstructed the LECA virus repertoire. We compiled an inventory of eukaryotic hosts of all major virus taxa and reconstructed the LECA virome by inferring the origins of these groups of viruses. The origin of the LECA virome can be traced back to a small set of bacterial-not archaeal-viruses. This provenance of the LECA virome is probably due to the bacterial origin of eukaryotic membranes, which is most compatible with two endosymbiosis events in a syntrophic model of eukaryogenesis. In the first endosymbiosis, a bacterial host engulfed an Asgard archaeon, preventing archaeal viruses from entry owing to a lack of archaeal virus receptors on the external membranes.}, } @article {pmid37105243, year = {2023}, author = {Su, H and Xu, J and Li, J and Yi, Z}, title = {Four ciliate-specific expansion events occurred during actin gene family evolution of eukaryotes.}, journal = {Molecular phylogenetics and evolution}, volume = {184}, number = {}, pages = {107789}, doi = {10.1016/j.ympev.2023.107789}, pmid = {37105243}, issn = {1095-9513}, mesh = {*Actins/genetics ; Phylogeny ; Multigene Family ; Transcriptome ; *Ciliophora/genetics ; Evolution, Molecular ; }, abstract = {Actin gene family is a divergent and ancient eukaryotic cellular cytoskeletal gene family, and participates in many essential cellular processes. Ciliated protists offer us an excellent opportunity to investigate gene family evolution, since their gene families evolved faster in ciliates than in other eukaryotes. Nonetheless, actin gene family is well studied in few model ciliate species but little is known about its evolutionary patterns in ciliates. Here, we analyzed the evolutionary pattern of eukaryotic actin gene family based on genomes/transcriptomes of 36 species covering ten ciliate classes, as well as those of nine non-ciliate eukaryotic species. Results showed: (1) Except for conventional actins and actin-related proteins (Arps) shared by various eukaryotes, at least four ciliate-specific subfamilies occurred during evolution of actin gene family. Expansions of Act2 and ArpC were supposed to have happened in the ciliate common ancestor, while expansions of ActI and ActII may have occurred in the ancestor of Armophorea, Muranotrichea, and Spirotrichea. (2) The number of actin isoforms varied greatly among ciliate species. Environmental adaptability, whole genome duplication (WGD) or segmental duplication events, distinct spatial and temporal patterns of expression might play driving forces for the variation of isoform numbers. (3) The 'birth and death' model of evolution could explain the evolution of actin gene family in ciliates. And actin genes have been generally under strong negative selection to maintain protein structures and physiological functions. Collectively, we provided meaningful information for understanding the evolution of eukaryotic actin gene family.}, } @article {pmid37071674, year = {2023}, author = {Libby, E and Kempes, CP and Okie, JG}, title = {Metabolic compatibility and the rarity of prokaryote endosymbioses.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {17}, pages = {e2206527120}, pmid = {37071674}, issn = {1091-6490}, mesh = {Phylogeny ; *Symbiosis/genetics ; *Prokaryotic Cells/metabolism ; Eukaryota/genetics ; Eukaryotic Cells/metabolism ; Biological Evolution ; }, abstract = {The evolution of the mitochondria was a significant event that gave rise to the eukaryotic lineage and most large complex life. Central to the origins of the mitochondria was an endosymbiosis between prokaryotes. Yet, despite the potential benefits that can stem from a prokaryotic endosymbiosis, their modern occurrence is exceptionally rare. While many factors may contribute to their rarity, we lack methods for estimating the extent to which they constrain the appearance of a prokaryotic endosymbiosis. Here, we address this knowledge gap by examining the role of metabolic compatibility between a prokaryotic host and endosymbiont. We use genome-scale metabolic flux models from three different collections (AGORA, KBase, and CarveMe) to assess the viability, fitness, and evolvability of potential prokaryotic endosymbioses. We find that while more than half of host-endosymbiont pairings are metabolically viable, the resulting endosymbioses have reduced growth rates compared to their ancestral metabolisms and are unlikely to gain mutations to overcome these fitness differences. In spite of these challenges, we do find that they may be more robust in the face of environmental perturbations at least in comparison with the ancestral host metabolism lineages. Our results provide a critical set of null models and expectations for understanding the forces that shape the structure of prokaryotic life.}, } @article {pmid36965057, year = {2023}, author = {Speijer, D}, title = {How mitochondria showcase evolutionary mechanisms and the importance of oxygen.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {45}, number = {6}, pages = {e2300013}, doi = {10.1002/bies.202300013}, pmid = {36965057}, issn = {1521-1878}, mesh = {*Biological Evolution ; *Oxygen/metabolism ; Eukaryota/metabolism ; Bacteria/genetics/metabolism ; Mitochondria/metabolism ; }, abstract = {Darwinian evolution can be simply stated: natural selection of inherited variations increasing differential reproduction. However, formulated thus, links with biochemistry, cell biology, ecology, and population dynamics remain unclear. To understand interactive contributions of chance and selection, higher levels of biological organization (e.g., endosymbiosis), complexities of competing selection forces, and emerging biological novelties (such as eukaryotes or meiotic sex), we must analyze actual examples. Focusing on mitochondria, I will illuminate how biology makes sense of life's evolution, and the concepts involved. First, looking at the bacterium - mitochondrion transition: merging with an archaeon, it lost its independence, but played a decisive role in eukaryogenesis, as an extremely efficient aerobic ATP generator and internal ROS source. Second, surveying later mitochondrion adaptations and diversifications illustrates concepts such as constructive neutral evolution, dynamic interactions between endosymbionts and hosts, the contingency of life histories, and metabolic reprogramming. Without oxygen, mitochondria disappear; with (intermittent) oxygen diversification occurs in highly complex ways, especially upon (temporary) phototrophic substrate supply. These expositions show the Darwinian model to be a highly fruitful paradigm.}, } @article {pmid36921606, year = {2023}, author = {Muñoz-Gómez, SA and Cadena, LR and Gardiner, AT and Leger, MM and Sheikh, S and Connell, LB and Bilý, T and Kopejtka, K and Beatty, JT and Koblížek, M and Roger, AJ and Slamovits, CH and Lukeš, J and Hashimi, H}, title = {Intracytoplasmic-membrane development in alphaproteobacteria involves the homolog of the mitochondrial crista-developing protein Mic60.}, journal = {Current biology : CB}, volume = {33}, number = {6}, pages = {1099-1111.e6}, doi = {10.1016/j.cub.2023.02.059}, pmid = {36921606}, issn = {1879-0445}, mesh = {*Mitochondrial Proteins/metabolism ; *Alphaproteobacteria/genetics/metabolism ; Mitochondrial Membranes/metabolism ; Mitochondria/metabolism ; Biological Evolution ; }, abstract = {Mitochondrial cristae expand the surface area of respiratory membranes and ultimately allow for the evolutionary scaling of respiration with cell volume across eukaryotes. The discovery of Mic60 homologs among alphaproteobacteria, the closest extant relatives of mitochondria, suggested that cristae might have evolved from bacterial intracytoplasmic membranes (ICMs). Here, we investigated the predicted structure and function of alphaproteobacterial Mic60, and a protein encoded by an adjacent gene Orf52, in two distantly related purple alphaproteobacteria, Rhodobacter sphaeroides and Rhodopseudomonas palustris. In addition, we assessed the potential physical interactors of Mic60 and Orf52 in R. sphaeroides. We show that the three α helices of mitochondrial Mic60's mitofilin domain, as well as its adjacent membrane-binding amphipathic helix, are present in alphaproteobacterial Mic60. The disruption of Mic60 and Orf52 caused photoheterotrophic growth defects, which are most severe under low light conditions, and both their disruption and overexpression led to enlarged ICMs in both studied alphaproteobacteria. We also found that alphaproteobacterial Mic60 physically interacts with BamA, the homolog of Sam50, one of the main physical interactors of eukaryotic Mic60. This interaction, responsible for making contact sites at mitochondrial envelopes, has been conserved in modern alphaproteobacteria despite more than a billion years of evolutionary divergence. Our results suggest a role for Mic60 in photosynthetic ICM development and contact site formation at alphaproteobacterial envelopes. Overall, we provide support for the hypothesis that mitochondrial cristae evolved from alphaproteobacterial ICMs and have therefore improved our understanding of the nature of the mitochondrial ancestor.}, } @article {pmid36792581, year = {2023}, author = {Filée, J and Becker, HF and Mellottee, L and Eddine, RZ and Li, Z and Yin, W and Lambry, JC and Liebl, U and Myllykallio, H}, title = {Bacterial origins of thymidylate metabolism in Asgard archaea and Eukarya.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {838}, pmid = {36792581}, issn = {2041-1723}, mesh = {*Archaea/metabolism ; *Eukaryota/genetics/metabolism ; Phylogeny ; Thymidylate Synthase/genetics/metabolism ; Bacteria/genetics/metabolism ; Amino Acids/metabolism ; Folic Acid/metabolism ; DNA/metabolism ; }, abstract = {Asgard archaea include the closest known archaeal relatives of eukaryotes. Here, we investigate the evolution and function of Asgard thymidylate synthases and other folate-dependent enzymes required for the biosynthesis of DNA, RNA, amino acids and vitamins, as well as syntrophic amino acid utilization. Phylogenies of Asgard folate-dependent enzymes are consistent with their horizontal transmission from various bacterial groups. We experimentally validate the functionality of thymidylate synthase ThyX of the cultured 'Candidatus Prometheoarchaeum syntrophicum'. The enzyme efficiently uses bacterial-like folates and is inhibited by mycobacterial ThyX inhibitors, even though the majority of experimentally tested archaea are known to use carbon carriers distinct from bacterial folates. Our phylogenetic analyses suggest that the eukaryotic thymidylate synthase, required for de novo DNA synthesis, is not closely related to archaeal enzymes and might have been transferred from bacteria to protoeukaryotes during eukaryogenesis. Altogether, our study suggests that the capacity of eukaryotic cells to duplicate their genetic material is a sum of archaeal (replisome) and bacterial (thymidylate synthase) characteristics. We also propose that recent prevalent lateral gene transfer from bacteria has markedly shaped the metabolism of Asgard archaea.}, } @article {pmid36752808, year = {2023}, author = {Bremer, N and Tria, FDK and Skejo, J and Martin, WF}, title = {The Ancestral Mitotic State: Closed Orthomitosis With Intranuclear Spindles in the Syncytial Last Eukaryotic Common Ancestor.}, journal = {Genome biology and evolution}, volume = {15}, number = {3}, pages = {}, pmid = {36752808}, issn = {1759-6653}, support = {101018894/ERC_/European Research Council/International ; }, mesh = {*Eukaryota/genetics ; *Eukaryotic Cells ; Mitosis ; Cell Nucleus ; Cytosol ; }, abstract = {All eukaryotes have linear chromosomes that are distributed to daughter nuclei during mitotic division, but the ancestral state of nuclear division in the last eukaryotic common ancestor (LECA) is so far unresolved. To address this issue, we have employed ancestral state reconstructions for mitotic states that can be found across the eukaryotic tree concerning the intactness of the nuclear envelope during mitosis (open or closed), the position of spindles (intranuclear or extranuclear), and the symmetry of spindles being either axial (orthomitosis) or bilateral (pleuromitosis). The data indicate that the LECA possessed closed orthomitosis with intranuclear spindles. Our reconstruction is compatible with recent findings indicating a syncytial state of the LECA, because it decouples three main processes: chromosome division, chromosome partitioning, and cell division (cytokinesis). The possession of closed mitosis using intranuclear spindles adds to the number of cellular traits that can now be attributed to LECA, providing insights into the lifestyle of this otherwise elusive biological entity at the origin of eukaryotic cells. Closed mitosis in a syncytial eukaryotic common ancestor would buffer mutations arising at the origin of mitotic division by allowing nuclei with viable chromosome sets to complement defective nuclei via mRNA in the cytosol.}, } @article {pmid36692278, year = {2022}, author = {Forterre, P and Gaïa, M}, title = {[Viruses and the evolution of modern eukaryotic cells].}, journal = {Medecine sciences : M/S}, volume = {38}, number = {12}, pages = {990-998}, doi = {10.1051/medsci/2022164}, pmid = {36692278}, issn = {1958-5381}, mesh = {Humans ; *Eukaryotic Cells ; Phylogeny ; *Viruses/genetics ; Eukaryota/genetics ; Cell Nucleus ; Evolution, Molecular ; Biological Evolution ; }, abstract = {It is now well accepted that viruses have played an important role in the evolution of modern eukaryotes. In this review, we suggest that interactions between ancient eukaryoviruses and proto-eukaryotes also played a major role in eukaryogenesis. We discuss phylogenetic analyses that highlight the viral origin of several key proteins in the molecular biology of eukaryotes. We also discuss recent observations that, by analogy, could suggest a viral origin of the cellular nucleus. Finally, we hypothesize that mechanisms of cell differentiation in multicellular organisms might have originated from mechanisms implemented by viruses to transform infected cells into virocells.}, } @article {pmid36672768, year = {2022}, author = {Santos, FB and Del-Bem, LE}, title = {The Evolution of tRNA Copy Number and Repertoire in Cellular Life.}, journal = {Genes}, volume = {14}, number = {1}, pages = {}, pmid = {36672768}, issn = {2073-4425}, mesh = {Animals ; *Anticodon ; *DNA Copy Number Variations ; RNA, Transfer/genetics ; RNA ; Eukaryota/genetics ; Archaea/genetics ; }, abstract = {tRNAs are universal decoders that bridge the gap between transcriptome and proteome. They can also be processed into small RNA fragments with regulatory functions. In this work, we show that tRNA copy number is largely controlled by genome size in all cellular organisms, in contrast to what is observed for protein-coding genes that stop expanding between ~20,000 and ~35,000 loci per haploid genome in eukaryotes, regardless of genome size. Our analyses indicate that after the bacteria/archaea split, the tRNA gene pool experienced the evolution of increased anticodon diversity in the archaeal lineage, along with a tRNA gene size increase and mature tRNA size decrease. The evolution and diversification of eukaryotes from archaeal ancestors involved further expansion of the tRNA anticodon repertoire, additional increase in tRNA gene size and decrease in mature tRNA length, along with an explosion of the tRNA gene copy number that emerged coupled with accelerated genome size expansion. Our findings support the notion that macroscopic eukaryotes with a high diversity of cell types, such as land plants and vertebrates, independently evolved a high diversity of tRNA anticodons along with high gene redundancy caused by the expansion of the tRNA copy number. The results presented here suggest that the evolution of tRNA genes played important roles in the early split between bacteria and archaea, and in eukaryogenesis and the later emergence of complex eukaryotes, with potential implications in protein translation and gene regulation through tRNA-derived RNA fragments.}, } @article {pmid36631250, year = {2023}, author = {Vosseberg, J and Stolker, D and von der Dunk, SHA and Snel, B}, title = {Integrating Phylogenetics With Intron Positions Illuminates the Origin of the Complex Spliceosome.}, journal = {Molecular biology and evolution}, volume = {40}, number = {1}, pages = {}, pmid = {36631250}, issn = {1537-1719}, mesh = {*Spliceosomes/genetics ; Introns ; Phylogeny ; *RNA Splicing ; Eukaryota/genetics ; Evolution, Molecular ; }, abstract = {Eukaryotic genes are characterized by the presence of introns that are removed from pre-mRNA by a spliceosome. This ribonucleoprotein complex is comprised of multiple RNA molecules and over a hundred proteins, which makes it one of the most complex molecular machines that originated during the prokaryote-to-eukaryote transition. Previous works have established that these introns and the spliceosomal core originated from self-splicing introns in prokaryotes. Yet, how the spliceosomal core expanded by recruiting many additional proteins remains largely elusive. In this study, we use phylogenetic analyses to infer the evolutionary history of 145 proteins that we could trace back to the spliceosome in the last eukaryotic common ancestor. We found that an overabundance of proteins derived from ribosome-related processes was added to the prokaryote-derived core. Extensive duplications of these proteins substantially increased the complexity of the emerging spliceosome. By comparing the intron positions between spliceosomal paralogs, we infer that most spliceosomal complexity postdates the spread of introns through the proto-eukaryotic genome. The reconstruction of early spliceosomal evolution provides insight into the driving forces behind the emergence of complexes with many proteins during eukaryogenesis.}, } @article {pmid36599981, year = {2023}, author = {Otsuka, S and Tempkin, JOB and Zhang, W and Politi, AZ and Rybina, A and Hossain, MJ and Kueblbeck, M and Callegari, A and Koch, B and Morero, NR and Sali, A and Ellenberg, J}, title = {A quantitative map of nuclear pore assembly reveals two distinct mechanisms.}, journal = {Nature}, volume = {613}, number = {7944}, pages = {575-581}, pmid = {36599981}, issn = {1476-4687}, support = {P41 GM109824/GM/NIGMS NIH HHS/United States ; R01 GM083960/GM/NIGMS NIH HHS/United States ; R01 GM112108/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Interphase ; Mitosis ; *Nuclear Pore/chemistry/metabolism ; *Nuclear Pore Complex Proteins/chemistry/metabolism ; Spectrometry, Fluorescence ; }, abstract = {Understanding how the nuclear pore complex (NPC) is assembled is of fundamental importance to grasp the mechanisms behind its essential function and understand its role during the evolution of eukaryotes[1-4]. There are at least two NPC assembly pathways-one during the exit from mitosis and one during nuclear growth in interphase-but we currently lack a quantitative map of these events. Here we use fluorescence correlation spectroscopy calibrated live imaging of endogenously fluorescently tagged nucleoporins to map the changes in the composition and stoichiometry of seven major modules of the human NPC during its assembly in single dividing cells. This systematic quantitative map reveals that the two assembly pathways have distinct molecular mechanisms, in which the order of addition of two large structural components, the central ring complex and nuclear filaments are inverted. The dynamic stoichiometry data was integrated to create a spatiotemporal model of the NPC assembly pathway and predict the structures of postmitotic NPC assembly intermediates.}, } @article {pmid36569058, year = {2022}, author = {Li, R and Song, X and Gao, S and Peng, S}, title = {Analysis on the interactions between the first introns and other introns in mitochondrial ribosomal protein genes.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1091698}, pmid = {36569058}, issn = {1664-302X}, abstract = {It is realized that the first intron plays a key role in regulating gene expression, and the interactions between the first introns and other introns must be related to the regulation of gene expression. In this paper, the sequences of mitochondrial ribosomal protein genes were selected as the samples, based on the Smith-Waterman method, the optimal matched segments between the first intron and the reverse complementary sequences of other introns of each gene were obtained, and the characteristics of the optimal matched segments were analyzed. The results showed that the lengths and the ranges of length distributions of the optimal matched segments are increased along with the evolution of eukaryotes. For the distributions of the optimal matched segments with different GC contents, the peak values are decreased along with the evolution of eukaryotes, but the corresponding GC content of the peak values are increased along with the evolution of eukaryotes, it means most introns of higher organisms interact with each other though weak bonds binding. By comparing the lengths and matching rates of optimal matched segments with those of siRNA and miRNA, it is found that some optimal matched segments may be related to non-coding RNA with special biological functions, just like siRNA and miRNA, they may play an important role in the process of gene expression and regulation. For the relative position of the optimal matched segments, the peaks of relative position distributions of optimal matched segments are increased during the evolution of eukaryotes, and the positions of the first two peaks exhibit significant conservatism.}, } @article {pmid36562617, year = {2023}, author = {Spang, A}, title = {Is an archaeon the ancestor of eukaryotes?.}, journal = {Environmental microbiology}, volume = {25}, number = {4}, pages = {775-779}, doi = {10.1111/1462-2920.16323}, pmid = {36562617}, issn = {1462-2920}, mesh = {*Archaea/genetics ; *Eukaryota/genetics ; Phylogeny ; Biological Evolution ; Eukaryotic Cells ; }, abstract = {The origin of complex cellular life is a key puzzle in evolutionary research, which has broad implications for various neighbouring scientific disciplines. Naturally, views on this topic vary widely depending on the world view and context from which this topic is approached. In the following, I will share my perspective about our current scientific knowledge on the origin of eukaryotic cells, that is, eukaryogenesis, from a biological point of view focusing on the question as to whether an archaeon was the ancestor of eukaryotes.}, } @article {pmid36533149, year = {2022}, author = {Guglielmini, J and Gaia, M and Da Cunha, V and Criscuolo, A and Krupovic, M and Forterre, P}, title = {Viral origin of eukaryotic type IIA DNA topoisomerases.}, journal = {Virus evolution}, volume = {8}, number = {2}, pages = {veac097}, pmid = {36533149}, issn = {2057-1577}, abstract = {Type II DNA topoisomerases of the family A (Topo IIAs) are present in all Bacteria (DNA gyrase) and eukaryotes. In eukaryotes, they play a major role in transcription, DNA replication, chromosome segregation, and modulation of chromosome architecture. The origin of eukaryotic Topo IIA remains mysterious since they are very divergent from their bacterial homologs and have no orthologs in Archaea. Interestingly, eukaryotic Topo IIAs have close homologs in viruses of the phylum Nucleocytoviricota, an expansive assemblage of large and giant viruses formerly known as the nucleocytoplasmic large DNA viruses. Topo IIAs are also encoded by some bacterioviruses of the class Caudoviricetes (tailed bacteriophages). To elucidate the origin of the eukaryotic Topo IIA, we performed in-depth phylogenetic analyses on a dataset combining viral and cellular Topo IIA homologs. Topo IIAs encoded by Bacteria and eukaryotes form two monophyletic groups nested within Topo IIA encoded by Caudoviricetes and Nucleocytoviricota, respectively. Importantly, Nucleocytoviricota remained well separated from eukaryotes after removing both Bacteria and Caudoviricetes from the data set, indicating that the separation of Nucleocytoviricota and eukaryotes is probably not due to long-branch attraction artifact. The topologies of our trees suggest that the eukaryotic Topo IIA was probably acquired from an ancestral member of the Nucleocytoviricota of the class Megaviricetes, before the emergence of the last eukaryotic common ancestor (LECA). This result further highlights a key role of these viruses in eukaryogenesis and suggests that early proto-eukaryotes used a Topo IIB instead of a Topo IIA for solving their DNA topological problems.}, } @article {pmid36472116, year = {2022}, author = {Cahill, MA}, title = {Quo vadis PGRMC? Grand-Scale Biology in Human Health and Disease.}, journal = {Frontiers in bioscience (Landmark edition)}, volume = {27}, number = {11}, pages = {318}, doi = {10.31083/j.fbl2711318}, pmid = {36472116}, issn = {2768-6698}, mesh = {Animals ; Humans ; *Receptors, Progesterone/genetics/metabolism ; *Eukaryota ; Biology ; Mammals/metabolism ; Membrane Proteins/genetics ; }, abstract = {The title usage of Latin Quo vadis 'where are you going' extends the question Unde venisti from where 'did you come?' posed in the accompanying paper and extends consideration of how ancient eukaryotic and eumetazoan functions of progesterone receptor membrane component (PGRMC) proteins (PGRMC1 and PGRMC2 in mammals) could influence modern human health and disease. This paper attempts to extrapolate to modern biology in terms of extensions of hypothetical ancestral functional states from early eukaryotes and the last eumetazoan common ancestor (LEUMCA), to relativize human metabolic physiology and disease. As novel cell types and functional specializations appeared in bilaterian animals, PGRMC functions are hypothesized to have continued to be part of the toolkit used to develop new cell types and manage increasingly complex tasks such as nerve-gut-microbiome neuronal and hormonal communication. A critical role of PGRMC (as one component of a new eumetazoan genetic machinery) is proposed in LEUMCA endocrinology, neurogenesis, and nerve-gut communication with possible involvement in circadian nicotinamide adenine dinucleotide synthesis. This model would explain the contribution of PGRMC to metabolic and differentiation/behavioral changes observed in age-related diseases like diabetes, cancer and perhaps aging itself. Consistent with proposed key regulation of neurogenesis in the LEUMCA, it is argued that Alzheimer's disease is the modern pathology that most closely reflects the suite of functions related to PGRMC biology, with the 'usual suspect' pathologies possibly being downstream of PGRMC1. Hopefully, these thoughts help to signpost directions for future research.}, } @article {pmid36472108, year = {2022}, author = {Cahill, MA}, title = {Unde venisti PGRMC? Grand-Scale Biology from Early Eukaryotes and Eumetazoan Animal Origins.}, journal = {Frontiers in bioscience (Landmark edition)}, volume = {27}, number = {11}, pages = {317}, doi = {10.31083/j.fbl2711317}, pmid = {36472108}, issn = {2768-6698}, mesh = {Animals ; Humans ; *Eukaryota ; *Proteomics ; Epigenesis, Genetic ; Receptors, Progesterone/metabolism ; Glycolysis ; Heme/metabolism ; Mammals/metabolism ; Membrane Proteins/genetics/metabolism ; }, abstract = {The title usage of Unde venisti 'from where have you come' is from a now dead language (Latin) that foundationally influenced modern English (not the major influence, but an essential formative one). This is an apt analogy for how both the ancient eukaryotic and eumetazoan functions of PGRMC proteins (PGRMC1 and PGRMC2 in mammals) probably influence modern human biology: via a formative trajectory from an evolutionarily foundational fulcrum. There is an arguable probability, although not a certainty, that PGRMC-like proteins were involved in eukaryogenesis. If so, then the proto-eukaryotic ancestral protein is modelled as having initiated the oxygen-induced and CYP450 (Cytochrome P450)-mediated synthesis of sterols in the endoplasmic reticulum to regulate proto-mitochondrial activity and heme homeostasis, as well as having enabled sterol transport between endoplasmic reticulum (ER) and mitochondria membranes involving the actin cytoskeleton, transport of heme from mitochondria, and possibly the regulation/origins of mitosis/meiosis. Later, during animal evolution, the last eumetazoan common ancestor (LEUMCA) acquired PGRMC phosphorylated tyrosines coincidentally with the gastrulation organizer, Netrin/deleted in colorectal carcinoma (DCC) signaling, muscle fibers, synapsed neurons, and neural recovery via a sleep-like process. Modern PGRMC proteins regulate multiple functions, including CYP450-mediated steroidogenesis, membrane trafficking, heme homeostasis, glycolysis/Warburg effect, fatty acid metabolism, mitochondrial regulation, and genomic CpG epigenetic regulation of gene expression. The latter imposes the system of differentiation status-sensitive cell-type specific proteomic complements in multi-tissued descendants of the LEUMCA. This paper attempts to trace PGRMC functions through time, proposing that key functions were involved in early eukaryotes, and were later added upon in the LEUMCA. An accompanying paper considers the implications of this awareness for human health and disease.}, } @article {pmid36461738, year = {2023}, author = {Ponlachantra, K and Suginta, W and Robinson, RC and Kitaoku, Y}, title = {AlphaFold2: A versatile tool to predict the appearance of functional adaptations in evolution: Profilin interactions in uncultured Asgard archaea: Profilin interactions in uncultured Asgard archaea.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {45}, number = {2}, pages = {e2200119}, doi = {10.1002/bies.202200119}, pmid = {36461738}, issn = {1521-1878}, support = {JPMJCR19S5//JST CREST/ ; //Moore-Simons Project/ ; GBMF9743//Origin of the Eukaryotic Cell/ ; //Vidyasirimedhi Institute of Science and Technology (VISTEC)/ ; }, mesh = {*Archaea/metabolism ; *Profilins/genetics/metabolism ; Actins ; Phylogeny ; Furylfuramide/metabolism ; Eukaryota/metabolism ; }, abstract = {The release of AlphaFold2 (AF2), a deep-learning-aided, open-source protein structure prediction program, from DeepMind, opened a new era of molecular biology. The astonishing improvement in the accuracy of the structure predictions provides the opportunity to characterize protein systems from uncultured Asgard archaea, key organisms in evolutionary biology. Despite the accumulation in metagenomics-derived Asgard archaea eukaryotic-like protein sequences, limited structural and biochemical information have restricted the insight in their potential functions. In this review, we focus on profilin, an actin-dynamics regulating protein, which in eukaryotes, modulates actin polymerization through (1) direct actin interaction, (2) polyproline binding, and (3) phospholipid binding. We assess AF2-predicted profilin structures in their potential abilities to participate in these activities. We demonstrate that AF2 is a powerful new tool for understanding the emergence of biological functional traits in evolution.}, } @article {pmid36399624, year = {2022}, author = {Field, MC and Rout, MP}, title = {Coatomer in the universe of cellular complexity.}, journal = {Molecular biology of the cell}, volume = {33}, number = {14}, pages = {}, pmid = {36399624}, issn = {1939-4586}, support = {P41 GM109824/GM/NIGMS NIH HHS/United States ; R01 CA228351/CA/NCI NIH HHS/United States ; R01 GM112108/GM/NIGMS NIH HHS/United States ; 204697/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Eukaryotic Cells/metabolism ; *Eukaryota/genetics ; Biological Evolution ; COP-Coated Vesicles ; Endosomal Sorting Complexes Required for Transport/metabolism ; }, abstract = {Eukaryotic cells possess considerable internal complexity, differentiating them from prokaryotes. Eukaryogenesis, an evolutionary transitional period culminating in the last eukaryotic common ancestor (LECA), marked the origin of the eukaryotic endomembrane system. LECA is reconstructed as possessing intracellular complexity akin to modern eukaryotes. Construction of endomembrane compartments involved three key gene families: coatomer, BAR-domain proteins, and ESCRT. Each has a distinct evolutionary origin, but of these coatomer and BAR proteins are eukaryote specific, while ESCRT has more ancient origins. We discuss the structural motifs defining these three membrane-coating complexes and suggest that compared with BAR and ESCRT, the coatomer architecture had a unique ability to be readily and considerably modified, unlocking functional diversity and enabling the development of the eukaryotic cell.}, } @article {pmid36373631, year = {2023}, author = {Mencía, M}, title = {Acid digestion and symbiont: Proton sharing at the origin of mitochondriogenesis?: Proton production by a symbiotic bacterium may have been the origin of two hallmark eukaryotic features, acid digestion and mitochondria: Proton production by a symbiotic bacterium may have been the origin of two hallmark eukaryotic features, acid digestion and mitochondria.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {45}, number = {1}, pages = {e2200136}, doi = {10.1002/bies.202200136}, pmid = {36373631}, issn = {1521-1878}, mesh = {*Protons ; Phylogeny ; *Eukaryota ; Symbiosis ; Bacteria ; Mitochondria ; Digestion ; Biological Evolution ; }, abstract = {The initial relationships between organisms leading to endosymbiosis and the first eukaryote are currently a topic of hot debate. Here, I present a theory that offers a gradual scenario in which the origins of phagocytosis and mitochondria are intertwined in such a way that the evolution of one would not be possible without the other. In this scenario, the premitochondrial bacterial symbiont became initially associated with a protophagocytic host on the basis of cooperation to kill prey with symbiont-produced toxins and reactive oxygen species (ROS). Subsequently, the cooperation was focused on the digestion stage, through the acidification of the protophagocytic cavities via exportation of protons produced by the aerobic respiration of the symbiont. The host gained an improved phagocytic capacity and the symbiont received organic compounds from prey. As the host gradually lost its membrane energetics to develop lysosomal digestion, respiration was centralized in the premitochondrial symbiont for energy production for the consortium.}, } @article {pmid36366773, year = {2023}, author = {van der Gulik, PTS and Hoff, WD and Speijer, D}, title = {Renewing Linnaean taxonomy: a proposal to restructure the highest levels of the Natural System.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {98}, number = {2}, pages = {584-602}, doi = {10.1111/brv.12920}, pmid = {36366773}, issn = {1469-185X}, mesh = {*Eukaryota ; *Biodiversity ; Phylogeny ; }, abstract = {During the last century enormous progress has been made in the understanding of biological diversity, involving a dramatic shift from macroscopic to microscopic organisms. The question now arises as to whether the Natural System introduced by Carl Linnaeus, which has served as the central system for organizing biological diversity, can accommodate the great expansion of diversity that has been discovered. Important discoveries regarding biological diversity have not been fully integrated into a formal, coherent taxonomic system. In addition, because of taxonomic challenges and conflicts, various proposals have been made to abandon key aspects of the Linnaean system. We review the current status of taxonomy of the living world, focussing on groups at the taxonomic level of phylum and above. We summarize the main arguments against and in favour of abandoning aspects of the Linnaean system. Based on these considerations, we conclude that retaining the Linnaean Natural System provides important advantages. We propose a relatively small number of amendments for extending this system, particularly to include the named rank of world (Latin alternative mundis) formally to include non-cellular entities (viruses), and the named rank of empire (Latin alternative imperium) to accommodate the depth of diversity in (unicellular) eukaryotes that has been uncovered. We argue that in the case of both the eukaryotic domain and the viruses the cladistic approach intrinsically fails. However, the resulting semi-cladistic system provides a productive way forward that can help resolve taxonomic challenges. The amendments proposed allow us to: (i) retain named taxonomic levels and the three-domain system, (ii) improve understanding of the main eukaryotic lineages, and (iii) incorporate viruses into the Natural System. Of note, the proposal described herein is intended to serve as the starting point for a broad scientific discussion regarding the modernization of the Linnaean system.}, } @article {pmid36355038, year = {2022}, author = {Raval, PK and Garg, SG and Gould, SB}, title = {Endosymbiotic selective pressure at the origin of eukaryotic cell biology.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {36355038}, issn = {2050-084X}, mesh = {*Eukaryotic Cells/physiology ; *Symbiosis/genetics ; Biological Evolution ; Eukaryota/genetics ; Archaea/genetics ; Cell Nucleus ; Meiosis ; Biology ; Phylogeny ; }, abstract = {The dichotomy that separates prokaryotic from eukaryotic cells runs deep. The transition from pro- to eukaryote evolution is poorly understood due to a lack of reliable intermediate forms and definitions regarding the nature of the first host that could no longer be considered a prokaryote, the first eukaryotic common ancestor, FECA. The last eukaryotic common ancestor, LECA, was a complex cell that united all traits characterising eukaryotic biology including a mitochondrion. The role of the endosymbiotic organelle in this radical transition towards complex life forms is, however, sometimes questioned. In particular the discovery of the asgard archaea has stimulated discussions regarding the pre-endosymbiotic complexity of FECA. Here we review differences and similarities among models that view eukaryotic traits as isolated coincidental events in asgard archaeal evolution or, on the contrary, as a result of and in response to endosymbiosis. Inspecting eukaryotic traits from the perspective of the endosymbiont uncovers that eukaryotic cell biology can be explained as having evolved as a solution to housing a semi-autonomous organelle and why the addition of another endosymbiont, the plastid, added no extra compartments. Mitochondria provided the selective pressures for the origin (and continued maintenance) of eukaryotic cell complexity. Moreover, they also provided the energetic benefit throughout eukaryogenesis for evolving thousands of gene families unique to eukaryotes. Hence, a synthesis of the current data lets us conclude that traits such as the Golgi apparatus, the nucleus, autophagosomes, and meiosis and sex evolved as a response to the selective pressures an endosymbiont imposes.}, } @article {pmid36313567, year = {2022}, author = {Cellier, MFM}, title = {Nramp: Deprive and conquer?.}, journal = {Frontiers in cell and developmental biology}, volume = {10}, number = {}, pages = {988866}, pmid = {36313567}, issn = {2296-634X}, abstract = {Solute carriers 11 (Slc11) evolved from bacterial permease (MntH) to eukaryotic antibacterial defense (Nramp) while continuously mediating proton (H[+])-dependent manganese (Mn[2+]) import. Also, Nramp horizontal gene transfer (HGT) toward bacteria led to mntH polyphyly. Prior demonstration that evolutionary rate-shifts distinguishing Slc11 from outgroup carriers dictate catalytic specificity suggested that resolving Slc11 family tree may provide a function-aware phylogenetic framework. Hence, MntH C (MC) subgroups resulted from HGTs of prototype Nramp (pNs) parologs while archetype Nramp (aNs) correlated with phagocytosis. PHI-Blast based taxonomic profiling confirmed MntH B phylogroup is confined to anaerobic bacteria vs. MntH A (MA)'s broad distribution; suggested niche-related spread of MC subgroups; established that MA-variant MH, which carries 'eukaryotic signature' marks, predominates in archaea. Slc11 phylogeny shows MH is sister to Nramp. Site-specific analysis of Slc11 charge network known to interact with the protonmotive force demonstrates sequential rate-shifts that recapitulate Slc11 evolution. 3D mapping of similarly coevolved sites across Slc11 hydrophobic core revealed successive targeting of discrete areas. The data imply that pN HGT could advantage recipient bacteria for H[+]-dependent Mn[2+] acquisition and Alphafold 3D models suggest conformational divergence among MC subgroups. It is proposed that Slc11 originated as a bacterial stress resistance function allowing Mn[2+]-dependent persistence in conditions adverse for growth, and that archaeal MH could contribute to eukaryogenesis as a Mn[2+] sequestering defense perhaps favoring intracellular growth-competent bacteria.}, } @article {pmid36221007, year = {2023}, author = {Nachmias, D and Melnikov, N and Zorea, A and Sharon, M and Yemini, R and De-Picchoto, Y and Tsirkas, I and Aharoni, A and Frohn, B and Schwille, P and Zarivach, R and Mizrahi, I and Elia, N}, title = {Asgard ESCRT-III and VPS4 reveal conserved chromatin binding properties of the ESCRT machinery.}, journal = {The ISME journal}, volume = {17}, number = {1}, pages = {117-129}, pmid = {36221007}, issn = {1751-7370}, mesh = {Animals ; Humans ; *Endosomal Sorting Complexes Required for Transport/genetics/chemistry/metabolism ; Saccharomyces cerevisiae/metabolism ; Archaea/genetics ; Chromatin/genetics/metabolism ; Mammals ; Adenosine Triphosphatases/genetics/metabolism ; *Saccharomyces cerevisiae Proteins/chemistry/genetics/metabolism ; }, abstract = {The archaeal Asgard superphylum currently stands as the most promising prokaryotic candidate, from which eukaryotic cells emerged. This unique superphylum encodes for eukaryotic signature proteins (ESP) that could shed light on the origin of eukaryotes, but the properties and function of these proteins is largely unresolved. Here, we set to understand the function of an Asgard archaeal protein family, namely the ESCRT machinery, that is conserved across all domains of life and executes basic cellular eukaryotic functions, including membrane constriction during cell division. We find that ESCRT proteins encoded in Loki archaea, express in mammalian and yeast cells, and that the Loki ESCRT-III protein, CHMP4-7, resides in the eukaryotic nucleus in both organisms. Moreover, Loki ESCRT-III proteins associated with chromatin, recruited their AAA-ATPase VPS4 counterpart to organize in discrete foci in the mammalian nucleus, and directly bind DNA. The human ESCRT-III protein, CHMP1B, exhibited similar nuclear properties and recruited both human and Asgard VPS4s to nuclear foci, indicating interspecies interactions. Mutation analysis revealed a role for the N terminal region of ESCRT-III in mediating these phenotypes in both human and Asgard ESCRTs. These findings suggest that ESCRT proteins hold chromatin binding properties that were highly preserved through the billion years of evolution separating Asgard archaea and humans. The conserved chromatin binding properties of the ESCRT membrane remodeling machinery, reported here, may have important implications for the origin of eukaryogenesis.}, } @article {pmid36218394, year = {2022}, author = {Chen, D and Zhang, T and Chen, Y and Ma, H and Qi, J}, title = {Tree2GD: a phylogenomic method to detect large-scale gene duplication events.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {23}, pages = {5317-5321}, doi = {10.1093/bioinformatics/btac669}, pmid = {36218394}, issn = {1367-4811}, support = {32070247//National Natural Science Foundation of China/ ; 2019M661344//China Postdoctoral Science Foundation/ ; //State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering in Fudan University/ ; }, mesh = {Animals ; *Gene Duplication ; Phylogeny ; Synteny ; *Eukaryota ; Sequence Alignment ; }, abstract = {MOTIVATION: Whole-genome duplication events have long been discovered throughout the evolution of eukaryotes, contributing to genome complexity and biodiversity and leaving traces in the descending organisms. Therefore, an accurate and rapid phylogenomic method is needed to identify the retained duplicated genes on various lineages across the target taxonomy.

RESULTS: Here, we present Tree2GD, an integrated method to identify large-scale gene duplication events by automatically perform multiple procedures, including sequence alignment, recognition of homolog, gene tree/species tree reconciliation, Ks distribution of gene duplicates and synteny analyses. Application of Tree2GD on 2 datasets, 12 metazoan genomes and 68 angiosperms, successfully identifies all reported whole-genome duplication events exhibited by these species, showing effectiveness and efficiency of Tree2GD on phylogenomic analyses of large-scale gene duplications.

Tree2GD is written in Python and C++ and is available at https://github.com/Dee-chen/Tree2gd.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36218381, year = {2022}, author = {Silva, VSD and Machado, CR}, title = {Sex in protists: A new perspective on the reproduction mechanisms of trypanosomatids.}, journal = {Genetics and molecular biology}, volume = {45}, number = {3}, pages = {e20220065}, pmid = {36218381}, issn = {1415-4757}, abstract = {The Protist kingdom individuals are the most ancestral representatives of eukaryotes. They have inhabited Earth since ancient times and are currently found in the most diverse environments presenting a great heterogeneity of life forms. The unicellular and multicellular algae, photosynthetic and heterotrophic organisms, as well as free-living and pathogenic protozoa represents the protist group. The evolution of sex is directly associated with the origin of eukaryotes being protists the earliest protagonists of sexual reproduction on earth. In eukaryotes, the recombination through genetic exchange is a ubiquitous mechanism that can be stimulated by DNA damage. Scientific evidences support the hypothesis that reactive oxygen species (ROS) induced DNA damage can promote sexual recombination in eukaryotes which might have been a decisive factor for the origin of sex. The fact that some recombination enzymes also participate in meiotic sex in modern eukaryotes reinforces the idea that sexual reproduction emerged as consequence of specific mechanisms to cope with mutations and alterations in genetic material. In this review we will discuss about origin of sex and different strategies of evolve sexual reproduction in some protists such that cause human diseases like malaria, toxoplasmosis, sleeping sickness, Chagas disease, and leishmaniasis.}, } @article {pmid36208292, year = {2022}, author = {Abrahim, M and Machado, E and Alvarez-Valín, F and de Miranda, AB and Catanho, M}, title = {Uncovering Pseudogenes and Intergenic Protein-coding Sequences in TriTryps' Genomes.}, journal = {Genome biology and evolution}, volume = {14}, number = {10}, pages = {}, pmid = {36208292}, issn = {1759-6653}, mesh = {Animals ; Pseudogenes ; Phylogeny ; Open Reading Frames ; Genome ; *Trypanosoma brucei brucei/genetics ; *Parasites/genetics ; }, abstract = {Trypanosomatids belong to a remarkable group of unicellular, parasitic organisms of the order Kinetoplastida, an early diverging branch of the phylogenetic tree of eukaryotes, exhibiting intriguing biological characteristics affecting gene expression (intronless polycistronic transcription, trans-splicing, and RNA editing), metabolism, surface molecules, and organelles (compartmentalization of glycolysis, variation of the surface molecules, and unique mitochondrial DNA), cell biology and life cycle (phagocytic vacuoles evasion and intricate patterns of cell morphogenesis). With numerous genomic-scale data of several trypanosomatids becoming available since 2005 (genomes, transcriptomes, and proteomes), the scientific community can further investigate the mechanisms underlying these unusual features and address other unexplored phenomena possibly revealing biological aspects of the early evolution of eukaryotes. One fundamental aspect comprises the processes and mechanisms involved in the acquisition and loss of genes throughout the evolutionary history of these primitive microorganisms. Here, we present a comprehensive in silico analysis of pseudogenes in three major representatives of this group: Leishmania major, Trypanosoma brucei, and Trypanosoma cruzi. Pseudogenes, DNA segments originating from altered genes that lost their original function, are genomic relics that can offer an essential record of the evolutionary history of functional genes, as well as clues about the dynamics and evolution of hosting genomes. Scanning these genomes with functional proteins as proxies to reveal intergenic regions with protein-coding features, relying on a customized threshold to distinguish statistically and biologically significant sequence similarities, and reassembling remnant sequences from their debris, we found thousands of pseudogenes and hundreds of open reading frames, with particular characteristics in each trypanosomatid: mutation profile, number, content, density, codon bias, average size, single- or multi-copy gene origin, number and type of mutations, putative primitive function, and transcriptional activity. These features suggest a common process of pseudogene formation, different patterns of pseudogene evolution and extant biological functions, and/or distinct genome organization undertaken by those parasites during evolution, as well as different evolutionary and/or selective pressures acting on distinct lineages.}, } @article {pmid36194551, year = {2022}, author = {Gäbelein, CG and Reiter, MA and Ernst, C and Giger, GH and Vorholt, JA}, title = {Engineering Endosymbiotic Growth of E. coli in Mammalian Cells.}, journal = {ACS synthetic biology}, volume = {11}, number = {10}, pages = {3388-3396}, pmid = {36194551}, issn = {2161-5063}, mesh = {Animals ; Humans ; *Symbiosis ; *Escherichia coli/genetics ; HeLa Cells ; Biological Evolution ; Bacteria ; Amino Acids, Aromatic ; Mammals ; }, abstract = {Endosymbioses are cellular mergers in which one cell lives within another cell and have led to major evolutionary transitions, most prominently to eukaryogenesis. Generation of synthetic endosymbioses aims to provide a defined starting point for studying fundamental processes in emerging endosymbiotic systems and enable the engineering of cells with novel properties. Here, we tested the potential of different bacteria for artificial endosymbiosis in mammalian cells. To this end, we adopted the fluidic force microscopy technology to inject diverse bacteria directly into the cytosol of HeLa cells and examined the endosymbiont-host interactions by real-time fluorescence microscopy. Among them, Escherichia coli grew exponentially within the cytoplasm, however, at a faster pace than its host cell. To slow down the intracellular growth of E. coli, we introduced auxotrophies in E. coli and demonstrated that the intracellular growth rate can be reduced by limiting the uptake of aromatic amino acids. In consequence, the survival of the endosymbiont-host pair was prolonged. The presented experimental framework enables studying endosymbiotic candidate systems at high temporal resolution and at the single cell level. Our work represents a starting point for engineering a stable, vertically inherited endosymbiosis.}, } @article {pmid36125740, year = {2022}, author = {Forterre, P}, title = {Archaea: A Goldmine for Molecular Biologists and Evolutionists.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2522}, number = {}, pages = {1-21}, pmid = {36125740}, issn = {1940-6029}, mesh = {*Archaea/genetics ; Bacteria/genetics ; *Biological Evolution ; Eukaryota/genetics ; Genome, Archaeal ; RNA, Ribosomal, 16S ; }, abstract = {The rebuttal of the prokaryote-eukaryote dichotomy and the elaboration of the three domains concept by Carl Woese and colleagues has been a breakthrough in biology. With the methodologies available at this time, they have shown that a single molecule, the 16S ribosomal RNA, could reveal the global organization of the living world. Later on, mining archaeal genomes led to major discoveries in archaeal molecular biology, providing a third model for comparative molecular biology. These analyses revealed the strong eukaryal flavor of the basic molecular fabric of Archaea and support rooting the universal tree between Bacteria and Arcarya (the clade grouping Archaea and Eukarya). However, in contradiction with this conclusion, it remains to understand why the archaeal and bacterial mobilomes are so similar and so different from the eukaryal one. These last years, the number of recognized archaea lineages (phyla?) has exploded. The archaeal nomenclature is now in turmoil and debates about the nature of the last universal common ancestor, the last archaeal common ancestor, and the topology of the tree of life are still going on. Interestingly, the expansion of the archaeal eukaryome, especially in the Asgard archaea, has provided new opportunities to study eukaryogenesis. In recent years, the application to Archaea of the new methodologies described in the various chapters of this book have opened exciting avenues to study the molecular biology and the physiology of these fascinating microorganisms.}, } @article {pmid36103518, year = {2022}, author = {Tricou, T and Tannier, E and de Vienne, DM}, title = {Ghost lineages can invalidate or even reverse findings regarding gene flow.}, journal = {PLoS biology}, volume = {20}, number = {9}, pages = {e3001776}, pmid = {36103518}, issn = {1545-7885}, mesh = {*Biological Evolution ; *Gene Flow ; Genome ; Phylogeny ; }, abstract = {Introgression, endosymbiosis, and gene transfer, i.e., horizontal gene flow (HGF), are primordial sources of innovation in all domains of life. Our knowledge on HGF relies on detection methods that exploit some of its signatures left on extant genomes. One of them is the effect of HGF on branch lengths of constructed phylogenies. This signature has been formalized in statistical tests for HGF detection and used for example to detect massive adaptive gene flows in malaria vectors or to order evolutionary events involved in eukaryogenesis. However, these studies rely on the assumption that ghost lineages (all unsampled extant and extinct taxa) have little influence. We demonstrate here with simulations and data reanalysis that when considering the more realistic condition that unsampled taxa are legion compared to sampled ones, the conclusion of these studies become unfounded or even reversed. This illustrates the necessity to recognize the existence of ghosts in evolutionary studies.}, } @article {pmid36045281, year = {2022}, author = {Akıl, C and Tran, LT and Orhant-Prioux, M and Baskaran, Y and Senju, Y and Takeda, S and Chotchuang, P and Muengsaen, D and Schulte, A and Manser, E and Blanchoin, L and Robinson, RC}, title = {Structural and biochemical evidence for the emergence of a calcium-regulated actin cytoskeleton prior to eukaryogenesis.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {890}, pmid = {36045281}, issn = {2399-3642}, mesh = {Actin Cytoskeleton/metabolism ; *Actins/metabolism ; Archaea/metabolism ; *Calcium/metabolism ; Gelsolin/chemistry/metabolism ; }, abstract = {Charting the emergence of eukaryotic traits is important for understanding the characteristics of organisms that contributed to eukaryogenesis. Asgard archaea and eukaryotes are the only organisms known to possess regulated actin cytoskeletons. Here, we determined that gelsolins (2DGels) from Lokiarchaeota (Loki) and Heimdallarchaeota (Heim) are capable of regulating eukaryotic actin dynamics in vitro and when expressed in eukaryotic cells. The actin filament severing and capping, and actin monomer sequestering, functionalities of 2DGels are strictly calcium controlled. We determined the X-ray structures of Heim and Loki 2DGels bound actin monomers. Each structure possesses common and distinct calcium-binding sites. Loki2DGel has an unusual WH2-like motif (LVDV) between its two gelsolin domains, in which the aspartic acid coordinates a calcium ion at the interface with actin. We conclude that the calcium-regulated actin cytoskeleton predates eukaryogenesis and emerged in the predecessors of the last common ancestor of Loki, Heim and Thorarchaeota.}, } @article {pmid36040076, year = {2022}, author = {Kontou, A and Herman, EK and Field, MC and Dacks, JB and Koumandou, VL}, title = {Evolution of factors shaping the endoplasmic reticulum.}, journal = {Traffic (Copenhagen, Denmark)}, volume = {23}, number = {9}, pages = {462-473}, pmid = {36040076}, issn = {1600-0854}, support = {204697/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Endoplasmic Reticulum/metabolism ; *Eukaryotic Cells ; Protein Transport ; }, abstract = {Endomembrane system compartments are significant elements in virtually all eukaryotic cells, supporting functions including protein synthesis, post-translational modifications and protein/lipid targeting. In terms of membrane area the endoplasmic reticulum (ER) is the largest intracellular organelle, but the origins of proteins defining the organelle and the nature of lineage-specific modifications remain poorly studied. To understand the evolution of factors mediating ER morphology and function we report a comparative genomics analysis of experimentally characterized ER-associated proteins involved in maintaining ER structure. We find that reticulons, REEPs, atlastins, Ufe1p, Use1p, Dsl1p, TBC1D20, Yip3p and VAPs are highly conserved, suggesting an origin at least as early as the last eukaryotic common ancestor (LECA), although many of these proteins possess additional non-ER functions in modern eukaryotes. Secondary losses are common in individual species and in certain lineages, for example lunapark is missing from the Stramenopiles and the Alveolata. Lineage-specific innovations include protrudin, Caspr1, Arl6IP1, p180, NogoR, kinectin and CLIMP-63, which are restricted to the Opisthokonta. Hence, much of the machinery required to build and maintain the ER predates the LECA, but alternative strategies for the maintenance and elaboration of ER shape and function are present in modern eukaryotes. Moreover, experimental investigations for ER maintenance factors in diverse eukaryotes are expected to uncover novel mechanisms.}, } @article {pmid36028415, year = {2022}, author = {Obado, SO and Rout, MP and Field, MC}, title = {Sending the message: specialized RNA export mechanisms in trypanosomes.}, journal = {Trends in parasitology}, volume = {38}, number = {10}, pages = {854-867}, pmid = {36028415}, issn = {1471-5007}, support = {P41 GM109824/GM/NIGMS NIH HHS/United States ; R01 AI140429/AI/NIAID NIH HHS/United States ; R01 GM112108/GM/NIGMS NIH HHS/United States ; 204697/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Active Transport, Cell Nucleus/genetics ; Animals ; Cell Nucleus/genetics/metabolism ; *RNA/genetics/metabolism ; RNA, Messenger/genetics ; *Trypanosoma/genetics/metabolism ; }, abstract = {Export of RNA from the nucleus is essential for all eukaryotic cells and has emerged as a major step in the control of gene expression. mRNA molecules are required to complete a complex series of processing events and pass a quality control system to protect the cytoplasm from the translation of aberrant proteins. Many of these events are highly conserved across eukaryotes, reflecting their ancient origin, but significant deviation from a canonical pathway as described from animals and fungi has emerged in the trypanosomatids. With significant implications for the mechanisms that control gene expression and hence differentiation, responses to altered environments and fitness as a parasite, these deviations may also reveal additional, previously unsuspected, mRNA export pathways.}, } @article {pmid35994648, year = {2022}, author = {Colnaghi, M and Lane, N and Pomiankowski, A}, title = {Repeat sequences limit the effectiveness of lateral gene transfer and favored the evolution of meiotic sex in early eukaryotes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {35}, pages = {e2205041119}, pmid = {35994648}, issn = {1091-6490}, support = {BB/V003542/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/S003681/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {Computer Simulation ; *DNA Repeat Expansion/genetics ; *Eukaryota/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal/genetics ; Genome/genetics ; *Meiosis/genetics ; Mutation ; Mutation Accumulation ; Phylogeny ; Prokaryotic Cells ; }, abstract = {The transition from prokaryotic lateral gene transfer to eukaryotic meiotic sex is poorly understood. Phylogenetic evidence suggests that it was tightly linked to eukaryogenesis, which involved an unprecedented rise in both genome size and the density of genetic repeats. Expansion of genome size raised the severity of Muller's ratchet, while limiting the effectiveness of lateral gene transfer (LGT) at purging deleterious mutations. In principle, an increase in recombination length combined with higher rates of LGT could solve this problem. Here, we show using a computational model that this solution fails in the presence of genetic repeats prevalent in early eukaryotes. The model demonstrates that dispersed repeat sequences allow ectopic recombination, which leads to the loss of genetic information and curtails the capacity of LGT to prevent mutation accumulation. Increasing recombination length in the presence of repeat sequences exacerbates the problem. Mutational decay can only be resisted with homology along extended sequences of DNA. We conclude that the transition to homologous pairing along linear chromosomes was a key innovation in meiotic sex, which was instrumental in the expansion of eukaryotic genomes and morphological complexity.}, } @article {pmid35881430, year = {2022}, author = {Schavemaker, PE and Lynch, M}, title = {Flagellar energy costs across the tree of life.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {35881430}, issn = {2050-084X}, support = {R35 GM122566/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaea ; Bacteria ; *Chlamydomonas reinhardtii/genetics ; *Flagella/metabolism ; }, abstract = {Flagellar-driven motility grants unicellular organisms the ability to gather more food and avoid predators, but the energetic costs of construction and operation of flagella are considerable. Paths of flagellar evolution depend on the deviations between fitness gains and energy costs. Using structural data available for all three major flagellar types (bacterial, archaeal, and eukaryotic), flagellar construction costs were determined for Escherichia coli, Pyrococcus furiosus, and Chlamydomonas reinhardtii. Estimates of cell volumes, flagella numbers, and flagellum lengths from the literature yield flagellar costs for another ~200 species. The benefits of flagellar investment were analysed in terms of swimming speed, nutrient collection, and growth rate; showing, among other things, that the cost-effectiveness of bacterial and eukaryotic flagella follows a common trend. However, a comparison of whole-cell costs and flagellum costs across the Tree of Life reveals that only cells with larger cell volumes than the typical bacterium could evolve the more expensive eukaryotic flagellum. These findings provide insight into the unsolved evolutionary question of why the three domains of life each carry their own type of flagellum.}, } @article {pmid35880421, year = {2022}, author = {Cerón-Romero, MA and Fonseca, MM and de Oliveira Martins, L and Posada, D and Katz, LA}, title = {Phylogenomic Analyses of 2,786 Genes in 158 Lineages Support a Root of the Eukaryotic Tree of Life between Opisthokonts and All Other Lineages.}, journal = {Genome biology and evolution}, volume = {14}, number = {8}, pages = {}, pmid = {35880421}, issn = {1759-6653}, support = {R15 HG010409/HG/NHGRI NIH HHS/United States ; }, mesh = {*Eukaryota/genetics ; *Eukaryotic Cells ; Guanosine Triphosphate ; Likelihood Functions ; Phylogeny ; }, abstract = {Advances in phylogenomics and high-throughput sequencing have allowed the reconstruction of deep phylogenetic relationships in the evolution of eukaryotes. Yet, the root of the eukaryotic tree of life remains elusive. The most popular hypothesis in textbooks and reviews is a root between Unikonta (Opisthokonta + Amoebozoa) and Bikonta (all other eukaryotes), which emerged from analyses of a single-gene fusion. Subsequent, highly cited studies based on concatenation of genes supported this hypothesis with some variations or proposed a root within Excavata. However, concatenation of genes does not consider phylogenetically-informative events like gene duplications and losses. A recent study using gene tree parsimony (GTP) suggested the root lies between Opisthokonta and all other eukaryotes, but only including 59 taxa and 20 genes. Here we use GTP with a duplication-loss model in a gene-rich and taxon-rich dataset (i.e., 2,786 gene families from two sets of 155 and 158 diverse eukaryotic lineages) to assess the root, and we iterate each analysis 100 times to quantify tree space uncertainty. We also contrasted our results and discarded alternative hypotheses from the literature using GTP and the likelihood-based method SpeciesRax. Our estimates suggest a root between Fungi or Opisthokonta and all other eukaryotes; but based on further analysis of genome size, we propose that the root between Opisthokonta and all other eukaryotes is the most likely.}, } @article {pmid35765784, year = {2022}, author = {Romei, M and Sapriel, G and Imbert, P and Jamay, T and Chomilier, J and Lecointre, G and Carpentier, M}, title = {Protein folds as synapomorphies of the tree of life.}, journal = {Evolution; international journal of organic evolution}, volume = {76}, number = {8}, pages = {1706-1719}, pmid = {35765784}, issn = {1558-5646}, mesh = {*Biological Evolution ; *Eukaryota ; Phylogeny ; Symbiosis ; }, abstract = {Several studies showed that folds (topology of protein secondary structures) distribution in proteomes may be a global proxy to build phylogeny. Then, some folds should be synapomorphies (derived characters exclusively shared among taxa). However, previous studies used methods that did not allow synapomorphy identification, which requires congruence analysis of folds as individual characters. Here, we map SCOP folds onto a sample of 210 species across the tree of life (TOL). Congruence is assessed using retention index of each fold for the TOL, and principal component analysis for deeper branches. Using a bicluster mapping approach, we define synapomorphic blocks of folds (SBF) sharing similar presence/absence patterns. Among the 1232 folds, 20% are universally present in our TOL, whereas 54% are reliable synapomorphies. These results are similar with CATH and ECOD databases. Eukaryotes are characterized by a large number of them, and several SBFs clearly support nested eukaryotic clades (divergence times from 1100 to 380 mya). Although clearly separated, the three superkingdoms reveal a strong mosaic pattern. This pattern is consistent with the dual origin of eukaryotes and witness secondary endosymbiosis in their phothosynthetic clades. Our study unveils direct analysis of folds synapomorphies as key characters to unravel evolutionary history of species.}, } @article {pmid35761090, year = {2022}, author = {Banciu, HL and Gridan, IM and Zety, AV and Baricz, A}, title = {Asgard archaea in saline environments.}, journal = {Extremophiles : life under extreme conditions}, volume = {26}, number = {2}, pages = {21}, pmid = {35761090}, issn = {1433-4909}, support = {PN-III-P4-ID-PCE-2020-1559//Ministry of Research, Innovation and Digitization, CNCS/CCCDI - UEFISCDI/ ; }, mesh = {*Archaea ; Eukaryotic Cells/metabolism ; *Genome, Archaeal ; Metagenome ; Phylogeny ; }, abstract = {Members of candidate Asgardarchaeota superphylum appear to share numerous eukaryotic-like attributes thus being broadly explored for their relevance to eukaryogenesis. On the contrast, the ecological roles of Asgard archaea remains understudied. Asgard archaea have been frequently associated to low-oxygen aquatic sedimentary environments worldwide spanning a broad but not extreme salinity range. To date, the available information on diversity and potential biogeochemical roles of Asgardarchaeota mostly sourced from marine habitats and to a much lesser extend from true saline environments (i.e., > 3% w/v total salinity). Here, we provide an overview on diversity and ecological implications of Asgard archaea distributed across saline environments and briefly explore their metagenome-resolved potential for osmoadaptation. Loki-, Thor- and Heimdallarchaeota are the dominant Asgard clades in saline habitats where they might employ anaerobic/microaerophilic organic matter degradation and autotrophic carbon fixation. Homologs of primary solute uptake ABC transporters seemingly prevail in Thorarchaeota, whereas those putatively involved in trehalose and ectoine biosynthesis were mostly inferred in Lokiarchaeota. We speculate that Asgardarchaeota might adopt compatible solute-accumulating ('salt-out') strategy as response to salt stress. Our current understanding on the distribution, ecology and salt-adaptive strategies of Asgardarchaeota in saline environments are, however, limited by insufficient sampling and incompleteness of the available metagenome-assembled genomes. Extensive sampling combined with 'omics'- and cultivation-based approaches seem, therefore, crucial to gain deeper knowledge on this particularly intriguing archaeal lineage.}, } @article {pmid35710309, year = {2022}, author = {Mallén-Ponce, MJ and Pérez-Pérez, ME and Crespo, JL}, title = {Deciphering the function and evolution of the target of rapamycin signaling pathway in microalgae.}, journal = {Journal of experimental botany}, volume = {73}, number = {20}, pages = {6993-7005}, pmid = {35710309}, issn = {1460-2431}, support = {PGC2018-099048-B-I00//Ministerio de Ciencia y Tecnología/ ; P20-00057//Regional Government of Andalucía/ ; }, mesh = {*Microalgae/metabolism ; Sirolimus/metabolism ; Signal Transduction ; Photosynthesis ; Eukaryota ; }, abstract = {Microalgae constitute a highly diverse group of photosynthetic microorganisms that are widely distributed on Earth. The rich diversity of microalgae arose from endosymbiotic events that took place early in the evolution of eukaryotes and gave rise to multiple lineages including green algae, the ancestors of land plants. In addition to their fundamental role as the primary source of marine and freshwater food chains, microalgae are essential producers of oxygen on the planet and a major biotechnological target for sustainable biofuel production and CO2 mitigation. Microalgae integrate light and nutrient signals to regulate cell growth. Recent studies identified the target of rapamycin (TOR) kinase as a central regulator of cell growth and a nutrient sensor in microalgae. TOR promotes protein synthesis and regulates processes that are induced under nutrient stress such as autophagy and the accumulation of triacylglycerol and starch. A detailed analysis of representative genomes from the entire microalgal lineage revealed that the highly conserved central components of the TOR pathway are likely to have been present in the last eukaryotic common ancestor, and the loss of specific TOR signaling elements at an early stage in the evolution of microalgae. Here we examine the evolutionary conservation of TOR signaling components in diverse microalgae and discuss recent progress of this signaling pathway in these organisms.}, } @article {pmid35667126, year = {2022}, author = {Gophna, U and Altman-Price, N}, title = {Horizontal Gene Transfer in Archaea-From Mechanisms to Genome Evolution.}, journal = {Annual review of microbiology}, volume = {76}, number = {}, pages = {481-502}, doi = {10.1146/annurev-micro-040820-124627}, pmid = {35667126}, issn = {1545-3251}, mesh = {*Archaea/genetics ; Bacteria/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {Archaea remains the least-studied and least-characterized domain of life despite its significance not just to the ecology of our planet but also to the evolution of eukaryotes. It is therefore unsurprising that research into horizontal gene transfer (HGT) in archaea has lagged behind that of bacteria. Indeed, several archaeal lineages may owe their very existence to large-scale HGT events, and thus understanding both the molecular mechanisms and the evolutionary impact of HGT in archaea is highly important. Furthermore, some mechanisms of gene exchange, such as plasmids that transmit themselves via membrane vesicles and the formation of cytoplasmic bridges that allows transfer of both chromosomal and plasmid DNA, may be archaea-specific. This review summarizes what we know about HGT in archaea, and the barriers that restrict it, highlighting exciting recent discoveries and pointing out opportunities for future research.}, } @article {pmid35662005, year = {2022}, author = {Kumar, P and Bhatnagar, A and Sankaranarayanan, R}, title = {Chiral proofreading during protein biosynthesis and its evolutionary implications.}, journal = {FEBS letters}, volume = {596}, number = {13}, pages = {1615-1627}, doi = {10.1002/1873-3468.14419}, pmid = {35662005}, issn = {1873-3468}, mesh = {Amino Acids/metabolism ; Glycine/metabolism ; *Protein Biosynthesis ; RNA, Transfer/genetics/metabolism ; RNA, Transfer, Amino Acyl/chemistry/metabolism ; *RNA, Transfer, Gly/metabolism ; }, abstract = {Homochirality of biomacromolecules is a prerequisite for their proper functioning and hence essential for all life forms. This underscores the role of cellular chiral checkpoints in enforcing homochirality during protein biosynthesis. d-Aminoacyl-tRNA deacylase (DTD) is an enzyme that performs 'chirality-based proofreading' to remove d-amino acids mistakenly attached to tRNAs, thus recycling them for further rounds of translation. Paradoxically, owing to its l-chiral rejection mode of action, DTD can remove glycine as well, which is an achiral amino acid. However, this activity is modulated by discriminator base (N73) in tRNA, a unique element that protects the cognate Gly-tRNA[Gly] . Here, we review our recent work showing various aspects of DTD and tRNA[Gly] coevolution and its key role in maintaining proper translation surveillance in both bacteria and eukaryotes. Moreover, we also discuss two major optimization events on DTD and tRNA that resolved compatibility issues among the archaeal and the bacterial translation apparatuses. Importantly, such optimizations are necessary for the emergence of mitochondria and successful eukaryogenesis.}, } @article {pmid35643186, year = {2022}, author = {Olovnikov, AM}, title = {Eco-crossover, or environmentally regulated crossing-over, and natural selection are two irreplaceable drivers of adaptive evolution: Eco-crossover hypothesis.}, journal = {Bio Systems}, volume = {218}, number = {}, pages = {104706}, doi = {10.1016/j.biosystems.2022.104706}, pmid = {35643186}, issn = {1872-8324}, mesh = {Chromosomes ; *Crossing Over, Genetic/genetics ; Eukaryota/genetics ; Genome ; Meiosis ; *RNA, Circular ; Selection, Genetic ; }, abstract = {The existence of an environmentally regulated version of meiotic crossing-over, or eco-crossover, is proposed, and the main consequences of this hypothesis are considered. Eco-crossover is a key source of partially directed genetic diversity of eukaryotes. In stressful environment, it creates ecologically justified and topologically specific genetic changes, and hence phenotypic variability, with which the selection works. If variability were random, then, in the face of rapid environmental changes, natural selection could not create life-saving adaptations in a timely manner. Owing to the eco-crossover activity, epimutations, i.e., eco-dependently marked chromosomal sites, are transforming into mutations. In its work, eco-crossover uses the eco-stress-dependent versions of circular RNAs ("ecological" circRNAs), which, against the background of eco-stresses, are synthesized as variants of alternative splicing. These ecological circRNAs, binding to homologous epimutations on the homologous parent chromosomes of the meiocyte, involve them in topologically specific recombinations. These recombinations can create random mutations in nonrandom genomic sites. These quasi-random mutations serve as a pivotal source for creating all adaptations of any level of complexity. The drivers of the adaptive evolution of eukaryotes, both in micro- and macroevolution, are two irreplaceable factors - eco-crossover and natural selection.}, } @article {pmid35642316, year = {2022}, author = {Bremer, N and Tria, FDK and Skejo, J and Garg, SG and Martin, WF}, title = {Ancestral State Reconstructions Trace Mitochondria But Not Phagocytosis to the Last Eukaryotic Common Ancestor.}, journal = {Genome biology and evolution}, volume = {14}, number = {6}, pages = {}, pmid = {35642316}, issn = {1759-6653}, support = {101018894/ERC_/European Research Council/International ; }, mesh = {Animals ; *Biological Evolution ; *Eukaryota/genetics ; Eukaryotic Cells/physiology ; Mitochondria/genetics ; Phagocytosis/physiology ; Phylogeny ; Symbiosis/genetics ; }, abstract = {Two main theories have been put forward to explain the origin of mitochondria in eukaryotes: phagotrophic engulfment (undigested food) and microbial symbiosis (physiological interactions). The two theories generate mutually exclusive predictions about the order in which mitochondria and phagocytosis arose. To discriminate the alternatives, we have employed ancestral state reconstructions (ASR) for phagocytosis as a trait, phagotrophy as a feeding habit, the presence of mitochondria, the presence of plastids, and the multinucleated organization across major eukaryotic lineages. To mitigate the bias introduced by assuming a particular eukaryotic phylogeny, we reconstructed the appearance of these traits across 1789 different rooted gene trees, each having species from opisthokonts, mycetozoa, hacrobia, excavate, archeplastida, and Stramenopiles, Alveolates and Rhizaria. The trees reflect conflicting relationships and different positions of the root. We employed a novel phylogenomic test that summarizes ASR across trees which reconstructs a last eukaryotic common ancestor that possessed mitochondria, was multinucleated, lacked plastids, and was non-phagotrophic as well as non-phagocytic. This indicates that both phagocytosis and phagotrophy arose subsequent to the origin of mitochondria, consistent with findings from comparative physiology. Furthermore, our ASRs uncovered multiple origins of phagocytosis and of phagotrophy across eukaryotes, indicating that, like wings in animals, these traits are useful but neither ancestral nor homologous across groups. The data indicate that mitochondria preceded the origin of phagocytosis, such that phagocytosis cannot have been the mechanism by which mitochondria were acquired.}, } @article {pmid35633668, year = {2022}, author = {Bell, PJL}, title = {Eukaryogenesis: The Rise of an Emergent Superorganism.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {858064}, pmid = {35633668}, issn = {1664-302X}, abstract = {Although it is widely taught that all modern life descended via modification from a last universal common ancestor (LUCA), this dominant paradigm is yet to provide a generally accepted explanation for the chasm in design between prokaryotic and eukaryotic cells. Counter to this dominant paradigm, the viral eukaryogenesis (VE) hypothesis proposes that the eukaryotes originated as an emergent superorganism and thus did not evolve from LUCA via descent with incremental modification. According to the VE hypothesis, the eukaryotic nucleus descends from a viral factory, the mitochondrion descends from an enslaved alpha-proteobacteria and the cytoplasm and plasma membrane descend from an archaeal host. A virus initiated the eukaryogenesis process by colonising an archaeal host to create a virocell that had its metabolism reprogrammed to support the viral factory. Subsequently, viral processes facilitated the entry of a bacterium into the archaeal cytoplasm which was also eventually reprogrammed to support the viral factory. As the viral factory increased control of the consortium, the archaeal genome was lost, the bacterial genome was greatly reduced and the viral factory eventually evolved into the nucleus. It is proposed that the interaction between these three simple components generated a superorganism whose emergent properties allowed the evolution of eukaryotic complexity. If the radical tenets of the VE hypothesis are ultimately accepted, current biological paradigms regarding viruses, cell theory, LUCA and the universal Tree of Life (ToL) should be fundamentally altered or completely abandoned.}, } @article {pmid35589959, year = {2022}, author = {Vosseberg, J and Schinkel, M and Gremmen, S and Snel, B}, title = {The spread of the first introns in proto-eukaryotic paralogs.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {476}, pmid = {35589959}, issn = {2399-3642}, mesh = {*Eukaryota/genetics ; Eukaryotic Cells ; *Evolution, Molecular ; Humans ; Introns/genetics ; Spliceosomes/genetics ; }, abstract = {Spliceosomal introns are a unique feature of eukaryotic genes. Previous studies have established that many introns were present in the protein-coding genes of the last eukaryotic common ancestor (LECA). Intron positions shared between genes that duplicated before LECA could in principle provide insight into the emergence of the first introns. In this study we use ancestral intron position reconstructions in two large sets of duplicated families to systematically identify these ancient paralogous intron positions. We found that 20-35% of introns inferred to have been present in LECA were shared between paralogs. These shared introns, which likely preceded ancient duplications, were wide spread across different functions, with the notable exception of nuclear transport. Since we observed a clear signal of pervasive intron loss prior to LECA, it is likely that substantially more introns were shared at the time of duplication than we can detect in LECA. The large extent of shared introns indicates an early origin of introns during eukaryogenesis and suggests an early origin of a nuclear structure, before most of the other complex eukaryotic features were established.}, } @article {pmid35525886, year = {2022}, author = {Camus, MF and Alexander-Lawrie, B and Sharbrough, J and Hurst, GDD}, title = {Inheritance through the cytoplasm.}, journal = {Heredity}, volume = {129}, number = {1}, pages = {31-43}, pmid = {35525886}, issn = {1365-2540}, mesh = {Cytoplasm/genetics ; *Eukaryota/genetics ; Genome ; *Inheritance Patterns ; Symbiosis ; }, abstract = {Most heritable information in eukaryotic cells is encoded in the nuclear genome, with inheritance patterns following classic Mendelian segregation. Genomes residing in the cytoplasm, however, prove to be a peculiar exception to this rule. Cytoplasmic genetic elements are generally maternally inherited, although there are several exceptions where these are paternally, biparentally or doubly-uniparentally inherited. In this review, we examine the diversity and peculiarities of cytoplasmically inherited genomes, and the broad evolutionary consequences that non-Mendelian inheritance brings. We first explore the origins of vertical transmission and uniparental inheritance, before detailing the vast diversity of cytoplasmic inheritance systems across Eukaryota. We then describe the evolution of genomic organisation across lineages, how this process has been shaped by interactions with the nuclear genome and population genetics dynamics. Finally, we discuss how both nuclear and cytoplasmic genomes have evolved to co-inhabit the same host cell via one of the longest symbiotic processes, and all the opportunities for intergenomic conflict that arise due to divergence in inheritance patterns. In sum, we cannot understand the evolution of eukaryotes without understanding hereditary symbiosis.}, } @article {pmid35449457, year = {2022}, author = {Mills, DB and Boyle, RA and Daines, SJ and Sperling, EA and Pisani, D and Donoghue, PCJ and Lenton, TM}, title = {Eukaryogenesis and oxygen in Earth history.}, journal = {Nature ecology & evolution}, volume = {6}, number = {5}, pages = {520-532}, pmid = {35449457}, issn = {2397-334X}, support = {BB/T012773/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Archaea ; *Atmosphere ; Eukaryota ; Fossils ; Humans ; Hypoxia ; *Oxygen/metabolism ; }, abstract = {The endosymbiotic origin of mitochondria during eukaryogenesis has long been viewed as an adaptive response to the oxygenation of Earth's surface environment, presuming a fundamentally aerobic lifestyle for the free-living bacterial ancestors of mitochondria. This oxygen-centric view has been robustly challenged by recent advances in the Earth and life sciences. While the permanent oxygenation of the atmosphere above trace concentrations is now thought to have occurred 2.2 billion years ago, large parts of the deep ocean remained anoxic until less than 0.5 billion years ago. Neither fossils nor molecular clocks correlate the origin of mitochondria, or eukaryogenesis more broadly, to either of these planetary redox transitions. Instead, mitochondria-bearing eukaryotes are consistently dated to between these two oxygenation events, during an interval of pervasive deep-sea anoxia and variable surface-water oxygenation. The discovery and cultivation of the Asgard archaea has reinforced metabolic evidence that eukaryogenesis was initially mediated by syntrophic H2 exchange between an archaeal host and an α-proteobacterial symbiont living under anoxia. Together, these results temporally, spatially and metabolically decouple the earliest stages of eukaryogenesis from the oxygen content of the surface ocean and atmosphere. Rather than reflecting the ancestral metabolic state, obligate aerobiosis in eukaryotes is most probably derived, having only become globally widespread over the past 1 billion years as atmospheric oxygen approached modern levels.}, } @article {pmid35394422, year = {2022}, author = {Meyer, BH and Adam, PS and Wagstaff, BA and Kolyfetis, GE and Probst, AJ and Albers, SV and Dorfmueller, HC}, title = {Agl24 is an ancient archaeal homolog of the eukaryotic N-glycan chitobiose synthesis enzymes.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {35394422}, issn = {2050-084X}, support = {109357/Z/15/Z//The Wellcome Trust and Royal Society Grant/ ; /WT_/Wellcome Trust/United Kingdom ; 105606/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Archaea/genetics ; Disaccharides ; *Eukaryota ; Phylogeny ; Polysaccharides ; }, abstract = {Protein N-glycosylation is a post-translational modification found in organisms of all domains of life. The crenarchaeal N-glycosylation begins with the synthesis of a lipid-linked chitobiose core structure, identical to that in Eukaryotes, although the enzyme catalyzing this reaction remains unknown. Here, we report the identification of a thermostable archaeal β-1,4-N-acetylglucosaminyltransferase, named archaeal glycosylation enzyme 24 (Agl24), responsible for the synthesis of the N-glycan chitobiose core. Biochemical characterization confirmed its function as an inverting β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol glycosyltransferase. Substitution of a conserved histidine residue, found also in the eukaryotic and bacterial homologs, demonstrated its functional importance for Agl24. Furthermore, bioinformatics and structural modeling revealed similarities of Agl24 to the eukaryotic Alg14/13 and a distant relation to the bacterial MurG, which are catalyzing the same or a similar reaction, respectively. Phylogenetic analysis of Alg14/13 homologs indicates that they are ancient in Eukaryotes, either as a lateral transfer or inherited through eukaryogenesis.}, } @article {pmid35333570, year = {2022}, author = {Akıl, C and Ali, S and Tran, LT and Gaillard, J and Li, W and Hayashida, K and Hirose, M and Kato, T and Oshima, A and Fujishima, K and Blanchoin, L and Narita, A and Robinson, RC}, title = {Structure and dynamics of Odinarchaeota tubulin and the implications for eukaryotic microtubule evolution.}, journal = {Science advances}, volume = {8}, number = {12}, pages = {eabm2225}, pmid = {35333570}, issn = {2375-2548}, mesh = {Eukaryota/metabolism ; *Eukaryotic Cells/metabolism ; Guanosine Triphosphate/metabolism ; Microtubules/metabolism ; *Tubulin/chemistry ; }, abstract = {Tubulins are critical for the internal organization of eukaryotic cells, and understanding their emergence is an important question in eukaryogenesis. Asgard archaea are the closest known prokaryotic relatives to eukaryotes. Here, we elucidated the apo and nucleotide-bound x-ray structures of an Asgard tubulin from hydrothermal living Odinarchaeota (OdinTubulin). The guanosine 5'-triphosphate (GTP)-bound structure resembles a microtubule protofilament, with GTP bound between subunits, coordinating the "+" end subunit through a network of water molecules and unexpectedly by two cations. A water molecule is located suitable for GTP hydrolysis. Time course crystallography and electron microscopy revealed conformational changes on GTP hydrolysis. OdinTubulin forms tubules at high temperatures, with short curved protofilaments coiling around the tubule circumference, more similar to FtsZ, rather than running parallel to its length, as in microtubules. Thus, OdinTubulin represents an evolutionary stage intermediate between prokaryotic FtsZ and eukaryotic microtubule-forming tubulins.}, } @article {pmid35328452, year = {2022}, author = {Wu, X and Han, J and Guo, C}, title = {Function of Nuclear Pore Complexes in Regulation of Plant Defense Signaling.}, journal = {International journal of molecular sciences}, volume = {23}, number = {6}, pages = {}, pmid = {35328452}, issn = {1422-0067}, support = {31770352//National Natural Science Foundation of China/ ; LY20C020002//Natural Science Foundation of Zhejiang Province/ ; }, mesh = {Active Transport, Cell Nucleus ; *Biological Phenomena ; Nuclear Envelope/metabolism ; *Nuclear Pore/metabolism ; Nuclear Pore Complex Proteins/metabolism ; Plant Breeding ; Plants/metabolism ; }, abstract = {In eukaryotes, the nucleus is the regulatory center of cytogenetics and metabolism, and it is critical for fundamental biological processes, including DNA replication and transcription, protein synthesis, and biological macromolecule transportation. The eukaryotic nucleus is surrounded by a lipid bilayer called the nuclear envelope (NE), which creates a microenvironment for sophisticated cellular processes. The NE is perforated by the nuclear pore complex (NPC), which is the channel for biological macromolecule bi-directional transport between the nucleus and cytoplasm. It is well known that NPC is the spatial designer of the genome and the manager of genomic function. Moreover, the NPC is considered to be a platform for the continual adaptation and evolution of eukaryotes. So far, a number of nucleoporins required for plant-defense processes have been identified. Here, we first provide an overview of NPC organization in plants, and then discuss recent findings in the plant NPC to elaborate on and dissect the distinct defensive functions of different NPC subcomponents in plant immune defense, growth and development, hormone signaling, and temperature response. Nucleoporins located in different components of NPC have their unique functions, and the link between the NPC and nucleocytoplasmic trafficking promotes crosstalk of different defense signals in plants. It is necessary to explore appropriate components of the NPC as potential targets for the breeding of high-quality and broad spectrum resistance crop varieties.}, } @article {pmid35275997, year = {2022}, author = {Jüttner, M and Ferreira-Cerca, S}, title = {Looking through the Lens of the Ribosome Biogenesis Evolutionary History: Possible Implications for Archaeal Phylogeny and Eukaryogenesis.}, journal = {Molecular biology and evolution}, volume = {39}, number = {4}, pages = {}, pmid = {35275997}, issn = {1537-1719}, mesh = {*Archaea/genetics ; Biological Evolution ; Eukaryota/genetics ; *Genome, Archaeal ; Phylogeny ; Ribosomes/genetics ; }, abstract = {Our understanding of microbial diversity and its evolutionary relationships has increased substantially over the last decade. Such an understanding has been greatly fueled by culture-independent metagenomics analyses. However, the outcome of some of these studies and their biological and evolutionary implications, such as the origin of the eukaryotic lineage from the recently discovered archaeal Asgard superphylum, is debated. The sequences of the ribosomal constituents are amongst the most used phylogenetic markers. However, the functional consequences underlying the analysed sequence diversity and their putative evolutionary implications are essentially not taken into consideration. Here, we propose to exploit additional functional hallmarks of ribosome biogenesis to help disentangle competing evolutionary hypotheses. Using selected examples, such as the multiple origins of halophily in archaea or the evolutionary relationship between the Asgard archaea and Eukaryotes, we illustrate and discuss how function-aware phylogenetic framework can contribute to refining our understanding of archaeal phylogeny and the origin of eukaryotic cells.}, } @article {pmid35218347, year = {2022}, author = {Spang, A and Mahendrarajah, TA and Offre, P and Stairs, CW}, title = {Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere.}, journal = {Genome biology and evolution}, volume = {14}, number = {6}, pages = {}, pmid = {35218347}, issn = {1759-6653}, mesh = {*Archaea ; Biological Evolution ; Eukaryota ; Phylogeny ; *Viruses/genetics ; }, abstract = {The tree of life (TOL) is a powerful framework to depict the evolutionary history of cellular organisms through time, from our microbial origins to the diversification of multicellular eukaryotes that shape the visible biosphere today. During the past decades, our perception of the TOL has fundamentally changed, in part, due to profound methodological advances, which allowed a more objective approach to studying organismal and viral diversity and led to the discovery of major new branches in the TOL as well as viral lineages. Phylogenetic and comparative genomics analyses of these data have, among others, revolutionized our understanding of the deep roots and diversity of microbial life, the origin of the eukaryotic cell, eukaryotic diversity, as well as the origin, and diversification of viruses. In this review, we provide an overview of some of the recent discoveries on the evolutionary history of cellular organisms and their viruses and discuss a variety of complementary techniques that we consider crucial for making further progress in our understanding of the TOL and its interconnection with the virosphere.}, } @article {pmid35174363, year = {2022}, author = {Albers, S and Ashmore, J and Pollard, T and Spang, A and Zhou, J}, title = {Origin of eukaryotes: What can be learned from the first successfully isolated Asgard archaeon.}, journal = {Faculty reviews}, volume = {11}, number = {}, pages = {3}, pmid = {35174363}, issn = {2732-432X}, abstract = {The origin of cellular complexity characterizing eukaryotic cells remains a central unresolved issue in the study of diversification of cellular life on Earth. The isolation by Imachi et al.[1] of a member of the Asgard archaea[2] - a contemporary relative of organisms thought to have given rise to eukaryotic cells about 2 billion years ago - now promises new insight. The complete genome sequence of the isolated Lokiarchaeum strain confirms that the eukaryotic signature proteins (ESPs) previously identified in the Lokiarchaeota[3] and other Asgard archaea[2] are indeed encoded by these archaeal genomes and do not represent contamination from eukaryotes. These ESPs encode homologs of eukaryotic actins, small GTPases and the ESCRT complex proteins and are required for the functioning of complex eukaryotic cells. The new, slowly growing, anaerobic laboratory strain allows a first direct look at these organisms and provides key insights into the morphology and metabolism of an Asgard archaeal organism. The work has provided valuable information for other laboratories that aim to isolate and characterize related organisms from other environments.}, } @article {pmid35167692, year = {2022}, author = {Hugoson, E and Guliaev, A and Ammunét, T and Guy, L}, title = {Host Adaptation in Legionellales Is 1.9 Ga, Coincident with Eukaryogenesis.}, journal = {Molecular biology and evolution}, volume = {39}, number = {3}, pages = {}, pmid = {35167692}, issn = {1537-1719}, mesh = {Bacteria ; *Gammaproteobacteria ; Host Adaptation ; *Legionella/genetics ; Virulence Factors ; }, abstract = {Bacteria adapting to living in a host cell caused the most salient events in the evolution of eukaryotes, namely the seminal fusion with an archaeon, and the emergence of both mitochondrion and chloroplast. A bacterial clade that may hold the key to understanding these events is the deep-branching gammaproteobacterial order Legionellales-containing among others Coxiella and Legionella-of which all known members grow inside eukaryotic cells. Here, by analyzing 35 novel Legionellales genomes mainly acquired through metagenomics, we show that this group is much more diverse than previously thought, and that key host-adaptation events took place very early in its evolution. Crucial virulence factors like the Type IVB secretion (Dot/Icm) system and two shared effector proteins were gained in the last Legionellales common ancestor (LLCA). Many metabolic gene families were lost in LLCA and its immediate descendants, including functions directly and indirectly related to molybdenum metabolism. On the other hand, genome sizes increased in the ancestors of the Legionella genus. We estimate that LLCA lived approximately 1.89 Ga, probably predating the last eukaryotic common ancestor by approximately 0.4-1.0 Gy. These elements strongly indicate that host adaptation arose only once in Legionellales, and that these bacteria were using advanced molecular machinery to exploit and manipulate host cells early in eukaryogenesis.}, } @article {pmid35154237, year = {2021}, author = {Medina-Chávez, NO and Travisano, M}, title = {Archaeal Communities: The Microbial Phylogenomic Frontier.}, journal = {Frontiers in genetics}, volume = {12}, number = {}, pages = {693193}, pmid = {35154237}, issn = {1664-8021}, abstract = {Archaea are a unique system for investigating the diversity of life. There are the most diverse group of organisms with the longest evolutionary history of life on Earth. Phylogenomic investigations reveal the complex evolutionary history of Archaea, overturning longstanding views of the history of life. They exist in the harshest environments and benign conditions, providing a system to investigate the basis for living in extreme environments. They are frequently members of microbial communities, albeit generally rare. Archaea were central in the evolution of Eukaryotes and can be used as a proxy for studying life on other planets. Future advances will depend not only upon phylogenomic studies but also on a better understanding of isolation and cultivation techniques.}, } @article {pmid35150280, year = {2022}, author = {Da Cunha, V and Gaia, M and Ogata, H and Jaillon, O and Delmont, TO and Forterre, P}, title = {Giant Viruses Encode Actin-Related Proteins.}, journal = {Molecular biology and evolution}, volume = {39}, number = {2}, pages = {}, pmid = {35150280}, issn = {1537-1719}, mesh = {Actins/genetics ; Eukaryota/genetics ; Eukaryotic Cells ; Evolution, Molecular ; *Giant Viruses/genetics ; Phylogeny ; }, abstract = {The emergence of the eukaryotic cytoskeleton is a critical yet puzzling step of eukaryogenesis. Actin and actin-related proteins (ARPs) are ubiquitous components of this cytoskeleton. The gene repertoire of the Last Eukaryotic Common Ancestor (LECA) would have therefore harbored both actin and various ARPs. Here, we report the presence and expression of actin-related genes in viral genomes (viractins) of some Imitervirales, a viral order encompassing the giant Mimiviridae. Phylogenetic analyses suggest an early recruitment of an actin-related gene by viruses from ancient protoeukaryotic hosts before the emergence of modern eukaryotes, possibly followed by a back transfer that gave rise to eukaryotic actins. This supports a coevolutionary scenario between pre-LECA lineages and their viruses, which could have contributed to the emergence of the modern eukaryotic cytoskeleton.}, } @article {pmid35084524, year = {2022}, author = {La, SR and Ndhlovu, A and Durand, PM}, title = {The Ancient Origins of Death Domains Support the 'Original Sin' Hypothesis for the Evolution of Programmed Cell Death.}, journal = {Journal of molecular evolution}, volume = {90}, number = {1}, pages = {95-113}, pmid = {35084524}, issn = {1432-1432}, mesh = {Apoptosis ; *Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; Caspases/genetics/metabolism ; Death Domain ; Evolution, Molecular ; *Genome, Archaeal/genetics ; Peptide Hydrolases/genetics/metabolism ; Phylogeny ; }, abstract = {The discovery of caspase homologs in bacteria highlighted the relationship between programmed cell death (PCD) evolution and eukaryogenesis. However, the origin of PCD genes in prokaryotes themselves (bacteria and archaea) is poorly understood and a source of controversy. Whether archaea also contain C14 peptidase enzymes and other death domains is largely unknown because of a historical dearth of genomic data. Archaeal genomic databases have grown significantly in the last decade, which allowed us to perform a detailed comparative study of the evolutionary histories of PCD-related death domains in major archaeal phyla, including the deepest branching phyla of Candidatus Aenigmarchaeota, Candidatus Woesearchaeota, and Euryarchaeota. We identified death domains associated with executioners of PCD, like the caspase homologs of the C14 peptidase family, in 321 archaea sequences. Of these, 15.58% were metacaspase type I orthologues and 84.42% were orthocaspases. Maximum likelihood phylogenetic analyses revealed a scattered distribution of orthocaspases and metacaspases in deep-branching bacteria and archaea. The tree topology was incongruent with the prokaryote 16S phylogeny suggesting a common ancestry of PCD genes in prokaryotes and subsequent massive horizontal gene transfer coinciding with the divergence of archaea and bacteria. Previous arguments for the origin of PCD were philosophical in nature with two popular propositions being the "addiction" and 'original sin' hypotheses. Our data support the 'original sin' hypothesis, which argues for a pleiotropic origin of the PCD toolkit with pro-life and pro-death functions tracing back to the emergence of cellular life-the Last Universal Common Ancestor State.}, } @article {pmid35027725, year = {2022}, author = {Muñoz-Gómez, SA and Susko, E and Williamson, K and Eme, L and Slamovits, CH and Moreira, D and López-García, P and Roger, AJ}, title = {Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria.}, journal = {Nature ecology & evolution}, volume = {6}, number = {3}, pages = {253-262}, pmid = {35027725}, issn = {2397-334X}, mesh = {*Alphaproteobacteria/genetics/metabolism ; Metagenome ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins ; Phylogeny ; }, abstract = {Determining the phylogenetic origin of mitochondria is key to understanding the ancestral mitochondrial symbiosis and its role in eukaryogenesis. However, the precise evolutionary relationship between mitochondria and their closest bacterial relatives remains hotly debated. The reasons include pervasive phylogenetic artefacts as well as limited protein and taxon sampling. Here we developed a new model of protein evolution that accommodates both across-site and across-branch compositional heterogeneity. We applied this site-and-branch-heterogeneous model (MAM60 + GFmix) to a considerably expanded dataset that comprises 108 mitochondrial proteins of alphaproteobacterial origin, and novel metagenome-assembled genomes from microbial mats, microbialites and sediments. The MAM60 + GFmix model fits the data much better and agrees with analyses of compositionally homogenized datasets with conventional site-heterogenous models. The consilience of evidence thus suggests that mitochondria are sister to the Alphaproteobacteria to the exclusion of MarineProteo1 and Magnetococcia. We also show that the ancestral presence of the crista-developing mitochondrial contact site and cristae organizing system (a mitofilin-domain-containing Mic60 protein) in mitochondria and the Alphaproteobacteria only supports their close relationship.}, } @article {pmid35027677, year = {2022}, author = {Wu, F and Speth, DR and Philosof, A and Crémière, A and Narayanan, A and Barco, RA and Connon, SA and Amend, JP and Antoshechkin, IA and Orphan, VJ}, title = {Unique mobile elements and scalable gene flow at the prokaryote-eukaryote boundary revealed by circularized Asgard archaea genomes.}, journal = {Nature microbiology}, volume = {7}, number = {2}, pages = {200-212}, pmid = {35027677}, issn = {2058-5276}, mesh = {Archaea/*genetics ; Archaeal Proteins/genetics ; Bacteria/genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; *Gene Flow ; *Genome, Archaeal ; Metagenomics ; Phylogeny ; Prokaryotic Cells/*metabolism ; }, abstract = {Eukaryotic genomes are known to have garnered innovations from both archaeal and bacterial domains but the sequence of events that led to the complex gene repertoire of eukaryotes is largely unresolved. Here, through the enrichment of hydrothermal vent microorganisms, we recovered two circularized genomes of Heimdallarchaeum species that belong to an Asgard archaea clade phylogenetically closest to eukaryotes. These genomes reveal diverse mobile elements, including an integrative viral genome that bidirectionally replicates in a circular form and aloposons, transposons that encode the 5,000 amino acid-sized proteins Otus and Ephialtes. Heimdallaechaeal mobile elements have garnered various genes from bacteria and bacteriophages, likely playing a role in shuffling functions across domains. The number of archaea- and bacteria-related genes follow strikingly different scaling laws in Asgard archaea, exhibiting a genome size-dependent ratio and a functional division resembling the bacteria- and archaea-derived gene repertoire across eukaryotes. Bacterial gene import has thus likely been a continuous process unaltered by eukaryogenesis and scaled up through genome expansion. Our data further highlight the importance of viewing eukaryogenesis in a pan-Asgard context, which led to the proposal of a conceptual framework, that is, the Heimdall nucleation-decentralized innovation-hierarchical import model that accounts for the emergence of eukaryotic complexity.}, } @article {pmid35013306, year = {2022}, author = {Sforna, MC and Loron, CC and Demoulin, CF and François, C and Cornet, Y and Lara, YJ and Grolimund, D and Ferreira Sanchez, D and Medjoubi, K and Somogyi, A and Addad, A and Fadel, A and Compère, P and Baudet, D and Brocks, JJ and Javaux, EJ}, title = {Intracellular bound chlorophyll residues identify 1 Gyr-old fossils as eukaryotic algae.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {146}, pmid = {35013306}, issn = {2041-1723}, mesh = {Biological Evolution ; Chlorophyll/*chemistry/history ; Chlorophyta/anatomy & histology/classification/physiology/*ultrastructure ; Coordination Complexes/*chemistry ; Democratic Republic of the Congo ; Ecosystem ; Eukaryotic Cells ; *Fossils ; Geologic Sediments/analysis ; History, Ancient ; Microscopy, Electron, Transmission ; Nickel/chemistry ; Photosynthesis/*physiology ; Phylogeny ; Plant Cells/physiology/ultrastructure ; Tetrapyrroles/chemistry ; X-Ray Absorption Spectroscopy ; }, abstract = {The acquisition of photosynthesis is a fundamental step in the evolution of eukaryotes. However, few phototrophic organisms are unambiguously recognized in the Precambrian record. The in situ detection of metabolic byproducts in individual microfossils is the key for the direct identification of their metabolisms. Here, we report a new integrative methodology using synchrotron-based X-ray fluorescence and absorption. We evidence bound nickel-geoporphyrins moieties in low-grade metamorphic rocks, preserved in situ within cells of a ~1 Gyr-old multicellular eukaryote, Arctacellularia tetragonala. We identify these moieties as chlorophyll derivatives, indicating that A. tetragonala was a phototrophic eukaryote, one of the first unambiguous algae. This new approach, applicable to overmature rocks, creates a strong new proxy to understand the evolution of phototrophy and diversification of early ecosystems.}, } @article {pmid35012979, year = {2022}, author = {Bellinger, MR and Wei, J and Hartmann, U and Cadiou, H and Winklhofer, M and Banks, MA}, title = {Conservation of magnetite biomineralization genes in all domains of life and implications for magnetic sensing.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {3}, pages = {}, pmid = {35012979}, issn = {1091-6490}, mesh = {Animals ; Biological Evolution ; Biomineralization/*genetics ; Ferrosoferric Oxide/*chemistry ; Genomics ; *Magnetic Phenomena ; Magnetosomes/genetics ; Salmon ; }, abstract = {Animals use geomagnetic fields for navigational cues, yet the sensory mechanism underlying magnetic perception remains poorly understood. One idea is that geomagnetic fields are physically transduced by magnetite crystals contained inside specialized receptor cells, but evidence for intracellular, biogenic magnetite in eukaryotes is scant. Certain bacteria produce magnetite crystals inside intracellular compartments, representing the most ancient form of biomineralization known and having evolved prior to emergence of the crown group of eukaryotes, raising the question of whether magnetite biomineralization in eukaryotes and prokaryotes might share a common evolutionary history. Here, we discover that salmonid olfactory epithelium contains magnetite crystals arranged in compact clusters and determine that genes differentially expressed in magnetic olfactory cells, contrasted to nonmagnetic olfactory cells, share ancestry with an ancient prokaryote magnetite biomineralization system, consistent with exaptation for use in eukaryotic magnetoreception. We also show that 11 prokaryote biomineralization genes are universally present among a diverse set of eukaryote taxa and that nine of those genes are present within the Asgard clade of archaea Lokiarchaeota that affiliates with eukaryotes in phylogenomic analysis. Consistent with deep homology, we present an evolutionary genetics hypothesis for magnetite formation among eukaryotes to motivate convergent approaches for examining magnetite-based magnetoreception, molecular origins of matrix-associated biomineralization processes, and eukaryogenesis.}, } @article {pmid34986784, year = {2022}, author = {Aouad, M and Flandrois, JP and Jauffrit, F and Gouy, M and Gribaldo, S and Brochier-Armanet, C}, title = {A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea.}, journal = {BMC ecology and evolution}, volume = {22}, number = {1}, pages = {1}, pmid = {34986784}, issn = {2730-7182}, mesh = {*Archaea/genetics ; *Eukaryota ; Phylogeny ; }, abstract = {BACKGROUND: The recent rise in cultivation-independent genome sequencing has provided key material to explore uncharted branches of the Tree of Life. This has been particularly spectacular concerning the Archaea, projecting them at the center stage as prominently relevant to understand early stages in evolution and the emergence of fundamental metabolisms as well as the origin of eukaryotes. Yet, resolving deep divergences remains a challenging task due to well-known tree-reconstruction artefacts and biases in extracting robust ancient phylogenetic signal, notably when analyzing data sets including the three Domains of Life. Among the various strategies aimed at mitigating these problems, divide-and-conquer approaches remain poorly explored, and have been primarily based on reconciliation among single gene trees which however notoriously lack ancient phylogenetic signal.

RESULTS: We analyzed sub-sets of full supermatrices covering the whole Tree of Life with specific taxonomic sampling to robustly resolve different parts of the archaeal phylogeny in light of their current diversity. Our results strongly support the existence and early emergence of two main clades, Cluster I and Cluster II, which we name Ouranosarchaea and Gaiarchaea, and we clarify the placement of important novel archaeal lineages within these two clades. However, the monophyly and branching of the fast evolving nanosized DPANN members remains unclear and worth of further study.

CONCLUSIONS: We inferred a well resolved rooted phylogeny of the Archaea that includes all recently described phyla of high taxonomic rank. This phylogeny represents a valuable reference to study the evolutionary events associated to the early steps of the diversification of the archaeal domain. Beyond the specifics of archaeal phylogeny, our results demonstrate the power of divide-and-conquer approaches to resolve deep phylogenetic relationships, which should be applied to progressively resolve the entire Tree of Life.}, } @article {pmid34964900, year = {2022}, author = {Rand, DM and Mossman, JA and Spierer, AN and Santiago, JA}, title = {Mitochondria as environments for the nuclear genome in Drosophila: mitonuclear G×G×E.}, journal = {The Journal of heredity}, volume = {113}, number = {1}, pages = {37-47}, pmid = {34964900}, issn = {1465-7333}, support = {1R35GM139607/NH/NIH HHS/United States ; R35 GM139607/GM/NIGMS NIH HHS/United States ; R01 GM067862/GM/NIGMS NIH HHS/United States ; T32 AG041688/AG/NIA NIH HHS/United States ; 2R01GM067862/NH/NIH HHS/United States ; }, mesh = {Animals ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; *Drosophila/genetics ; Epistasis, Genetic ; *Genome, Mitochondrial ; Mitochondria/genetics ; }, abstract = {Mitochondria evolved from a union of microbial cells belonging to distinct lineages that were likely anaerobic. The evolution of eukaryotes required a massive reorganization of the 2 genomes and eventual adaptation to aerobic environments. The nutrients and oxygen that sustain eukaryotic metabolism today are processed in mitochondria through coordinated expression of 37 mitochondrial genes and over 1000 nuclear genes. This puts mitochondria at the nexus of gene-by-gene (G×G) and gene-by-environment (G×E) interactions that sustain life. Here we use a Drosophila model of mitonuclear genetic interactions to explore the notion that mitochondria are environments for the nuclear genome, and vice versa. We construct factorial combinations of mtDNA and nuclear chromosomes to test for epistatic interactions (G×G), and expose these mitonuclear genotypes to altered dietary environments to examine G×E interactions. We use development time and genome-wide RNAseq analyses to assess the relative contributions of mtDNA, nuclear chromosomes, and environmental effects on these traits (mitonuclear G×G×E). We show that the nuclear transcriptional response to alternative mitochondrial "environments" (G×G) has significant overlap with the transcriptional response of mitonuclear genotypes to altered dietary environments. These analyses point to specific transcription factors (e.g., giant) that mediated these interactions, and identified coexpressed modules of genes that may account for the overlap in differentially expressed genes. Roughly 20% of the transcriptome includes G×G genes that are concordant with G×E genes, suggesting that mitonuclear interactions are part of an organism's environment.}, } @article {pmid34949483, year = {2022}, author = {Cohen, PA and Kodner, RB}, title = {The earliest history of eukaryotic life: uncovering an evolutionary story through the integration of biological and geological data.}, journal = {Trends in ecology & evolution}, volume = {37}, number = {3}, pages = {246-256}, doi = {10.1016/j.tree.2021.11.005}, pmid = {34949483}, issn = {1872-8383}, mesh = {Biological Evolution ; *Ecosystem ; *Eukaryota/genetics ; Eukaryotic Cells ; Fossils ; Geology ; Phylogeny ; }, abstract = {While there is significant data on eukaryogenesis and the early development of the eukaryotic lineage, major uncertainties regarding their origins and evolution remain, including questions of taxonomy, timing, and paleoecology. Here we examine the origin and diversification of the eukaryotes in the Proterozoic Eon as viewed through fossils, organic biomarkers, molecular clocks, phylogenies, and redox proxies. Our interpretation of the integration of these data suggest that eukaryotes were likely aerobic and established in Proterozoic ecosystems. We argue that we must closely examine and integrate both biological and geological evidence and examine points of agreement and contention to gain new insights into the true origin and early evolutionary history of this vastly important group.}, } @article {pmid34863611, year = {2022}, author = {Nobs, SJ and MacLeod, FI and Wong, HL and Burns, BP}, title = {Eukarya the chimera: eukaryotes, a secondary innovation of the two domains of life?.}, journal = {Trends in microbiology}, volume = {30}, number = {5}, pages = {421-431}, doi = {10.1016/j.tim.2021.11.003}, pmid = {34863611}, issn = {1878-4380}, mesh = {Archaea/genetics ; Bacteria/genetics ; *Biological Evolution ; *Eukaryota/genetics ; Eukaryotic Cells ; Phylogeny ; }, abstract = {One of the most significant events in the evolution of life is the origin of the eukaryotic cell, an increase in cellular complexity that occurred approximately 2 billion years ago. Ground-breaking research has centered around unraveling the characteristics of the Last Eukaryotic Common Ancestor (LECA) and the nuanced archaeal and bacterial contributions in eukaryogenesis, resulting in fundamental changes in our understanding of the Tree of Life. The archaeal and bacterial roles are covered by theories of endosymbiogenesis wherein an ancestral host archaeon and a bacterial endosymbiont merged to create a new complex cell type - Eukarya - and its mitochondrion. Eukarya is often regarded as a unique and distinct domain due to complex innovations not found in archaea or bacteria, despite housing a chimeric genome containing genes of both archaeal and bacterial origin. However, the discovery of complex cell machineries in recently described Asgard archaeal lineages, and the growing support for diverse bacterial gene transfers prior to and during the time of LECA, is redefining our understanding of eukaryogenesis. Indeed, the uniqueness of Eukarya, as a domain, is challenged. It is likely that many microbial syntrophies, encompassing a 'microbial village', were required to 'raise' a eukaryote during the process of eukaryogenesis.}, } @article {pmid34830325, year = {2021}, author = {Borao, S and Ayté, J and Hümmer, S}, title = {Evolution of the Early Spliceosomal Complex-From Constitutive to Regulated Splicing.}, journal = {International journal of molecular sciences}, volume = {22}, number = {22}, pages = {}, pmid = {34830325}, issn = {1422-0067}, support = {BFU2018-PGC2018-097248-B-I00//Ministry of Economy, Industry and Competitiveness/ ; CEX2018-000792-M//Ministry of Economy, Industry and Competitiveness/ ; }, mesh = {*Alternative Splicing ; Animals ; Base Sequence ; Evolution, Molecular ; Exons ; Humans ; Introns ; Mammals/*genetics/metabolism ; RNA Precursors/*genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Ribonucleoprotein, U1 Small Nuclear/genetics/metabolism ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Schizosaccharomyces/*genetics/metabolism ; Spliceosomes/chemistry/*genetics/metabolism ; Splicing Factor U2AF/genetics/metabolism ; }, abstract = {Pre-mRNA splicing is a major process in the regulated expression of genes in eukaryotes, and alternative splicing is used to generate different proteins from the same coding gene. Splicing is a catalytic process that removes introns and ligates exons to create the RNA sequence that codifies the final protein. While this is achieved in an autocatalytic process in ancestral group II introns in prokaryotes, the spliceosome has evolved during eukaryogenesis to assist in this process and to finally provide the opportunity for intron-specific splicing. In the early stage of splicing, the RNA 5' and 3' splice sites must be brought within proximity to correctly assemble the active spliceosome and perform the excision and ligation reactions. The assembly of this first complex, termed E-complex, is currently the least understood process. We focused in this review on the formation of the E-complex and compared its composition and function in three different organisms. We highlight the common ancestral mechanisms in S. cerevisiae, S. pombe, and mammals and conclude with a unifying model for intron definition in constitutive and regulated co-transcriptional splicing.}, } @article {pmid34826191, year = {2022}, author = {Wang, L and Yang, J and Zhang, H and Tao, Q and Zhang, Y and Dang, Z and Zhang, F and Luo, Z}, title = {Sequence coverage required for accurate genotyping by sequencing in polyploid species.}, journal = {Molecular ecology resources}, volume = {22}, number = {4}, pages = {1417-1426}, doi = {10.1111/1755-0998.13558}, pmid = {34826191}, issn = {1755-0998}, support = {31871240//National Natural Science Foundation of China/ ; BB/N008952/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Alleles ; Diploidy ; Genotype ; *Genotyping Techniques ; *High-Throughput Nucleotide Sequencing/methods ; *Plants/genetics ; *Polyploidy ; }, abstract = {Polyploidy plays an important role in the evolution of eukaryotes, especially for flowering plants. Many of ecologically or agronomically important plant or crop species are polyploids, including sycamore maple (tetraploid), the world second and third largest food crops wheat (hexaploid) and potato (tetraploid) as well as economically important aquaculture animals such as Atlantic salmon and trout. The next generation sequencing data enables to allocate genotype at a sequence variant site, known as genotyping by sequencing (GBS). GBS has stimulated enormous interests in population based genomics studies in almost all diploid and many polyploid organisms. DNA sequence polymorphisms are codominant and thus fully informative about the underlying genotype at the polymorphic site, making GBS a straightforward task in diploids. However, sequence data may usually be uninformative in polyploid species, making GBS a far more challenging task in polyploids. This paper presents novel and rigorous statistical methods for predicting the number of sequence reads needed to ensure accurate GBS at a polymorphic site bared by the reads in polyploids and shows that a dozen of reads can ensure a probability of 95% to recover all constituent alleles of any tetraploid genotype but several hundreds of reads are needed to accurately uncover the genotype with probability confidence of 90%, subverting the proposition of GBS using low coverage sequence data in the literature. The theoretical prediction was tested by use of RAD-seq data from tetraploid potato cultivars. The paper provides polyploid experimentalists with theoretical guides and methods for designing and conducting their sequence-based studies.}, } @article {pmid34472688, year = {2022}, author = {Kořený, L and Oborník, M and Horáková, E and Waller, RF and Lukeš, J}, title = {The convoluted history of haem biosynthesis.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {97}, number = {1}, pages = {141-162}, doi = {10.1111/brv.12794}, pmid = {34472688}, issn = {1469-185X}, support = {214298/Z/18/Z//Wellcome Investigator Award/ ; }, mesh = {Biological Evolution ; *Eukaryota/genetics ; *Heme/genetics/metabolism ; Metabolic Networks and Pathways ; }, abstract = {The capacity of haem to transfer electrons, bind diatomic gases, and catalyse various biochemical reactions makes it one of the essential biomolecules on Earth and one that was likely used by the earliest forms of cellular life. Since the description of haem biosynthesis, our understanding of this multi-step pathway has been almost exclusively derived from a handful of model organisms from narrow taxonomic contexts. Recent advances in genome sequencing and functional studies of diverse and previously neglected groups have led to discoveries of alternative routes of haem biosynthesis that deviate from the 'classical' pathway. In this review, we take an evolutionarily broad approach to illuminate the remarkable diversity and adaptability of haem synthesis, from prokaryotes to eukaryotes, showing the range of strategies that organisms employ to obtain and utilise haem. In particular, the complex evolutionary histories of eukaryotes that involve multiple endosymbioses and horizontal gene transfers are reflected in the mosaic origin of numerous metabolic pathways with haem biosynthesis being a striking case. We show how different evolutionary trajectories and distinct life strategies resulted in pronounced tensions and differences in the spatial organisation of the haem biosynthesis pathway, in some cases leading to a complete loss of a haem-synthesis capacity and, rarely, even loss of a requirement for haem altogether.}, } @article {pmid34436602, year = {2021}, author = {Petrů, M and Dohnálek, V and Füssy, Z and Doležal, P}, title = {Fates of Sec, Tat, and YidC Translocases in Mitochondria and Other Eukaryotic Compartments.}, journal = {Molecular biology and evolution}, volume = {38}, number = {12}, pages = {5241-5254}, pmid = {34436602}, issn = {1537-1719}, mesh = {*Escherichia coli Proteins/genetics ; *Eukaryota/genetics/metabolism ; Evolution, Molecular ; Membrane Transport Proteins/genetics/metabolism ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/genetics/metabolism ; Protein Transport ; }, abstract = {Formation of mitochondria by the conversion of a bacterial endosymbiont was a key moment in the evolution of eukaryotes. It was made possible by outsourcing the endosymbiont's genetic control to the host nucleus, while developing the import machinery for proteins synthesized on cytosolic ribosomes. The original protein export machines of the nascent organelle remained to be repurposed or were completely abandoned. This review follows the evolutionary fates of three prokaryotic inner membrane translocases Sec, Tat, and YidC. Homologs of all three translocases can still be found in current mitochondria, but with different importance for mitochondrial function. Although the mitochondrial YidC homolog, Oxa1, became an omnipresent independent insertase, the other two remained only sporadically present in mitochondria. Only a single substrate is known for the mitochondrial Tat and no function has yet been assigned for the mitochondrial Sec. Finally, this review compares these ancestral mitochondrial proteins with their paralogs operating in the plastids and the endomembrane system.}, } @article {pmid34378142, year = {2022}, author = {Xie, R and Wang, Y and Huang, D and Hou, J and Li, L and Hu, H and Zhao, X and Wang, F}, title = {Expanding Asgard members in the domain of Archaea sheds new light on the origin of eukaryotes.}, journal = {Science China. Life sciences}, volume = {65}, number = {4}, pages = {818-829}, pmid = {34378142}, issn = {1869-1889}, mesh = {*Archaea/genetics/metabolism ; *Eukaryota/genetics ; Eukaryotic Cells/metabolism ; Phylogeny ; }, abstract = {The hypothesis that eukaryotes originated from within the domain Archaea has been strongly supported by recent phylogenomic analyses placing Heimdallarchaeota-Wukongarchaeota branch from the Asgard superphylum as the closest known archaeal sister-group to eukaryotes. However, our understanding is still limited in terms of the relationship between eukaryotes and archaea, as well as the evolution and ecological functions of the Asgard archaea. Here, we describe three previously unknown phylum-level Asgard archaeal lineages, tentatively named Sigyn-, Freyr- and Njordarchaeota. Additional members in Wukongarchaeota and Baldrarchaeota from distinct environments are also reported here, further expanding their ecological roles and metabolic capacities. Comprehensive phylogenomic analyses further supported the origin of eukaryotes within Asgard archaea and a new lineage Njordarchaeota was supposed as the known closest branch with the eukaryotic nuclear host lineage. Metabolic reconstruction suggests that Njordarchaeota may have a heterotrophic lifestyle with capability of peptides and amino acids utilization, while Sigynarchaeota and Freyrarchaeota also have the potentials to fix inorganic carbon via the Wood-Ljungdahl pathway and degrade organic matters. Additionally, the Ack/Pta pathway for homoacetogenesis and de novo anaerobic cobalamin biosynthesis pathway were found in Freyrarchaeota and Wukongrarchaeota, respectively. Some previously unidentified eukaryotic signature proteins for intracellular membrane trafficking system, and the homologue of mu/sigma subunit of adaptor protein complex, were identified in Freyrarchaeota. This study expands the Asgard superphylum, sheds new light on the evolution of eukaryotes and improves our understanding of ecological functions of the Asgard archaea.}, } @article {pmid34343017, year = {2021}, author = {Gabaldón, T}, title = {Origin and Early Evolution of the Eukaryotic Cell.}, journal = {Annual review of microbiology}, volume = {75}, number = {}, pages = {631-647}, doi = {10.1146/annurev-micro-090817-062213}, pmid = {34343017}, issn = {1545-3251}, mesh = {*Biological Evolution ; Eukaryota/genetics ; *Eukaryotic Cells/metabolism ; Phylogeny ; Prokaryotic Cells/metabolism ; Symbiosis ; }, abstract = {The origin of eukaryotes has been defined as the major evolutionary transition since the origin of life itself. Most hallmark traits of eukaryotes, such as their intricate intracellular organization, can be traced back to a putative common ancestor that predated the broad diversity of extant eukaryotes. However, little is known about the nature and relative order of events that occurred in the path from preexisting prokaryotes to this already sophisticated ancestor. The origin of mitochondria from the endosymbiosis of an alphaproteobacterium is one of the few robustly established events to which most hypotheses on the origin of eukaryotes are anchored, but the debate is still open regarding the time of this acquisition, the nature of the host, and the ecological and metabolic interactions between the symbiotic partners. After the acquisition of mitochondria, eukaryotes underwent a fast radiation into several major clades whose phylogenetic relationships have been largely elusive. Recent progress in the comparative analyses of a growing number of genomes is shedding light on the early events of eukaryotic evolution as well as on the root and branching patterns of the tree of eukaryotes. Here I discuss current knowledge and debates on the origin and early evolution of eukaryotes. I focus particularly on how phylogenomic analyses have challenged some of the early assumptions about eukaryotic evolution, including the widespread idea that mitochondrial symbiosis in an archaeal host was the earliest event in eukaryogenesis.}, } @article {pmid34282823, year = {2021}, author = {Makarov, AA and Padilla-Mejia, NE and Field, MC}, title = {Evolution and diversification of the nuclear pore complex.}, journal = {Biochemical Society transactions}, volume = {49}, number = {4}, pages = {1601-1619}, pmid = {34282823}, issn = {1470-8752}, support = {/WT_/Wellcome Trust/United Kingdom ; 204697/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Biological Evolution ; Biological Transport ; Membrane Proteins/metabolism ; Mitosis ; Nuclear Pore/*metabolism ; RNA, Messenger/metabolism ; }, abstract = {The nuclear pore complex (NPC) is responsible for transport between the cytoplasm and nucleoplasm and one of the more intricate structures of eukaryotic cells. Typically composed of over 300 polypeptides, the NPC shares evolutionary origins with endo-membrane and intraflagellar transport system complexes. The modern NPC was fully established by the time of the last eukaryotic common ancestor and, hence, prior to eukaryote diversification. Despite the complexity, the NPC structure is surprisingly flexible with considerable variation between lineages. Here, we review diversification of the NPC in major taxa in view of recent advances in genomic and structural characterisation of plant, protist and nucleomorph NPCs and discuss the implications for NPC evolution. Furthermore, we highlight these changes in the context of mRNA export and consider how this process may have influenced NPC diversity. We reveal the NPC as a platform for continual evolution and adaptation.}, } @article {pmid34252921, year = {2021}, author = {Anselmetti, Y and El-Mabrouk, N and Lafond, M and Ouangraoua, A}, title = {Gene tree and species tree reconciliation with endosymbiotic gene transfer.}, journal = {Bioinformatics (Oxford, England)}, volume = {37}, number = {Suppl_1}, pages = {i120-i132}, pmid = {34252921}, issn = {1367-4811}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; //Fonds de recherche Nature et Technologie, Québec/ ; }, mesh = {Algorithms ; *Evolution, Molecular ; Gene Duplication ; *Gene Transfer, Horizontal ; Genome ; Phylogeny ; Symbiosis/genetics ; }, abstract = {MOTIVATION: It is largely established that all extant mitochondria originated from a unique endosymbiotic event integrating an α-proteobacterial genome into an eukaryotic cell. Subsequently, eukaryote evolution has been marked by episodes of gene transfer, mainly from the mitochondria to the nucleus, resulting in a significant reduction of the mitochondrial genome, eventually completely disappearing in some lineages. However, in other lineages such as in land plants, a high variability in gene repertoire distribution, including genes encoded in both the nuclear and mitochondrial genome, is an indication of an ongoing process of Endosymbiotic Gene Transfer (EGT). Understanding how both nuclear and mitochondrial genomes have been shaped by gene loss, duplication and transfer is expected to shed light on a number of open questions regarding the evolution of eukaryotes, including rooting of the eukaryotic tree.

RESULTS: We address the problem of inferring the evolution of a gene family through duplication, loss and EGT events, the latter considered as a special case of horizontal gene transfer occurring between the mitochondrial and nuclear genomes of the same species (in one direction or the other). We consider both EGT events resulting in maintaining (EGTcopy) or removing (EGTcut) the gene copy in the source genome. We present a linear-time algorithm for computing the DLE (Duplication, Loss and EGT) distance, as well as an optimal reconciled tree, for the unitary cost, and a dynamic programming algorithm allowing to output all optimal reconciliations for an arbitrary cost of operations. We illustrate the application of our EndoRex software and analyze different costs settings parameters on a plant dataset and discuss the resulting reconciled trees.

EndoRex implementation and supporting data are available on the GitHub repository via https://github.com/AEVO-lab/EndoRex.}, } @article {pmid34247240, year = {2021}, author = {Vargová, R and Wideman, JG and Derelle, R and Klimeš, V and Kahn, RA and Dacks, JB and Eliáš, M}, title = {A Eukaryote-Wide Perspective on the Diversity and Evolution of the ARF GTPase Protein Family.}, journal = {Genome biology and evolution}, volume = {13}, number = {8}, pages = {}, pmid = {34247240}, issn = {1759-6653}, support = {R21 ES021028/ES/NIEHS NIH HHS/United States ; R35 GM122568/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Eukaryota/genetics ; Eukaryotic Cells ; Evolution, Molecular ; *GTP Phosphohydrolases/genetics ; Genome ; Phylogeny ; }, abstract = {The evolution of eukaryotic cellular complexity is interwoven with the extensive diversification of many protein families. One key family is the ARF GTPases that act in eukaryote-specific processes, including membrane traffic, tubulin assembly, actin dynamics, and cilia-related functions. Unfortunately, our understanding of the evolution of this family is limited. Sampling an extensive set of available genome and transcriptome sequences, we have assembled a data set of over 2,000 manually curated ARF family genes from 114 eukaryotic species, including many deeply diverged protist lineages, and carried out comprehensive molecular phylogenetic analyses. These reconstructed as many as 16 ARF family members present in the last eukaryotic common ancestor, nearly doubling the previously inferred ancient system complexity. Evidence for the wide occurrence and ancestral origin of Arf6, Arl13, and Arl16 is presented for the first time. Moreover, Arl17, Arl18, and SarB, newly described here, are absent from well-studied model organisms and as a result their function(s) remain unknown. Analyses of our data set revealed a previously unsuspected diversity of membrane association modes and domain architectures within the ARF family. We detail the step-wise expansion of the ARF family in the metazoan lineage, including discovery of several new animal-specific family members. Delving back to its earliest evolution in eukaryotes, the resolved relationship observed between the ARF family paralogs sets boundaries for scenarios of vesicle coat origins during eukaryogenesis. Altogether, our work fundamentally broadens the understanding of the diversity and evolution of a protein family underpinning the structural and functional complexity of the eukaryote cells.}, } @article {pmid34229349, year = {2021}, author = {Devos, DP}, title = {Reconciling Asgardarchaeota Phylogenetic Proximity to Eukaryotes and Planctomycetes Cellular Features in the Evolution of Life.}, journal = {Molecular biology and evolution}, volume = {38}, number = {9}, pages = {3531-3542}, pmid = {34229349}, issn = {1537-1719}, mesh = {Archaea/genetics ; Biological Evolution ; *Eukaryota/genetics ; Phylogeny ; *Planctomycetes ; }, abstract = {The relationship between the three domains of life-Archaea, Bacteria, and Eukarya-is one of Biology's greatest mysteries. Current favored models imply two ancestral domains, Bacteria and Archaea, with eukaryotes originating within Archaea. This type of models has been supported by the recent description of the Asgardarchaeota, the closest prokaryotic relatives of eukaryotes. However, there are many problems associated with any scenarios implying that eukaryotes originated from within the Archaea, including genome mosaicism, phylogenies, the cellular organization of the Archaea, and their ancestral character. By contrast, all models of eukaryogenesis fail to consider two relevant discoveries: the detection of membrane coat proteins, and of phagocytosis-related processes in Planctomycetes, which are among the bacteria with the most developed endomembrane system. Consideration of these often overlooked features and others found in Planctomycetes and related bacteria suggest an evolutionary model based on a single ancestral domain. In this model, the proximity of Asgard and eukaryotes is not rejected but instead, Asgard are considered as diverging away from a common ancestor instead of on the way toward the eukaryotic ancestor. This model based on a single ancestral domain solves most of the ambiguities associated with the ones based on two ancestral domains. The single-domain model is better suited to explain the origin and evolution of all three domains of life, blurring the distinctions between them. Support for this model as well as the opportunities that it presents not only for reinterpreting previous results, but also for planning future experiments, are explored.}, } @article {pmid34228793, year = {2021}, author = {Zhang, S and Hama, Y and Mizushima, N}, title = {The evolution of autophagy proteins - diversification in eukaryotes and potential ancestors in prokaryotes.}, journal = {Journal of cell science}, volume = {134}, number = {13}, pages = {}, doi = {10.1242/jcs.233742}, pmid = {34228793}, issn = {1477-9137}, mesh = {Archaea/genetics ; Autophagy/genetics ; *Eukaryota/genetics ; Eukaryotic Cells ; Evolution, Molecular ; Phylogeny ; *Prokaryotic Cells ; }, abstract = {Autophagy is a degradative pathway for cytoplasmic constituents, and is conserved across eukaryotes. Autophagy-related (ATG) genes have undergone extensive multiplications and losses in different eukaryotic lineages, resulting in functional diversification and specialization. Notably, even though bacteria and archaea do not possess an autophagy pathway, they do harbor some remote homologs of Atg proteins, suggesting that preexisting proteins were recruited when the autophagy pathway developed during eukaryogenesis. In this Review, we summarize our current knowledge on the distribution of Atg proteins within eukaryotes and outline the major multiplication and loss events within the eukaryotic tree. We also discuss the potential prokaryotic homologs of Atg proteins identified to date, emphasizing the evolutionary relationships and functional differences between prokaryotic and eukaryotic proteins.}, } @article {pmid34217168, year = {2021}, author = {Tan, DX}, title = {Genesis of the nucleus from bacterial sporulation: A simple hypothesis of eukaryotic origin.}, journal = {Neuro endocrinology letters}, volume = {42}, number = {2}, pages = {113-127}, pmid = {34217168}, issn = {2354-4716}, abstract = {The most complexed issue of eukaryogenesis is the origin of the nucleus. Many hypotheses have been forwarded to explain this. Most of them are complicated and intangible. Here, a new and relatively simple hypothesis to address this unresolved problem has been hypothesized. This hypothesis is denominated as "Theory of Nucleus Origin from Bacterial Sporulation" (TNOBS). The hypothesis points out that the nucleus may be derived from a bacterial endospore, particularly, when sporulation is arrested at stage 4 due to a gene mutation. At this stage, a double membrane structure containing a chromosome (foreospore) has developed, which is reminiscent of a nucleus. In addition to the forespore, the mother cell also contains an additional chromosome. This morphologically specific cell is referred as a proto-nucleate cell (PTC). The PTC requires additional energy to maintain their newly formed endomembrane compartment (protonucleus). This energy demand has the potential of driving the expression of genes for energy production from the cytosolic chromosome which finally evolves to mitochondria, whereas the forespore develops to the nucleus. This TNOBS considers the nucleus and mitochondrion having derived simultaneously in the same cell. Moreover, this scenario avoids the difficulty to explain how an α-proteobacterium (precursor of mitochondria) can be taken up by the host despite of lacking capacity for classic endocytosis. It is further suggested that PTC generation may not be an extremely rare event in nature due to the widely existing spore-forming bacteria and frequent mutations. TNOBS is comparably simple and may, in some of its principle traits, be even reproducible under laboratory conditions.}, } @article {pmid34203645, year = {2021}, author = {Almojil, D and Bourgeois, Y and Falis, M and Hariyani, I and Wilcox, J and Boissinot, S}, title = {The Structural, Functional and Evolutionary Impact of Transposable Elements in Eukaryotes.}, journal = {Genes}, volume = {12}, number = {6}, pages = {}, pmid = {34203645}, issn = {2073-4425}, mesh = {Animals ; *DNA Transposable Elements ; *Evolution, Molecular ; Humans ; Plants/genetics ; }, abstract = {Transposable elements (TEs) are nearly ubiquitous in eukaryotes. The increase in genomic data, as well as progress in genome annotation and molecular biology techniques, have revealed the vast number of ways mobile elements have impacted the evolution of eukaryotes. In addition to being the main cause of difference in haploid genome size, TEs have affected the overall organization of genomes by accumulating preferentially in some genomic regions, by causing structural rearrangements or by modifying the recombination rate. Although the vast majority of insertions is neutral or deleterious, TEs have been an important source of evolutionary novelties and have played a determinant role in the evolution of fundamental biological processes. TEs have been recruited in the regulation of host genes and are implicated in the evolution of regulatory networks. They have also served as a source of protein-coding sequences or even entire genes. The impact of TEs on eukaryotic evolution is only now being fully appreciated and the role they may play in a number of biological processes, such as speciation and adaptation, remains to be deciphered.}, } @article {pmid34166615, year = {2021}, author = {Liu, J and Tassinari, M and Souza, DP and Naskar, S and Noel, JK and Bohuszewicz, O and Buck, M and Williams, TA and Baum, B and Low, HH}, title = {Bacterial Vipp1 and PspA are members of the ancient ESCRT-III membrane-remodeling superfamily.}, journal = {Cell}, volume = {184}, number = {14}, pages = {3660-3673.e18}, pmid = {34166615}, issn = {1097-4172}, support = {MC_UP_1201/27/MRC_/Medical Research Council/United Kingdom ; 215553/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; 200074/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; 203276/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; BB/P001440/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/chemistry/isolation & purification/*metabolism/ultrastructure ; Cell Membrane/*metabolism ; Chickens ; Cryoelectron Microscopy ; Endosomal Sorting Complexes Required for Transport/chemistry/*metabolism ; Evolution, Molecular ; Heat-Shock Proteins/chemistry/*metabolism/ultrastructure ; Humans ; Models, Molecular ; *Multigene Family ; Nostoc/*metabolism ; Protein Structure, Secondary ; Sequence Homology, Amino Acid ; Thermodynamics ; }, abstract = {Membrane remodeling and repair are essential for all cells. Proteins that perform these functions include Vipp1/IM30 in photosynthetic plastids, PspA in bacteria, and ESCRT-III in eukaryotes. Here, using a combination of evolutionary and structural analyses, we show that these protein families are homologous and share a common ancient evolutionary origin that likely predates the last universal common ancestor. This homology is evident in cryo-electron microscopy structures of Vipp1 rings from the cyanobacterium Nostoc punctiforme presented over a range of symmetries. Each ring is assembled from rungs that stack and progressively tilt to form dome-shaped curvature. Assembly is facilitated by hinges in the Vipp1 monomer, similar to those in ESCRT-III proteins, which allow the formation of flexible polymers. Rings have an inner lumen that is able to bind and deform membranes. Collectively, these data suggest conserved mechanistic principles that underlie Vipp1, PspA, and ESCRT-III-dependent membrane remodeling across all domains of life.}, } @article {pmid34131078, year = {2021}, author = {Hoshino, Y and Gaucher, EA}, title = {Evolution of bacterial steroid biosynthesis and its impact on eukaryogenesis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {25}, pages = {}, pmid = {34131078}, issn = {1091-6490}, support = {R01 AR069137/AR/NIAMS NIH HHS/United States ; }, mesh = {Archaea/genetics ; Bacteria/genetics/*metabolism ; Bayes Theorem ; *Biosynthetic Pathways/genetics ; Cell Membrane/metabolism ; Eukaryotic Cells/*metabolism ; *Evolution, Molecular ; Genes, Bacterial ; Phylogeny ; Steroids/*biosynthesis ; }, abstract = {Steroids are components of the eukaryotic cellular membrane and have indispensable roles in the process of eukaryotic endocytosis by regulating membrane fluidity and permeability. In particular, steroids may have been a structural prerequisite for the acquisition of mitochondria via endocytosis during eukaryogenesis. While eukaryotes are inferred to have evolved from an archaeal lineage, there is little similarity between the eukaryotic and archaeal cellular membranes. As such, the evolution of eukaryotic cellular membranes has limited our understanding of eukaryogenesis. Despite evolving from archaea, the eukaryotic cellular membrane is essentially a fatty acid bacterial-type membrane, which implies a substantial bacterial contribution to the evolution of the eukaryotic cellular membrane. Here, we address the evolution of steroid biosynthesis in eukaryotes by combining ancestral sequence reconstruction and comprehensive phylogenetic analyses of steroid biosynthesis genes. Contrary to the traditional assumption that eukaryotic steroid biosynthesis evolved within eukaryotes, most steroid biosynthesis genes are inferred to be derived from bacteria. In particular, aerobic deltaproteobacteria (myxobacteria) seem to have mediated the transfer of key genes for steroid biosynthesis to eukaryotes. Analyses of resurrected steroid biosynthesis enzymes suggest that the steroid biosynthesis pathway in early eukaryotes may have been similar to the pathway seen in modern plants and algae. These resurrected proteins also experimentally demonstrate that molecular oxygen was required to establish the modern eukaryotic cellular membrane during eukaryogenesis. Our study provides unique insight into relationships between early eukaryotes and other bacteria in addition to the well-known endosymbiosis with alphaproteobacteria.}, } @article {pmid34021750, year = {2021}, author = {Wright, GSA}, title = {Bacterial Evolutionary Precursors of Eukaryotic Copper-Zinc Superoxide Dismutases.}, journal = {Molecular biology and evolution}, volume = {38}, number = {9}, pages = {3789-3803}, pmid = {34021750}, issn = {1537-1719}, support = {WRIGHT/OCT18/969-799/MNDA_/Motor Neurone Disease Association/United Kingdom ; }, mesh = {Bacteria/genetics/metabolism ; *Copper/metabolism ; *Eukaryota/metabolism ; Humans ; Superoxide Dismutase/chemistry/genetics/metabolism ; Zinc ; }, abstract = {Internalization of a bacteria by an archaeal cell expedited eukaryotic evolution. An important feature of the species that diversified into the great variety of eukaryotic life visible today was the ability to combat oxidative stress with a copper-zinc superoxide dismutase (CuZnSOD) enzyme activated by a specific, high-affinity copper chaperone. Adoption of a single protein interface that facilitates homodimerization and heterodimerization was essential; however, its evolution has been difficult to rationalize given the structural differences between bacterial and eukaryotic enzymes. In contrast, no consistent strategy for the maturation of periplasmic bacterial CuZnSODs has emerged. Here, 34 CuZnSODs are described that closely resemble the eukaryotic form but originate predominantly from aquatic bacteria. Crystal structures of a Bacteroidetes bacterium CuZnSOD portray both prokaryotic and eukaryotic characteristics and propose a mechanism for self-catalyzed disulfide maturation. Unification of a bacterial but eukaryotic-like CuZnSOD along with a ferredoxin-fold MXCXXC copper-binding domain within a single polypeptide created the advanced copper delivery system for CuZnSODs exemplified by the human copper chaperone for superoxide dismutase-1. The development of this system facilitated evolution of large and compartmentalized cells following endosymbiotic eukaryogenesis.}, } @article {pmid34008202, year = {2021}, author = {Speijer, D}, title = {Zombie ideas about early endosymbiosis: Which entry mechanisms gave us the "endo" in different endosymbionts?.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {43}, number = {7}, pages = {e2100069}, doi = {10.1002/bies.202100069}, pmid = {34008202}, issn = {1521-1878}, mesh = {Bacteria/genetics ; Biological Evolution ; Eukaryota ; *Eukaryotic Cells ; Phylogeny ; *Symbiosis ; }, abstract = {Recently, a review regarding the mechanics and evolution of mitochondrial fission appeared in Nature. Surprisingly, it stated authoritatively that the mitochondrial outer membrane, in contrast with the inner membrane of bacterial descent, was acquired from the host, presumably during uptake. However, it has been known for quite some time that this membrane was also derived from the Gram-negative, alpha-proteobacterium related precursor of present-day mitochondria. The zombie idea of the host membrane still surrounding the endosymbiont is not only wrong, but more importantly, might hamper the proper conception of possible scenarios of eukaryogenesis. Why? Because it steers the imagination not only with regard to possible uptake mechanisms, but also regarding what went on before. Here I critically discuss both the evidence for the continuity of the bacterial outer membrane, the reasons for the persistence of the erroneous host membrane hypothesis and the wider implications of these misconceptions for the ideas regarding events occurring during the first steps towards the evolution of the eukaryotes and later major eukaryotic differentiations. I will also highlight some of the latest insights regarding different instances of endosymbiont evolution.}, } @article {pmid33984158, year = {2021}, author = {Lineweaver, CH and Bussey, KJ and Blackburn, AC and Davies, PCW}, title = {Cancer progression as a sequence of atavistic reversions.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {43}, number = {7}, pages = {e2000305}, pmid = {33984158}, issn = {1521-1878}, support = {U54 CA217376/CA/NCI NIH HHS/United States ; U54-CA143682/CA/NCI NIH HHS/United States ; }, mesh = {*Biological Evolution ; Eukaryota ; Eukaryotic Cells ; Humans ; *Neoplasms/genetics ; Phenotype ; }, abstract = {It has long been recognized that cancer onset and progression represent a type of reversion to an ancestral quasi-unicellular phenotype. This general concept has been refined into the atavistic model of cancer that attempts to provide a quantitative analysis and testable predictions based on genomic data. Over the past decade, support for the multicellular-to-unicellular reversion predicted by the atavism model has come from phylostratigraphy. Here, we propose that cancer onset and progression involve more than a one-off multicellular-to-unicellular reversion, and are better described as a series of reversionary transitions. We make new predictions based on the chronology of the unicellular-eukaryote-to-multicellular-eukaryote transition. We also make new predictions based on three other evolutionary transitions that occurred in our lineage: eukaryogenesis, oxidative phosphorylation and the transition to adaptive immunity. We propose several modifications to current phylostratigraphy to improve age resolution to test these predictions. Also see the video abstract here: https://youtu.be/3unEu5JYJrQ.}, } @article {pmid33963405, year = {2021}, author = {Skejo, J and Garg, SG and Gould, SB and Hendriksen, M and Tria, FDK and Bremer, N and Franjević, D and Blackstone, NW and Martin, WF}, title = {Evidence for a Syncytial Origin of Eukaryotes from Ancestral State Reconstruction.}, journal = {Genome biology and evolution}, volume = {13}, number = {7}, pages = {}, pmid = {33963405}, issn = {1759-6653}, mesh = {Archaea/genetics ; *Biological Evolution ; *Eukaryota/genetics ; Eukaryotic Cells ; Phylogeny ; Prokaryotic Cells ; }, abstract = {Modern accounts of eukaryogenesis entail an endosymbiotic encounter between an archaeal host and a proteobacterial endosymbiont, with subsequent evolution giving rise to a unicell possessing a single nucleus and mitochondria. The mononucleate state of the last eukaryotic common ancestor (LECA) is seldom, if ever, questioned, even though cells harboring multiple (syncytia, coenocytes, and polykaryons) are surprisingly common across eukaryotic supergroups. Here, we present a survey of multinucleated forms. Ancestral character state reconstruction for representatives of 106 eukaryotic taxa using 16 different possible roots and supergroup sister relationships, indicate that LECA, in addition to being mitochondriate, sexual, and meiotic, was multinucleate. LECA exhibited closed mitosis, which is the rule for modern syncytial forms, shedding light on the mechanics of its chromosome segregation. A simple mathematical model shows that within LECA's multinucleate cytosol, relationships among mitochondria and nuclei were neither one-to-one, nor one-to-many, but many-to-many, placing mitonuclear interactions and cytonuclear compatibility at the evolutionary base of eukaryotic cell origin. Within a syncytium, individual nuclei and individual mitochondria function as the initial lower-level evolutionary units of selection, as opposed to individual cells, during eukaryogenesis. Nuclei within a syncytium rescue each other's lethal mutations, thereby postponing selection for viable nuclei and cytonuclear compatibility to the generation of spores, buffering transitional bottlenecks at eukaryogenesis. The prokaryote-to-eukaryote transition is traditionally thought to have left no intermediates, yet if eukaryogenesis proceeded via a syncytial common ancestor, intermediate forms have persisted to the present throughout the eukaryotic tree as syncytia but have so far gone unrecognized.}, } @article {pmid33923118, year = {2021}, author = {Filip, E and Skuza, L}, title = {Horizontal Gene Transfer Involving Chloroplasts.}, journal = {International journal of molecular sciences}, volume = {22}, number = {9}, pages = {}, pmid = {33923118}, issn = {1422-0067}, mesh = {Cell Nucleus/*genetics ; Chloroplasts/*genetics ; Endophytes/genetics ; *Gene Transfer, Horizontal ; Genome ; Mitochondria/*genetics ; Plants/genetics ; Plastids/genetics ; }, abstract = {Horizontal gene transfer (HGT)- is defined as the acquisition of genetic material from another organism. However, recent findings indicate a possible role of HGT in the acquisition of traits with adaptive significance, suggesting that HGT is an important driving force in the evolution of eukaryotes as well as prokaryotes. It has been noted that, in eukaryotes, HGT is more prevalent than originally thought. Mitochondria and chloroplasts lost a large number of genes after their respective endosymbiotic events occurred. Even after this major content loss, organelle genomes still continue to lose their own genes. Many of these are subsequently acquired by intracellular gene transfer from the original plastid. The aim of our review was to elucidate the role of chloroplasts in the transfer of genes. This review also explores gene transfer involving mitochondrial and nuclear genomes, though recent studies indicate that chloroplast genomes are far more active in HGT as compared to these other two DNA-containing cellular compartments.}, } @article {pmid33911286, year = {2021}, author = {Liu, Y and Makarova, KS and Huang, WC and Wolf, YI and Nikolskaya, AN and Zhang, X and Cai, M and Zhang, CJ and Xu, W and Luo, Z and Cheng, L and Koonin, EV and Li, M}, title = {Expanded diversity of Asgard archaea and their relationships with eukaryotes.}, journal = {Nature}, volume = {593}, number = {7860}, pages = {553-557}, pmid = {33911286}, issn = {1476-4687}, mesh = {Archaea/*classification ; Biological Evolution ; Eukaryota ; *Genome, Archaeal ; Metagenomics ; *Phylogeny ; }, abstract = {Asgard is a recently discovered superphylum of archaea that appears to include the closest archaeal relatives of eukaryotes[1-5]. Debate continues as to whether the archaeal ancestor of eukaryotes belongs within the Asgard superphylum or whether this ancestor is a sister group to all other archaea (that is, a two-domain versus a three-domain tree of life)[6-8]. Here we present a comparative analysis of 162 complete or nearly complete genomes of Asgard archaea, including 75 metagenome-assembled genomes that-to our knowledge-have not previously been reported. Our results substantially expand the phylogenetic diversity of Asgard and lead us to propose six additional phyla that include a deep branch that we have provisionally named Wukongarchaeota. Our phylogenomic analysis does not resolve unequivocally the evolutionary relationship between eukaryotes and Asgard archaea, but instead-depending on the choice of species and conserved genes used to build the phylogeny-supports either the origin of eukaryotes from within Asgard (as a sister group to the expanded Heimdallarchaeota-Wukongarchaeota branch) or a deeper branch for the eukaryote ancestor within archaea. Our comprehensive protein domain analysis using the 162 Asgard genomes results in a major expansion of the set of eukaryotic signature proteins. The Asgard eukaryotic signature proteins show variable phyletic distributions and domain architectures, which is suggestive of dynamic evolution through horizontal gene transfer, gene loss, gene duplication and domain shuffling. The phylogenomics of the Asgard archaea points to the accumulation of the components of the mobile archaeal 'eukaryome' in the archaeal ancestor of eukaryotes (within or outside Asgard) through extensive horizontal gene transfer.}, } @article {pmid33892498, year = {2021}, author = {Knopp, M and Stockhorst, S and van der Giezen, M and Garg, SG and Gould, SB}, title = {The Asgard Archaeal-Unique Contribution to Protein Families of the Eukaryotic Common Ancestor Was 0.3.}, journal = {Genome biology and evolution}, volume = {13}, number = {6}, pages = {}, pmid = {33892498}, issn = {1759-6653}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Eukaryota/*genetics ; *Multigene Family ; }, abstract = {The identification of the asgard archaea has fueled speculations regarding the nature of the archaeal host in eukaryogenesis and its level of complexity prior to endosymbiosis. Here, we analyzed the coding capacity of 150 eukaryotes, 1,000 bacteria, and 226 archaea, including the only cultured member of the asgard archaea. Clustering methods that consistently recover endosymbiotic contributions to eukaryotic genomes recover an asgard archaeal-unique contribution of a mere 0.3% to protein families present in the last eukaryotic common ancestor, while simultaneously suggesting that this group's diversity rivals that of all other archaea combined. The number of homologs shared exclusively between asgard archaea and eukaryotes is only 27 on average. This tiny asgard archaeal-unique contribution to the root of eukaryotic protein families questions claims that archaea evolved complexity prior to eukaryogenesis. Genomic and cellular complexity remains a eukaryote-specific feature and is best understood as the archaeal host's solution to housing an endosymbiont.}, } @article {pmid33871607, year = {2021}, author = {Wang, J and Han, GZ}, title = {Unearthing LTR Retrotransposon gag Genes Co-opted in the Deep Evolution of Eukaryotes.}, journal = {Molecular biology and evolution}, volume = {38}, number = {8}, pages = {3267-3278}, pmid = {33871607}, issn = {1537-1719}, mesh = {Animals ; *Biological Evolution ; Eukaryota/*genetics ; *Genes, gag ; Retroelements/*genetics ; Selection, Genetic ; }, abstract = {LTR retrotransposons comprise a major component of the genomes of eukaryotes. On occasion, retrotransposon genes can be recruited by their hosts for diverse functions, a process formally referred to as co-option. However, a comprehensive picture of LTR retrotransposon gag gene co-option in eukaryotes is still lacking, with several documented cases exclusively involving Ty3/Gypsy retrotransposons in animals. Here, we use a phylogenomic approach to systemically unearth co-option of retrotransposon gag genes above the family level of taxonomy in 2,011 eukaryotes, namely co-option occurring during the deep evolution of eukaryotes. We identify a total of 14 independent gag gene co-option events across more than 740 eukaryote families, eight of which have not been reported previously. Among these retrotransposon gag gene co-option events, nine, four, and one involve gag genes of Ty3/Gypsy, Ty1/Copia, and Bel-Pao retrotransposons, respectively. Seven, four, and three co-option events occurred in animals, plants, and fungi, respectively. Interestingly, two co-option events took place in the early evolution of angiosperms. Both selective pressure and gene expression analyses further support that these co-opted gag genes might perform diverse cellular functions in their hosts, and several co-opted gag genes might be subject to positive selection. Taken together, our results provide a comprehensive picture of LTR retrotransposon gag gene co-option events that occurred during the deep evolution of eukaryotes and suggest paucity of LTR retrotransposon gag gene co-option during the deep evolution of eukaryotes.}, } @article {pmid33860546, year = {2021}, author = {Brandeis, M}, title = {Were eukaryotes made by sex?: Sex might have been vital for merging endosymbiont and host genomes giving rise to eukaryotes.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {43}, number = {6}, pages = {e2000256}, doi = {10.1002/bies.202000256}, pmid = {33860546}, issn = {1521-1878}, mesh = {Archaea/genetics ; *Biological Evolution ; *Eukaryota/genetics ; Eukaryotic Cells ; Phylogeny ; Symbiosis/genetics ; }, abstract = {I hypothesize that the appearance of sex facilitated the merging of the endosymbiont and host genomes during early eukaryote evolution. Eukaryotes were formed by symbiosis between a bacterium that entered an archaeon, eventually giving rise to mitochondria. This entry was followed by the gradual transfer of most bacterial endosymbiont genes into the archaeal host genome. I argue that the merging of the mitochondrial genes into the host genome was vital for the evolution of genuine eukaryotes. At the time this process commenced it was unprecedented and required a novel mechanism. I suggest that this mechanism was meiotic sex, and that its appearance might have been THE crucial step that enabled the evolution of proper eukaryotes from early endosymbiont containing proto-eukaryotes. Sex might continue to be essential today for keeping genome insertions in check. Also see the video abstract here: https://youtu.be/aVMvWMpomac.}, } @article {pmid33857537, year = {2021}, author = {Deonath, A}, title = {Evolution of eukaryotes as a story of survival and growth of mitochondrial DNA over two billion years.}, journal = {Bio Systems}, volume = {206}, number = {}, pages = {104426}, doi = {10.1016/j.biosystems.2021.104426}, pmid = {33857537}, issn = {1872-8324}, mesh = {Animals ; *Biological Evolution ; Cell Survival/physiology ; DNA, Mitochondrial/*physiology ; Eukaryota/genetics/*growth & development ; Eukaryotic Cells/*physiology ; *Evolution, Molecular ; Humans ; Mitochondria/physiology ; Time Factors ; }, abstract = {Mitochondria's significance in human diseases and in functioning, health and death of eukaryotic cell has been acknowledged widely. Yet our perspective in cell biology and evolution remains nucleocentric. Mitochondrial DNA, by virtue of its omnipresence and species-level conservation, is used as a barcode in animal taxonomy. This article analyses various levels of containment structures that enclose mitochondrial DNA and advocates a fresh perspective wherein evolution of organic structures of the eukarya domain seem to support and facilitate survival and proliferation of mitochondrial DNA by splitting containers as they age and by directing them along two distinct pathways: destruction of containers with more mutant mitochondrial DNA and rejuvenation of containers with less mutant mitochondrial DNA.}, } @article {pmid33837594, year = {2021}, author = {Nasir, A and Mughal, F and Caetano-Anollés, G}, title = {The tree of life describes a tripartite cellular world.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {43}, number = {6}, pages = {e2000343}, doi = {10.1002/bies.202000343}, pmid = {33837594}, issn = {1521-1878}, mesh = {*Archaea/genetics ; Biological Evolution ; *Eukaryota ; Eukaryotic Cells ; Evolution, Molecular ; Phylogeny ; }, abstract = {The canonical view of a 3-domain (3D) tree of life was recently challenged by the discovery of Asgardarchaeota encoding eukaryote signature proteins (ESPs), which were treated as missing links of a 2-domain (2D) tree. Here we revisit the debate. We discuss methodological limitations of building trees with alignment-dependent approaches, which often fail to satisfactorily address the problem of ''gaps.'' In addition, most phylogenies are reconstructed unrooted, neglecting the power of direct rooting methods. Alignment-free methodologies lift most difficulties but require employing realistic evolutionary models. We argue that the discoveries of Asgards and ESPs, by themselves, do not rule out the 3D tree, which is strongly supported by comparative and evolutionary genomic analyses and vast genomic and biochemical superkingdom distinctions. Given uncertainties of retrodiction and interpretation difficulties, we conclude that the 3D view has not been falsified but instead has been strengthened by genomic analyses. In turn, the objections to the 2D model have not been lifted. The debate remains open. Also see the video abstract here: https://youtu.be/-6TBN0bubI8.}, } @article {pmid33812918, year = {2021}, author = {Mikhailovsky, GE and Gordon, R}, title = {LUCA to LECA, the Lucacene: A model for the gigayear delay from the first prokaryote to eukaryogenesis.}, journal = {Bio Systems}, volume = {205}, number = {}, pages = {104415}, doi = {10.1016/j.biosystems.2021.104415}, pmid = {33812918}, issn = {1872-8324}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Biological Evolution ; Computer Simulation ; Eukaryota/*genetics ; *Gene Transfer, Horizontal ; *Models, Biological ; Mutation ; *Systems Biology ; Time Factors ; }, abstract = {It is puzzling why life on Earth consisted of prokaryotes for up to 2.5 ± 0.5 billion years (Gy) before the appearance of the first eukaryotes. This period, from LUCA (Last Universal Common Ancestor) to LECA (Last Eucaryotic Common Ancestor), we have named the Lucacene, to suggest all prokaryotic descendants of LUCA before the appearance of LECA. Here we present a simple model based on horizontal gene transfer (HGT). It is the process of HGT from Bacteria to Archaea and its reverse that we wish to simulate and estimate its duration until eukaryogenesis. Rough quantitation of its parameters shows that the model may explain the long duration of the Lucacene.}, } @article {pmid33748102, year = {2021}, author = {Dhakshinamoorthy, R and Singh, SP}, title = {Evolution of Reproductive Division of Labor - Lessons Learned From the Social Amoeba Dictyostelium discoideum During Its Multicellular Development.}, journal = {Frontiers in cell and developmental biology}, volume = {9}, number = {}, pages = {599525}, pmid = {33748102}, issn = {2296-634X}, abstract = {The origin of multicellular life from unicellular beings is an epochal step in the evolution of eukaryotes. There are several factors influencing cell fate choices during differentiation and morphogenesis of an organism. Genetic make-up of two cells that unite and fertilize is the key factor to signal the formation of various cell-types in due course of development. Although ploidy of the cell-types determines the genetics of an individual, the role of ploidy in cell fate decisions remains unclear. Dictyostelium serves as a versatile model to study the emergence of multicellular life from unicellular life forms. In this work, we investigate the role played by ploidy status of a cell on cell fate commitments during Dictyostelium development. To answer this question, we created Dictyostelium cells of different ploidy: haploid parents and derived isogenic diploids, allowing them to undergo development. The diploid strains used in this study were generated using parasexual genetics. The ploidy status of the haploids and diploids were confirmed by microscopy, flow cytometry, and karyotyping. Prior to reconstitution, we labeled the cells by two methods. First, intragenic expression of red fluorescent protein (RFP) and second, staining the amoebae with a vital, fluorescent dye carboxyfluorescein succinimidyl ester (CFSE). RFP labeled haploid cells allowed us to track the haploids in the chimeric aggregates, slugs, and fruiting bodies. The CFSE labeling method allowed us to track both the haploids and the diploids in the chimeric developmental structures. Our findings illustrate that the haploids demonstrate sturdy cell fate commitment starting from the aggregation stage. The haploids remain crowded at the aggregation centers of the haploid-diploid chimeric aggregates. At the slug stage haploids are predominantly occupying the slug posterior, and are visible in the spore population in the fruiting bodies. Our findings show that cell fate decisions during D. discoideum development are highly influenced by the ploidy status of a cell, adding a new aspect to already known factors Here, we report that ploidy status of a cell could also play a crucial role in regulating the cell fate commitments.}, } @article {pmid33744400, year = {2021}, author = {Lazcano, A and Peretó, J}, title = {Prokaryotic symbiotic consortia and the origin of nucleated cells: A critical review of Lynn Margulis hypothesis.}, journal = {Bio Systems}, volume = {204}, number = {}, pages = {104408}, doi = {10.1016/j.biosystems.2021.104408}, pmid = {33744400}, issn = {1872-8324}, mesh = {Basal Bodies ; *Biological Evolution ; Cell Movement ; Centromere ; *Eukaryotic Cells ; Flagella ; Genome, Mitochondrial ; Genome, Plastid ; Microbial Consortia ; Organelles/genetics ; *Prokaryotic Cells ; *Symbiosis ; }, abstract = {The publication in the late 1960s of Lynn Margulis endosymbiotic proposal is a scientific milestone that brought to the fore of evolutionary discussions the issue of the origin of nucleated cells. Although it is true that the times were ripe, the timely publication of Lynn Margulis' original paper was the product of an intellectually bold 29-years old scientist, who based on the critical analysis of the available scientific information produced an all-encompassing, sophisticated narrative scheme on the origin of eukaryotic cells as a result of the evolution of prokaryotic consortia and, in bold intellectual stroke, put it all in the context of planetary evolution. A critical historical reassessment of her original proposal demonstrates that her hypothesis was not a simple archival outline of past schemes, but a renewed historical narrative of prokaryotic evolution and the role of endosymbiosis in the origin of eukaryotes. Although it is now accepted that the closest bacterial relatives of mitochondria and plastids are α-proteobacteria and cyanobacteria, respectively, comparative genomics demonstrates the mosaic character of the organelle genomes. The available evidence has completely refuted Margulis' proposal of an exogenous origin for eukaryotic flagella, the (9 + 2) basal bodies, and centromeres, but we discuss in detail the reasons that led her to devote considerable efforts to argue for a symbiotic origin of the eukaryotic motility. An analysis of the arguments successfully employed by Margulis in her persuasive advocacy of endosymbiosis, combined with the discussions of her flaws and the scientific atmosphere during the period in which she formulated her proposals, are critical for a proper appraisal of the historical conditions that shaped her theory and its acceptance.}, } @article {pmid33621507, year = {2021}, author = {Roger, AJ and Susko, E and Leger, MM}, title = {Evolution: Reconstructing the Timeline of Eukaryogenesis.}, journal = {Current biology : CB}, volume = {31}, number = {4}, pages = {R193-R196}, doi = {10.1016/j.cub.2020.12.035}, pmid = {33621507}, issn = {1879-0445}, mesh = {*Eukaryota/genetics ; *Eukaryotic Cells ; *Evolution, Molecular ; Humans ; *Phylogeny ; Time Factors ; }, abstract = {Timing the events in the evolution of eukaryotic cells is crucial to understanding this major transition. A recent study reconstructs the origins of thousands of gene families ancestral to eukaryotes and, using a controversial approach, aims to order the events of eukaryogenesis.}, } @article {pmid33591272, year = {2021}, author = {Zhu, X and Boulet, A and Buckley, KM and Phillips, CB and Gammon, MG and Oldfather, LE and Moore, SA and Leary, SC and Cobine, PA}, title = {Mitochondrial copper and phosphate transporter specificity was defined early in the evolution of eukaryotes.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {33591272}, issn = {2050-084X}, support = {R01 GM120211/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; *Biological Evolution ; Cell Line ; Copper Transport Proteins/genetics/metabolism ; Eukaryota ; Mice ; Mitochondria ; Mitochondrial Proteins/*genetics/metabolism ; Mutagenesis, Site-Directed ; Phosphate Transport Proteins/genetics/metabolism ; Phylogeny ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/*genetics/metabolism ; }, abstract = {The mitochondrial carrier family protein SLC25A3 transports both copper and phosphate in mammals, yet in Saccharomyces cerevisiae the transport of these substrates is partitioned across two paralogs: PIC2 and MIR1. To understand the ancestral state of copper and phosphate transport in mitochondria, we explored the evolutionary relationships of PIC2 and MIR1 orthologs across the eukaryotic tree of life. Phylogenetic analyses revealed that PIC2-like and MIR1-like orthologs are present in all major eukaryotic supergroups, indicating an ancient gene duplication created these paralogs. To link this phylogenetic signal to protein function, we used structural modeling and site-directed mutagenesis to identify residues involved in copper and phosphate transport. Based on these analyses, we generated an L175A variant of mouse SLC25A3 that retains the ability to transport copper but not phosphate. This work highlights the utility of using an evolutionary framework to uncover amino acids involved in substrate recognition by mitochondrial carrier family proteins.}, } @article {pmid33571133, year = {2021}, author = {Carlisle, EM and Jobbins, M and Pankhania, V and Cunningham, JA and Donoghue, PCJ}, title = {Experimental taphonomy of organelles and the fossil record of early eukaryote evolution.}, journal = {Science advances}, volume = {7}, number = {5}, pages = {}, pmid = {33571133}, issn = {2375-2548}, support = {BB/N000919/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T012773/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {The timing of origin of eukaryotes and the sequence of eukaryogenesis are poorly constrained because their fossil record is difficult to interpret. Claims of fossilized organelles have been discounted on the unsubstantiated perception that they decay too quickly for fossilization. We experimentally characterized the pattern and time scale of decay of nuclei, chloroplasts, and pyrenoids in red and green algae, demonstrating that they persist for many weeks postmortem as physical substrates available for preservation, a time scale consistent with known mechanisms of fossilization. Chloroplasts exhibit greater decay resistance than nuclei; pyrenoids are unlikely to be preserved, but their presence could be inferred from spaces within fossil chloroplasts. Our results are compatible with differential organelle preservation in seed plants. Claims of fossilized organelles in Proterozoic fossils can no longer be dismissed on grounds of plausibility, prompting reinterpretation of the early eukaryotic fossil record and the prospect of a fossil record of eukaryogenesis.}, } @article {pmid33549602, year = {2021}, author = {Baluška, F and Lyons, S}, title = {Archaeal Origins of Eukaryotic Cell and Nucleus.}, journal = {Bio Systems}, volume = {203}, number = {}, pages = {104375}, doi = {10.1016/j.biosystems.2021.104375}, pmid = {33549602}, issn = {1872-8324}, mesh = {Actin Cytoskeleton ; Archaea/*cytology ; Biological Evolution ; Cell Biology ; *Cell Nucleus ; Cytoskeleton ; Eukaryota/*cytology ; *Mitochondria ; *Plastids ; *Symbiosis ; Trimethoprim, Sulfamethoxazole Drug Combination ; Tubulin ; }, abstract = {Symbiosis is a major evolutionary force, especially at the cellular level. Here we discuss several older and new discoveries suggesting that besides mitochondria and plastids, eukaryotic nuclei also have symbiotic origins. We propose an archaea-archaea scenario for the evolutionary origin of the eukaryotic cells. We suggest that two ancient archaea-like cells, one based on the actin cytoskeleton and another one based on the tubulin-centrin cytoskeleton, merged together to form the first nucleated eukaryotic cell. This archaeal endosymbiotic origin of eukaryotic cells and their nuclei explains several features of eukaryotic cells which are incompatible with the currently preferred autogenous scenarios of eukaryogenesis.}, } @article {pmid33538295, year = {2021}, author = {Collens, AB and Katz, LA}, title = {Opinion: Genetic Conflict With Mobile Elements Drives Eukaryotic Genome Evolution, and Perhaps Also Eukaryogenesis.}, journal = {The Journal of heredity}, volume = {112}, number = {1}, pages = {140-144}, pmid = {33538295}, issn = {1465-7333}, mesh = {*DNA Transposable Elements ; Epigenesis, Genetic ; Eukaryota/*genetics ; *Evolution, Molecular ; *Models, Genetic ; }, abstract = {Through analyses of diverse microeukaryotes, we have previously argued that eukaryotic genomes are dynamic systems that rely on epigenetic mechanisms to distinguish germline (i.e., DNA to be inherited) from soma (i.e., DNA that undergoes polyploidization, genome rearrangement, etc.), even in the context of a single nucleus. Here, we extend these arguments by including two well-documented observations: (1) eukaryotic genomes interact frequently with mobile genetic elements (MGEs) like viruses and transposable elements (TEs), creating genetic conflict, and (2) epigenetic mechanisms regulate MGEs. Synthesis of these ideas leads to the hypothesis that genetic conflict with MGEs contributed to the evolution of a dynamic eukaryotic genome in the last eukaryotic common ancestor (LECA), and may have contributed to eukaryogenesis (i.e., may have been a driver in the evolution of FECA, the first eukaryotic common ancestor). Sex (i.e., meiosis) may have evolved within the context of the development of germline-soma distinctions in LECA, as this process resets the germline genome by regulating/eliminating somatic (i.e., polyploid, rearranged) genetic material. Our synthesis of these ideas expands on hypotheses of the origin of eukaryotes by integrating the roles of MGEs and epigenetics.}, } @article {pmid33487111, year = {2021}, author = {Wan, KY and Jékely, G}, title = {Origins of eukaryotic excitability.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {376}, number = {1820}, pages = {20190758}, pmid = {33487111}, issn = {1471-2970}, mesh = {*Biological Evolution ; Eukaryota/*physiology ; Eukaryotic Cells/*physiology ; }, abstract = {All living cells interact dynamically with a constantly changing world. Eukaryotes, in particular, evolved radically new ways to sense and react to their environment. These advances enabled new and more complex forms of cellular behaviour in eukaryotes, including directional movement, active feeding, mating, and responses to predation. But what are the key events and innovations during eukaryogenesis that made all of this possible? Here we describe the ancestral repertoire of eukaryotic excitability and discuss five major cellular innovations that enabled its evolutionary origin. The innovations include a vastly expanded repertoire of ion channels, the emergence of cilia and pseudopodia, endomembranes as intracellular capacitors, a flexible plasma membrane and the relocation of chemiosmotic ATP synthesis to mitochondria, which liberated the plasma membrane for more complex electrical signalling involved in sensing and reacting. We conjecture that together with an increase in cell size, these new forms of excitability greatly amplified the degrees of freedom associated with cellular responses, allowing eukaryotes to vastly outperform prokaryotes in terms of both speed and accuracy. This comprehensive new perspective on the evolution of excitability enriches our view of eukaryogenesis and emphasizes behaviour and sensing as major contributors to the success of eukaryotes. This article is part of the theme issue 'Basal cognition: conceptual tools and the view from the single cell'.}, } @article {pmid33462601, year = {2021}, author = {Garg, SG and Kapust, N and Lin, W and Knopp, M and Tria, FDK and Nelson-Sathi, S and Gould, SB and Fan, L and Zhu, R and Zhang, C and Martin, WF}, title = {Anomalous Phylogenetic Behavior of Ribosomal Proteins in Metagenome-Assembled Asgard Archaea.}, journal = {Genome biology and evolution}, volume = {13}, number = {1}, pages = {}, pmid = {33462601}, issn = {1759-6653}, mesh = {Archaea/*genetics ; Ecosystem ; Eukaryota/genetics ; Eukaryotic Cells ; Evolution, Molecular ; *Genome, Archaeal ; Genomics ; *Metagenome ; Metagenomics ; *Phylogeny ; Ribosomal Proteins/*classification/*genetics ; }, abstract = {Metagenomic studies permit the exploration of microbial diversity in a defined habitat, and binning procedures enable phylogenomic analyses, taxon description, and even phenotypic characterizations in the absence of morphological evidence. Such lineages include asgard archaea, which were initially reported to represent archaea with eukaryotic cell complexity, although the first images of such an archaeon show simple cells with prokaryotic characteristics. However, these metagenome-assembled genomes (MAGs) might suffer from data quality problems not encountered in sequences from cultured organisms due to two common analytical procedures of bioinformatics: assembly of metagenomic sequences and binning of assembled sequences on the basis of innate sequence properties and abundance across samples. Consequently, genomic sequences of distantly related taxa, or domains, can in principle be assigned to the same MAG and result in chimeric sequences. The impacts of low-quality or chimeric MAGs on phylogenomic and metabolic prediction remain unknown. Debates that asgard archaeal data are contaminated with eukaryotic sequences are overshadowed by the lack of evidence indicating that individual asgard MAGs stem from the same chromosome. Here, we show that universal proteins including ribosomal proteins of asgard archaeal MAGs fail to meet the basic phylogenetic criterion fulfilled by genome sequences of cultured archaea investigated to date: These proteins do not share common evolutionary histories to the same extent as pure culture genomes do, pointing to a chimeric nature of asgard archaeal MAGs. Our analysis suggests that some asgard archaeal MAGs represent unnatural constructs, genome-like patchworks of genes resulting from assembly and/or the binning process.}, } @article {pmid33453317, year = {2021}, author = {Slijepcevic, P}, title = {Serial Endosymbiosis Theory: From biology to astronomy and back to the origin of life.}, journal = {Bio Systems}, volume = {202}, number = {}, pages = {104353}, doi = {10.1016/j.biosystems.2021.104353}, pmid = {33453317}, issn = {1872-8324}, mesh = {Astronomy/methods/*trends ; *Biological Evolution ; Biology/methods/*trends ; Eukaryota/physiology ; Humans ; *Origin of Life ; Phylogeny ; Symbiosis/*physiology ; }, abstract = {Serial Endosymbiosis Theory, or SET, was conceived and developed by Lynn Margulis, to explain the greatest discontinuity in the history of life, the origin of eukaryotic cells. Some predictions of SET, namely the origin of mitochondria and chloroplasts, withstood the test of the most recent evidence from a variety of disciplines including phylogenetics, biochemistry, and cell biology. Even though some other predictions fared less well, SET remains a seminal theory in biology. In this paper, I focus on two aspects of SET. First, using the concept of "universal symbiogenesis", developed by Freeman Dyson to search for commonalities in astronomy and biology, I propose that SET can be extended beyond eukaryogenesis. The extension refers to the possibility that even prokaryotic organisms, themselves subject to the process of symbiogenesis in SET, could have emerged symbiotically. Second, I contrast a recent "viral eukaryogenesis" hypothesis, according to which the nucleus evolved from a complex DNA virus, with a view closer to SET, according to which the nucleus evolved through the interplay of the archaeal host, the eubacterial symbiont, and a non-LTR transposon, or telomerase. Viruses joined in later, through the process of viral endogenization, to shape eukaryotic chromosomes in the process of karyotype evolution. These two proposals based on SET are a testament to its longevity as a scientific theory.}, } @article {pmid33435791, year = {2021}, author = {Padilla-Mejia, NE and Makarov, AA and Barlow, LD and Butterfield, ER and Field, MC}, title = {Evolution and diversification of the nuclear envelope.}, journal = {Nucleus (Austin, Tex.)}, volume = {12}, number = {1}, pages = {21-41}, pmid = {33435791}, issn = {1949-1042}, support = {MR/P009018/1/MRC_/Medical Research Council/United Kingdom ; MR/N010558/1/MRC_/Medical Research Council/United Kingdom ; 203134/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 204697/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Cell Nucleus/genetics ; Endoplasmic Reticulum ; *Nuclear Envelope ; Nuclear Pore/genetics ; *Proteomics ; }, abstract = {Eukaryotic cells arose ~1.5 billion years ago, with the endomembrane system a central feature, facilitating evolution of intracellular compartments. Endomembranes include the nuclear envelope (NE) dividing the cytoplasm and nucleoplasm. The NE possesses universal features: a double lipid bilayer membrane, nuclear pore complexes (NPCs), and continuity with the endoplasmic reticulum, indicating common evolutionary origin. However, levels of specialization between lineages remains unclear, despite distinct mechanisms underpinning various nuclear activities. Several distinct modes of molecular evolution facilitate organellar diversification and to understand which apply to the NE, we exploited proteomic datasets of purified nuclear envelopes from model systems for comparative analysis. We find enrichment of core nuclear functions amongst the widely conserved proteins to be less numerous than lineage-specific cohorts, but enriched in core nuclear functions. This, together with consideration of additional evidence, suggests that, despite a common origin, the NE has evolved as a highly diverse organelle with significant lineage-specific functionality.}, } @article {pmid33422486, year = {2021}, author = {Austin, S and Nowikovsky, K}, title = {Mitochondrial osmoregulation in evolution, cation transport and metabolism.}, journal = {Biochimica et biophysica acta. Bioenergetics}, volume = {1862}, number = {5}, pages = {148368}, doi = {10.1016/j.bbabio.2021.148368}, pmid = {33422486}, issn = {1879-2650}, mesh = {Animals ; Cations/*metabolism ; *Evolution, Molecular ; Humans ; Ion Transport ; Mitochondria/*metabolism ; *Osmoregulation ; }, abstract = {This review provides a retrospective on the role of osmotic regulation in the process of eukaryogenesis. Specifically, it focuses on the adjustments which must have been made by the original colonizing α-proteobacteria that led to the evolution of modern mitochondria. We focus on the cations that are fundamentally involved in volume determination and cellular metabolism and define the transporter landscape in relation to these ions in mitochondria as we know today. We provide analysis on how the cations interplay and together maintain osmotic balance that allows for effective ATP synthesis in the organelle.}, } @article {pmid33421755, year = {2021}, author = {Dey, G and Baum, B}, title = {Nuclear envelope remodelling during mitosis.}, journal = {Current opinion in cell biology}, volume = {70}, number = {}, pages = {67-74}, pmid = {33421755}, issn = {1879-0410}, support = {/WT_/Wellcome Trust/United Kingdom ; MC_UP_1201/27/MRC_/Medical Research Council/United Kingdom ; 203276/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Cell Nucleus ; Cytoplasm ; Humans ; *Mitosis ; *Nuclear Envelope ; Nuclear Pore ; }, abstract = {The defining feature of the eukaryotic cell, the nucleus, is bounded by a double envelope. This envelope and the nuclear pores within it play a critical role in separating the genome from the cytoplasm. It also presents cells with a challenge. How are cells to remodel the nuclear compartment boundary during mitosis without compromising nuclear function? In the two billion years since the emergence of the first cells with a nucleus, eukaryotes have evolved a range of strategies to do this. At one extreme, the nucleus is disassembled upon entry into mitosis and then reassembled anew in the two daughter cells. At the other, cells maintain an intact nuclear compartment boundary throughout the division process. In this review, we discuss common features of the division process that underpin remodelling mechanisms, the topological challenges involved and speculate on the selective pressures that may drive the evolution of distinct modes of division.}, } @article {pmid33307359, year = {2021}, author = {Prokina, KI and Keeling, PJ and Tikhonenkov, DV}, title = {Heterotrophic flagellates and centrohelid heliozoans from marine waters of Curacao, the Netherlands Antilles.}, journal = {European journal of protistology}, volume = {77}, number = {}, pages = {125758}, doi = {10.1016/j.ejop.2020.125758}, pmid = {33307359}, issn = {1618-0429}, mesh = {Aquatic Organisms/*classification/ultrastructure ; *Biodiversity ; Curacao ; Eukaryota/*classification/ultrastructure ; Microscopy, Electron, Transmission ; Seawater/*parasitology ; Species Specificity ; }, abstract = {Recent progress in understanding the early evolution of eukaryotes was tied to morphological identification of flagellates and heliozoans from natural samples, isolation of their culture and genomic and ultrastructural investigations. These protists are the smallest and least studied microbial eukaryotes but play an important role in the functioning of microbial food webs. Using light and electron microscopy, we have studied the diversity of heterotrophic flagellates and centrohelid heliozoans from marine waters of Curacao (The Netherlands Antilles), and provide micrographs and morphological descriptions of observed species. Among 86 flagellates and 3 centrohelids encountered in this survey, five heterotrophic flagellates and one сentrohelid heliozoan were not identified even to the genus. Some flagellate protists have a unique morphology, and may represent undescribed lineages of eukaryotes of high taxonomic rank. The vast majority (89%) of identified flagellates is characterized by wide geographical distribution and have been reported previously from all hemispheres and various climatic regions. More than half of the species were previously observed not only from marine, but also from freshwater habitats. The parameters of the species accumulation curve indicate that our species list obtained for the Curacao study sites is far from complete, and each new sample should yield new species.}, } @article {pmid33293849, year = {2020}, author = {Checa, J and Aran, JM}, title = {Reactive Oxygen Species: Drivers of Physiological and Pathological Processes.}, journal = {Journal of inflammation research}, volume = {13}, number = {}, pages = {1057-1073}, pmid = {33293849}, issn = {1178-7031}, abstract = {Since the Great Oxidation Event, about 2.4 billion years ago, the Earth is immersed in an oxidizing atmosphere. Thus, it has been proposed that excess oxygen, originally a waste product of photosynthetic cyanobacteria, induced oxidative stress and the production of reactive oxygen species (ROS), which have since acted as fundamental drivers of biologic evolution and eukaryogenesis. Indeed, throughout an organism's lifespan, ROS affect directly (as mutagens) or indirectly (as messengers and regulators) all structural and functional components of cells, and many aspects of cell biology. Whether left unchecked by protective antioxidant systems, excess ROS not only cause genomic mutations but also induce irreversible oxidative modification of proteins (protein oxidation and peroxidation), lipids and glycans (advanced lipoxidation and glycation end products), impairing their function and promoting disease or cell death. Conversely, low-level local ROS play an important role both as redox-signaling molecules in a wide spectrum of pathways involved in the maintenance of cellular homeostasis (MAPK/ERK, PTK/PTP, PI3K-AKT-mTOR), and regulating key transcription factors (NFκB/IκB, Nrf2/KEAP1, AP-1, p53, HIF-1). Consequently, ROS can shape a variety of cellular functions, including proliferation, differentiation, migration and apoptosis. In this review, we will give a brief overview of the relevance of ROS in both physiological and pathological processes, particularly inflammation and aging. In-depth knowledge of the molecular mechanisms of ROS actuation and their influence under steady-state and stressful conditions will pave the way for the development of novel therapeutic interventions. This will mitigate the harmful outcomes of ROS in the onset and progression of a variety of chronic inflammatory and age-related diseases.}, } @article {pmid33279568, year = {2021}, author = {Kowallik, KV and Martin, WF}, title = {The origin of symbiogenesis: An annotated English translation of Mereschkowsky's 1910 paper on the theory of two plasma lineages.}, journal = {Bio Systems}, volume = {199}, number = {}, pages = {104281}, pmid = {33279568}, issn = {1872-8324}, mesh = {Animals ; *Autotrophic Processes ; Bacteria, Anaerobic/genetics/*metabolism ; Cell Nucleus/genetics/*metabolism ; Eukaryota/genetics/*metabolism ; Humans ; Phylogeny ; Plants/genetics/*metabolism ; Russia ; *Symbiosis ; Translating ; }, abstract = {In 1910, the Russian biologist Konstantin Sergejewitch Mereschkowsky (Константин Сергеевич Мережковский, in standard transliterations also written as Konstantin Sergeevič Merežkovskij and Konstantin Sergeevich Merezhkovsky) published a notable synthesis of observations and inferences concerning the origin of life and the origin of nucleated cells. His theory was based on physiology and leaned heavily upon the premise that thermophilic autotrophs were ancient. The ancestors of plants and animals were inferred as ancestrally mesophilic anucleate heterotrophs (Monera) that became complex and diverse through endosymbiosis. He placed a phylogenetic root in the tree of life among anaerobic autotrophic bacteria that lack chlorophyll. His higher level classification of all microbes and macrobes in the living world was based upon the presence or absence of past endosymbiotic events. The paper's primary aim was to demonstrate that all life forms descend from two fundamentally distinct organismal lineages, called mykoplasma and amoeboplasma, whose very nature was so different that, in his view, they could only have arisen independently of one another and at different times during Earth history. The mykoplasma arose at a time when the young Earth was still hot, it later gave rise to cyanobacteria, which in turn gave rise to plastids. The product of the second origin of life, the amoeboplasma, arose after the Earth had cooled and autotrophs had generated substrates for heterotrophic growth. Lineage diversification of that second plasma brought forth, via serial endosymbioses, animals (one symbiosis) and then plants (two symbioses, the second being the plastid). The paper was published in German, rendering it inaccessible to many interested scholars. Here we translate the 1910 paper in full and briefly provide some context.}, } @article {pmid33263877, year = {2020}, author = {Lupette, J and Maréchal, E}, title = {The Puzzling Conservation and Diversification of Lipid Droplets from Bacteria to Eukaryotes.}, journal = {Results and problems in cell differentiation}, volume = {69}, number = {}, pages = {281-334}, pmid = {33263877}, issn = {0080-1844}, mesh = {Bacteria/*chemistry/genetics ; Biological Evolution ; Eukaryota/*chemistry/genetics ; Lipid Droplets/*chemistry ; Organelles ; Plastids ; Symbiosis ; }, abstract = {Membrane compartments are amongst the most fascinating markers of cell evolution from prokaryotes to eukaryotes, some being conserved and the others having emerged via a series of primary and secondary endosymbiosis events. Membrane compartments comprise the system limiting cells (one or two membranes in bacteria, a unique plasma membrane in eukaryotes) and a variety of internal vesicular, subspherical, tubular, or reticulated organelles. In eukaryotes, the internal membranes comprise on the one hand the general endomembrane system, a dynamic network including organelles like the endoplasmic reticulum, the Golgi apparatus, the nuclear envelope, etc. and also the plasma membrane, which are linked via direct lateral connectivity (e.g. between the endoplasmic reticulum and the nuclear outer envelope membrane) or indirectly via vesicular trafficking. On the other hand, semi-autonomous organelles, i.e. mitochondria and chloroplasts, are disconnected from the endomembrane system and request vertical transmission following cell division. Membranes are organized as lipid bilayers in which proteins are embedded. The budding of some of these membranes, leading to the formation of the so-called lipid droplets (LDs) loaded with hydrophobic molecules, most notably triacylglycerol, is conserved in all clades. The evolution of eukaryotes is marked by the acquisition of mitochondria and simple plastids from Gram-positive bacteria by primary endosymbiosis events and the emergence of extremely complex plastids, collectively called secondary plastids, bounded by three to four membranes, following multiple and independent secondary endosymbiosis events. There is currently no consensus view of the evolution of LDs in the Tree of Life. Some features are conserved; others show a striking level of diversification. Here, we summarize the current knowledge on the architecture, dynamics, and multitude of functions of the lipid droplets in prokaryotes and in eukaryotes deriving from primary and secondary endosymbiosis events.}, } @article {pmid33229320, year = {2020}, author = {Gao, ZW and Wang, L}, title = {[Progress in elucidating the origin of eukaryotes].}, journal = {Yi chuan = Hereditas}, volume = {42}, number = {10}, pages = {929-948}, doi = {10.16288/j.yczz.20-107}, pmid = {33229320}, issn = {0253-9772}, mesh = {Archaea/classification/genetics ; *Biological Evolution ; *Eukaryota/classification/genetics ; Research/trends ; }, abstract = {Knowledge of the origin of eukaryotes is key to broadening our understanding of the eukaryotic genome and the relationship among internal structures within a eukaryotic cell. Since the discovery of archaea in 1977 and the proposal of three-domain tree of life by the American microbiologist Carl Woese, the intimate relationship in evolution between eukaryotes and archaea has been demonstrated by considerable experiments and analyses. From the beginning of the 21st century, with the development of phylogenetic methods and the discovery of new archaeal phyla more related to eukaryotes, increasing evidence has shown that Eukarya and Archaea should be merged into one domain, leading to a two-domain tree of life. Nowadays, the Asgard superphylum discovered via metagenomic analysis is regarded as the closest prokaryotes to eukaryotes. Nevertheless, several key questions are still under debate, such as what the ancestors of the eukaryotes were and when mitochondria emerged. Here, we review the current research progress regarding the changes of the tree of life and the detailed eukaryotic evolutionary mechanism. We show that the recent findings have greatly improved our knowledge on the origin of eukaryotes, which will pave the way for future studies.}, } @article {pmid33223169, year = {2021}, author = {Cai, M and Richter-Heitmann, T and Yin, X and Huang, WC and Yang, Y and Zhang, C and Duan, C and Pan, J and Liu, Y and Liu, Y and Friedrich, MW and Li, M}, title = {Ecological features and global distribution of Asgard archaea.}, journal = {The Science of the total environment}, volume = {758}, number = {}, pages = {143581}, doi = {10.1016/j.scitotenv.2020.143581}, pmid = {33223169}, issn = {1879-1026}, mesh = {*Archaea/genetics ; *Eukaryota ; Geologic Sediments ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; }, abstract = {Asgard is a newly proposed archaeal superphylum, which has been suggested to hold the key to decipher the origin of Eukaryotes. However, their ecology remains largely unknown. Here, we conducted a meta-analysis of publicly available Asgard-associated 16S rRNA gene fragments, and found that just three previously proposed clades (Lokiarchaeota, Thorarchaeota, and Asgard clade 4) are widely distributed, whereas the other seven clades (phylum or class level) are restricted to the sediment biosphere. Asgard archaea, especially Loki- and Thorarchaeota, seem to adapt to marine sediments, and water depth (the depth of the sediment below water surface) and salinity might be crucial factors for the proportion of these microorganisms as revealed by multivariate regression analyses. However, the abundance of Asgard archaea exhibited distinct environmental drivers at the clade-level; for instance, the proportion of Asgard clade 4 was higher in less saline environments (salinity <6.35 psu), while higher for Heimdallarchaeota-AAG and Asgard clade 2 in more saline environment (salinity ≥35 psu). Furthermore, co-occurrence analysis allowed us to find a significant non-random association of different Asgard clades with other groups (e.g., Lokiarchaeota with Deltaproteobacteria and Anaerolineae; Odinarchaeota with Bathyarchaeota), suggesting different interaction potentials among these clades. Overall, these findings reveal Asgard archaea as a ubiquitous group worldwide and provide initial insights into their ecological features on a global scale.}, } @article {pmid33216655, year = {2021}, author = {Snyder-Beattie, AE and Sandberg, A and Drexler, KE and Bonsall, MB}, title = {The Timing of Evolutionary Transitions Suggests Intelligent Life is Rare.}, journal = {Astrobiology}, volume = {21}, number = {3}, pages = {265-278}, pmid = {33216655}, issn = {1557-8070}, mesh = {Bayes Theorem ; Biological Evolution ; Earth, Planet ; *Exobiology ; Extraterrestrial Environment ; Intelligence ; *Planets ; }, abstract = {It is unknown how abundant extraterrestrial life is, or whether such life might be complex or intelligent. On Earth, the emergence of complex intelligent life required a preceding series of evolutionary transitions such as abiogenesis, eukaryogenesis, and the evolution of sexual reproduction, multicellularity, and intelligence itself. Some of these transitions could have been extraordinarily improbable, even in conducive environments. The emergence of intelligent life late in Earth's lifetime is thought to be evidence for a handful of rare evolutionary transitions, but the timing of other evolutionary transitions in the fossil record is yet to be analyzed in a similar framework. Using a simplified Bayesian model that combines uninformative priors and the timing of evolutionary transitions, we demonstrate that expected evolutionary transition times likely exceed the lifetime of Earth, perhaps by many orders of magnitude. Our results corroborate the original argument suggested by Brandon Carter that intelligent life in the Universe is exceptionally rare, assuming that intelligent life elsewhere requires analogous evolutionary transitions. Arriving at the opposite conclusion would require exceptionally conservative priors, evidence for much earlier transitions, multiple instances of transitions, or an alternative model that can explain why evolutionary transitions took hundreds of millions of years without appealing to rare chance events. Although the model is simple, it provides an initial basis for evaluating how varying biological assumptions and fossil record data impact the probability of evolving intelligent life, and also provides a number of testable predictions, such as that some biological paradoxes will remain unresolved and that planets orbiting M dwarf stars are uninhabitable.}, } @article {pmid33137653, year = {2021}, author = {Ryan, DG and Frezza, C and O'Neill, LA}, title = {TCA cycle signalling and the evolution of eukaryotes.}, journal = {Current opinion in biotechnology}, volume = {68}, number = {}, pages = {72-88}, pmid = {33137653}, issn = {1879-0429}, support = {109443/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; MC_UU_12022/6/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Archaea/genetics ; *Biological Evolution ; *Eukaryota/genetics ; Eukaryotic Cells ; Phylogeny ; Prokaryotic Cells ; Symbiosis ; }, abstract = {A major question remaining in the field of evolutionary biology is how prokaryotic organisms made the leap to complex eukaryotic life. The prevailing theory depicts the origin of eukaryotic cell complexity as emerging from the symbiosis between an α-proteobacterium, the ancestor of present-day mitochondria, and an archaeal host (endosymbiont theory). A primary contribution of mitochondria to eukaryogenesis has been attributed to the mitochondrial genome, which enabled the successful internalisation of bioenergetic membranes and facilitated remarkable genome expansion. It has also been postulated that a key contribution of the archaeal host during eukaryogenesis was in providing 'archaeal histones' that would enable compaction and regulation of an expanded genome. Yet, how the communication between the host and the symbiont evolved is unclear. Here, we propose an evolutionary concept in which mitochondrial TCA cycle signalling was also a crucial player during eukaryogenesis enabling the dynamic control of an expanded genome via regulation of DNA and histone modifications. Furthermore, we discuss how TCA cycle remodelling is a common evolutionary strategy invoked by eukaryotic organisms to coordinate stress responses and gene expression programmes, with a particular focus on the TCA cycle-derived metabolite itaconate.}, } @article {pmid33106602, year = {2021}, author = {Vosseberg, J and van Hooff, JJE and Marcet-Houben, M and van Vlimmeren, A and van Wijk, LM and Gabaldón, T and Snel, B}, title = {Timing the origin of eukaryotic cellular complexity with ancient duplications.}, journal = {Nature ecology & evolution}, volume = {5}, number = {1}, pages = {92-100}, pmid = {33106602}, issn = {2397-334X}, support = {724173/ERC_/European Research Council/International ; }, mesh = {Archaea/genetics ; *Biological Evolution ; Eukaryota/genetics ; *Eukaryotic Cells ; Humans ; Phylogeny ; }, abstract = {Eukaryogenesis is one of the most enigmatic evolutionary transitions, during which simple prokaryotic cells gave rise to complex eukaryotic cells. While evolutionary intermediates are lacking, gene duplications provide information on the order of events by which eukaryotes originated. Here we use a phylogenomics approach to reconstruct successive steps during eukaryogenesis. We find that gene duplications roughly doubled the proto-eukaryotic gene repertoire, with families inherited from the Asgard archaea-related host being duplicated most. By relatively timing events using phylogenetic distances, we inferred that duplications in cytoskeletal and membrane-trafficking families were among the earliest events, whereas most other families expanded predominantly after mitochondrial endosymbiosis. Altogether, we infer that the host that engulfed the proto-mitochondrion had some eukaryote-like complexity, which drastically increased upon mitochondrial acquisition. This scenario bridges the signs of complexity observed in Asgard archaeal genomes to the proposed role of mitochondria in triggering eukaryogenesis.}, } @article {pmid33050064, year = {2020}, author = {Schrumpfová, PP and Fajkus, J}, title = {Composition and Function of Telomerase-A Polymerase Associated with the Origin of Eukaryotes.}, journal = {Biomolecules}, volume = {10}, number = {10}, pages = {}, pmid = {33050064}, issn = {2218-273X}, support = {20-01331X//Grantová Agentura České Republiky/International ; CEITEC 2020 (LQ1601)//Ministry of Education, Youth and Sports of the Czech Republic/International ; project SYMBIT, reg. no.CZ.02.1.01/0.0/0.0/15_003/0000477//European Regional Development Fund/International ; }, mesh = {Animals ; *Biological Evolution ; Eukaryota/classification/genetics/metabolism ; History, 20th Century ; History, 21st Century ; Humans ; Phylogeny ; RNA/physiology ; Telomerase/*chemistry/*physiology ; Telomere/metabolism ; }, abstract = {The canonical DNA polymerases involved in the replication of the genome are unable to fully replicate the physical ends of linear chromosomes, called telomeres. Chromosomal termini thus become shortened in each cell cycle. The maintenance of telomeres requires telomerase-a specific RNA-dependent DNA polymerase enzyme complex that carries its own RNA template and adds telomeric repeats to the ends of chromosomes using a reverse transcription mechanism. Both core subunits of telomerase-its catalytic telomerase reverse transcriptase (TERT) subunit and telomerase RNA (TR) component-were identified in quick succession in Tetrahymena more than 30 years ago. Since then, both telomerase subunits have been described in various organisms including yeasts, mammals, birds, reptiles and fish. Despite the fact that telomerase activity in plants was described 25 years ago and the TERT subunit four years later, a genuine plant TR has only recently been identified by our group. In this review, we focus on the structure, composition and function of telomerases. In addition, we discuss the origin and phylogenetic divergence of this unique RNA-dependent DNA polymerase as a witness of early eukaryotic evolution. Specifically, we discuss the latest information regarding the recently discovered TR component in plants, its conservation and its structural features.}, } @article {pmid33014348, year = {2020}, author = {Muñoz-Gómez, SA and Snyder, SN and Montoya, SJ and Wideman, JG}, title = {Independent accretion of TIM22 complex subunits in the animal and fungal lineages.}, journal = {F1000Research}, volume = {9}, number = {}, pages = {1060}, pmid = {33014348}, issn = {2046-1402}, mesh = {Animals ; Fungi/genetics ; *Mitochondrial Membrane Transport Proteins ; *Mitochondrial Membranes/metabolism ; Phylogeny ; Protein Transport ; }, abstract = {Background: The mitochondrial protein import complexes arose early in eukaryogenesis. Most of the components of the protein import pathways predate the last eukaryotic common ancestor. For example, the carrier-insertase TIM22 complex comprises the widely conserved Tim22 channel core. However, the auxiliary components of fungal and animal TIM22 complexes are exceptions to this ancient conservation. Methods: Using comparative genomics and phylogenetic approaches, we identified precisely when each TIM22 accretion occurred. Results: In animals, we demonstrate that Tim29 and Tim10b arose early in the holozoan lineage. Tim29 predates the metazoan lineage being present in the animal sister lineages, choanoflagellate and filastereans, whereas the erroneously named Tim10b arose from a duplication of Tim9 at the base of metazoans. In fungi, we show that Tim54 has representatives present in every holomycotan lineage including microsporidians and fonticulids, whereas Tim18 and Tim12 appeared much later in fungal evolution. Specifically, Tim18 and Tim12 arose from duplications of Sdh3 and Tim10, respectively, early in the Saccharomycotina. Surprisingly, we show that Tim54 is distantly related to AGK suggesting that AGK and Tim54 are extremely divergent orthologues and the origin of AGK/Tim54 interaction with Tim22 predates the divergence of animals and fungi. Conclusions: We argue that the evolutionary history of the TIM22 complex is best understood as the neutral structural divergence of an otherwise strongly functionally conserved protein complex. This view suggests that many of the differences in structure/subunit composition of multi-protein complexes are non-adaptive. Instead, most of the phylogenetic variation of functionally conserved molecular machines, which have been under stable selective pressures for vast phylogenetic spans, such as the TIM22 complex, is most likely the outcome of the interplay of random genetic drift and mutation pressure.}, } @article {pmid33013805, year = {2020}, author = {Takemura, M}, title = {Medusavirus Ancestor in a Proto-Eukaryotic Cell: Updating the Hypothesis for the Viral Origin of the Nucleus.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {571831}, pmid = {33013805}, issn = {1664-302X}, abstract = {The mechanistic evolutionary origin of the eukaryotic cell nucleus remains unknown. Among several plausible hypotheses, the most controversial is that large DNA viruses, such as poxviruses, led to the emergence of the eukaryotic cell nucleus. Several recent findings, including the discovery of a nucleus-like structure in prokaryotic viruses and prokaryotes possessing nucleus-like inner membranes, suggest genomic DNA compartmentalization not only in eukaryotes but also in prokaryotes. The sophisticated viral machinery of mimiviruses is thought to resemble the eukaryotic nucleus: DNA replicates both inside the viral factory and nucleus, which is at least partially surrounded by membranes and is devoid of ribosomes. Furthermore, several features of the recently identified Acanthamoeba castellanii medusavirus suggest that the evolutionary relationship between ancestral viral factory and eukaryotic nucleus. Notably, Ran, DNA polymerase, and histones show molecular fossils of lateral transfer of nuclear genes between the virus and host. These results suggest viral innovation in the emergence of the eukaryotic nucleus. According to these results, a new scenario explaining the origin of the eukaryotic nucleus from the perspective of viral participation is proposed. This new scenario could substantially impact the study of eukaryogenesis and stimulate further discussion about viral contributions to the evolution of the eukaryotic nucleus.}, } @article {pmid32985518, year = {2020}, author = {Haq, SR and Survery, S and Hurtig, F and Lindås, AC and Chi, CN}, title = {NMR resonance assignment and dynamics of profilin from Heimdallarchaeota.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {15867}, pmid = {32985518}, issn = {2045-2322}, support = {203276/F/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Archaeal Proteins/*chemistry/*metabolism ; Dyscalculia ; *Nuclear Magnetic Resonance, Biomolecular ; Profilins/*chemistry/*metabolism ; }, abstract = {The origin of the eukaryotic cell is an unsettled scientific question. The Asgard superphylum has emerged as a compelling target for studying eukaryogenesis due to the previously unseen diversity of eukaryotic signature proteins. However, our knowledge about these proteins is still relegated to metagenomic data and very little is known about their structural properties. Additionally, it is still unclear if these proteins are functionally homologous to their eukaryotic counterparts. Here, we expressed, purified and structurally characterized profilin from Heimdallarchaeota in the Asgard superphylum. The structural analysis shows that while this profilin possesses similar secondary structural elements as eukaryotic profilin, it contains additional secondary structural elements that could be critical for its function and an indication of divergent evolution.}, } @article {pmid32979052, year = {2020}, author = {Miles, JA and Davies, TA and Hayman, RD and Lorenzen, G and Taylor, J and Anjarwalla, M and Allen, SJR and Graham, JWD and Taylor, PC}, title = {A Case Study of Eukaryogenesis: The Evolution of Photoreception by Photolyase/Cryptochrome Proteins.}, journal = {Journal of molecular evolution}, volume = {88}, number = {8-9}, pages = {662-673}, pmid = {32979052}, issn = {1432-1432}, mesh = {Amino Acid Sequence ; *Cryptochromes/genetics ; *Deoxyribodipyrimidine Photo-Lyase/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Photoreceptors, Microbial/*genetics ; *Phylogeny ; Tryptophan ; }, abstract = {Eukaryogenesis, the origin of the eukaryotes, is still poorly understood. Herein, we show how a detailed all-kingdom phylogenetic analysis overlaid with a map of key biochemical features can provide valuable clues. The photolyase/cryptochrome family of proteins are well known to repair DNA in response to potentially harmful effects of sunlight and to entrain circadian rhythms. Phylogenetic analysis of photolyase/cryptochrome protein sequences from a wide range of prokaryotes and eukaryotes points to a number of horizontal gene transfer events between ancestral bacteria and ancestral eukaryotes. Previous experimental research has characterised patterns of tryptophan residues in these proteins that are important for photoreception, specifically a tryptophan dyad, a canonical tryptophan triad, an alternative tryptophan triad, a tryptophan tetrad and an alternative tetrad. Our results suggest that the spread of the different triad and tetrad motifs across the kingdoms of life accompanied the putative horizontal gene transfers and is consistent with multiple bacterial contributions to eukaryogenesis.}, } @article {pmid32961211, year = {2020}, author = {Bell, PJL}, title = {Evidence supporting a viral origin of the eukaryotic nucleus.}, journal = {Virus research}, volume = {289}, number = {}, pages = {198168}, doi = {10.1016/j.virusres.2020.198168}, pmid = {32961211}, issn = {1872-7492}, mesh = {Archaea/*genetics ; Biological Evolution ; *Cell Nucleus ; DNA Viruses ; Eukaryota/*genetics ; Eukaryotic Cells/*cytology ; *Evolution, Molecular ; }, abstract = {The defining feature of the eukaryotic cell is the possession of a nucleus that uncouples transcription from translation. According to the updated Viral Eukaryogenesis (VE) hypothesis presented here, the eukaryotic nucleus descends from the viral factory of a DNA virus that infected the archaeal ancestor of the eukaryotes. The VE hypothesis implies that many unique features of the nucleus, including the mechanisms by which the eukaryotic nucleus uncouples transcription from translation, should be viral rather than cellular in origin. The modern eukaryotic nucleus uncouples transcription from translation using a complex process employing hundreds of eukaryotic specific genes acting in concert. This intricate process is primed by the eukaryote specific 7-methylguanylate (m7G) cap on eukaryotic mRNA that targets mRNA for splicing, nuclear export, and cytoplasmic translation. It is shown here that homologues of the eukaryotic m7G capping apparatus are present in viruses of the Mimiviridae yet are apparently absent from archaea generally, and specifically from Lokiarchaeota, a proposed archaeal relative of the eukaryotes. Phylogenetic analysis of the m7G capping apparatus shows that eukaryotic nuclei and Mimiviridae obtained this shared pathway from a common ancestral source that predated the origin of the Last Eukaryotic Common Ancestor (LECA). These results are consistent with the hypothesis that the eukaryotic nucleus and the Mimiviridae obtained these abilities from an ancient virus that could be considered the 'First Eukaryotic Nuclear Ancestor' (FENA).}, } @article {pmid32923644, year = {2020}, author = {Stairs, CW and Dharamshi, JE and Tamarit, D and Eme, L and Jørgensen, SL and Spang, A and Ettema, TJG}, title = {Chlamydial contribution to anaerobic metabolism during eukaryotic evolution.}, journal = {Science advances}, volume = {6}, number = {35}, pages = {eabb7258}, pmid = {32923644}, issn = {2375-2548}, support = {310039/ERC_/European Research Council/International ; 817834/ERC_/European Research Council/International ; }, abstract = {The origin of eukaryotes is a major open question in evolutionary biology. Multiple hypotheses posit that eukaryotes likely evolved from a syntrophic relationship between an archaeon and an alphaproteobacterium based on H2 exchange. However, there are no strong indications that modern eukaryotic H2 metabolism originated from archaea or alphaproteobacteria. Here, we present evidence for the origin of H2 metabolism genes in eukaryotes from an ancestor of the Anoxychlamydiales-a group of anaerobic chlamydiae, newly described here, from marine sediments. Among Chlamydiae, these bacteria uniquely encode genes for H2 metabolism and other anaerobiosis-associated pathways. Phylogenetic analyses of several components of H2 metabolism reveal that Anoxychlamydiales homologs are the closest relatives to eukaryotic sequences. We propose that an ancestor of the Anoxychlamydiales contributed these key genes during the evolution of eukaryotes, supporting a mosaic evolutionary origin of eukaryotic metabolism.}, } @article {pmid32911339, year = {2020}, author = {Feltrin, RDS and Segatto, ALA and de Souza, TA and Schuch, AP}, title = {Open gaps in the evolution of the eukaryotic nucleotide excision repair.}, journal = {DNA repair}, volume = {95}, number = {}, pages = {102955}, doi = {10.1016/j.dnarep.2020.102955}, pmid = {32911339}, issn = {1568-7856}, mesh = {Animals ; Conserved Sequence ; DNA Repair/*genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; Humans ; Introns/genetics ; Phylogeny ; }, abstract = {Nucleotide excision repair (NER) is the most versatile DNA repair pathway as it removes different kinds of bulky lesions. Due to its essential role for genome integrity, it has appeared early in the evolution of species. However, most published studies are focused on humans, mice, yeast or bacteria. Considering the large amount of information on genome databases, it is currently possible to retrieve sequences from NER components in many organisms. Therefore, we have characterized the potential orthologs of 10 critical components of the human NER pathway in 12 eukaryotic species by using similarity and structural criteria through the use of bioinformatics tools. This approach has allowed us to characterize gene and protein structures comparatively, taking a glance at some evolutionary aspects of the NER pathway. We have obtained significant search results for the majority of the proteins in most of the organisms studied, mainly for factors that play a pivotal role in the pathway. However, we have revisited significant differences and found new aspects that may imply a distinct functioning of this pathway in different organisms. Through the demonstration of the heterogeneity of the gene structures and a variety in the protein architecture of the NER components evaluated, our results show important differences between human NER and evolutionarily distant eukaryotes. We highlight the lack of a canonical XPD in chicken, the divergence of XPA in plants and protozoans and the absence of XPE in the invertebrate species analyzed. In spite of this, it is remarkable the presence of this excision repair mechanism in a high number of evolutionary distant organisms, being present since the origin of eukaryotes.}, } @article {pmid32816285, year = {2021}, author = {Militello, G and Bich, L and Moreno, A}, title = {Functional Integration and Individuality in Prokaryotic Collective Organisations.}, journal = {Acta biotheoretica}, volume = {69}, number = {3}, pages = {391-415}, pmid = {32816285}, issn = {1572-8358}, support = {IT1228-19//Eusko Jaurlaritza/ ; RYC-2016-19798//Ministerio de Ciencia, Innovación y Universidades/ ; PID2019-104576GB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; PIF17/31//Euskal Herriko Unibertsitatea/ ; }, mesh = {*Biological Evolution ; Humans ; *Prokaryotic Cells ; Symbiosis ; }, abstract = {Both physiological and evolutionary criteria of biological individuality are underpinned by the idea that an individual is a functionally integrated whole. However, a precise account of functional integration has not been provided so far, and current notions are not developed in the details, especially in the case of composite systems. To address this issue, this paper focuses on the organisational dimension of two representative associations of prokaryotes: biofilms and the endosymbiosis between prokaryotes. Some critical voices have been raised against the thesis that biofilms are biological individuals. Nevertheless, it has not been investigated which structural and functional obstacles may prevent them from being fully integrated physiological or evolutionary units. By contrast, the endosymbiotic association of different species of prokaryotes has the potential for achieving a different type of physiological integration based on a common boundary and interlocked functions. This type of association had made it possible, under specific conditions, to evolve endosymbionts into fully integrated organelles. This paper therefore has three aims: first, to analyse the organisational conditions and the physiological mechanisms that enable integration in prokaryotic associations; second, to discuss the organisational differences between biofilms and prokaryotic endosymbiosis and the types of integration they achieve; finally, to provide a more precise account of functional integration based on these case studies.}, } @article {pmid32747565, year = {2020}, author = {Akıl, C and Tran, LT and Orhant-Prioux, M and Baskaran, Y and Manser, E and Blanchoin, L and Robinson, RC}, title = {Insights into the evolution of regulated actin dynamics via characterization of primitive gelsolin/cofilin proteins from Asgard archaea.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {33}, pages = {19904-19913}, pmid = {32747565}, issn = {1091-6490}, mesh = {Actin Depolymerizing Factors/chemistry/genetics/*metabolism ; Actins/chemistry/genetics/*metabolism ; Amino Acid Sequence ; Archaea/chemistry/genetics/*metabolism ; Archaeal Proteins/chemistry/genetics/*metabolism ; Cytoskeleton/chemistry/genetics/metabolism ; Evolution, Molecular ; Gelsolin/chemistry/genetics/*metabolism ; Genome, Archaeal ; Polymerization ; Protein Conformation, alpha-Helical ; Sequence Alignment ; }, abstract = {Asgard archaea genomes contain potential eukaryotic-like genes that provide intriguing insight for the evolution of eukaryotes. The eukaryotic actin polymerization/depolymerization cycle is critical for providing force and structure in many processes, including membrane remodeling. In general, Asgard genomes encode two classes of actin-regulating proteins from sequence analysis, profilins and gelsolins. Asgard profilins were demonstrated to regulate actin filament nucleation. Here, we identify actin filament severing, capping, annealing and bundling, and monomer sequestration activities by gelsolin proteins from Thorarchaeota (Thor), which complete a eukaryotic-like actin depolymerization cycle, and indicate complex actin cytoskeleton regulation in Asgard organisms. Thor gelsolins have homologs in other Asgard archaea and comprise one or two copies of the prototypical gelsolin domain. This appears to be a record of an initial preeukaryotic gene duplication event, since eukaryotic gelsolins are generally comprise three to six domains. X-ray structures of these proteins in complex with mammalian actin revealed similar interactions to the first domain of human gelsolin or cofilin with actin. Asgard two-domain, but not one-domain, gelsolins contain calcium-binding sites, which is manifested in calcium-controlled activities. Expression of two-domain gelsolins in mammalian cells enhanced actin filament disassembly on ionomycin-triggered calcium release. This functional demonstration, at the cellular level, provides evidence for a calcium-controlled Asgard actin cytoskeleton, indicating that the calcium-regulated actin cytoskeleton predates eukaryotes. In eukaryotes, dynamic bundled actin filaments are responsible for shaping filopodia and microvilli. By correlation, we hypothesize that the formation of the protrusions observed from Lokiarchaeota cell bodies may involve the gelsolin-regulated actin structures.}, } @article {pmid32731621, year = {2020}, author = {Garrido, C and Caspari, OD and Choquet, Y and Wollman, FA and Lafontaine, I}, title = {Evidence Supporting an Antimicrobial Origin of Targeting Peptides to Endosymbiotic Organelles.}, journal = {Cells}, volume = {9}, number = {8}, pages = {}, pmid = {32731621}, issn = {2073-4409}, mesh = {Anti-Infective Agents/*metabolism ; Humans ; Organelles/*metabolism ; Peptides/*metabolism ; Symbiosis/*genetics ; }, abstract = {Mitochondria and chloroplasts emerged from primary endosymbiosis. Most proteins of the endosymbiont were subsequently expressed in the nucleo-cytosol of the host and organelle-targeted via the acquisition of N-terminal presequences, whose evolutionary origin remains enigmatic. Using a quantitative assessment of their physico-chemical properties, we show that organelle targeting peptides, which are distinct from signal peptides targeting other subcellular compartments, group with a subset of antimicrobial peptides. We demonstrate that extant antimicrobial peptides target a fluorescent reporter to either the mitochondria or the chloroplast in the green alga Chlamydomonas reinhardtii and, conversely, that extant targeting peptides still display antimicrobial activity. Thus, we provide strong computational and functional evidence for an evolutionary link between organelle-targeting and antimicrobial peptides. Our results support the view that resistance of bacterial progenitors of organelles to the attack of host antimicrobial peptides has been instrumental in eukaryogenesis and in the emergence of photosynthetic eukaryotes.}, } @article {pmid32727863, year = {2020}, author = {Salcher, MM and Andrei, AŞ and Bulzu, PA and Keresztes, ZG and Banciu, HL and Ghai, R}, title = {Visualization of Lokiarchaeia and Heimdallarchaeia (Asgardarchaeota) by Fluorescence In Situ Hybridization and Catalyzed Reporter Deposition (CARD-FISH).}, journal = {mSphere}, volume = {5}, number = {4}, pages = {}, pmid = {32727863}, issn = {2379-5042}, mesh = {Archaea/classification/*genetics ; Geologic Sediments/microbiology ; In Situ Hybridization, Fluorescence/*methods ; Microscopy, Fluorescence ; Oligonucleotide Probes/*genetics ; Phylogeny ; }, abstract = {Metagenome-assembled genomes (MAGs) of Asgardarchaeota have been recovered from a variety of habitats, broadening their environmental distribution and providing access to the genetic makeup of this archaeal lineage. The recent success in cultivating the first representative of Lokiarchaeia was a breakthrough in science at large and gave rise to new hypotheses about the evolution of eukaryotes. Despite their singular phylogenetic position at the base of the eukaryotic tree of life, the morphology of these bewildering organisms remains a mystery, except for the report of an unusual morphology with long, branching protrusions of the cultivated Lokiarchaeion strain "Candidatus Prometheoarchaeum syntrophicum" MK-D1. In order to visualize this elusive group, we applied a combination of fluorescence in situ hybridization and catalyzed reporter deposition (CARD-FISH) and epifluorescence microscopy on coastal hypersaline sediment samples, using specifically designed CARD-FISH probes for Heimdallarchaeia and Lokiarchaeia lineages, and provide the first visual evidence for Heimdallarchaeia and new images of a lineage of Lokiarchaeia that is different from the cultured representative. Here, we show that while Heimdallarchaeia are characterized by a uniform cellular morphology typified by a centralized DNA localization, Lokiarchaeia display a plethora of shapes and sizes that likely reflect their broad phylogenetic diversity and ecological distribution.IMPORTANCE Asgardarchaeota are considered to be the closest relatives to modern eukaryotes. These enigmatic microbes have been mainly studied using metagenome-assembled genomes (MAGs). Only very recently, a first member of Lokiarchaeia was isolated and characterized in detail; it featured a striking morphology with long, branching protrusions. In order to visualize additional members of the phylum Asgardarchaeota, we applied a fluorescence in situ hybridization technique and epifluorescence microscopy on coastal hypersaline sediment samples, using specifically designed probes for Heimdallarchaeia and Lokiarchaeia lineages. We provide the first visual evidence for Heimdallarchaeia that are characterized by a uniform cellular morphology typified by an apparently centralized DNA localization. Further, we provide new images of a lineage of Lokiarchaeia that is different from the cultured representative and with multiple morphologies, ranging from small ovoid cells to long filaments. This diversity in observed cell shapes is likely owing to the large phylogenetic diversity within Asgardarchaeota, the vast majority of which remain uncultured.}, } @article {pmid32714303, year = {2020}, author = {Skejo, J and Franjević, D}, title = {Eukaryotes Are a Holophyletic Group of Polyphyletic Origin.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1380}, pmid = {32714303}, issn = {1664-302X}, } @article {pmid32685134, year = {2020}, author = {Harish, A and Morrison, D}, title = {The deep(er) roots of Eukaryotes and Akaryotes.}, journal = {F1000Research}, volume = {9}, number = {}, pages = {112}, pmid = {32685134}, issn = {2046-1402}, mesh = {Archaea/*classification ; *Biological Evolution ; Eukaryota/*classification ; *Phylogeny ; Protein Domains ; Sequence Alignment ; Sequence Analysis, Protein ; }, abstract = {Background: Locating the root node of the "tree of life" (ToL) is one of the hardest problems in phylogenetics, given the time depth. The root-node, or the universal common ancestor (UCA), groups descendants into organismal clades/domains. Two notable variants of the two-domains ToL (2D-ToL) have gained support recently. One 2D-ToL posits that eukaryotes (organisms with nuclei) and akaryotes (organisms without nuclei) are sister clades that diverged from the UCA, and that Asgard archaea are sister to other archaea. The other 2D-ToL proposes that eukaryotes emerged from within archaea and places Asgard archaea as sister to eukaryotes. Williams et al. (Nature Ecol. Evol. 4: 138-147; 2020) re-evaluated the data and methods that support the competing two-domains proposals and concluded that eukaryotes are the closest relatives of Asgard archaea. Critique: The poor resolution of the archaea in their analysis, despite employing amino acid alignments from thousands of proteins and the best-fitting substitution models, contradicts their conclusions. We argue that they overlooked important aspects of estimating evolutionary relatedness and assessing phylogenetic signal in empirical data. Which 2D-ToL is better supported depends on which kind of molecular features are better for resolving common ancestors at the roots of clades - protein-domains or their component amino acids. We focus on phylogenetic character reconstructions necessary to describe the UCA or its closest descendants in the absence of reliable fossils. Clarifications: It is well known that different character types present different perspectives on evolutionary history that relate to different phylogenetic depths. We show that protein structural-domains support more reliable phylogenetic reconstructions of deep-diverging clades in the ToL. Accordingly, Eukaryotes and Akaryotes are better supported clades in a 2D-ToL.}, } @article {pmid32642057, year = {2020}, author = {Mills, DB}, title = {The origin of phagocytosis in Earth history.}, journal = {Interface focus}, volume = {10}, number = {4}, pages = {20200019}, pmid = {32642057}, issn = {2042-8898}, abstract = {Phagocytosis, or 'cell eating', is a eukaryote-specific process where particulate matter is engulfed via invaginations of the plasma membrane. The origin of phagocytosis has been central to discussions on eukaryogenesis for decades-, where it is argued as being either a prerequisite for, or consequence of, the acquisition of the ancestral mitochondrion. Recently, genomic and cytological evidence has increasingly supported the view that the pre-mitochondrial host cell-a bona fide archaeon branching within the 'Asgard' archaea-was incapable of phagocytosis and used alternative mechanisms to incorporate the alphaproteobacterial ancestor of mitochondria. Indeed, the diversity and variability of proteins associated with phagosomes across the eukaryotic tree suggest that phagocytosis, as seen in a variety of extant eukaryotes, may have evolved independently several times within the eukaryotic crown-group. Since phagocytosis is critical to the functioning of modern marine food webs (without it, there would be no microbial loop or animal life), multiple late origins of phagocytosis could help explain why many of the ecological and evolutionary innovations of the Neoproterozoic Era (e.g. the advent of eukaryotic biomineralization, the 'Rise of Algae' and the origin of animals) happened when they did.}, } @article {pmid32642050, year = {2020}, author = {Porter, SM}, title = {Insights into eukaryogenesis from the fossil record.}, journal = {Interface focus}, volume = {10}, number = {4}, pages = {20190105}, pmid = {32642050}, issn = {2042-8898}, abstract = {Eukaryogenesis-the process by which the eukaryotic cell emerged-has long puzzled scientists. It has been assumed that the fossil record has little to say about this process, in part because important characters such as the nucleus and mitochondria are rarely preserved, and in part because the prevailing model of early eukaryotes implies that eukaryogenesis occurred before the appearance of the first eukaryotes recognized in the fossil record. Here, I propose a different scenario for early eukaryote evolution than is widely assumed. Rather than crown group eukaryotes originating in the late Paleoproterozoic and remaining ecologically minor components for more than half a billion years in a prokaryote-dominated world, I argue for a late Mesoproterozoic origin of the eukaryotic crown group, implying that eukaryogenesis can be studied using the fossil record. I review the proxy records of four crown group characters: the capacity to form cysts as evidenced by the presence of excystment structures; a complex cytoskeleton as evidenced by spines or pylomes; sterol synthesis as evidenced by steranes; and aerobic respiration-and therefore mitochondria-as evidenced by eukaryotes living in oxic environments, and argue that it might be possible to use these proxy records to infer the order in which these characters evolved. The records indicate that both cyst formation and a complex cytoskeleton appeared by late Paleoproterozoic time, and sterol synthesis appeared in the late Mesoproterozioc or early Neoproterozoic. The origin of aerobic respiration cannot as easily be pinned down, but current evidence permits the possibility that it evolved sometime in the Mesoproterozoic.}, } @article {pmid32636606, year = {2020}, author = {Long, X and Xue, H and Wong, JT}, title = {Descent of Bacteria and Eukarya From an Archaeal Root of Life.}, journal = {Evolutionary bioinformatics online}, volume = {16}, number = {}, pages = {1176934320908267}, pmid = {32636606}, issn = {1176-9343}, abstract = {The 3 biological domains delineated based on small subunit ribosomal RNAs (SSU rRNAs) are confronted by uncertainties regarding the relationship between Archaea and Bacteria, and the origin of Eukarya. The similarities between the paralogous valyl-tRNA and isoleucyl-tRNA synthetases in 5398 species estimated by BLASTP, which decreased from Archaea to Bacteria and further to Eukarya, were consistent with vertical gene transmission from an archaeal root of life close to Methanopyrus kandleri through a Primitive Archaea Cluster to an Ancestral Bacteria Cluster, and to Eukarya. The predominant similarities of the ribosomal proteins (rProts) of eukaryotes toward archaeal rProts relative to bacterial rProts established that an archaeal parent rather than a bacterial parent underwent genome merger with bacteria to generate eukaryotes with mitochondria. Eukaryogenesis benefited from the predominantly archaeal accelerated gene adoption (AGA) phenotype pertaining to horizontally transferred genes from other prokaryotes and expedited genome evolution via both gene-content mutations and nucleotidyl mutations. Archaeons endowed with substantial AGA activity were accordingly favored as candidate archaeal parents. Based on the top similarity bitscores displayed by their proteomes toward the eukaryotic proteomes of Giardia and Trichomonas, and high AGA activity, the Aciduliprofundum archaea were identified as leading candidates of the archaeal parent. The Asgard archaeons and a number of bacterial species were among the foremost potential contributors of eukaryotic-like proteins to Eukarya.}, } @article {pmid32581834, year = {2020}, author = {Mannella, CA}, title = {Consequences of Folding the Mitochondrial Inner Membrane.}, journal = {Frontiers in physiology}, volume = {11}, number = {}, pages = {536}, pmid = {32581834}, issn = {1664-042X}, support = {P41 RR001219/RR/NCRR NIH HHS/United States ; }, abstract = {A fundamental first step in the evolution of eukaryotes was infolding of the chemiosmotic membrane of the endosymbiont. This allowed the proto-eukaryote to amplify ATP generation while constraining the volume dedicated to energy production. In mitochondria, folding of the inner membrane has evolved into a highly regulated process that creates specialized compartments (cristae) tuned to optimize function. Internalizing the inner membrane also presents complications in terms of generating the folds and maintaining mitochondrial integrity in response to stresses. This review describes mechanisms that have evolved to regulate inner membrane topology and either preserve or (when appropriate) rupture the outer membrane.}, } @article {pmid32442459, year = {2020}, author = {Neveu, E and Khalifeh, D and Salamin, N and Fasshauer, D}, title = {Prototypic SNARE Proteins Are Encoded in the Genomes of Heimdallarchaeota, Potentially Bridging the Gap between the Prokaryotes and Eukaryotes.}, journal = {Current biology : CB}, volume = {30}, number = {13}, pages = {2468-2480.e5}, doi = {10.1016/j.cub.2020.04.060}, pmid = {32442459}, issn = {1879-0445}, mesh = {Amino Acid Sequence ; Archaea/*genetics/metabolism ; Archaeal Proteins/chemistry/*genetics/metabolism ; *Evolution, Molecular ; Genome, Archaeal ; SNARE Proteins/chemistry/*genetics/metabolism ; }, abstract = {A defining feature of eukaryotic cells is the presence of numerous membrane-bound organelles that subdivide the intracellular space into distinct compartments. How the eukaryotic cell acquired its internal complexity is still poorly understood. Material exchange among most organelles occurs via vesicles that bud off from a source and specifically fuse with a target compartment. Central players in the vesicle fusion process are the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins. These small tail-anchored (TA) membrane proteins zipper into elongated four-helix bundles that pull membranes together. SNARE proteins are highly conserved among eukaryotes but are thought to be absent in prokaryotes. Here, we identified SNARE-like factors in the genomes of uncultured organisms of Asgard archaea of the Heimdallarchaeota clade, which are thought to be the closest living relatives of eukaryotes. Biochemical experiments show that the archaeal SNARE-like proteins can interact with eukaryotic SNARE proteins. We did not detect SNAREs in α-proteobacteria, the closest relatives of mitochondria, but identified several genes encoding for SNARE proteins in γ-proteobacteria of the order Legionellales, pathogens that live inside eukaryotic cells. Very probably, their SNAREs stem from lateral gene transfer from eukaryotes. Together, this suggests that the diverse set of eukaryotic SNAREs evolved from an archaeal precursor. However, whether Heimdallarchaeota actually have a simplified endomembrane system will only be seen when we succeed studying these organisms under the microscope.}, } @article {pmid32430475, year = {2020}, author = {Speijer, D and Hammond, M and Lukeš, J}, title = {Comparing Early Eukaryotic Integration of Mitochondria and Chloroplasts in the Light of Internal ROS Challenges: Timing is of the Essence.}, journal = {mBio}, volume = {11}, number = {3}, pages = {}, pmid = {32430475}, issn = {2150-7511}, mesh = {Biological Evolution ; Chloroplasts/genetics/*metabolism ; Cyanobacteria/genetics/*metabolism ; Eukaryota/*genetics/*metabolism ; Mitochondria/genetics/*metabolism ; Reactive Oxygen Species/*metabolism ; Time Factors ; }, abstract = {When trying to reconstruct the evolutionary trajectories during early eukaryogenesis, one is struck by clear differences in the developments of two organelles of endosymbiotic origin: the mitochondrion and the chloroplast. From a symbiogenic perspective, eukaryotic development can be interpreted as a process in which many of the defining eukaryotic characteristics arose as a result of mutual adaptions of both prokaryotes (an archaeon and a bacterium) involved. This implies that many steps during the bacterium-to-mitochondrion transition trajectory occurred in an intense period of dramatic and rapid changes. In contrast, the subsequent cyanobacterium-to-chloroplast development in a specific eukaryotic subgroup, leading to the photosynthetic lineages, occurred in a full-fledged eukaryote. The commonalities and differences in the two trajectories shed an interesting light on early, and ongoing, eukaryotic evolutionary driving forces, especially endogenous reactive oxygen species (ROS) formation. Differences between organellar ribosomes, changes to the electron transport chain (ETC) components, and mitochondrial codon reassignments in nonplant mitochondria can be understood when mitochondrial ROS formation, e.g., during high energy consumption in heterotrophs, is taken into account.IMPORTANCE The early eukaryotic evolution was deeply influenced by the acquisition of two endosymbiotic organelles - the mitochondrion and the chloroplast. Here we discuss the possibly important role of reactive oxygen species in these processes.}, } @article {pmid32430468, year = {2020}, author = {Lu, Z and Fu, T and Li, T and Liu, Y and Zhang, S and Li, J and Dai, J and Koonin, EV and Li, G and Chu, H and Li, M}, title = {Coevolution of Eukaryote-like Vps4 and ESCRT-III Subunits in the Asgard Archaea.}, journal = {mBio}, volume = {11}, number = {3}, pages = {}, pmid = {32430468}, issn = {2150-7511}, mesh = {Adenosine Triphosphatases/genetics ; Archaea/*classification ; Archaeal Proteins/*genetics/metabolism ; Biological Transport ; Endosomal Sorting Complexes Required for Transport/*genetics/metabolism ; *Evolution, Molecular ; Models, Molecular ; Molecular Docking Simulation ; *Phylogeny ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/genetics ; }, abstract = {The emergence of the endomembrane system is a key step in the evolution of cellular complexity during eukaryogenesis. The endosomal sorting complex required for transport (ESCRT) machinery is essential and required for the endomembrane system functions in eukaryotic cells. Recently, genes encoding eukaryote-like ESCRT protein components have been identified in the genomes of Asgard archaea, a newly proposed archaeal superphylum that is thought to include the closest extant prokaryotic relatives of eukaryotes. However, structural and functional features of Asgard ESCRT remain uncharacterized. Here, we show that Vps4, Vps2/24/46, and Vps20/32/60, the core functional components of the Asgard ESCRT, coevolved eukaryote-like structural and functional features. Phylogenetic analysis shows that Asgard Vps4, Vps2/24/46, and Vps20/32/60 are closely related to their eukaryotic counterparts. Molecular dynamics simulation and biochemical assays indicate that Asgard Vps4 contains a eukaryote-like microtubule-interacting and transport (MIT) domain that binds the distinct type 1 MIT-interacting motif and type 2 MIT-interacting motif in Vps2/24/46 and Vps20/32/60, respectively. The Asgard Vps4 partly, but much more efficiently than homologs from other archaea, complements the vps4 null mutant of Saccharomyces cerevisiae, further supporting the functional similarity between the membrane remodeling machineries of Asgard archaea and eukaryotes. Thus, this work provides evidence that the ESCRT complexes from Asgard archaea and eukaryotes are evolutionarily related and functionally similar. Thus, despite the apparent absence of endomembranes in Asgard archaea, the eukaryotic ESCRT seems to have been directly inherited from an Asgard ancestor, to become a key component of the emerging endomembrane system.IMPORTANCE The discovery of Asgard archaea has changed the existing ideas on the origins of eukaryotes. Researchers propose that eukaryotic cells evolved from Asgard archaea. This hypothesis partly stems from the presence of multiple eukaryotic signature proteins in Asgard archaea, including homologs of ESCRT proteins that are essential components of the endomembrane system in eukaryotes. However, structural and functional features of Asgard ESCRT remain unknown. Our study provides evidence that Asgard ESCRT is functionally comparable to the eukaryotic counterparts, suggesting that despite the apparent absence of endomembranes in archaea, eukaryotic ESCRT was inherited from an Asgard archaeal ancestor, alongside the emergence of endomembrane system during eukaryogenesis.}, } @article {pmid32428484, year = {2020}, author = {Lane, N}, title = {How energy flow shapes cell evolution.}, journal = {Current biology : CB}, volume = {30}, number = {10}, pages = {R471-R476}, doi = {10.1016/j.cub.2020.03.055}, pmid = {32428484}, issn = {1879-0445}, mesh = {Archaea/genetics/metabolism ; *Biological Evolution ; DNA, Mitochondrial/genetics ; Eukaryota/*genetics/*physiology ; Gene Deletion ; Mitochondria/genetics/*physiology ; }, abstract = {How mitochondria shaped the evolution of eukaryotic complexity has been controversial for decades. The discovery of the Asgard archaea, which harbor close phylogenetic ties to the eukaryotes, supports the idea that a critical endosymbiosis between an archaeal host and a bacterial endosymbiont transformed the selective constraints present at the origin of eukaryotes. Cultured Asgard archaea are typically prokaryotic in both size and internal morphology, albeit featuring extensive protrusions. The acquisition of the mitochondrial predecessor by an archaeal host cell fundamentally altered the topology of genes in relation to bioenergetic membranes. Mitochondria internalised not only the bioenergetic membranes but also the genetic machinery needed for local control of oxidative phosphorylation. Gene loss from mitochondria enabled expansion of the nuclear genome, giving rise to an extreme genomic asymmetry that is ancestral to all extant eukaryotes. This genomic restructuring gave eukaryotes thousands of fold more energy availability per gene. In principle, that difference can support more and larger genes, far more non-coding DNA, greater regulatory complexity, and thousands of fold more protein synthesis per gene. These changes released eukaryotes from the bioenergetic constraints on prokaryotes, facilitating the evolution of morphological complexity.}, } @article {pmid32367054, year = {2020}, author = {Baker, BJ and De Anda, V and Seitz, KW and Dombrowski, N and Santoro, AE and Lloyd, KG}, title = {Diversity, ecology and evolution of Archaea.}, journal = {Nature microbiology}, volume = {5}, number = {7}, pages = {887-900}, pmid = {32367054}, issn = {2058-5276}, mesh = {*Archaea/classification/genetics/growth & development/metabolism ; *Biodiversity ; *Biological Evolution ; *Ecology ; Energy Metabolism ; Environmental Microbiology ; Genetic Variation ; Genome, Archaeal ; Phylogeny ; }, abstract = {Compared to bacteria, our knowledge of archaeal biology is limited. Historically, microbiologists have mostly relied on culturing and single-gene diversity surveys to understand Archaea in nature. However, only six of the 27 currently proposed archaeal phyla have cultured representatives. Advances in genomic sequencing and computational approaches are revolutionizing our understanding of Archaea. The recovery of genomes belonging to uncultured groups from the environment has resulted in the description of several new phyla, many of which are globally distributed and are among the predominant organisms on the planet. In this Review, we discuss how these genomes, together with long-term enrichment studies and elegant in situ measurements, are providing insights into the metabolic capabilities of the Archaea. We also debate how such studies reveal how important Archaea are in mediating an array of ecological processes, including global carbon and nutrient cycles, and how this increase in archaeal diversity has expanded our view of the tree of life and early archaeal evolution, and has provided new insights into the origin of eukaryotes.}, } @article {pmid32345370, year = {2020}, author = {Bateman, A}, title = {Division of labour in a matrix, rather than phagocytosis or endosymbiosis, as a route for the origin of eukaryotic cells.}, journal = {Biology direct}, volume = {15}, number = {1}, pages = {8}, pmid = {32345370}, issn = {1745-6150}, mesh = {*Biological Evolution ; Eukaryotic Cells/*physiology ; Extracellular Space/*physiology ; *Microbial Interactions ; Models, Biological ; Phagocytosis ; Prokaryotic Cells/*physiology ; Symbiosis ; }, abstract = {Two apparently irreconcilable models dominate research into the origin of eukaryotes. In one model, amitochondrial proto-eukaryotes emerged autogenously from the last universal common ancestor of all cells. Proto-eukaryotes subsequently acquired mitochondrial progenitors by the phagocytic capture of bacteria. In the second model, two prokaryotes, probably an archaeon and a bacterial cell, engaged in prokaryotic endosymbiosis, with the species resident within the host becoming the mitochondrial progenitor. Both models have limitations. A search was therefore undertaken for alternative routes towards the origin of eukaryotic cells. The question was addressed by considering classes of potential pathways from prokaryotic to eukaryotic cells based on considerations of cellular topology. Among the solutions identified, one, called here the "third-space model", has not been widely explored. A version is presented in which an extracellular space (the third-space), serves as a proxy cytoplasm for mixed populations of archaea and bacteria to "merge" as a transitionary complex without obligatory endosymbiosis or phagocytosis and to form a precursor cell. Incipient nuclei and mitochondria diverge by division of labour. The third-space model can accommodate the reorganization of prokaryote-like genomes to a more eukaryote-like genome structure. Nuclei with multiple chromosomes and mitosis emerge as a natural feature of the model. The model is compatible with the loss of archaeal lipid biochemistry while retaining archaeal genes and provides a route for the development of membranous organelles such as the Golgi apparatus and endoplasmic reticulum. Advantages, limitations and variations of the "third-space" models are discussed. REVIEWERS: This article was reviewed by Damien Devos, Buzz Baum and Michael Gray.}, } @article {pmid32341569, year = {2020}, author = {López-García, P and Moreira, D}, title = {The Syntrophy hypothesis for the origin of eukaryotes revisited.}, journal = {Nature microbiology}, volume = {5}, number = {5}, pages = {655-667}, pmid = {32341569}, issn = {2058-5276}, mesh = {Archaea/genetics/*metabolism ; Bacteria/genetics ; *Biological Evolution ; Cell Nucleus ; Eukaryota/genetics/*metabolism ; Eukaryotic Cells/*metabolism ; Genome, Archaeal ; Hydrogen/metabolism ; Membranes/metabolism ; Mitochondria/metabolism ; Oxidation-Reduction ; *Phylogeny ; Sulfur/metabolism ; Symbiosis/physiology ; }, abstract = {The discovery of Asgard archaea, phylogenetically closer to eukaryotes than other archaea, together with improved knowledge of microbial ecology, impose new constraints on emerging models for the origin of the eukaryotic cell (eukaryogenesis). Long-held views are metamorphosing in favour of symbiogenetic models based on metabolic interactions between archaea and bacteria. These include the classical Searcy's and Hydrogen hypothesis, and the more recent Reverse Flow and Entangle-Engulf-Endogenize models. Two decades ago, we put forward the Syntrophy hypothesis for the origin of eukaryotes based on a tripartite metabolic symbiosis involving a methanogenic archaeon (future nucleus), a fermentative myxobacterial-like deltaproteobacterium (future eukaryotic cytoplasm) and a metabolically versatile methanotrophic alphaproteobacterium (future mitochondrion). A refined version later proposed the evolution of the endomembrane and nuclear membrane system by invagination of the deltaproteobacterial membrane. Here, we adapt the Syntrophy hypothesis to contemporary knowledge, shifting from the original hydrogen and methane-transfer-based symbiosis (HM Syntrophy) to a tripartite hydrogen and sulfur-transfer-based model (HS Syntrophy). We propose a sensible ecological scenario for eukaryogenesis in which eukaryotes originated in early Proterozoic microbial mats from the endosymbiosis of a hydrogen-producing Asgard archaeon within a complex sulfate-reducing deltaproteobacterium. Mitochondria evolved from versatile, facultatively aerobic, sulfide-oxidizing and, potentially, anoxygenic photosynthesizing alphaproteobacterial endosymbionts that recycled sulfur in the consortium. The HS Syntrophy hypothesis accounts for (endo)membrane, nucleus and metabolic evolution in a realistic ecological context. We compare and contrast the HS Syntrophy hypothesis to other models of eukaryogenesis, notably in terms of the mode and tempo of eukaryotic trait evolution, and discuss several model predictions and how these can be tested.}, } @article {pmid32305250, year = {2020}, author = {Meinnel, T and Dian, C and Giglione, C}, title = {Myristoylation, an Ancient Protein Modification Mirroring Eukaryogenesis and Evolution.}, journal = {Trends in biochemical sciences}, volume = {45}, number = {7}, pages = {619-632}, doi = {10.1016/j.tibs.2020.03.007}, pmid = {32305250}, issn = {0968-0004}, mesh = {*Biological Evolution ; Catalysis ; Eukaryotic Cells/metabolism ; Myristic Acid/*metabolism ; Protein Processing, Post-Translational ; Substrate Specificity ; }, abstract = {N-myristoylation (MYR) is a crucial fatty acylation catalyzed by N-myristoyltransferases (NMTs) that is likely to have appeared over 2 billion years ago. Proteome-wide approaches have now delivered an exhaustive list of substrates undergoing MYR across approximately 2% of any proteome, with constituents, several unexpected, associated with different membrane compartments. A set of <10 proteins conserved in eukaryotes probably represents the original set of N-myristoylated targets, marking major changes occurring throughout eukaryogenesis. Recent findings have revealed unexpected mechanisms and reactivity, suggesting competition with other acylations that are likely to influence cellular homeostasis and the steady state of the modification landscape. Here, we review recent advances in NMT catalysis, substrate specificity, and MYR proteomics, and discuss concepts regarding MYR during evolution.}, } @article {pmid32302567, year = {2020}, author = {López-García, P and Moreira, D}, title = {Cultured Asgard Archaea Shed Light on Eukaryogenesis.}, journal = {Cell}, volume = {181}, number = {2}, pages = {232-235}, doi = {10.1016/j.cell.2020.03.058}, pmid = {32302567}, issn = {1097-4172}, mesh = {*Archaea/genetics ; *Eukaryota/genetics ; Eukaryotic Cells ; Genome, Archaeal ; Phylogeny ; }, abstract = {The first cultured Asgard archaeon lives in metabolic symbiosis with hydrogen-scavenging microbes. Its full-genome analysis authenticates the existence of Asgard archaea, previously only known from metagenome-assembled genomes, confirms their closer phylogenetic relatedness to eukaryotes and reinforces the idea that the eukaryotic cell evolved from an integrated archaeal-bacterial syntrophic consortium.}, } @article {pmid32269557, year = {2020}, author = {Domínguez-Santos, R and Pérez-Cobas, AE and Artacho, A and Castro, JA and Talón, I and Moya, A and García-Ferris, C and Latorre, A}, title = {Unraveling Assemblage, Functions and Stability of the Gut Microbiota of Blattella germanica by Antibiotic Treatment.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {487}, pmid = {32269557}, issn = {1664-302X}, abstract = {Symbiosis between prokaryotes and eukaryotes is a widespread phenomenon that has contributed to the evolution of eukaryotes. In cockroaches, two types of symbionts coexist: an endosymbiont in the fat body (Blattabacterium), and a rich gut microbiota. The transmission mode of Blattabacterium is vertical, while the gut microbiota of a new generation is mainly formed by bacterial species present in feces. We have carried out a metagenomic analysis of Blattella germanica populations, treated and non-treated with two antibiotics (vancomycin and ampicillin) over two generations to (1) determine the core of bacterial communities and potential functions of the gut microbiota and (2) to gain insights into the mechanisms of resistance and resilience of the gut microbiota. Our results indicate that the composition and functions of the bacteria were affected by treatment, more severely in the case of vancomycin. Further results demonstrated that in an untreated second-generation population that comes from antibiotic-treated first-generation, the microbiota is not yet stabilized at nymphal stages but can fully recover in adults when feces of a control population were added to the diet. This signifies the existence of a stable core in either composition and functions in lab-reared populations. The high microbiota diversity as well as the observed functional redundancy point toward the microbiota of cockroach hindguts as a robust ecosystem that can recover from perturbations, with recovery being faster when feces are added to the diet.}, } @article {pmid32231287, year = {2020}, author = {Mendez-Bermudez, A and Giraud-Panis, MJ and Ye, J and Gilson, E}, title = {Heterochromatin replication goes hand in hand with telomere protection.}, journal = {Nature structural & molecular biology}, volume = {27}, number = {4}, pages = {313-318}, pmid = {32231287}, issn = {1545-9985}, mesh = {Chromatin/*genetics/ultrastructure ; DNA Replication/genetics ; Heterochromatin/*genetics/ultrastructure ; Humans ; Proteins/chemistry/*genetics/ultrastructure ; Telomere/*genetics/ultrastructure ; }, abstract = {Telomeres arose from the need to stabilize natural chromosome ends, resulting in terminal chromatin structures with specific protective functions. Their constituent proteins also execute general functions within heterochromatin, mediating late replication and facilitating fork progression. Emerging insights into the mechanisms governing heterochromatin replication suggest telomeres and heterochromatin act in concert during development and aging. They also suggest a common evolutionary origin for these two chromosome regions that arose during eukaryogenesis.}, } @article {pmid32201928, year = {2020}, author = {Cai, M and Liu, Y and Yin, X and Zhou, Z and Friedrich, MW and Richter-Heitmann, T and Nimzyk, R and Kulkarni, A and Wang, X and Li, W and Pan, J and Yang, Y and Gu, JD and Li, M}, title = {Diverse Asgard archaea including the novel phylum Gerdarchaeota participate in organic matter degradation.}, journal = {Science China. Life sciences}, volume = {63}, number = {6}, pages = {886-897}, pmid = {32201928}, issn = {1869-1889}, mesh = {Amino Acids/metabolism ; Archaea/*enzymology ; Carbon Cycle ; Ecosystem ; Fatty Acids/metabolism ; Genomics ; Geologic Sediments/*chemistry ; *Metagenome ; Peptides/metabolism ; *Phylogeny ; }, abstract = {Asgard is an archaeal superphylum that might hold the key to understand the origin of eukaryotes, but its diversity and ecological roles remain poorly understood. Here, we reconstructed 15 metagenomic-assembled genomes from coastal sediments covering most known Asgard archaea and a novel group, which is proposed as a new Asgard phylum named as the "Gerdarchaeota". Genomic analyses predict that Gerdarchaeota are facultative anaerobes in utilizing both organic and inorganic carbon. Unlike their closest relatives Heimdallarchaeota, Gerdarchaeota have genes encoding for cellulase and enzymes involved in the tetrahydromethanopterin-based Wood-Ljungdahl pathway. Transcriptomics showed that most of our identified Asgard archaea are capable of degrading organic matter, including peptides, amino acids and fatty acids, occupying ecological niches in different depths of layers of the sediments. Overall, this study broadens the diversity of the mysterious Asgard archaea and provides evidence for their ecological roles in coastal sediments.}, } @article {pmid32157725, year = {2020}, author = {Speijer, D}, title = {Debating Eukaryogenesis-Part 2: How Anachronistic Reasoning Can Lure Us into Inventing Intermediates.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {42}, number = {5}, pages = {e1900153}, doi = {10.1002/bies.201900153}, pmid = {32157725}, issn = {1521-1878}, mesh = {Archaea/genetics ; *Biological Evolution ; *Eukaryota ; Eukaryotic Cells ; Phylogeny ; Symbiosis ; }, abstract = {Eukaryotic origins are inextricably linked with the arrival of a pre-mitochondrion of alphaproteobacterial-like ancestry. However, the nature of the "host" cell and the mode of entry are subject to heavy debate. It is becoming clear that the mutual adaptation of a relatively simple, archaeal host and the endosymbiont has been the defining influence at the beginning of the eukaryotic lineage; however, many still resist such symbiogenic models. In part 1, it is posited that a symbiotic stage before uptake ("pre-symbiosis") seems essential to allow further metabolic integration of the two partners ending in endosymbiosis. Thus, the author argued against phagocytic mechanisms (in which the bacterium is prey or parasite) as the mode of entry. Such positions are still broadly unpopular. Here it is explained why. Evolutionary thinking, especially in the case of eukaryogenesis, is still dominated by anachronistic reasoning, in which highly derived protozoan organisms are seen as in some way representative of intermediate steps during eukaryotic evolution, hence poisoning the debate. This reasoning reflects a mind-set that ignores that Darwinian evolution is a fundamentally historic process. Numerous examples of this kind of erroneous reasoning are given, and some basic precautions against its use are formulated. Also see the video abstract here https://youtu.be/ekqtNleVJpU.}, } @article {pmid32153618, year = {2020}, author = {Peska, V and Garcia, S}, title = {Origin, Diversity, and Evolution of Telomere Sequences in Plants.}, journal = {Frontiers in plant science}, volume = {11}, number = {}, pages = {117}, pmid = {32153618}, issn = {1664-462X}, abstract = {Telomeres are basic structures of eukaryote genomes. They distinguish natural chromosome ends from double-stranded breaks in DNA and protect chromosome ends from degradation or end-to-end fusion with other chromosomes. Telomere sequences are usually tandemly arranged minisatellites, typically following the formula (TxAyGz)n. Although they are well conserved across large groups of organisms, recent findings in plants imply that their diversity has been underestimated. Changes in telomeres are of enormous evolutionary importance as they can affect whole-genome stability. Even a small change in the telomere motif of each repeat unit represents an important interference in the system of sequence-specific telomere binding proteins. Here, we provide an overview of telomere sequences, considering the latest phylogenomic evolutionary framework of plants in the broad sense (Archaeplastida), in which new telomeric sequences have recently been found in diverse and economically important families such as Solanaceae and Amaryllidaceae. In the family Lentibulariaceae and in many groups of green algae, deviations from the typical plant telomeric sequence have also been detected recently. Ancestry and possible homoplasy in telomeric motifs, as well as extant gaps in knowledge are discussed. With the increasing availability of genomic approaches, it is likely that more telomeric diversity will be uncovered in the future. We also discuss basic methods used for telomere identification and we explain the implications of the recent discovery of plant telomerase RNA on further research about the role of telomerase in eukaryogenesis or on the molecular causes and consequences of telomere variability.}, } @article {pmid32125435, year = {2020}, author = {Santana-Molina, C and Rivas-Marin, E and Rojas, AM and Devos, DP}, title = {Origin and Evolution of Polycyclic Triterpene Synthesis.}, journal = {Molecular biology and evolution}, volume = {37}, number = {7}, pages = {1925-1941}, pmid = {32125435}, issn = {1537-1719}, mesh = {Carotenoids/*metabolism ; Eukaryota/metabolism ; *Evolution, Molecular ; Farnesyl-Diphosphate Farnesyltransferase/*genetics/metabolism ; Genes, Bacterial ; *Phylogeny ; Squalene/*metabolism ; Sterols/biosynthesis ; }, abstract = {Polycyclic triterpenes are members of the terpene family produced by the cyclization of squalene. The most representative polycyclic triterpenes are hopanoids and sterols, the former are mostly found in bacteria, whereas the latter are largely limited to eukaryotes, albeit with a growing number of bacterial exceptions. Given their important role and omnipresence in most eukaryotes, contrasting with their scant representation in bacteria, sterol biosynthesis was long thought to be a eukaryotic innovation. Thus, their presence in some bacteria was deemed to be the result of lateral gene transfer from eukaryotes. Elucidating the origin and evolution of the polycyclic triterpene synthetic pathways is important to understand the role of these compounds in eukaryogenesis and their geobiological value as biomarkers in fossil records. Here, we have revisited the phylogenies of the main enzymes involved in triterpene synthesis, performing gene neighborhood analysis and phylogenetic profiling. Squalene can be biosynthesized by two different pathways containing the HpnCDE or Sqs proteins. Our results suggest that the HpnCDE enzymes are derived from carotenoid biosynthesis ones and that they assembled in an ancestral squalene pathway in bacteria, while remaining metabolically versatile. Conversely, the Sqs enzyme is prone to be involved in lateral gene transfer, and its emergence is possibly related to the specialization of squalene biosynthesis. The biosynthesis of hopanoids seems to be ancestral in the Bacteria domain. Moreover, no triterpene cyclases are found in Archaea, invoking a potential scenario in which eukaryotic genes for sterol biosynthesis assembled from ancestral bacterial contributions in early eukaryotic lineages.}, } @article {pmid32121565, year = {2020}, author = {Tiwari, P and Bae, H}, title = {Horizontal Gene Transfer and Endophytes: An Implication for the Acquisition of Novel Traits.}, journal = {Plants (Basel, Switzerland)}, volume = {9}, number = {3}, pages = {}, pmid = {32121565}, issn = {2223-7747}, support = {PJ013655022020//Rural Development Administration/ ; }, abstract = {Horizontal gene transfer (HGT), an important evolutionary mechanism observed in prokaryotes, is the transmission of genetic material across phylogenetically distant species. In recent years, the availability of complete genomes has facilitated the comprehensive analysis of HGT and highlighted its emerging role in the adaptation and evolution of eukaryotes. Endophytes represent an ecologically favored association, which highlights its beneficial attributes to the environment, in agriculture and in healthcare. The HGT phenomenon in endophytes, which features an important biological mechanism for their evolutionary adaptation within the host plant and simultaneously confers "novel traits" to the associated microbes, is not yet completely understood. With a focus on the emerging implications of HGT events in the evolution of biological species, the present review discusses the occurrence of HGT in endophytes and its socio-economic importance in the current perspective. To our knowledge, this review is the first report that provides a comprehensive insight into the impact of HGT in the adaptation and evolution of endophytes.}, } @article {pmid32117448, year = {2020}, author = {Schäffer, DE and Iyer, LM and Burroughs, AM and Aravind, L}, title = {Functional Innovation in the Evolution of the Calcium-Dependent System of the Eukaryotic Endoplasmic Reticulum.}, journal = {Frontiers in genetics}, volume = {11}, number = {}, pages = {34}, pmid = {32117448}, issn = {1664-8021}, abstract = {The origin of eukaryotes was marked by the emergence of several novel subcellular systems. One such is the calcium (Ca[2+])-stores system of the endoplasmic reticulum, which profoundly influences diverse aspects of cellular function including signal transduction, motility, division, and biomineralization. We use comparative genomics and sensitive sequence and structure analyses to investigate the evolution of this system. Our findings reconstruct the core form of the Ca[2+]-stores system in the last eukaryotic common ancestor as having at least 15 proteins that constituted a basic system for facilitating both Ca[2+] flux across endomembranes and Ca[2+]-dependent signaling. We present evidence that the key EF-hand Ca[2+]-binding components had their origins in a likely bacterial symbiont other than the mitochondrial progenitor, whereas the protein phosphatase subunit of the ancestral calcineurin complex was likely inherited from the asgard archaeal progenitor of the stem eukaryote. This further points to the potential origin of the eukaryotes in a Ca[2+]-rich biomineralized environment such as stromatolites. We further show that throughout eukaryotic evolution there were several acquisitions from bacteria of key components of the Ca[2+]-stores system, even though no prokaryotic lineage possesses a comparable system. Further, using quantitative measures derived from comparative genomics we show that there were several rounds of lineage-specific gene expansions, innovations of novel gene families, and gene losses correlated with biological innovation such as the biomineralized molluscan shells, coccolithophores, and animal motility. The burst of innovation of new genes in animals included the wolframin protein associated with Wolfram syndrome in humans. We show for the first time that it contains previously unidentified Sel1, EF-hand, and OB-fold domains, which might have key roles in its biochemistry.}, } @article {pmid32112800, year = {2020}, author = {Li, J and Liu, G and Li, L and Yao, Z and Huang, J}, title = {Research progress on the effect of autophagy-lysosomal pathway on tumor drug resistance.}, journal = {Experimental cell research}, volume = {389}, number = {2}, pages = {111925}, doi = {10.1016/j.yexcr.2020.111925}, pmid = {32112800}, issn = {1090-2422}, mesh = {Animals ; *Autophagy ; *Drug Resistance, Neoplasm ; *Homeostasis ; Humans ; Lysosomes/*pathology ; Neoplasms/*pathology ; }, abstract = {Autophagy is an intracellular degradation pathway that is highly conserved during the evolution of eukaryotes and is based on lysosome. Under nutritional deficiencies or stress, cells can clear damaged and necrotic organelles and proteins through autophagy to maintain the homeostasis of cells and organisms. Studies have found that abnormal autophagy is closely related to the occurrence and development of neurodegenerative diseases and tumors. In order to further understand the relationship between lysosomes and autophagy, tumorigenesis and drug resistance, the role of autophagy-lysosomal pathway in tumor resistance and related mechanisms and the relationship between drug resistance and hypoxia-induced autophagy are discussed in this paper.}, } @article {pmid32080867, year = {2020}, author = {Speijer, D}, title = {Debating Eukaryogenesis-Part 1: Does Eukaryogenesis Presuppose Symbiosis Before Uptake?.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {42}, number = {4}, pages = {e1900157}, doi = {10.1002/bies.201900157}, pmid = {32080867}, issn = {1521-1878}, mesh = {Adaptation, Physiological ; Archaea/*metabolism ; Bacteria/*metabolism ; Biological Evolution ; Eukaryota/*metabolism ; Eukaryotic Cells/*metabolism ; Mitochondria/metabolism ; Phagocytosis/physiology ; Phylogeny ; Reactive Oxygen Species/metabolism ; Signal Transduction/physiology ; Symbiosis/*physiology ; }, abstract = {Eukaryotic origins are heavily debated. The author as well as others have proposed that they are inextricably linked with the arrival of a pre-mitochondrion of alphaproteobacterial-like ancestry, in a so-called symbiogenic scenario. The ensuing mutual adaptation of archaeal host and endosymbiont seems to have been a defining influence during the processes leading to the last eukaryotic common ancestor. An unresolved question in this scenario deals with the means by which the bacterium ends up inside. Older hypotheses revolve around the application of known antagonistic interactions, the bacterium being prey or parasite. Here, in reviewing the field, the author argues that such models share flaws, hence making them less likely, and that a "pre-symbiotic stage" would have eased ongoing metabolic integration. Based on this the author will speculate about the nature of the (endo) symbiosis that started eukaryotic evolution-in the context of bacterial entry being a relatively "early" event-and stress the differences between this uptake and subsequent ones. He will also briefly discuss how the mutual adaptation following the merger progressed and how many eukaryotic hallmarks can be understood in light of coadaptation. Also see the video abstract here https://youtu.be/ekqtNleVJpU.}, } @article {pmid32049644, year = {2020}, author = {Kornmann, B}, title = {The endoplasmic reticulum-mitochondria encounter structure: coordinating lipid metabolism across membranes.}, journal = {Biological chemistry}, volume = {401}, number = {6-7}, pages = {811-820}, doi = {10.1515/hsz-2020-0102}, pmid = {32049644}, issn = {1437-4315}, support = {214291/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Cell Membrane/chemistry/*metabolism ; Endoplasmic Reticulum/*metabolism ; Lipid Metabolism ; Lipids/*chemistry ; Mitochondria/chemistry/*metabolism ; }, abstract = {Endosymbiosis, the beginning of a collaboration between an archaeon and a bacterium and a founding step in the evolution of eukaryotes, owes its success to the establishment of communication routes between the host and the symbiont to allow the exchange of metabolites. As far as lipids are concerned, it is the host that has learnt the symbiont's language, as eukaryote lipids appear to have been borrowed from the bacterial symbiont. Mitochondria exchange lipids with the rest of the cell at membrane contact sites. In fungi, the endoplasmic reticulum-mitochondria encounter structure (ERMES) is one of the best understood membrane tethering complexes. Its discovery has yielded crucial insight into the mechanisms of intracellular lipid trafficking. Despite a wealth of data, our understanding of ERMES formation and its exact role(s) remains incomplete. Here, I endeavour to summarise our knowledge on the ERMES complex and to identify lingering gaps.}, } @article {pmid32044287, year = {2020}, author = {Kuwabara, T and Igarashi, K}, title = {Thermotogales origin scenario of eukaryogenesis.}, journal = {Journal of theoretical biology}, volume = {492}, number = {}, pages = {110192}, doi = {10.1016/j.jtbi.2020.110192}, pmid = {32044287}, issn = {1095-8541}, mesh = {*Archaea/genetics ; Bacteria/genetics ; Biological Evolution ; *Eukaryota/genetics ; Eukaryotic Cells ; Evolution, Molecular ; Phylogeny ; }, abstract = {How eukaryotes were generated is an enigma of evolutionary biology. Widely accepted archaeal-origin eukaryogenesis scenarios, based on similarities of genes and related characteristics between archaea and eukaryotes, cannot explain several eukaryote-specific features of the last eukaryotic common ancestor, such as glycerol-3-phosphate-type membrane lipids, large cells and genomes, and endomembrane formation. Thermotogales spheroids, having multicopy-integrated large nucleoids and producing progeny in periplasm, may explain all of these features as well as endoplasmic reticulum-type signal cleavage sites, although they cannot divide. We hypothesize that the progeny chromosome is formed by random joining small DNAs in immature progeny, followed by reorganization by mechanisms including homologous recombination enabled with multicopy-integrated large genome (MILG). We propose that Thermotogales ancestor spheroids came to divide owing to the archaeal cell division genes horizontally transferred via virus-related particles, forming the first eukaryotic common ancestor (FECA). Referring to the hypothesis, the archaeal information-processing system would have been established in FECA by random joining DNAs excised from the MILG, which contained horizontally transferred archaeal and bacterial DNAs, followed by reorganization by the MILG-enabled homologous recombination. Thus, the large genome may have been a prerequisite, but not a consequence, of eukaryogenesis. The random joining of DNAs likely provided the basic mechanisms for eukaryotic evolution: producing the diversity by the formations of supergroups, novel genes, and introns that are involved in exon shuffling.}, } @article {pmid32008087, year = {2020}, author = {Zachar, I and Boza, G}, title = {Endosymbiosis before eukaryotes: mitochondrial establishment in protoeukaryotes.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {77}, number = {18}, pages = {3503-3523}, pmid = {32008087}, issn = {1420-9071}, support = {NKFI-K124438//National Research, Development, and Innovation Office/ ; GINOP-2.3.2-15-2016-00057//National Research, Development, and Innovation Office/ ; }, mesh = {Biological Evolution ; Eukaryotic Cells/metabolism ; Microbial Consortia ; Mitochondria/*metabolism ; Mitochondrial ADP, ATP Translocases/metabolism ; Plastids ; Prokaryotic Cells/*metabolism ; *Symbiosis ; }, abstract = {Endosymbiosis and organellogenesis are virtually unknown among prokaryotes. The single presumed example is the endosymbiogenetic origin of mitochondria, which is hidden behind the event horizon of the last eukaryotic common ancestor. While eukaryotes are monophyletic, it is unlikely that during billions of years, there were no other prokaryote-prokaryote endosymbioses as symbiosis is extremely common among prokaryotes, e.g., in biofilms. Therefore, it is even more precarious to draw conclusions about potentially existing (or once existing) prokaryotic endosymbioses based on a single example. It is yet unknown if the bacterial endosymbiont was captured by a prokaryote or by a (proto-)eukaryote, and if the process of internalization was parasitic infection, slow engulfment, or phagocytosis. In this review, we accordingly explore multiple mechanisms and processes that could drive the evolution of unicellular microbial symbioses with a special attention to prokaryote-prokaryote interactions and to the mitochondrion, possibly the single prokaryotic endosymbiosis that turned out to be a major evolutionary transition. We investigate the ecology and evolutionary stability of inter-species microbial interactions based on dependence, physical proximity, cost-benefit budget, and the types of benefits, investments, and controls. We identify challenges that had to be conquered for the mitochondrial host to establish a stable eukaryotic lineage. Any assumption about the initial interaction of the mitochondrial ancestor and its contemporary host based solely on their modern relationship is rather perilous. As a result, we warn against assuming an initial mutually beneficial interaction based on modern mitochondria-host cooperation. This assumption is twice fallacious: (i) endosymbioses are known to evolve from exploitative interactions and (ii) cooperativity does not necessarily lead to stable mutualism. We point out that the lack of evidence so far on the evolution of endosymbiosis from mutual syntrophy supports the idea that mitochondria emerged from an exploitative (parasitic or phagotrophic) interaction rather than from syntrophy.}, } @article {pmid31942073, year = {2020}, author = {Imachi, H and Nobu, MK and Nakahara, N and Morono, Y and Ogawara, M and Takaki, Y and Takano, Y and Uematsu, K and Ikuta, T and Ito, M and Matsui, Y and Miyazaki, M and Murata, K and Saito, Y and Sakai, S and Song, C and Tasumi, E and Yamanaka, Y and Yamaguchi, T and Kamagata, Y and Tamaki, H and Takai, K}, title = {Isolation of an archaeon at the prokaryote-eukaryote interface.}, journal = {Nature}, volume = {577}, number = {7791}, pages = {519-525}, pmid = {31942073}, issn = {1476-4687}, mesh = {Amino Acids/metabolism ; Archaea/*classification/*isolation & purification/metabolism/ultrastructure ; Eukaryotic Cells/*classification/cytology/metabolism/ultrastructure ; Evolution, Molecular ; Genome, Archaeal/genetics ; Geologic Sediments/microbiology ; Lipids/analysis/chemistry ; *Models, Biological ; Phylogeny ; Prokaryotic Cells/*classification/cytology/metabolism/ultrastructure ; Symbiosis ; }, abstract = {The origin of eukaryotes remains unclear[1-4]. Current data suggest that eukaryotes may have emerged from an archaeal lineage known as 'Asgard' archaea[5,6]. Despite the eukaryote-like genomic features that are found in these archaea, the evolutionary transition from archaea to eukaryotes remains unclear, owing to the lack of cultured representatives and corresponding physiological insights. Here we report the decade-long isolation of an Asgard archaeon related to Lokiarchaeota from deep marine sediment. The archaeon-'Candidatus Prometheoarchaeum syntrophicum' strain MK-D1-is an anaerobic, extremely slow-growing, small coccus (around 550 nm in diameter) that degrades amino acids through syntrophy. Although eukaryote-like intracellular complexes have been proposed for Asgard archaea[6], the isolate has no visible organelle-like structure. Instead, Ca. P. syntrophicum is morphologically complex and has unique protrusions that are long and often branching. On the basis of the available data obtained from cultivation and genomics, and reasoned interpretations of the existing literature, we propose a hypothetical model for eukaryogenesis, termed the entangle-engulf-endogenize (also known as E[3]) model.}, } @article {pmid31900730, year = {2020}, author = {Cavalier-Smith, T and Chao, EE}, title = {Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria).}, journal = {Protoplasma}, volume = {257}, number = {3}, pages = {621-753}, pmid = {31900730}, issn = {1615-6102}, support = {NE/E004156/1//Natural Environment Research Council/ ; }, mesh = {Archaea/*chemistry ; Biological Evolution ; Eukaryota/*chemistry ; *Phylogeny ; Ribosomes/*chemistry ; }, abstract = {Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.}, } @article {pmid31880779, year = {2020}, author = {Caspermeyer, J}, title = {Scientists Identify Rare Evolutionary Intermediates That Help to Understand the Origin of Eukaryotes.}, journal = {Molecular biology and evolution}, volume = {37}, number = {1}, pages = {305-306}, doi = {10.1093/molbev/msz246}, pmid = {31880779}, issn = {1537-1719}, mesh = {*Archaeal Proteins ; Biological Evolution ; Cell Nucleus ; *Eukaryota ; Nuclear Localization Signals ; Ribosomal Proteins ; }, } @article {pmid31873205, year = {2020}, author = {Orsi, WD and Vuillemin, A and Rodriguez, P and Coskun, ÖK and Gomez-Saez, GV and Lavik, G and Mohrholz, V and Ferdelman, TG}, title = {Metabolic activity analyses demonstrate that Lokiarchaeon exhibits homoacetogenesis in sulfidic marine sediments.}, journal = {Nature microbiology}, volume = {5}, number = {2}, pages = {248-255}, pmid = {31873205}, issn = {2058-5276}, mesh = {Anaerobiosis ; Archaea/classification/*genetics/*metabolism ; Carbon Cycle ; Energy Metabolism ; Fermentation ; Genome, Archaeal ; Geologic Sediments/microbiology ; Metagenomics ; Models, Biological ; Oxidation-Reduction ; Sulfides/metabolism ; }, abstract = {The genomes of the Asgard superphylum of Archaea hold clues pertaining to the nature of the host cell that acquired the mitochondrion at the origin of eukaryotes[1-4]. Representatives of the Asgard candidate phylum Candidatus Lokiarchaeota (Lokiarchaeon) have the capacity for acetogenesis and fermentation[5-7], but how their metabolic activity responds to environmental conditions is poorly understood. Here, we show that in anoxic Namibian shelf sediments, Lokiarchaeon gene expression levels are higher than those of bacterial phyla and increase with depth below the seafloor. Lokiarchaeon gene expression was significantly different across a hypoxic-sulfidic redox gradient, whereby genes involved in growth, fermentation and H2-dependent carbon fixation had the highest expression under the most reducing (sulfidic) conditions. Quantitative stable isotope probing revealed that anaerobic utilization of CO2 and diatomaceous extracellular polymeric substances by Lokiarchaeon was higher than the bacterial average, consistent with higher expression of Lokiarchaeon genes, including those involved in transport and fermentation of sugars and amino acids. The quantitative stable isotope probing and gene expression data demonstrate homoacetogenic activity of Candidatus Lokiarchaeota, whereby fermentative H2 production from organic substrates is coupled with the Wood-Ljungdahl carbon fixation pathway[8]. The high energetic efficiency provided by homoacetogenesis[8] helps to explain the elevated metabolic activity of Lokiarchaeon in this anoxic, energy-limited setting.}, } @article {pmid31866780, year = {2019}, author = {Durand, PM and Barreto Filho, MM and Michod, RE}, title = {Cell Death in Evolutionary Transitions in Individuality.}, journal = {The Yale journal of biology and medicine}, volume = {92}, number = {4}, pages = {651-662}, pmid = {31866780}, issn = {1551-4056}, mesh = {Animals ; *Apoptosis ; *Biological Evolution ; Ecological and Environmental Phenomena ; Eukaryotic Cells/cytology/metabolism ; Humans ; Insecta/physiology ; Signal Transduction ; }, abstract = {Programmed cell death (PCD) in cell groups and microbial communities affects population structures, nutrient recycling, and sociobiological interactions. A less explored area is the role played by PCD in the emergence of higher-level individuals. Here, we examine how cell death impacted evolutionary transitions in individuality (ETIs). The focus is on three specific ETIs - the emergence of the eukaryote cell, multicellularity, and social insects - and we review the theoretical and empirical evidence for the role of PCD in these three transitions. We find that PCD likely contributed to many of the processes involved in eukaryogenesis and the transition to multicellularity. PCD is important for the formation of cooperative groups and is a mechanism by which mutual dependencies between individuals evolve. PCD is also a conflict mediator and involved in division of labor in social groups and in the origin of new cell types. In multicellularity, PCD facilitates the transfer of fitness to the higher-level individual. In eusocial insects, PCD of the gonadal cells in workers is the basis for conflict mediation and the division of labor in the colony. In the three ETIs discussed here, PCD likely played an essential role, without which alternate mechanisms would have been necessary for these increases in complexity to occur.}, } @article {pmid31781075, year = {2019}, author = {Poole, AM and Hendrickson, HL}, title = {Response: Commentary: Manifold Routes to a Nucleus.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2585}, pmid = {31781075}, issn = {1664-302X}, } @article {pmid31754032, year = {2019}, author = {Desfougères, Y and Wilson, MSC and Laha, D and Miller, GJ and Saiardi, A}, title = {ITPK1 mediates the lipid-independent synthesis of inositol phosphates controlled by metabolism.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {49}, pages = {24551-24561}, pmid = {31754032}, issn = {1091-6490}, support = {MC_UU_00012/4/MRC_/Medical Research Council/United Kingdom ; MC_UU_12018/4/MRC_/Medical Research Council/United Kingdom ; R15 GM106322/GM/NIGMS NIH HHS/United States ; MC_UU12018/4/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Archaeal Proteins/metabolism ; Conserved Sequence ; HCT116 Cells ; Humans ; Hydrolysis ; Inositol/metabolism ; Inositol Phosphates/*biosynthesis/metabolism ; Phosphorylation ; Phosphotransferases (Alcohol Group Acceptor)/chemistry/genetics/*metabolism ; Saccharomyces cerevisiae/metabolism ; Sphingolipids/metabolism ; Type C Phospholipases/metabolism ; }, abstract = {Inositol phosphates (IPs) comprise a network of phosphorylated molecules that play multiple signaling roles in eukaryotes. IPs synthesis is believed to originate with IP3 generated from PIP2 by phospholipase C (PLC). Here, we report that in mammalian cells PLC-generated IPs are rapidly recycled to inositol, and uncover the enzymology behind an alternative "soluble" route to synthesis of IPs. Inositol tetrakisphosphate 1-kinase 1 (ITPK1)-found in Asgard archaea, social amoeba, plants, and animals-phosphorylates I(3)P1 originating from glucose-6-phosphate, and I(1)P1 generated from sphingolipids, to enable synthesis of IP6 We also found using PAGE mass assay that metabolic blockage by phosphate starvation surprisingly increased IP6 levels in a ITPK1-dependent manner, establishing a route to IP6 controlled by cellular metabolic status, that is not detectable by traditional [[3]H]-inositol labeling. The presence of ITPK1 in archaeal clades thought to define eukaryogenesis indicates that IPs had functional roles before the appearance of the eukaryote.}, } @article {pmid31738880, year = {2020}, author = {Di Giulio, M}, title = {Common ancestry of eukaryotes and Asgardarchaeota: Three, two or more cellular domains of life?.}, journal = {Journal of theoretical biology}, volume = {486}, number = {}, pages = {110083}, doi = {10.1016/j.jtbi.2019.110083}, pmid = {31738880}, issn = {1095-8541}, mesh = {*Archaea/genetics ; Biological Evolution ; *Eukaryota/genetics ; Eukaryotic Cells ; Evolution, Molecular ; Phylogeny ; }, abstract = {There is much evidence that eukaryotes have many traits in common with archaea and in phylogenetic analyses they are closely linked. In particular, it has been suggested that Asgardarchaeota would be part of the same clade of eukaryotes. If so - and being the difference between Asgardarchaeota and eukaryotes very large - then all this would imply that their common ancestor was a progenote, i.e. a protocell in which the relationship between genotype and phenotype was still evolving. This, in turn, would imply that true cells would appear on the tree of life only later, that is to say, only when the ancestor of Asgardarchaeota and the one of eukaryotes appeared. However, this way of seeing would define these ancestors as primary fundamental cells, namely, as cellular domains of life because it would be in this evolutionary stage that true cells would appear for the first time. Finally, the Asgardarchaeota-eukaryote transition is discussed, that is, some aspects of eukaryogenesis and the taxonomic rank of eukaryotes are analyzed.}, } @article {pmid31736534, year = {2019}, author = {Chen, J and Wang, N}, title = {Tissue cell differentiation and multicellular evolution via cytoskeletal stiffening in mechanically stressed microenvironments.}, journal = {Acta mechanica Sinica = Li xue xue bao}, volume = {35}, number = {2}, pages = {270-274}, pmid = {31736534}, issn = {0567-7718}, support = {R01 GM072744/GM/NIGMS NIH HHS/United States ; }, abstract = {Evolution of eukaryotes from simple cells to complex multicellular organisms remains a mystery. Our postulate is that cytoskeletal stiffening is a necessary condition for evolution of complex multicellular organisms from early simple eukaryotes. Recent findings show that embryonic stem cells are as soft as primitive eukaryotes-amoebae and that differentiated tissue cells can be two orders of magnitude stiffer than embryonic stem cells. Soft embryonic stem cells become stiff as they differentiate into tissue cells of the complex multicellular organisms to match their microenvironment stiffness. We perhaps see in differentiation of embryonic stem cells (derived from inner cell mass cells) the echo of those early evolutionary events. Early soft unicellular organisms might have evolved to stiffen their cytoskeleton to protect their structural integrity from external mechanical stresses while being able to maintain form, to change shape, and to move.}, } @article {pmid31595505, year = {2020}, author = {Rockwell, NC and Lagarias, JC}, title = {Phytochrome evolution in 3D: deletion, duplication, and diversification.}, journal = {The New phytologist}, volume = {225}, number = {6}, pages = {2283-2300}, pmid = {31595505}, issn = {1469-8137}, support = {R01 GM068552/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biological Evolution ; Cyanobacteria/*genetics ; Gene Duplication ; Gene Transfer, Horizontal ; *Genes, Plant ; *Phylogeny ; Phytochrome/*genetics/metabolism ; Plant Physiological Phenomena/*genetics ; Plants/*genetics/metabolism ; Sequence Deletion ; Symbiosis ; }, abstract = {Canonical plant phytochromes are master regulators of photomorphogenesis and the shade avoidance response. They are also part of a widespread superfamily of photoreceptors with diverse spectral and biochemical properties. Plant phytochromes belong to a clade including other phytochromes from glaucophyte, prasinophyte, and streptophyte algae (all members of the Archaeplastida) and those from cryptophyte algae. This is consistent with recent analyses supporting the existence of an AC (Archaeplastida + Cryptista) clade. AC phytochromes have been proposed to arise from ancestral cyanobacterial genes via endosymbiotic gene transfer (EGT), but most recent studies instead support multiple horizontal gene transfer (HGT) events to generate extant eukaryotic phytochromes. In principle, this scenario would be compared to the emerging understanding of early events in eukaryotic evolution to generate a coherent picture. Unfortunately, there is currently a major discrepancy between the evolution of phytochromes and the evolution of eukaryotes; phytochrome evolution is thus not a solved problem. We therefore examine phytochrome evolution in a broader context. Within this context, we can identify three important themes in phytochrome evolution: deletion, duplication, and diversification. These themes drive phytochrome evolution as organisms evolve in response to environmental challenges.}, } @article {pmid31587641, year = {2019}, author = {Keeling, PJ}, title = {Combining morphology, behaviour and genomics to understand the evolution and ecology of microbial eukaryotes.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {374}, number = {1786}, pages = {20190085}, pmid = {31587641}, issn = {1471-2970}, mesh = {Eukaryota/cytology/genetics/*physiology ; Genomics ; }, abstract = {Microbial eukaryotes (protists) are structurally, developmentally and behaviourally more complex than their prokaryotic cousins. This complexity makes it more difficult to translate genomic and metagenomic data into accurate functional inferences about systems ranging all the way from molecular and cellular levels to global ecological networks. This problem can be traced back to the advent of the cytoskeleton and endomembrane systems at the origin of eukaryotes, which endowed them with a range of complex structures and behaviours that still largely dominate how they evolve and interact within microbial communities. But unlike the diverse metabolic properties that evolved within prokaryotes, the structural and behavioural characteristics that strongly define how protists function in the environment cannot readily be inferred from genomic data, since there is generally no simple correlation between a gene and a discrete activity or function. A deeper understanding of protists at both cellular and ecological levels, therefore, requires not only high-throughput genomics but also linking such data to direct observations of natural history and cell biology. This is challenging since these observations typically require cultivation, which is lacking for most protists. Potential remedies with current technology include developing a more phylogenetically diverse range of model systems to better represent the diversity, as well as combining high-throughput, single-cell genomics with microscopic documentation of the subject cells to link sequence with structure and behaviour. This article is part of a discussion meeting issue 'Single cell ecology'.}, } @article {pmid31495194, year = {2019}, author = {Starr, DA}, title = {A network of nuclear envelope proteins and cytoskeletal force generators mediates movements of and within nuclei throughout Caenorhabditis elegans development.}, journal = {Experimental biology and medicine (Maywood, N.J.)}, volume = {244}, number = {15}, pages = {1323-1332}, pmid = {31495194}, issn = {1535-3699}, support = {R01 GM073874/GM/NIGMS NIH HHS/United States ; R35 GM134859/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Caenorhabditis elegans/embryology/*physiology ; Cell Nucleus/*physiology ; Cytoskeleton/*physiology ; Nuclear Envelope/*physiology ; }, abstract = {UNLABELLED: Nuclear migration and anchorage, together referred to as nuclear positioning, are central to many cellular and developmental events. Nuclear positioning is mediated by a conserved network of nuclear envelope proteins that interacts with force generators in the cytoskeleton. At the heart of this network are linker of nucleoskeleton and cytoskeleton (LINC) complexes made of Sad1 and UNC-84 (SUN) proteins at the inner nuclear membrane and Klarsicht, ANC-1, and Syne homology (KASH) proteins in the outer nuclear membrane. LINC complexes span the nuclear envelope, maintain nuclear envelope architecture, designate the surface of nuclei distinctly from the contiguous endoplasmic reticulum, and were instrumental in the early evolution of eukaryotes. LINC complexes interact with lamins in the nucleus and with various cytoplasmic KASH effectors from the surface of nuclei. These effectors regulate the cytoskeleton, leading to a variety of cellular outputs including pronuclear migration, nuclear migration through constricted spaces, nuclear anchorage, centrosome attachment to nuclei, meiotic chromosome movements, and DNA damage repair. How LINC complexes are regulated and how they function are reviewed here. The focus is on recent studies elucidating the best-understood network of LINC complexes, those used throughout Caenorhabditis elegans development.

IMPACT STATEMENT: Defects in nuclear positioning disrupt development in many mammalian tissues. In human development, LINC complexes play important cellular functions including nuclear positioning, homolog pairing in meiosis, DNA damage repair, wound healing, and gonadogenesis. The topics reviewed here are relevant to public health because defects in nuclear positioning and mutations in LINC components are associated with a wide variety of human diseases including muscular dystrophies, neurological disorders, progeria, aneurysms, hearing loss, blindness, sterility, and multiple cancers. Although this review focuses on findings in the model nematode Caenorhabditis elegans, the studies are relevant because almost all the findings originally made in C. elegans are conserved to humans. Furthermore, C. elegans remains the best described network for how LINC complexes are regulated and function.}, } @article {pmid31222170, year = {2019}, author = {López-García, P and Moreira, D}, title = {Eukaryogenesis, a syntrophy affair.}, journal = {Nature microbiology}, volume = {4}, number = {7}, pages = {1068-1070}, pmid = {31222170}, issn = {2058-5276}, support = {322669/ERC_/European Research Council/International ; }, mesh = {*Archaea ; Biological Evolution ; *Eukaryotic Cells ; Phylogeny ; }, abstract = {Eukaryotes evolved from a symbiosis involving alphaproteobacteria and archaea phylogenetically nested within the Asgard clade. Two recent studies explore the metabolic capabilities of Asgard lineages, supporting refined symbiotic metabolic interactions that might have operated at the dawn of eukaryogenesis.}, } @article {pmid31203379, year = {2020}, author = {Bloomfield, G}, title = {The molecular foundations of zygosis.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {77}, number = {2}, pages = {323-330}, pmid = {31203379}, issn = {1420-9071}, mesh = {Animals ; Biological Evolution ; Cell Membrane/metabolism/physiology ; Eukaryota/metabolism/physiology ; Germ Cells/metabolism ; Phylogeny ; Transcription Factors/metabolism ; Zygote/metabolism/*physiology ; }, abstract = {Zygosis is the generation of new biological individuals by the sexual fusion of gamete cells. Our current understanding of eukaryotic phylogeny indicates that sex is ancestral to all extant eukaryotes. Although sexual development is extremely diverse, common molecular elements have been retained. HAP2-GCS1, a protein that promotes the fusion of gamete cell membranes that is related in structure to certain viral fusogens, is conserved in many eukaryotic lineages, even though gametes vary considerably in form and behaviour between species. Similarly, although zygotes have dramatically different forms and fates in different organisms, diverse eukaryotes share a common developmental programme in which homeodomain-containing transcription factors play a central role. These common mechanistic elements suggest possible common evolutionary histories that, if correct, would have profound implications for our understanding of eukaryogenesis.}, } @article {pmid31196150, year = {2018}, author = {Gerlitz, M and Knopp, M and Kapust, N and Xavier, JC and Martin, WF}, title = {Elusive data underlying debate at the prokaryote-eukaryote divide.}, journal = {Biology direct}, volume = {13}, number = {1}, pages = {21}, pmid = {31196150}, issn = {1745-6150}, mesh = {*Biological Evolution ; Energy Metabolism ; Eukaryotic Cells/*physiology ; Mitochondria/metabolism ; Prokaryotic Cells/*physiology ; }, abstract = {BACKGROUND: The origin of eukaryotic cells was an important transition in evolution. The factors underlying the origin and evolutionary success of the eukaryote lineage are still discussed. One camp argues that mitochondria were essential for eukaryote origin because of the unique configuration of internalized bioenergetic membranes that they conferred to the common ancestor of all known eukaryotic lineages. A recent paper by Lynch and Marinov concluded that mitochondria were energetically irrelevant to eukaryote origin, a conclusion based on analyses of previously published numbers of various molecules and ribosomes per cell and cell volumes as a presumed proxy for the role of mitochondria in evolution. Their numbers were purportedly extracted from the literature.

RESULTS: We have examined the numbers upon which the recent study was based. We report that for a sample of 80 numbers that were purportedly extracted from the literature and that underlie key inferences of the recent study, more than 50% of the values do not exist in the cited papers to which the numbers are attributed. The published result cannot be independently reproduced. Other numbers that the recent study reports differ inexplicably from those in the literature to which they are ascribed. We list the discrepancies between the recently published numbers and the purported literature sources of those numbers in a head to head manner so that the discrepancies are readily evident, although the source of error underlying the discrepancies remains obscure.

CONCLUSION: The data purportedly supporting the view that mitochondria had no impact upon eukaryotic evolution data exhibits notable irregularities. The paper in question evokes the impression that the published numbers are of up to seven significant digit accuracy, when in fact more than half the numbers are nowhere to be found in the literature to which they are attributed. Though the reasons for the discrepancies are unknown, it is important to air these issues, lest the prominent paper in question become a point source of a snowballing error through the literature or become interpreted as a form of evidence that mitochondria were irrelevant to eukaryote evolution.

REVIEWERS: This article was reviewed by Eric Bapteste, Jianzhi Zhang and Martin Lercher.}, } @article {pmid31127038, year = {2019}, author = {Tromer, EC and van Hooff, JJE and Kops, GJPL and Snel, B}, title = {Mosaic origin of the eukaryotic kinetochore.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {26}, pages = {12873-12882}, pmid = {31127038}, issn = {1091-6490}, mesh = {Bacteria/classification/genetics ; Bacterial Proteins/chemistry/genetics ; Eukaryota/classification/genetics ; *Evolution, Molecular ; Gene Duplication ; Kinetochores/*chemistry/classification ; Microtubule Proteins/chemistry/genetics ; *Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {The emergence of eukaryotes from ancient prokaryotic lineages embodied a remarkable increase in cellular complexity. While prokaryotes operate simple systems to connect DNA to the segregation machinery during cell division, eukaryotes use a highly complex protein assembly known as the kinetochore. Although conceptually similar, prokaryotic segregation systems and the eukaryotic kinetochore are not homologous. Here we investigate the origins of the kinetochore before the last eukaryotic common ancestor (LECA) using phylogenetic trees, sensitive profile-versus-profile homology detection, and structural comparisons of its protein components. We show that LECA's kinetochore proteins share deep evolutionary histories with proteins involved in a few prokaryotic systems and a multitude of eukaryotic processes, including ubiquitination, transcription, and flagellar and vesicular transport systems. We find that gene duplications played a major role in shaping the kinetochore; more than half of LECA's kinetochore proteins have other kinetochore proteins as closest homologs. Some of these have no detectable homology to any other eukaryotic protein, suggesting that they arose as kinetochore-specific folds before LECA. We propose that the primordial kinetochore evolved from proteins involved in various (pre)eukaryotic systems as well as evolutionarily novel folds, after which a subset duplicated to give rise to the complex kinetochore of LECA.}, } @article {pmid31076245, year = {2019}, author = {Brunk, CF and Martin, WF}, title = {Archaeal Histone Contributions to the Origin of Eukaryotes.}, journal = {Trends in microbiology}, volume = {27}, number = {8}, pages = {703-714}, doi = {10.1016/j.tim.2019.04.002}, pmid = {31076245}, issn = {1878-4380}, mesh = {Archaea/*physiology ; *Biological Evolution ; DNA ; Eukaryotic Cells/*physiology ; Histones/*physiology ; Mitochondria/physiology ; Symbiosis ; }, abstract = {The eukaryotic lineage arose from bacterial and archaeal cells that underwent a symbiotic merger. At the origin of the eukaryote lineage, the bacterial partner contributed genes, metabolic energy, and the building blocks of the endomembrane system. What did the archaeal partner donate that made the eukaryotic experiment a success? The archaeal partner provided the potential for complex information processing. Archaeal histones were crucial in that regard by providing the basic functional unit with which eukaryotes organize DNA into nucleosomes, exert epigenetic control of gene expression, transcribe genes with CCAAT-box promoters, and a manifest cell cycle with condensed chromosomes. While mitochondrial energy lifted energetic constraints on eukaryotic protein production, histone-based chromatin organization paved the path to eukaryotic genome complexity, a critical hurdle en route to the evolution of complex cells.}, } @article {pmid31001417, year = {2019}, author = {Field, MC and Rout, MP}, title = {Pore timing: the evolutionary origins of the nucleus and nuclear pore complex.}, journal = {F1000Research}, volume = {8}, number = {}, pages = {}, pmid = {31001417}, issn = {2046-1402}, support = {MR/P009018/1/MRC_/Medical Research Council/United Kingdom ; MR/N010558/1/MRC_/Medical Research Council/United Kingdom ; 203134/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; R01 GM112108/GM/NIGMS NIH HHS/United States ; P41 GM109824/GM/NIGMS NIH HHS/United States ; R01 GM117212/GM/NIGMS NIH HHS/United States ; 204697/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Biological Evolution ; *Cell Nucleus ; *Eukaryotic Cells ; *Nuclear Pore ; *Prokaryotic Cells ; }, abstract = {The name "eukaryote" is derived from Greek, meaning "true kernel", and describes the domain of organisms whose cells have a nucleus. The nucleus is thus the defining feature of eukaryotes and distinguishes them from prokaryotes (Archaea and Bacteria), whose cells lack nuclei. Despite this, we discuss the intriguing possibility that organisms on the path from the first eukaryotic common ancestor to the last common ancestor of all eukaryotes did not possess a nucleus at all-at least not in a form we would recognize today-and that the nucleus in fact arrived relatively late in the evolution of eukaryotes. The clues to this alternative evolutionary path lie, most of all, in recent discoveries concerning the structure of the nuclear pore complex. We discuss the evidence for such a possibility and how this impacts our views of eukaryote origins and how eukaryotes have diversified subsequent to their last common ancestor.}, } @article {pmid30936488, year = {2019}, author = {Spang, A and Stairs, CW and Dombrowski, N and Eme, L and Lombard, J and Caceres, EF and Greening, C and Baker, BJ and Ettema, TJG}, title = {Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism.}, journal = {Nature microbiology}, volume = {4}, number = {7}, pages = {1138-1148}, pmid = {30936488}, issn = {2058-5276}, mesh = {Archaea/classification/*genetics/*metabolism ; Archaeal Proteins/genetics ; *Biological Evolution ; Eukaryotic Cells/metabolism/*physiology ; Genome, Archaeal/genetics ; Heterotrophic Processes ; Hydrogen/metabolism ; Metabolic Networks and Pathways ; *Models, Biological ; Oxidation-Reduction ; *Phylogeny ; Symbiosis ; }, abstract = {The origin of eukaryotes represents an unresolved puzzle in evolutionary biology. Current research suggests that eukaryotes evolved from a merger between a host of archaeal descent and an alphaproteobacterial endosymbiont. The discovery of the Asgard archaea, a proposed archaeal superphylum that includes Lokiarchaeota, Thorarchaeota, Odinarchaeota and Heimdallarchaeota suggested to comprise the closest archaeal relatives of eukaryotes, has helped to elucidate the identity of the putative archaeal host. Whereas Lokiarchaeota are assumed to employ a hydrogen-dependent metabolism, little is known about the metabolic potential of other members of the Asgard superphylum. We infer the central metabolic pathways of Asgard archaea using comparative genomics and phylogenetics to be able to refine current models for the origin of eukaryotes. Our analyses indicate that Thorarchaeota and Lokiarchaeota encode proteins necessary for carbon fixation via the Wood-Ljungdahl pathway and for obtaining reducing equivalents from organic substrates. By contrast, Heimdallarchaeum LC2 and LC3 genomes encode enzymes potentially enabling the oxidation of organic substrates using nitrate or oxygen as electron acceptors. The gene repertoire of Heimdallarchaeum AB125 and Odinarchaeum indicates that these organisms can ferment organic substrates and conserve energy by coupling ferredoxin reoxidation to respiratory proton reduction. Altogether, our genome analyses suggest that Asgard representatives are primarily organoheterotrophs with variable capacity for hydrogen consumption and production. On this basis, we propose the 'reverse flow model', an updated symbiogenetic model for the origin of eukaryotes that involves electron or hydrogen flow from an organoheterotrophic archaeal host to a bacterial symbiont.}, } @article {pmid30884919, year = {2019}, author = {Akashi, M and Takemura, M}, title = {Gram-Positive Bacteria-Like DNA Binding Machineries Involved in Replication Initiation and Termination Mechanisms of Mimivirus.}, journal = {Viruses}, volume = {11}, number = {3}, pages = {}, pmid = {30884919}, issn = {1999-4915}, mesh = {Bacterial Proteins/genetics ; Computational Biology ; DNA Helicases ; DNA Repair/genetics ; *DNA Replication ; Exodeoxyribonucleases/genetics ; Gram-Positive Bacteria/enzymology/genetics ; Mimiviridae/enzymology/*genetics ; Mitochondria/genetics ; Open Reading Frames ; *Peptide Chain Termination, Translational ; *Replication Origin ; Rickettsia/genetics ; }, abstract = {The detailed mechanisms of replication initiation, termination and segregation events were not yet known in Acanthamoeba polyphaga mimivirus (APMV). Here, we show detailed bioinformatics-based analyses of chromosomal replication in APMV from initiation to termination mediated by proteins bound to specific DNA sequences. Using GC/AT skew and coding sequence skew analysis, we estimated that the replication origin is located at 382 kb in the APMV genome. We performed homology-modeling analysis of the gamma domain of APMV-FtsK (DNA translocase coordinating chromosome segregation) related to FtsK-orienting polar sequences (KOPS) binding, suggesting that there was an insertion in the gamma domain which maintains the structure of the DNA binding motif. Furthermore, UvrD/Rep-like helicase in APMV was homologous to Bacillus subtilis AddA, while the chi-like quartet sequence 5'-CCGC-3' was frequently found in the estimated ori region, suggesting that chromosomal replication of APMV is initiated via chi-like sequence recognition by UvrD/Rep-like helicase. Therefore, the replication initiation, termination and segregation of APMV are presumably mediated by DNA repair machineries derived from gram-positive bacteria. Moreover, the other frequently observed quartet sequence 5'-CGGC-3' in the ori region was homologous to the mitochondrial signal sequence of replication initiation, while the comparison of quartet sequence composition in APMV/Rickettsia-genome showed significantly similar values, suggesting that APMV also conserves the mitochondrial replication system acquired from an ancestral genome of mitochondria during eukaryogenesis.}, } @article {pmid30854543, year = {2019}, author = {Albertini, E and Barcaccia, G and Carman, JG and Pupilli, F}, title = {Did apomixis evolve from sex or was it the other way around?.}, journal = {Journal of experimental botany}, volume = {70}, number = {11}, pages = {2951-2964}, doi = {10.1093/jxb/erz109}, pmid = {30854543}, issn = {1460-2431}, mesh = {*Apomixis ; *Biological Evolution ; Magnoliopsida/*physiology ; Reproduction ; }, abstract = {In angiosperms, there are two pathways of reproduction through seeds: sexual, or amphimictic, and asexual, or apomictic. The essential feature of apomixis is that an embryo in an ovule is formed autonomously. It may form from a cell of the nucellus or integuments in an otherwise sexual ovule, a process referred to as adventitious embryony. Alternatively, the embryo may form by parthenogenesis from an unreduced egg that forms in an unreduced embryo sac. The latter may form from an ameiotic megasporocyte, in which case it is referred to as diplospory, or from a cell of the nucellus or integument, in which case it is referred to as apospory. Progeny of apomictic plants are generally identical to the mother plant. Apomixis has been seen over the years as either a gain- or loss-of-function over sexuality, implying that the latter is the default condition. Here, we consider an additional point of view, that apomixis may be anciently polyphenic with sex and that both reproductive phenisms involve anciently canalized components of complex molecular processes. This polyphenism viewpoint suggests that apomixis fails to occur in obligately sexual eukaryotes because genetic or epigenetic modifications have silenced the primitive sex apomixis switch and/or disrupted molecular capacities for apomixis. In eukaryotes where sex and apomixis are clearly polyphenic, apomixis exponentially drives clonal fecundity during reproductively favorable conditions, while stress induces sex for stress-tolerant spore or egg formation. The latter often guarantees species survival during environmentally harsh seasons.}, } @article {pmid30740457, year = {2019}, author = {Gruber, A}, title = {What's in a name? How organelles of endosymbiotic origin can be distinguished from endosymbionts.}, journal = {Microbial cell (Graz, Austria)}, volume = {6}, number = {2}, pages = {123-133}, pmid = {30740457}, issn = {2311-2638}, abstract = {Mitochondria and plastids evolved from free-living bacteria, but are now considered integral parts of the eukaryotic species in which they live. Therefore, they are implicitly called by the same eukaryotic species name. Historically, mitochondria and plastids were known as "organelles", even before their bacterial origin became fully established. However, since organelle evolution by endosymbiosis has become an established theory in biology, more and more endosymbiotic systems have been discovered that show various levels of host/symbiont integration. In this context, the distinction between "host/symbiont" and "eukaryote/organelle" systems is currently unclear. The criteria that are commonly considered are genetic integration (via gene transfer from the endosymbiont to the nucleus), cellular integration (synchronization of the cell cycles), and metabolic integration (the mutual dependency of the metabolisms). Here, I suggest that these criteria should be evaluated according to the resulting coupling of genetic recombination between individuals and congruence of effective population sizes, which determines if independent speciation is possible for either of the partners. I would like to call this aspect of integration "sexual symbiont integration". If the partners lose their independence in speciation, I think that they should be considered one species. The partner who maintains its genetic recombination mechanisms and life cycle should then be the name giving "host"; the other one would be the organelle. Distinguishing between organelles and symbionts according to their sexual symbiont integration is independent of any particular mechanism or structural property of the endosymbiont/host system under investigation.}, } @article {pmid30670662, year = {2019}, author = {Bloomfield, G and Paschke, P and Okamoto, M and Stevens, TJ and Urushihara, H}, title = {Triparental inheritance in Dictyostelium.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {6}, pages = {2187-2192}, pmid = {30670662}, issn = {1091-6490}, support = {MC_U105115237/MRC_/Medical Research Council/United Kingdom ; MC_U105178783/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Sex promotes the recombination and reassortment of genetic material and is prevalent across eukaryotes, although our knowledge of the molecular details of sexual inheritance is scant in several major lineages. In social amoebae, sex involves a promiscuous mixing of cytoplasm before zygotes consume the majority of cells, but for technical reasons, sexual progeny have been difficult to obtain and study. We report here genome-wide characterization of meiotic progeny in Dictyostelium discoideum We find that recombination occurs at high frequency in pairwise crosses between all three mating types, despite the absence of the Spo11 enzyme that is normally required to initiate crossover formation. Fusions of more than two gametes to form transient syncytia lead to frequent triparental inheritance, with haploid meiotic progeny bearing recombined nuclear haplotypes from two parents and the mitochondrial genome from a third. Cells that do not contribute genetically to the Dictyostelium zygote nucleus thereby have a stake in the next haploid generation. D. discoideum mitochondrial genomes are polymorphic, and our findings raise the possibility that some of this variation might be a result of sexual selection on genes that can promote the spread of individual organelle genomes during sex. This kind of self-interested mitochondrial behavior may have had important consequences during eukaryogenesis and the initial evolution of sex.}, } @article {pmid30621777, year = {2018}, author = {Lynch, M and Marinov, GK}, title = {Response to Martin and colleagues: mitochondria do not boost the bioenergetic capacity of eukaryotic cells.}, journal = {Biology direct}, volume = {13}, number = {1}, pages = {26}, pmid = {30621777}, issn = {1745-6150}, support = {R35 GM122566/GM/NIGMS NIH HHS/United States ; }, mesh = {*Energy Metabolism ; *Eukaryotic Cells ; Mitochondria ; Prokaryotic Cells ; }, abstract = {A recent paper by (Gerlitz et al., Biol Direct 13:21, 2018) questions the validity of the data underlying prior analyses on the bioenergetics capacities of cells, and continues to promote the idea that the mitochondrion endowed eukaryotic cells with energetic superiority over prokaryotes. The former point has been addressed previously, with no resultant changes in the conclusions, and the latter point remains inconsistent with multiple lines of empirical data.}, } @article {pmid30504522, year = {2019}, author = {Kanduc, D}, title = {The comparative biochemistry of viruses and humans: an evolutionary path towards autoimmunity.}, journal = {Biological chemistry}, volume = {400}, number = {5}, pages = {629-638}, doi = {10.1515/hsz-2018-0271}, pmid = {30504522}, issn = {1437-4315}, mesh = {Amino Acid Sequence ; *Autoimmunity ; Borna disease virus/*immunology ; Humans ; Influenza A virus/*immunology ; Measles virus/*immunology ; Mumps virus/*immunology ; Peptides/*immunology ; Rubella virus/*immunology ; }, abstract = {Analyses of the peptide sharing between five common human viruses (Borna disease virus, influenza A virus, measles virus, mumps virus and rubella virus) and the human proteome highlight a massive viral vs. human peptide overlap that is mathematically unexpected. Evolutionarily, the data underscore a strict relationship between viruses and the origin of eukaryotic cells. Indeed, according to the viral eukaryogenesis hypothesis and in light of the endosymbiotic theory, the first eukaryotic cell (our lineage) originated as a consortium consisting of an archaeal ancestor of the eukaryotic cytoplasm, a bacterial ancestor of the mitochondria and a viral ancestor of the nucleus. From a pathologic point of view, the peptide sequence similarity between viruses and humans may provide a molecular platform for autoimmune crossreactions during immune responses following viral infections/immunizations.}, } @article {pmid30466901, year = {2019}, author = {Hampl, V and Čepička, I and Eliáš, M}, title = {Was the Mitochondrion Necessary to Start Eukaryogenesis?.}, journal = {Trends in microbiology}, volume = {27}, number = {2}, pages = {96-104}, doi = {10.1016/j.tim.2018.10.005}, pmid = {30466901}, issn = {1878-4380}, mesh = {Adenosine Triphosphate ; Archaea/physiology ; *Biological Evolution ; Eukaryota/genetics/*physiology ; Eukaryotic Cells/*physiology ; Genome ; Mitochondria/genetics/*physiology ; Phagocytosis ; Prokaryotic Cells/physiology ; Symbiosis ; }, abstract = {Arguments based on cell energetics favour the view that a mitochondrion capable of oxidative phosphorylation was a prerequisite for the evolution of other features of the eukaryotic cell, including increased volume, genome size and, eventually, phagotrophy. Contrary to this we argue that: (i) extant amitochondriate eukaryotes possess voluminous phagotrophic cells with large genomes; (ii) picoeukaryotes demonstrate that phagotrophy is feasible at prokaryotic cell sizes; and (iii) the assumption that evolution of complex features requires extra ATP, often mentioned in this context, is unfounded and should not be used in such considerations. We claim that the diversity of cell organisations and functions observed today in eukaryotes gives no reason to postulate that a mitochondrion must have preceded phagocytosis in eukaryogenesis.}, } @article {pmid30422680, year = {2019}, author = {Avni, E and Snir, S}, title = {A New Quartet-Based Statistical Method for Comparing Sets of Gene Trees Is Developed Using a Generalized Hoeffding Inequality.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {26}, number = {1}, pages = {27-37}, doi = {10.1089/cmb.2018.0129}, pmid = {30422680}, issn = {1557-8666}, mesh = {Algorithms ; Animals ; Evolution, Molecular ; Gene Transfer, Horizontal ; Humans ; *Multigene Family ; Phylogeny ; }, abstract = {Extracting the strength of the tree signal that is encompassed by a collection of gene trees is an exceptionally challenging problem in phylogenomics. Often, this problem not only involves the construction of individual phylogenies based on different genes, which may be a difficult endeavor on its own, but is also exacerbated by many factors that create conflicts between the evolutionary histories of different gene families, such as duplications or losses of genes; hybridization events; incomplete lineage sorting; and horizontal gene transfer, the latter two play central roles in the evolution of eukaryotes and prokaryotes, respectively. In this work, we tackle the aforementioned problem by focusing on quartet trees, which are the most basic unit of information in the context of unrooted phylogenies. In the first part, we show how a theorem of Janson that generalizes the classical Hoeffding inequality can be used to develop a statistical test involving quartets. In the second part, we study real and simulated data using this theoretical advancement, thus demonstrating how the significance of the differences between sets of quartets can be assessed. Our results are particularly intriguing since they nonstandardly require the analysis of dependent random variables.}, } @article {pmid30401812, year = {2018}, author = {Lutfullahoğlu-Bal, G and Seferoğlu, AB and Keskin, A and Akdoğan, E and Dunn, CD}, title = {A bacteria-derived tail anchor localizes to peroxisomes in yeast and mammalian cells.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16374}, pmid = {30401812}, issn = {2045-2322}, support = {637649/ERC_/European Research Council/International ; }, mesh = {Amino Acid Sequence ; Escherichia coli/genetics/metabolism ; Escherichia coli Proteins/chemistry/*metabolism ; Gene Transfer, Horizontal ; HEK293 Cells ; Humans ; Mixed Function Oxygenases/chemistry/*metabolism ; Peroxisomes/*metabolism ; Protein Transport ; Saccharomyces cerevisiae/*cytology/metabolism ; }, abstract = {Prokaryotes can provide new genetic information to eukaryotes by horizontal gene transfer (HGT), and such transfers are likely to have been particularly consequential in the era of eukaryogenesis. Since eukaryotes are highly compartmentalized, it is worthwhile to consider the mechanisms by which newly transferred proteins might reach diverse organellar destinations. Toward this goal, we have focused our attention upon the behavior of bacteria-derived tail anchors (TAs) expressed in the eukaryote Saccharomyces cerevisiae. In this study, we report that a predicted membrane-associated domain of the Escherichia coli YgiM protein is specifically trafficked to peroxisomes in budding yeast, can be found at a pre-peroxisomal compartment (PPC) upon disruption of peroxisomal biogenesis, and can functionally replace an endogenous, peroxisome-directed TA. Furthermore, the YgiM(TA) can localize to peroxisomes in mammalian cells. Since the YgiM(TA) plays no endogenous role in peroxisomal function or assembly, this domain is likely to serve as an excellent tool allowing further illumination of the mechanisms by which TAs can travel to peroxisomes. Moreover, our findings emphasize the ease with which bacteria-derived sequences might target to organelles in eukaryotic cells following HGT, and we discuss the importance of flexible recognition of organelle targeting information during and after eukaryogenesis.}, } @article {pmid30358047, year = {2018}, author = {Gabaldón, T}, title = {Relative timing of mitochondrial endosymbiosis and the "pre-mitochondrial symbioses" hypothesis.}, journal = {IUBMB life}, volume = {70}, number = {12}, pages = {1188-1196}, pmid = {30358047}, issn = {1521-6551}, mesh = {Archaea/genetics/metabolism ; *Biological Evolution ; Eukaryotic Cells/metabolism ; Mitochondria/*genetics ; *Phylogeny ; Prokaryotic Cells/metabolism ; Symbiosis/*genetics ; }, abstract = {The origin of eukaryotes stands as a major open question in biology. Central to this question is the nature and timing of the origin of the mitochondrion, an ubiquitous eukaryotic organelle originated by the endosymbiosis of an alphaproteobacterial ancestor. Different hypotheses disagree, among other aspects, on whether mitochondria were acquired early or late during eukaryogenesis. Similarly, the nature and complexity of the receiving host is debated, with models ranging from a simple prokaryotic host to an already complex proto-eukaryote. Here, I will discuss recent findings from phylogenomics analyses of extant genomes that are shedding light into the evolutionary origins of the eukaryotic ancestor, and which suggest a later acquisition of alpha-proteobacterial derived proteins as compared to those with different bacterial ancestries. I argue that simple eukaryogenesis models that assume a binary symbiosis between an archaeon host and an alpha-proteobacterial proto-mitochondrion cannot explain the complex chimeric nature that is inferred for the eukaryotic ancestor. To reconcile existing hypotheses with the new data, I propose the "pre-mitochondrial symbioses" hypothesis that provides a framework for eukaryogenesis scenarios involving alternative symbiotic interactions that predate the acquisition of mitochondria. © 2018 The Authors. IUBMB Life published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology, 70(12):1188-1196, 2018.}, } @article {pmid30158917, year = {2018}, author = {Fournier, GP and Poole, AM}, title = {A Briefly Argued Case That Asgard Archaea Are Part of the Eukaryote Tree.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1896}, pmid = {30158917}, issn = {1664-302X}, abstract = {The recent discovery of the Lokiarchaeota and other members of the Asgard superphylum suggests that closer analysis of the cell biology and evolution of these groups may help shed light on the origin of the eukaryote cell. Asgard lineages often appear in molecular phylogenies as closely related to eukaryotes, and possess "Eukaryote Signature Proteins" coded by genes previously thought to be unique to eukaryotes. This phylogenetic affinity to eukaryotes has been widely interpreted as indicating that Asgard lineages are "eukaryote-like archaea," with eukaryotes evolving from within a paraphyletic Archaea. Guided by the established principles of systematics, we examine the potential implications of the monophyly of Asgard lineages and Eukarya. We show that a helpful parallel case is that of Synapsida, a group that includes modern mammals and their more "reptile-like" ancestors, united by shared derived characters that evolved in their common ancestor. While this group contains extinct members that share many similarities with modern reptiles and their extinct relatives, they are evolutionarily distinct from Sauropsida, the group which includes modern birds, reptiles, and all other amniotes. Similarly, Asgard lineages and eukaryotes are united by shared derived characters to the exclusion of all other groups. Consequently, the Asgard group is not only highly informative for our understanding of eukaryogenesis, but may be better understood as being early diverging members of a broader group including eukaryotes, for which we propose the name "Eukaryomorpha." Significantly, this means that the relationship between Eukarya and Asgard lineages cannot, on its own, resolve the debate over 2 vs. 3 Domains of life; instead, resolving this debate depends upon identifying the root of Archaea with respect to Bacteria.}, } @article {pmid30060189, year = {2018}, author = {Río Bártulos, C and Rogers, MB and Williams, TA and Gentekaki, E and Brinkmann, H and Cerff, R and Liaud, MF and Hehl, AB and Yarlett, NR and Gruber, A and Kroth, PG and van der Giezen, M}, title = {Mitochondrial Glycolysis in a Major Lineage of Eukaryotes.}, journal = {Genome biology and evolution}, volume = {10}, number = {9}, pages = {2310-2325}, pmid = {30060189}, issn = {1759-6653}, support = {//Wellcome Trust/United Kingdom ; 078566/A/05/Z//Wellcome Trust/United Kingdom ; }, mesh = {Biological Evolution ; Blastocystis/cytology/enzymology/genetics/*metabolism ; Diatoms/cytology/enzymology/genetics/*metabolism ; Energy Metabolism ; Genome, Mitochondrial ; *Glycolysis ; Mitochondria/genetics/*metabolism ; Symbiosis ; Transformation, Genetic ; }, abstract = {The establishment of the mitochondrion is seen as a transformational step in the origin of eukaryotes. With the mitochondrion came bioenergetic freedom to explore novel evolutionary space leading to the eukaryotic radiation known today. The tight integration of the bacterial endosymbiont with its archaeal host was accompanied by a massive endosymbiotic gene transfer resulting in a small mitochondrial genome which is just a ghost of the original incoming bacterial genome. This endosymbiotic gene transfer resulted in the loss of many genes, both from the bacterial symbiont as well the archaeal host. Loss of genes encoding redundant functions resulted in a replacement of the bulk of the host's metabolism for those originating from the endosymbiont. Glycolysis is one such metabolic pathway in which the original archaeal enzymes have been replaced by bacterial enzymes from the endosymbiont. Glycolysis is a major catabolic pathway that provides cellular energy from the breakdown of glucose. The glycolytic pathway of eukaryotes appears to be bacterial in origin, and in well-studied model eukaryotes it takes place in the cytosol. In contrast, here we demonstrate that the latter stages of glycolysis take place in the mitochondria of stramenopiles, a diverse and ecologically important lineage of eukaryotes. Although our work is based on a limited sample of stramenopiles, it leaves open the possibility that the mitochondrial targeting of glycolytic enzymes in stramenopiles might represent the ancestral state for eukaryotes.}, } @article {pmid29987711, year = {2018}, author = {Maréchal, E}, title = {Primary Endosymbiosis: Emergence of the Primary Chloroplast and the Chromatophore, Two Independent Events.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1829}, number = {}, pages = {3-16}, doi = {10.1007/978-1-4939-8654-5_1}, pmid = {29987711}, issn = {1940-6029}, mesh = {Alphaproteobacteria/genetics ; Cell Membrane/metabolism ; Chlamydia/genetics/metabolism ; Chloroplasts/*pathology ; Chromatophores/*physiology ; Cyanobacteria/metabolism ; Eukaryota/physiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Glaucophyta/genetics/metabolism ; Inheritance Patterns ; Mitochondria/genetics/metabolism ; Rhizaria ; *Symbiosis ; }, abstract = {The emergence of semiautonomous organelles, such as the mitochondrion, the chloroplast, and more recently, the chromatophore, are critical steps in the evolution of eukaryotes. They resulted from primary endosymbiotic events that seem to share general features, i.e., an acquisition of a bacterium/cyanobacteria likely via a phagocytic membrane, a genome reduction coinciding with an escape of genes from the organelle to the nucleus, and finally the appearance of an active system translocating nuclear-encoded proteins back to the organelles. An intense mobilization of foreign genes of bacterial origin, via horizontal gene transfers, plays a critical role. Some third partners, like Chlamydia, might have facilitated the transition from cyanobacteria to the early chloroplast. This chapter describes our current understanding of primary endosymbiosis, with a specific focus on primary chloroplasts considered to have emerged more than one billion years ago, and on the chromatophore, having emerged about one hundred million years ago.}, } @article {pmid29802659, year = {2018}, author = {Tilquin, A and Christie, JR and Kokko, H}, title = {Mitochondrial complementation: a possible neglected factor behind early eukaryotic sex.}, journal = {Journal of evolutionary biology}, volume = {31}, number = {8}, pages = {1152-1164}, doi = {10.1111/jeb.13293}, pmid = {29802659}, issn = {1420-9101}, mesh = {Animals ; *Biological Evolution ; Eukaryota/*genetics/*physiology ; *Mitochondria ; Models, Biological ; Reproduction/*genetics/*physiology ; }, abstract = {Sex is ancestral in eukaryotes. Meiotic sex differs from bacterial ways of exchanging genetic material by involving the fusion of two cells. We examine the hypothesis that fusion evolved in early eukaryotes because it was directly beneficial, rather than a passive side effect of meiotic sex. We assume that the uptake of (proto)mitochondria into eukaryotes preceded the evolution of cell fusion and that Muller's ratchet operating within symbiont lineages led to the accumulation of lineage-specific sets of mutations in asexual host cells. We examine whether cell fusion, and the consequent biparental inheritance of symbionts, helps to mitigate the effects of this mutational meltdown of mitochondria. In our model, host cell fitness improves when two independently evolved mitochondrial strains co-inhabit a single cytoplasm, mirroring mitochondrial complementation found in modern eukaryotes. If fusion incurs no cost, we find that an allele coding for fusion can invade a population of nonfusers. If fusion is costly, there are two thresholds. The first describes a maximal fusing rate (probability of fusion per round of cell division) that is able to fix. An allele that codes for a rate above this threshold can reach a polymorphic equilibrium with nonfusers, as long as the rate is below the second threshold, above which the fusion allele is counter-selected. Whenever it evolves, fusion increases the population-wide level of heteroplasmy, which allows mitochondrial complementation and increases population fitness. We conclude that beneficial interactions between mitochondria are a potential factor that selected for cell fusion in early eukaryotes.}, } @article {pmid29675831, year = {2018}, author = {Kauko, A and Lehto, K}, title = {Eukaryote specific folds: Part of the whole.}, journal = {Proteins}, volume = {86}, number = {8}, pages = {868-881}, doi = {10.1002/prot.25517}, pmid = {29675831}, issn = {1097-0134}, mesh = {Archaea/genetics ; Bacteria/classification ; Biological Evolution ; Databases, Protein ; Eukaryota/*classification ; Eukaryotic Cells/classification ; Evolution, Molecular ; Genes, Bacterial ; Genes, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; Proteins/genetics ; Symbiosis/*genetics ; }, abstract = {The origin of eukaryotes is one of the central transitions in the history of life; without eukaryotes there would be no complex multicellular life. The most accepted scenarios suggest the endosymbiosis of a mitochondrial ancestor with a complex archaeon, even though the details regarding the host and the triggering factors are still being discussed. Accordingly, phylogenetic analyses have demonstrated archaeal affiliations with key informational systems, while metabolic genes are often related to bacteria, mostly to the mitochondrial ancestor. Despite of this, there exists a large number of protein families and folds found only in eukaryotes. In this study, we have analyzed structural superfamilies and folds that probably appeared during eukaryogenesis. These folds typically represent relatively small binding domains of larger multidomain proteins. They are commonly involved in biological processes that are particularly complex in eukaryotes, such as signaling, trafficking/cytoskeleton, ubiquitination, transcription and RNA processing, but according to recent studies, these processes also have prokaryotic roots. Thus the folds originating from an eukaryotic stem seem to represent accessory parts that have contributed in the expansion of several prokaryotic processes to a new level of complexity. This might have taken place as a co-evolutionary process where increasing complexity and fold innovations have supported each other.}, } @article {pmid29534719, year = {2018}, author = {Méheust, R and Bhattacharya, D and Pathmanathan, JS and McInerney, JO and Lopez, P and Bapteste, E}, title = {Formation of chimeric genes with essential functions at the origin of eukaryotes.}, journal = {BMC biology}, volume = {16}, number = {1}, pages = {30}, pmid = {29534719}, issn = {1741-7007}, mesh = {Chimera/*genetics/*metabolism ; *Databases, Genetic ; Eukaryotic Cells/*physiology ; *Evolution, Molecular ; *Phylogeny ; }, abstract = {BACKGROUND: Eukaryotes evolved from the symbiotic association of at least two prokaryotic partners, and a good deal is known about the timings, mechanisms, and dynamics of these evolutionary steps. Recently, it was shown that a new class of nuclear genes, symbiogenetic genes (S-genes), was formed concomitant with endosymbiosis and the subsequent evolution of eukaryotic photosynthetic lineages. Understanding their origins and contributions to eukaryogenesis would provide insights into the ways in which cellular complexity has evolved.

RESULTS: Here, we show that chimeric nuclear genes (S-genes), built from prokaryotic domains, are critical for explaining the leap forward in cellular complexity achieved during eukaryogenesis. A total of 282 S-gene families contributed solutions to many of the challenges faced by early eukaryotes, including enhancing the informational machinery, processing spliceosomal introns, tackling genotoxicity within the cell, and ensuring functional protein interactions in a larger, more compartmentalized cell. For hundreds of S-genes, we confirmed the origins of their components (bacterial, archaeal, or generally prokaryotic) by maximum likelihood phylogenies. Remarkably, Bacteria contributed nine-fold more S-genes than Archaea, including a two-fold greater contribution to informational functions. Therefore, there is an additional, large bacterial contribution to the evolution of eukaryotes, implying that fundamental eukaryotic properties do not strictly follow the traditional informational/operational divide for archaeal/bacterial contributions to eukaryogenesis.

CONCLUSION: This study demonstrates the extent and process through which prokaryotic fragments from bacterial and archaeal genes inherited during eukaryogenesis underly the creation of novel chimeric genes with important functions.}, } @article {pmid29484479, year = {2018}, author = {Zhou, Z and Liu, Y and Li, M and Gu, JD}, title = {Two or three domains: a new view of tree of life in the genomics era.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {7}, pages = {3049-3058}, doi = {10.1007/s00253-018-8831-x}, pmid = {29484479}, issn = {1432-0614}, support = {31622002//National Natural Science Foundation of China/ ; 41506163//National Natural Science Foundation of China/ ; }, mesh = {Archaea/*classification ; Biological Evolution ; Eukaryota/*classification ; Evolution, Molecular ; *Genomics ; *Phylogeny ; }, abstract = {The deep phylogenetic topology of tree of life is in the center of a long-time dispute. The Woeseian three-domain tree theory, with the Eukarya evolving as a sister clade to Archaea, competes with the two-domain tree theory (the eocyte tree), with the Eukarya branched within Archaea. Revealed by the ongoing debate over the last three decades, sophisticated and proper phylogenetic methods should necessarily be paid with more emphasis, especially these are focusing on the compositional heterogeneity of sites and lineages, and the heterotachy issue. The newly emerging archaeal lineages with numerous eukaryotic-like features, such as membrane trafficking and cellular compartmentalization, are phylogenetically the closest to eukaryotes currently. These findings highlight the evolutionary history from an ancient archaeon to a more complex archaeon with protoeukaryotic-like features and complex cellular structures, thus providing clues to understand eukaryogenesis process. The increasing repertoire of precise genomic contents provides great advantages on understanding the deep phylogeny of tree of life and ancient evolutionary events on Eukarya branching process.}, } @article {pmid29480472, year = {2018}, author = {Jain, A and Roustan, V and Weckwerth, W and Ebersberger, I}, title = {Studying AMPK in an Evolutionary Context.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1732}, number = {}, pages = {111-142}, doi = {10.1007/978-1-4939-7598-3_8}, pmid = {29480472}, issn = {1940-6029}, mesh = {AMP-Activated Protein Kinases/*genetics/metabolism ; Archaea/*genetics ; Bacteria/*genetics ; Databases as Topic ; Eukaryota/*genetics ; *Evolution, Molecular ; Metabolic Networks and Pathways/genetics ; Phylogeny ; Protein Interaction Maps/genetics ; Sequence Homology, Amino Acid ; Software ; }, abstract = {The AMPK protein kinase forms the heart of a complex network controlling the metabolic activities in a eukaryotic cell. Unraveling the steps by which this pathway evolved from its primordial roots in the last eukaryotic common ancestor to its present status in contemporary species has the potential to shed light on the evolution of eukaryotes. A homolog search for the proteins interacting in this pathway is considerably straightforward. However, interpreting the results, when reconstructing the evolutionary history of the pathway over larger evolutionary distances, bears a number of pitfalls. With this in mind, we present a protocol to trace a metabolic pathway across contemporary species and backward in evolutionary time. Alongside the individual analysis steps, we provide guidelines for data interpretation generalizing beyond the analysis of AMPK.}, } @article {pmid29436502, year = {2018}, author = {Hörandl, E and Speijer, D}, title = {How oxygen gave rise to eukaryotic sex.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1872}, pages = {}, pmid = {29436502}, issn = {1471-2954}, mesh = {*Biological Evolution ; Eukaryota/*physiology ; Oxygen/*metabolism ; Reactive Oxygen Species/metabolism ; *Sex ; Symbiosis/physiology ; }, abstract = {How did full meiotic eukaryotic sex evolve and what was the immediate advantage allowing it to develop? We propose that the crucial determinant can be found in internal reactive oxygen species (ROS) formation at the start of eukaryotic evolution approximately 2 × 10[9] years ago. The large amount of ROS coming from a bacterial endosymbiont gave rise to DNA damage and vast increases in host genome mutation rates. Eukaryogenesis and chromosome evolution represent adaptations to oxidative stress. The host, an archaeon, most probably already had repair mechanisms based on DNA pairing and recombination, and possibly some kind of primitive cell fusion mechanism. The detrimental effects of internal ROS formation on host genome integrity set the stage allowing evolution of meiotic sex from these humble beginnings. Basic meiotic mechanisms thus probably evolved in response to endogenous ROS production by the 'pre-mitochondrion'. This alternative to mitosis is crucial under novel, ROS-producing stress situations, like extensive motility or phagotrophy in heterotrophs and endosymbiontic photosynthesis in autotrophs. In multicellular eukaryotes with a germline-soma differentiation, meiotic sex with diploid-haploid cycles improved efficient purging of deleterious mutations. Constant pressure of endogenous ROS explains the ubiquitous maintenance of meiotic sex in practically all eukaryotic kingdoms. Here, we discuss the relevant observations underpinning this model.}, } @article {pmid29253329, year = {2018}, author = {Boamah, D and Lin, T and Poppinga, FA and Basu, S and Rahman, S and Essel, F and Chakravarty, S}, title = {Characteristics of a PHD Finger Subtype.}, journal = {Biochemistry}, volume = {57}, number = {5}, pages = {525-539}, pmid = {29253329}, issn = {1520-4995}, support = {R15 GM116040/GM/NIGMS NIH HHS/United States ; }, mesh = {Binding Sites ; CCAAT-Enhancer-Binding Proteins/chemistry/metabolism ; DNA-Binding Proteins/chemistry/metabolism ; Histone Acetyltransferases/chemistry/metabolism ; Histones/chemistry/metabolism ; Humans ; Models, Molecular ; *PHD Zinc Fingers ; Protein Binding ; Transcription Factors/chemistry/metabolism ; Ubiquitin-Protein Ligases ; }, abstract = {Although the plant homeodomain (PHD) finger superfamily is known for its site-specific readouts of histone tails, the origins of the mechanistic differences in histone H3 readout by different PHD subtypes remain less clear. We show that sequences containing the xCDxCDx motif in the PHD treble clef (xCDxCDx-PHD) constitute a distinct subtype, based on the following observations: (i) the amino acid composition of the binding site is strikingly different from other subtypes due to position-specific enrichment of negatively charged and bulky nonpolar residues, (ii) the binding site positions are mutually and positively correlated, and this correlation is absent in other subtypes, and (iii) there are only small structural deviations, despite low sequence similarity. The xCDxCDx-PHD constitutes ∼20% of the PHD family, and the double PHD fingers (DPFs) are 10% of the total number of xCDxCDx-PHDs. This subtype originated early in the evolution of eukaryotes but has diversified within the metazoan lineage. Despite sequence diversification, the positions of the enriched nonpolar residues, in particular, show very small structural deviations, suggesting critical contributions of nonpolar residues in the binding mechanism of this subtype. Using mutagenesis, we probed the contributions of the binding-site positions enriched in nonpolar residues in four xCDxCDx-PHD proteins and found that they contribute to the tight packing of the H3 residues. This effect may potentially be exploited, as we observed affinity enhancement upon substituting a bulky nonpolar residue at the same binding site in another histone reader. Overall, we present a detailed characterization of PHD subtypes.}, } @article {pmid29191215, year = {2017}, author = {Vosseberg, J and Snel, B}, title = {Domestication of self-splicing introns during eukaryogenesis: the rise of the complex spliceosomal machinery.}, journal = {Biology direct}, volume = {12}, number = {1}, pages = {30}, pmid = {29191215}, issn = {1745-6150}, support = {016.160.638//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, mesh = {Eukaryota/*genetics ; *Evolution, Molecular ; Introns/*genetics ; Spliceosomes/*genetics ; }, abstract = {UNLABELLED: ᅟ: The spliceosome is a eukaryote-specific complex that is essential for the removal of introns from pre-mRNA. It consists of five small nuclear RNAs (snRNAs) and over a hundred proteins, making it one of the most complex molecular machineries. Most of this complexity has emerged during eukaryogenesis, a period that is characterised by a drastic increase in cellular and genomic complexity. Although not fully resolved, recent findings have started to shed some light on how and why the spliceosome originated. In this paper we review how the spliceosome has evolved and discuss its origin and subsequent evolution in light of different general hypotheses on the evolution of complexity. Comparative analyses have established that the catalytic core of this ribonucleoprotein (RNP) complex, as well as the spliceosomal introns, evolved from self-splicing group II introns. Most snRNAs evolved from intron fragments and the essential Prp8 protein originated from the protein that is encoded by group II introns. Proteins that functioned in other RNA processes were added to this core and extensive duplications of these proteins substantially increased the complexity of the spliceosome prior to the eukaryotic diversification. The splicing machinery became even more complex in animals and plants, yet was simplified in eukaryotes with streamlined genomes. Apparently, the spliceosome did not evolve its complexity gradually, but in rapid bursts, followed by stagnation or even simplification. We argue that although both adaptive and neutral evolution have been involved in the evolution of the spliceosome, especially the latter was responsible for the emergence of an enormously complex eukaryotic splicing machinery from simple self-splicing sequences.

REVIEWERS: This article was reviewed by W. Ford Doolittle, Eugene V. Koonin and Vivek Anantharaman.}, } @article {pmid29176585, year = {2018}, author = {Eme, L and Spang, A and Lombard, J and Stairs, CW and Ettema, TJG}, title = {Archaea and the origin of eukaryotes.}, journal = {Nature reviews. Microbiology}, volume = {16}, number = {2}, pages = {120}, pmid = {29176585}, issn = {1740-1534}, abstract = {This corrects the article DOI: 10.1038/nrmicro.2017.133.}, } @article {pmid29174886, year = {2017}, author = {Janouškovec, J and Tikhonenkov, DV and Burki, F and Howe, AT and Rohwer, FL and Mylnikov, AP and Keeling, PJ}, title = {A New Lineage of Eukaryotes Illuminates Early Mitochondrial Genome Reduction.}, journal = {Current biology : CB}, volume = {27}, number = {23}, pages = {3717-3724.e5}, doi = {10.1016/j.cub.2017.10.051}, pmid = {29174886}, issn = {1879-0445}, mesh = {Alveolata/classification/*genetics ; *Evolution, Molecular ; *Genome, Mitochondrial ; Phylogeny ; }, abstract = {The origin of eukaryotic cells represents a key transition in cellular evolution and is closely tied to outstanding questions about mitochondrial endosymbiosis [1, 2]. For example, gene-rich mitochondrial genomes are thought to be indicative of an ancient divergence, but this relies on unexamined assumptions about endosymbiont-to-host gene transfer [3-5]. Here, we characterize Ancoracysta twista, a new predatory flagellate that is not closely related to any known lineage in 201-protein phylogenomic trees and has a unique morphology, including a novel type of extrusome (ancoracyst). The Ancoracysta mitochondrion has a gene-rich genome with a coding capacity exceeding that of all other eukaryotes except the distantly related jakobids and Diphylleia, and it uniquely possesses heterologous, nucleus-, and mitochondrion-encoded cytochrome c maturase systems. To comprehensively examine mitochondrial genome reduction, we also assembled mitochondrial genomes from picozoans and colponemids and re-annotated existing mitochondrial genomes using hidden Markov model gene profiles. This revealed over a dozen previously overlooked mitochondrial genes at the level of eukaryotic supergroups. Analysis of trends over evolutionary time demonstrates that gene transfer to the nucleus was non-linear, that it occurred in waves of exponential decrease, and that much of it took place comparatively early, massively independently, and with lineage-specific rates. This process has led to differential gene retention, suggesting that gene-rich mitochondrial genomes are not a product of their early divergence. Parallel transfer of mitochondrial genes and their functional replacement by new nuclear factors are important in models for the origin of eukaryotes, especially as major gaps in our knowledge of eukaryotic diversity at the deepest level remain unfilled.}, } @article {pmid29153408, year = {2018}, author = {Lin, SC and Hardie, DG}, title = {AMPK: Sensing Glucose as well as Cellular Energy Status.}, journal = {Cell metabolism}, volume = {27}, number = {2}, pages = {299-313}, doi = {10.1016/j.cmet.2017.10.009}, pmid = {29153408}, issn = {1932-7420}, support = {204766/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; C37030/A15101/CRUK_/Cancer Research UK/United Kingdom ; 097726/Z/11/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {AMP-Activated Protein Kinases/chemistry/*metabolism ; Adenine Nucleotides/metabolism ; Animals ; Binding Sites ; Biological Evolution ; *Energy Metabolism ; Glucose/*metabolism ; Humans ; }, abstract = {Mammalian AMPK is known to be activated by falling cellular energy status, signaled by rising AMP/ATP and ADP/ATP ratios. We review recent information about how this occurs but also discuss new studies suggesting that AMPK is able to sense glucose availability independently of changes in adenine nucleotides. The glycolytic intermediate fructose-1,6-bisphosphate (FBP) is sensed by aldolase, which binds to the v-ATPase on the lysosomal surface. In the absence of FBP, interactions between aldolase and the v-ATPase are altered, allowing formation of an AXIN-based AMPK-activation complex containing the v-ATPase, Ragulator, AXIN, LKB1, and AMPK, causing increased Thr172 phosphorylation and AMPK activation. This nutrient-sensing mechanism activates AMPK but also primes it for further activation if cellular energy status subsequently falls. Glucose sensing at the lysosome, in which AMPK and other components of the activation complex act antagonistically with another key nutrient sensor, mTORC1, may have been one of the ancestral roles of AMPK.}, } @article {pmid29153324, year = {2017}, author = {Hartmann, AC and Baird, AH and Knowlton, N and Huang, D}, title = {The Paradox of Environmental Symbiont Acquisition in Obligate Mutualisms.}, journal = {Current biology : CB}, volume = {27}, number = {23}, pages = {3711-3716.e3}, doi = {10.1016/j.cub.2017.10.036}, pmid = {29153324}, issn = {1879-0445}, mesh = {Animals ; Anthozoa/*physiology ; Biological Evolution ; Dinoflagellida/*physiology ; *Symbiosis ; }, abstract = {Mutually beneficial interactions between species (mutualisms) shaped the evolution of eukaryotes and remain critical to the survival of species globally [1, 2]. Theory predicts that hosts should pass mutualist symbionts to their offspring (vertical transmission) [3-8]. However, offspring acquire symbionts from the environment in a surprising number of species (horizontal acquisition) [9-12]. A classic example of this paradox is the reef-building corals, in which 71% of species horizontally acquire algal endosymbionts [9]. An untested hypothesis explaining this paradox suggests that horizontal acquisition allows offspring to avoid symbiont-induced harm early in life. We reconstructed the evolution of symbiont transmission across 252 coral species and detected evolutionary transitions consistent with costs of vertical transmission among broadcast spawners, whose eggs tend to be positively buoyant and aggregate at the sea surface. Broadcasters with vertical transmission produce eggs with traits that favor reduced buoyancy (less wax ester lipid) and rapid development to the swimming stage (small egg size), both of which decrease the amount of time offspring spend at the sea surface. Wax ester provisioning decreased after vertically transmitting species evolved brooding from broadcasting, indicating that reduced buoyancy evolves only when offspring bear symbionts. We conclude that horizontal acquisition protects offspring from damage caused by high light and temperatures near the sea surface while providing benefits from enhanced fertilization and outcrossing. These findings help explain why modes of symbiont transmission and reproduction are strongly associated in corals and highlight benefits of delaying mutualist partnerships, offering an additional hypothesis for the pervasiveness of this theoretically paradoxical strategy.}, } @article {pmid29123225, year = {2017}, author = {Eme, L and Spang, A and Lombard, J and Stairs, CW and Ettema, TJG}, title = {Archaea and the origin of eukaryotes.}, journal = {Nature reviews. Microbiology}, volume = {15}, number = {12}, pages = {711-723}, pmid = {29123225}, issn = {1740-1534}, mesh = {Archaea/*genetics ; *Biological Evolution ; Eukaryota/*genetics ; Pharmacogenomic Variants ; }, abstract = {Woese and Fox's 1977 paper on the discovery of the Archaea triggered a revolution in the field of evolutionary biology by showing that life was divided into not only prokaryotes and eukaryotes. Rather, they revealed that prokaryotes comprise two distinct types of organisms, the Bacteria and the Archaea. In subsequent years, molecular phylogenetic analyses indicated that eukaryotes and the Archaea represent sister groups in the tree of life. During the genomic era, it became evident that eukaryotic cells possess a mixture of archaeal and bacterial features in addition to eukaryotic-specific features. Although it has been generally accepted for some time that mitochondria descend from endosymbiotic alphaproteobacteria, the precise evolutionary relationship between eukaryotes and archaea has continued to be a subject of debate. In this Review, we outline a brief history of the changing shape of the tree of life and examine how the recent discovery of a myriad of diverse archaeal lineages has changed our understanding of the evolutionary relationships between the three domains of life and the origin of eukaryotes. Furthermore, we revisit central questions regarding the process of eukaryogenesis and discuss what can currently be inferred about the evolutionary transition from the first to the last eukaryotic common ancestor.}, } @article {pmid29044824, year = {2018}, author = {Pavani, RS and Vitarelli, MO and Fernandes, CAH and Mattioli, FF and Morone, M and Menezes, MC and Fontes, MRM and Cano, MIN and Elias, MC}, title = {Replication Protein A-1 Has a Preference for the Telomeric G-rich Sequence in Trypanosoma cruzi.}, journal = {The Journal of eukaryotic microbiology}, volume = {65}, number = {3}, pages = {345-356}, doi = {10.1111/jeu.12478}, pmid = {29044824}, issn = {1550-7408}, mesh = {Chagas Disease/parasitology ; Chromatin/metabolism ; DNA, Single-Stranded/genetics ; Humans ; Protein Binding/genetics ; Replication Protein A/*metabolism ; Telomerase/*metabolism ; Telomere/genetics/*metabolism ; Telomere Homeostasis/physiology ; Trypanosoma cruzi/*genetics/metabolism ; }, abstract = {Replication protein A (RPA), the major eukaryotic single-stranded binding protein, is a heterotrimeric complex formed by RPA-1, RPA-2, and RPA-3. RPA is a fundamental player in replication, repair, recombination, and checkpoint signaling. In addition, increasing evidences have been adding functions to RPA in telomere maintenance, such as interaction with telomerase to facilitate its activity and also involvement in telomere capping in some conditions. Trypanosoma cruzi, the etiological agent of Chagas disease is a protozoa parasite that appears early in the evolution of eukaryotes. Recently, we have showed that T. cruziRPA presents canonical functions being involved with DNA replication and DNA damage response. Here, we found by FISH/IF assays that T. cruziRPA localizes at telomeres even outside replication (S) phase. In vitro analysis showed that one telomeric repeat is sufficient to bind RPA-1. Telomeric DNA induces different secondary structural modifications on RPA-1 in comparison with other types of DNA. In addition, RPA-1 presents a higher affinity for telomeric sequence compared to randomic sequence, suggesting that RPA may play specific roles in T. cruzi telomeric region.}, } @article {pmid29026213, year = {2017}, author = {Nakayama, T and Inagaki, Y}, title = {Genomic divergence within non-photosynthetic cyanobacterial endosymbionts in rhopalodiacean diatoms.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {13075}, pmid = {29026213}, issn = {2045-2322}, mesh = {Cyanobacteria/classification/*genetics/*physiology ; Diatoms/*microbiology ; Evolution, Molecular ; Genomics ; Phylogeny ; Symbiosis/genetics/*physiology ; }, abstract = {Organelle acquisitions via endosymbioses with prokaryotes were milestones in the evolution of eukaryotes. Still, quite a few uncertainties have remained for the evolution in the early stage of organellogenesis. In this respect, rhopalodiacean diatoms and their obligate cyanobacterial endosymbionts, called spheroid bodies, are emerging as new models for the study of organellogenesis. The genome for the spheroid body of Epithemia turgida, a rhopalodiacean diatom, has unveiled its unique metabolic nature lacking the photosynthetic ability. Nevertheless, the genome sequence of a spheroid body from a single lineage may not be sufficient to depict the evolution of these cyanobacterium-derived intracellular structures as a whole. Here, we report on the complete genome for the spheroid body of Rhopalodia gibberula, a lineage distinct from E. turgida, of which genome has been fully determined. Overall, features in genome structure and metabolic capacity, including a lack of photosynthetic ability, were highly conserved between the two spheroid bodies. However, our comparative genomic analyses revealed that the genome of the R. gibberula spheroid body exhibits a lower non-synonymous substitution rate and a slower progression of pseudogenisation than those of E. turgida, suggesting that a certain degree of diversity exists amongst the genomes of obligate endosymbionts in unicellular eukaryotes.}, } @article {pmid28927381, year = {2017}, author = {van der Gulik, PTS and Hoff, WD and Speijer, D}, title = {In defence of the three-domains of life paradigm.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {218}, pmid = {28927381}, issn = {1471-2148}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Biological Evolution ; Classification ; Eukaryota/*genetics ; Phylogeny ; }, abstract = {BACKGROUND: Recently, important discoveries regarding the archaeon that functioned as the "host" in the merger with a bacterium that led to the eukaryotes, its "complex" nature, and its phylogenetic relationship to eukaryotes, have been reported. Based on these new insights proposals have been put forward to get rid of the three-domain Model of life, and replace it with a two-domain model.

RESULTS: We present arguments (both regarding timing, complexity, and chemical nature of specific evolutionary processes, as well as regarding genetic structure) to resist such proposals. The three-domain Model represents an accurate description of the differences at the most fundamental level of living organisms, as the eukaryotic lineage that arose from this unique merging event is distinct from both Archaea and Bacteria in a myriad of crucial ways.

CONCLUSIONS: We maintain that "a natural system of organisms", as proposed when the three-domain Model of life was introduced, should not be revised when considering the recent discoveries, however exciting they may be.}, } @article {pmid28922368, year = {2017}, author = {Jayaswal, PK and Dogra, V and Shanker, A and Sharma, TR and Singh, NK}, title = {A tree of life based on ninety-eight expressed genes conserved across diverse eukaryotic species.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0184276}, pmid = {28922368}, issn = {1932-6203}, mesh = {Animals ; *Evolution, Molecular ; *Fungi/genetics/metabolism ; Gene Expression Regulation, Fungal/*physiology ; Gene Expression Regulation, Plant/*physiology ; Genes, Fungal/*physiology ; Genes, Plant/*physiology ; *Phylogeny ; *Plants/genetics/metabolism ; }, abstract = {Rapid advances in DNA sequencing technologies have resulted in the accumulation of large data sets in the public domain, facilitating comparative studies to provide novel insights into the evolution of life. Phylogenetic studies across the eukaryotic taxa have been reported but on the basis of a limited number of genes. Here we present a genome-wide analysis across different plant, fungal, protist, and animal species, with reference to the 36,002 expressed genes of the rice genome. Our analysis revealed 9831 genes unique to rice and 98 genes conserved across all 49 eukaryotic species analysed. The 98 genes conserved across diverse eukaryotes mostly exhibited binding and catalytic activities and shared common sequence motifs; and hence appeared to have a common origin. The 98 conserved genes belonged to 22 functional gene families including 26S protease, actin, ADP-ribosylation factor, ATP synthase, casein kinase, DEAD-box protein, DnaK, elongation factor 2, glyceraldehyde 3-phosphate, phosphatase 2A, ras-related protein, Ser/Thr protein phosphatase family protein, tubulin, ubiquitin and others. The consensus Bayesian eukaryotic tree of life developed in this study demonstrated widely separated clades of plants, fungi, and animals. Musa acuminata provided an evolutionary link between monocotyledons and dicotyledons, and Salpingoeca rosetta provided an evolutionary link between fungi and animals, which indicating that protozoan species are close relatives of fungi and animals. The divergence times for 1176 species pairs were estimated accurately by integrating fossil information with synonymous substitution rates in the comprehensive set of 98 genes. The present study provides valuable insight into the evolution of eukaryotes.}, } @article {pmid28916841, year = {2017}, author = {Dunn, CD}, title = {Some Liked It Hot: A Hypothesis Regarding Establishment of the Proto-Mitochondrial Endosymbiont During Eukaryogenesis.}, journal = {Journal of molecular evolution}, volume = {85}, number = {3-4}, pages = {99-106}, pmid = {28916841}, issn = {1432-1432}, support = {637649/ERC_/European Research Council/International ; }, mesh = {Archaea/*genetics/metabolism ; Bacteria/genetics ; *Biological Evolution ; Energy Metabolism ; Eukaryota/*genetics/metabolism ; *Hot Temperature ; Mitochondria/genetics/*metabolism/physiology ; *Symbiosis ; }, abstract = {Eukaryotic cells are characterized by a considerable increase in subcellular compartmentalization when compared to prokaryotes. Most evidence suggests that the earliest eukaryotes consisted of mitochondria derived from an α-proteobacterial ancestor enclosed within an archaeal host cell. However, what benefits the archaeal host and the proto-mitochondrial endosymbiont might have obtained at the beginning of this endosymbiotic relationship remains unclear. In this work, I argue that heat generated by the proto-mitochondrion initially permitted an archaeon living at high temperatures to colonize a cooler environment, thereby removing apparent limitations on cellular complexity. Furthermore, heat generation by the endosymbiont would have provided phenotypic flexibility not available through fixed alleles selected for fitness at specific temperatures. Finally, a role for heat production by the proto-mitochondrion bridges a conceptual gap between initial endosymbiont entry to the archaeal host and a later role for mitochondrial ATP production in permitting increased cellular complexity.}, } @article {pmid28826970, year = {2017}, author = {Aanen, DK and Eggleton, P}, title = {Symbiogenesis: Beyond the endosymbiosis theory?.}, journal = {Journal of theoretical biology}, volume = {434}, number = {}, pages = {99-103}, doi = {10.1016/j.jtbi.2017.08.001}, pmid = {28826970}, issn = {1095-8541}, mesh = {Animals ; *Biological Evolution ; Gastrointestinal Tract/anatomy & histology ; Isoptera/anatomy & histology ; *Phylogeny ; *Symbiosis ; }, abstract = {Symbiogenesis, literally 'becoming by living together', refers to the crucial role of symbiosis in major evolutionary innovations. The term usually is reserved for the major transition to eukaryotes and to photosynthesising eukaryotic algae and plants by endosymbiosis. However, in some eukaryote lineages endosymbionts have been lost secondarily, showing that symbiosis can trigger a major evolutionary innovation, even if symbionts were lost secondarily. This leads to the intriguing possibility that symbiosis has played a role in other major evolutionary innovations as well, even if not all extant representatives of such groups still have the symbiotic association. We evaluate this hypothesis for two innovations in termites (Termitoidae, also known informally as "Isoptera"): i) the role of flagellate gut protist symbionts in the transition to eusociality from cockroach-like ancestors, and ii) the role of non-gut associated symbionts in the transition to 'higher' termites, characterized by the absence of flagellate gut protists. In both cases we identify a crucial role for symbionts, even though in both cases, subsequently, symbionts were lost again in some lineages. We also briefly discuss additional possible examples of symbiogenesis. We conclude that symbiogenesis is more broadly applicable than just for the endosymbiotic origin of eukaryotes and photosynthetic eukaryotes, and may be a useful concept to acknowledge the important role of symbiosis for evolutionary innovation. However, we do not accept Lynn Margulis's view that symbiogenesis will lead to a paradigm shift from neoDarwinism, as the role of symbiosis in evolutionary change can be integrated with existing theory perfectly.}, } @article {pmid28818345, year = {2017}, author = {Novikova, O and Belfort, M}, title = {Mobile Group II Introns as Ancestral Eukaryotic Elements.}, journal = {Trends in genetics : TIG}, volume = {33}, number = {11}, pages = {773-783}, pmid = {28818345}, issn = {0168-9525}, support = {R01 GM039422/GM/NIGMS NIH HHS/United States ; R01 GM044844/GM/NIGMS NIH HHS/United States ; R37 GM039422/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Eukaryotic Cells ; Interspersed Repetitive Sequences ; *Introns ; RNA, Catalytic/genetics ; Spliceosomes ; }, abstract = {The duality of group II introns, capable of carrying out both self-splicing and retromobility reactions, is hypothesized to have played a profound role in the evolution of eukaryotes. These introns likely provided the framework for the emergence of eukaryotic retroelements, spliceosomal introns and other key components of the spliceosome. Group II introns are found in all three domains of life and are therefore considered to be exceptionally successful mobile genetic elements. Initially identified in organellar genomes, group II introns are found in bacteria, chloroplasts, and mitochondria of plants and fungi, but not in nuclear genomes. Although there is no doubt that prokaryotic and organellar group II introns are evolutionary related, there are remarkable differences in survival strategies between them. Furthermore, an evolutionary relationship of group II introns to eukaryotic retroelements, including telomeres, and spliceosomes is unmistakable.}, } @article {pmid28813669, year = {2017}, author = {Chaikeeratisak, V and Nguyen, K and Egan, ME and Erb, ML and Vavilina, A and Pogliano, J}, title = {The Phage Nucleus and Tubulin Spindle Are Conserved among Large Pseudomonas Phages.}, journal = {Cell reports}, volume = {20}, number = {7}, pages = {1563-1571}, pmid = {28813669}, issn = {2211-1247}, support = {P30 NS047101/NS/NINDS NIH HHS/United States ; R01 GM104556/GM/NIGMS NIH HHS/United States ; R35 GM118099/GM/NIGMS NIH HHS/United States ; T32 GM007240/GM/NIGMS NIH HHS/United States ; }, mesh = {Conserved Sequence ; DNA, Viral/*genetics/metabolism/ultrastructure ; Microscopy, Fluorescence ; Pseudomonas Phages/classification/*genetics/metabolism/ultrastructure ; Pseudomonas aeruginosa/ultrastructure/*virology ; Ribosomes/genetics/metabolism/ultrastructure ; Tubulin/*genetics/metabolism/ultrastructure ; Viral Proteins/*genetics/metabolism/ultrastructure ; Virus Replication ; }, abstract = {We recently demonstrated that the large Pseudomonas chlororaphis bacteriophage 201φ2-1 assembles a nucleus-like structure that encloses phage DNA and segregates proteins according to function, with DNA processing proteins inside and metabolic enzymes and ribosomes outside the nucleus. Here, we investigate the replication pathway of the Pseudomonas aeruginosa bacteriophages φKZ and φPA3. Bacteriophages φKZ and φPA3 encode a proteinaceous shell that assembles a nucleus-like structure that compartmentalizes proteins and DNA during viral infection. We show that the tubulin-like protein PhuZ encoded by each phage assembles a bipolar spindle that displays dynamic instability and positions the nucleus at midcell. Our results suggest that the phage spindle and nucleus play the same functional role in all three phages, 201φ2-1, φKZ, and φPA3, demonstrating that these key structures are conserved among large Pseudomonas phages.}, } @article {pmid28806979, year = {2017}, author = {Zachar, I and Szathmáry, E}, title = {Breath-giving cooperation: critical review of origin of mitochondria hypotheses : Major unanswered questions point to the importance of early ecology.}, journal = {Biology direct}, volume = {12}, number = {1}, pages = {19}, pmid = {28806979}, issn = {1745-6150}, mesh = {*Biological Evolution ; Energy Metabolism ; Genome, Mitochondrial ; *Mitochondria ; *Models, Biological ; Phagocytosis ; Phylogeny ; }, abstract = {UNLABELLED: The origin of mitochondria is a unique and hard evolutionary problem, embedded within the origin of eukaryotes. The puzzle is challenging due to the egalitarian nature of the transition where lower-level units took over energy metabolism. Contending theories widely disagree on ancestral partners, initial conditions and unfolding of events. There are many open questions but there is no comparative examination of hypotheses. We have specified twelve questions about the observable facts and hidden processes leading to the establishment of the endosymbiont that a valid hypothesis must address. We have objectively compared contending hypotheses under these questions to find the most plausible course of events and to draw insight on missing pieces of the puzzle. Since endosymbiosis borders evolution and ecology, and since a realistic theory has to comply with both domains' constraints, the conclusion is that the most important aspect to clarify is the initial ecological relationship of partners. Metabolic benefits are largely irrelevant at this initial phase, where ecological costs could be more disruptive. There is no single theory capable of answering all questions indicating a severe lack of ecological considerations. A new theory, compliant with recent phylogenomic results, should adhere to these criteria.

REVIEWERS: This article was reviewed by Michael W. Gray, William F. Martin and Purificación López-García.}, } @article {pmid31967573, year = {2017}, author = {Forterre, P and Raoult, D}, title = {The transformation of a bacterium into a nucleated virocell reminds the viral eukaryogenesis hypothesis.}, journal = {Virologie (Montrouge, France)}, volume = {21}, number = {4}, pages = {28-30}, doi = {10.1684/vir.2017.0700}, pmid = {31967573}, issn = {1267-8694}, } @article {pmid28750604, year = {2017}, author = {Aledo, JC}, title = {Inferring Methionine Sulfoxidation and serine Phosphorylation crosstalk from Phylogenetic analyses.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {171}, pmid = {28750604}, issn = {1471-2148}, mesh = {Eukaryotic Initiation Factor-2/chemistry ; Evolution, Molecular ; Heat-Shock Proteins/metabolism ; Humans ; Likelihood Functions ; Markov Chains ; Methionine/*metabolism ; Oxidation-Reduction ; Phosphorylation ; Phosphoserine/*metabolism ; *Phylogeny ; Protein Processing, Post-Translational ; Proteins/chemistry ; Stochastic Processes ; Sulfur/*metabolism ; }, abstract = {BACKGROUND: The sulfoxidation of methionine residues within the phosphorylation motif of protein kinase substrates, may provide a mechanism to couple oxidative signals to changes in protein phosphorylation. Herein, we hypothesize that if the residues within a pair of phosphorylatable-sulfoxidable sites are functionally linked, then they might have been coevolving. To test this hypothesis a number of site pairs previously detected on human stress-related proteins has been subjected to analysis using eukaryote ortholog sequences and a phylogenetic approach.

RESULTS: Overall, the results support the conclusion that in the eIF2α protein, serine phosphorylation at position 218 and methionine oxidation at position 222, belong to the same functional network. First, the observed data were much better fitted by Markovian models that assumed coevolution of both sites, with respect to their counterparts assuming independent evolution (p-value = 0.003). Second, this conclusion was robust with respect to the methods used to reconstruct the phylogenetic relationship between the 233 eukaryotic species analyzed. Third, the co-distribution of phosphorylatable and sulfoxidable residues at these positions showed multiple origins throughout the evolution of eukaryotes, which further supports the view of an adaptive value for this co-occurrence. Fourth, the possibility that the coevolution of these two sites might be due to structure-driven compensatory mutations was evaluated. The results suggested that factors other than those merely structural were behind the observed coevolution. Finally, the relationship detected between other modifiable site pairs from ataxin-2 (S814-M815), ataxin-2-like (S211-M215) and Pumilio homolog 1 (S124-M125), reinforce the view of a role for phosphorylation-sulfoxidation crosstalk.

CONCLUSIONS: For the four stress-related proteins analyzed herein, their respective pairs of PTM sites (phosphorylatable serine and sulfoxidable methionine) were found to be evolving in a correlated fashion, which suggests a relevant role for methionine sulfoxidation and serine phosphorylation crosstalk in the control of protein translation under stress conditions.}, } @article {pmid28738827, year = {2017}, author = {Lutfullahoğlu-Bal, G and Keskin, A and Seferoğlu, AB and Dunn, CD}, title = {Bacterial tail anchors can target to the mitochondrial outer membrane.}, journal = {Biology direct}, volume = {12}, number = {1}, pages = {16}, pmid = {28738827}, issn = {1745-6150}, support = {637649/ERC_/European Research Council/International ; }, mesh = {Escherichia coli Proteins/chemistry/*metabolism ; Eukaryotic Cells/metabolism/ultrastructure ; Mitochondria/metabolism ; Mitochondrial Membranes/*metabolism ; Organelle Biogenesis ; Protein Sorting Signals/physiology ; Protein Transport ; Saccharomyces cerevisiae/*metabolism/ultrastructure ; }, abstract = {BACKGROUND: During the generation and evolution of the eukaryotic cell, a proteobacterial endosymbiont was re-fashioned into the mitochondrion, an organelle that appears to have been present in the ancestor of all present-day eukaryotes. Mitochondria harbor proteomes derived from coding information located both inside and outside the organelle, and the rate-limiting step toward the formation of eukaryotic cells may have been development of an import apparatus allowing protein entry to mitochondria. Currently, a widely conserved translocon allows proteins to pass from the cytosol into mitochondria, but how proteins encoded outside of mitochondria were first directed to these organelles at the dawn of eukaryogenesis is not clear. Because several proteins targeted by a carboxyl-terminal tail anchor (TA) appear to have the ability to insert spontaneously into the mitochondrial outer membrane (OM), it is possible that self-inserting, tail-anchored polypeptides obtained from bacteria might have formed the first gate allowing proteins to access mitochondria from the cytosol.

RESULTS: Here, we tested whether bacterial TAs are capable of targeting to mitochondria. In a survey of proteins encoded by the proteobacterium Escherichia coli, predicted TA sequences were directed to specific subcellular locations within the yeast Saccharomyces cerevisiae. Importantly, TAs obtained from DUF883 family members ElaB and YqjD were abundantly localized to and inserted at the mitochondrial OM.

CONCLUSIONS: Our results support the notion that eukaryotic cells are able to utilize membrane-targeting signals present in bacterial proteins obtained by lateral gene transfer, and our findings make plausible a model in which mitochondrial protein translocation was first driven by tail-anchored proteins.

REVIEWERS: This article was reviewed by Michael Ryan and Thomas Simmen.}, } @article {pmid28684295, year = {2017}, author = {Lazcano, A and Peretó, J}, title = {On the origin of mitosing cells: A historical appraisal of Lynn Margulis endosymbiotic theory.}, journal = {Journal of theoretical biology}, volume = {434}, number = {}, pages = {80-87}, doi = {10.1016/j.jtbi.2017.06.036}, pmid = {28684295}, issn = {1095-8541}, mesh = {*Biological Evolution ; Chloroplasts ; Eukaryota/genetics ; Genome ; History, 20th Century ; Metabolic Networks and Pathways ; Mitochondria ; Symbiosis/*physiology ; }, abstract = {Although for a long-time symbiosis was considered to be quite rare and with no role in evolutionary processes, Lynn Margulis demonstrated that endosymbiotic events played a key role in the origin and evolution of eukaryotic cells. Starting with her seminal assay in the Journal of Theoretical Biology in 1967 (authored as Lynn Sagan), her lifelong work on eukaryogenesis and the role of symbiosis in evolution stands as a valid and authoritative contribution to science. As was quick to acknowledge, she was not the first to discuss the significance of symbiosis to explain the origin of mitochondria and chloroplasts, but no one else had done it to her extent and depth, nor had anyone provided a variety of testable hypotheses. While it is true that some of her proposals were incomplete or mistaken, morphological, biochemical and geochemical evidence together with phylogenomic analyses of mitochondria, chloroplasts and eukaryotic nuclear genomes have demonstrated the validity of her evolutionary scheme, as well that of her specific predictions on the chimeric nature of genomes and the mosaicism of metabolic pathways in eukaryotic cells.}, } @article {pmid28659892, year = {2017}, author = {Heimerl, T and Flechsler, J and Pickl, C and Heinz, V and Salecker, B and Zweck, J and Wanner, G and Geimer, S and Samson, RY and Bell, SD and Huber, H and Wirth, R and Wurch, L and Podar, M and Rachel, R}, title = {A Complex Endomembrane System in the Archaeon Ignicoccus hospitalis Tapped by Nanoarchaeum equitans.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1072}, pmid = {28659892}, issn = {1664-302X}, abstract = {Based on serial sectioning, focused ion beam scanning electron microscopy (FIB/SEM), and electron tomography, we depict in detail the highly unusual anatomy of the marine hyperthermophilic crenarchaeon, Ignicoccus hospitalis. Our data support a complex and dynamic endomembrane system consisting of cytoplasmic protrusions, and with secretory function. Moreover, we reveal that the cytoplasm of the putative archaeal ectoparasite Nanoarchaeum equitans can get in direct contact with this endomembrane system, complementing and explaining recent proteomic, transcriptomic and metabolomic data on this inter-archaeal relationship. In addition, we identified a matrix of filamentous structures and/or tethers in the voluminous inter-membrane compartment (IMC) of I. hospitalis, which might be responsible for membrane dynamics. Overall, this unusual cellular compartmentalization, ultrastructure and dynamics in an archaeon that belongs to the recently proposed TACK superphylum prompts speculation that the eukaryotic endomembrane system might originate from Archaea.}, } @article {pmid28637850, year = {2017}, author = {Heim, NA and Payne, JL and Finnegan, S and Knope, ML and Kowalewski, M and Lyons, SK and McShea, DW and Novack-Gottshall, PM and Smith, FA and Wang, SC}, title = {Hierarchical complexity and the size limits of life.}, journal = {Proceedings. Biological sciences}, volume = {284}, number = {1857}, pages = {}, pmid = {28637850}, issn = {1471-2954}, mesh = {*Biological Evolution ; Earth, Planet ; *Eukaryota ; *Prokaryotic Cells ; }, abstract = {Over the past 3.8 billion years, the maximum size of life has increased by approximately 18 orders of magnitude. Much of this increase is associated with two major evolutionary innovations: the evolution of eukaryotes from prokaryotic cells approximately 1.9 billion years ago (Ga), and multicellular life diversifying from unicellular ancestors approximately 0.6 Ga. However, the quantitative relationship between organismal size and structural complexity remains poorly documented. We assessed this relationship using a comprehensive dataset that includes organismal size and level of biological complexity for 11 172 extant genera. We find that the distributions of sizes within complexity levels are unimodal, whereas the aggregate distribution is multimodal. Moreover, both the mean size and the range of size occupied increases with each additional level of complexity. Increases in size range are non-symmetric: the maximum organismal size increases more than the minimum. The majority of the observed increase in organismal size over the history of life on the Earth is accounted for by two discrete jumps in complexity rather than evolutionary trends within levels of complexity. Our results provide quantitative support for an evolutionary expansion away from a minimal size constraint and suggest a fundamental rescaling of the constraints on minimal and maximal size as biological complexity increases.}, } @article {pmid28622586, year = {2017}, author = {Dacks, JB and Robinson, MS}, title = {Outerwear through the ages: evolutionary cell biology of vesicle coats.}, journal = {Current opinion in cell biology}, volume = {47}, number = {}, pages = {108-116}, doi = {10.1016/j.ceb.2017.04.001}, pmid = {28622586}, issn = {1879-0410}, support = {086598//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Archaea/classification/cytology ; *Biological Evolution ; Biological Transport ; Coated Vesicles/chemistry/*genetics/metabolism ; Eukaryotic Cells/classification/*cytology/metabolism ; Humans ; Membrane Proteins/genetics/metabolism ; }, abstract = {Vesicular transport was key to the evolution of eukaryotes, and is essential for eukaryotic life today. All modern eukaryotes have a set of vesicle coat proteins, which couple cargo selection to vesicle budding in the secretory and endocytic pathways. Although these coats share common features (e.g. recruitment via small GTPases, β-propeller-α-solenoid proteins acting as scaffolds), the relationships between them are not always clear. Structural studies on the coats themselves, comparative genomics and cell biology in diverse eukaryotes, and the recent discovery of the Asgard archaea and their 'eukaryotic signature proteins' are helping us to piece together how coats may have evolved during the prokaryote-to-eukaryote transition.}, } @article {pmid28615286, year = {2017}, author = {Martin, WF and Tielens, AGM and Mentel, M and Garg, SG and Gould, SB}, title = {The Physiology of Phagocytosis in the Context of Mitochondrial Origin.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {81}, number = {3}, pages = {}, pmid = {28615286}, issn = {1098-5557}, mesh = {Adenosine Triphosphate/metabolism ; Archaea/genetics ; Biological Evolution ; Endocytosis/physiology ; Energy Metabolism ; Eukaryotic Cells/*physiology ; Metagenomics ; Mitochondria/*physiology ; Phagocytosis/*physiology ; Phylogeny ; Prokaryotic Cells/*physiology ; Symbiosis ; }, abstract = {How mitochondria came to reside within the cytosol of their host has been debated for 50 years. Though current data indicate that the last eukaryote common ancestor possessed mitochondria and was a complex cell, whether mitochondria or complexity came first in eukaryotic evolution is still discussed. In autogenous models (complexity first), the origin of phagocytosis poses the limiting step at eukaryote origin, with mitochondria coming late as an undigested growth substrate. In symbiosis-based models (mitochondria first), the host was an archaeon, and the origin of mitochondria was the limiting step at eukaryote origin, with mitochondria providing bacterial genes, ATP synthesis on internalized bioenergetic membranes, and mitochondrion-derived vesicles as the seed of the eukaryote endomembrane system. Metagenomic studies are uncovering new host-related archaeal lineages that are reported as complex or phagocytosing, although images of such cells are lacking. Here we review the physiology and components of phagocytosis in eukaryotes, critically inspecting the concept of a phagotrophic host. From ATP supply and demand, a mitochondrion-lacking phagotrophic archaeal fermenter would have to ingest about 34 times its body weight in prokaryotic prey to obtain enough ATP to support one cell division. It would lack chemiosmotic ATP synthesis at the plasma membrane, because phagocytosis and chemiosmosis in the same membrane are incompatible. It would have lived from amino acid fermentations, because prokaryotes are mainly protein. Its ATP yield would have been impaired relative to typical archaeal amino acid fermentations, which involve chemiosmosis. In contrast, phagocytosis would have had great physiological benefit for a mitochondrion-bearing cell.}, } @article {pmid28577249, year = {2017}, author = {Kuwabara, T and Igarashi, K}, title = {Progeny production in the periplasm of Thermosipho globiformans.}, journal = {Extremophiles : life under extreme conditions}, volume = {21}, number = {4}, pages = {805-815}, pmid = {28577249}, issn = {1433-4909}, mesh = {Bacteria/*metabolism ; Microscopy/methods ; Periplasm/*metabolism ; Temperature ; }, abstract = {Thermotogales are rod-shaped, Gram-negative, anaerobic, (hyper) thermophiles distinguished by an outer sheath-like toga, which comprises an outer membrane (OM) and an amorphous layer (AL). Thermosipho globiformans bacteria can transform into spheroids with multiple cells concurrently with AL disintegration during early growth; the cell is defined as the cytoplasmic membrane (CM) plus the entity surrounded by the CM. Spheroids eventually produce rapidly moving periplasmic 'progenies' through an unknown mechanism. Here, we used high-temperature microscopy (HTM) to directly observe spheroid generation and growth. Rod OMs abruptly inflated to form ~2 μm-diameter balloons. Concurrently, multiple globular cells emerged in the balloons, suggesting their translocation and transformation from the rod state. During spheroid growth, the cells elongated and acquired a large dish shape by possible fusion. Spheroids with dish-shaped cells further enlarged to ~12 μm in diameter. HTM and epifluorescence-microscopy results collectively indicated that the nucleoids of dish-shaped cells transformed to form a ring shape, which then distorted to form a lip shape as the spheroid enlarged. HTM showed that 'progenies' were produced in the spheroid periplasm. Transmission electron microscopy results suggested that the 'progenies' represented immature progenies lacking togas, which were acquired subsequently.}, } @article {pmid28541439, year = {2017}, author = {Fort, P and Blangy, A}, title = {The Evolutionary Landscape of Dbl-Like RhoGEF Families: Adapting Eukaryotic Cells to Environmental Signals.}, journal = {Genome biology and evolution}, volume = {9}, number = {6}, pages = {1471-1486}, pmid = {28541439}, issn = {1759-6653}, mesh = {Adaptation, Biological ; Animals ; Eukaryotic Cells/cytology/*physiology ; *Evolution, Molecular ; Fungi/genetics ; Humans ; *Metagenomics ; Phylogeny ; Rho Guanine Nucleotide Exchange Factors/*genetics ; Signal Transduction ; Vertebrates/genetics ; }, abstract = {The dynamics of cell morphology in eukaryotes is largely controlled by small GTPases of the Rho family. Rho GTPases are activated by guanine nucleotide exchange factors (RhoGEFs), of which diffuse B-cell lymphoma (Dbl)-like members form the largest family. Here, we surveyed Dbl-like sequences from 175 eukaryotic genomes and illuminate how the Dbl family evolved in all eukaryotic supergroups. By combining probabilistic phylogenetic approaches and functional domain analysis, we show that the human Dbl-like family is made of 71 members, structured into 20 subfamilies. The 71 members were already present in ancestral jawed vertebrates, but several members were subsequently lost in specific clades, up to 12% in birds. The jawed vertebrate repertoire was established from two rounds of duplications that occurred between tunicates, cyclostomes, and jawed vertebrates. Duplicated members showed distinct tissue distributions, conserved at least in Amniotes. All 20 subfamilies have members in Deuterostomes and Protostomes. Nineteen subfamilies are present in Porifera, the first phylum that diverged in Metazoa, 14 in Choanoflagellida and Filasterea, single-celled organisms closely related to Metazoa and three in Fungi, the sister clade to Metazoa. Other eukaryotic supergroups show an extraordinary variability of Dbl-like repertoires as a result of repeated and independent gain and loss events. Last, we observed that in Metazoa, the number of Dbl-like RhoGEFs varies in proportion of cell signaling complexity. Overall, our analysis supports the conclusion that Dbl-like RhoGEFs were present at the origin of eukaryotes and evolved as highly adaptive cell signaling mediators.}, } @article {pmid28501637, year = {2017}, author = {Lane, N}, title = {Serial endosymbiosis or singular event at the origin of eukaryotes?.}, journal = {Journal of theoretical biology}, volume = {434}, number = {}, pages = {58-67}, doi = {10.1016/j.jtbi.2017.04.031}, pmid = {28501637}, issn = {1095-8541}, mesh = {*Biological Evolution ; Energy Metabolism ; Eukaryota/*cytology ; Genomics ; Membranes/metabolism ; Organelles ; Organogenesis/*genetics ; Symbiosis/*genetics ; }, abstract = {'On the Origin of Mitosing Cells' heralded a new way of seeing cellular evolution, with symbiosis at its heart. Lynn Margulis (then Sagan) marshalled an impressive array of evidence for endosymbiosis, from cell biology to atmospheric chemistry and Earth history. Despite her emphasis on symbiosis, she saw plenty of evidence for gradualism in eukaryotic evolution, with multiple origins of mitosis and sex, repeated acquisitions of plastids, and putative evolutionary intermediates throughout the microbial world. Later on, Margulis maintained her view of multiple endosymbioses giving rise to other organelles such as hydrogenosomes, in keeping with the polyphyletic assumptions of the serial endosymbiosis theory. She stood at the threshold of the phylogenetic era, and anticipated its potential. Yet while predicting that the nucleotide sequences of genes would enable a detailed reconstruction of eukaryotic evolution, Margulis did not, and could not, imagine the radically different story that would eventually emerge from comparative genomics. The last eukaryotic common ancestor now seems to have been essentially a modern eukaryotic cell that had already evolved mitosis, meiotic sex, organelles and endomembrane systems. The long search for missing evolutionary intermediates has failed to turn up a single example, and those discussed by Margulis turn out to have evolved reductively from more complex ancestors. Strikingly, Margulis argued that all eukaryotes had mitochondria in her 1967 paper (a conclusion that she later disavowed). But she developed her ideas in the context of atmospheric oxygen and aerobic respiration, neither of which is consistent with more recent geological and phylogenetic findings. Instead, a modern synthesis of genomics and bioenergetics points to the endosymbiotic restructuring of eukaryotic genomes in relation to bioenergetic membranes as the singular event that permitted the evolution of morphological complexity.}, } @article {pmid28500533, year = {2017}, author = {Lindås, AC and Valegård, K and Ettema, TJG}, title = {Archaeal Actin-Family Filament Systems.}, journal = {Sub-cellular biochemistry}, volume = {84}, number = {}, pages = {379-392}, doi = {10.1007/978-3-319-53047-5_13}, pmid = {28500533}, issn = {0306-0225}, mesh = {Actins/genetics/*metabolism ; Archaea/genetics/*metabolism ; Archaeal Proteins/genetics/*metabolism ; Cytoskeleton ; Phylogeny ; Pyrobaculum/genetics/metabolism ; }, abstract = {Actin represents one of the most abundant and conserved eukaryotic proteins over time, and has an important role in many different cellular processes such as cell shape determination, motility, force generation, cytokinesis, amongst many others. Eukaryotic actin has been studied for decades and was for a long time considered a eukaryote-specific trait. However, in the early 2000s a bacterial actin homolog, MreB, was identified, characterized and found to have a cytoskeletal function and group within the superfamily of actin proteins. More recently, an actin cytoskeleton was also identified in archaea. The genome of the hyperthermophilic crenarchaeon Pyrobaculum calidifontis contains a five-gene cluster named Arcade encoding for an actin homolog, Crenactin, polymerizing into helical filaments spanning the whole length of the cell. Phylogenetic and structural studies place Crenactin closer to the eukaryotic actin than to the bacterial homologues. A significant difference, however, is that Crenactin can form single helical filaments in addition to filaments containing two intertwined proto filaments. The genome of the recently discovered Lokiarchaeota encodes several different actin homologues, termed Lokiactins, which are even more closely related to the eukaryotic actin than Crenactin. A primitive, dynamic actin-based cytoskeleton in archaea could have enabled the engulfment of the alphaproteobacterial progenitor of the mitochondria, a key-event in the evolution of eukaryotes.}, } @article {pmid28495966, year = {2017}, author = {Gray, MW}, title = {Lynn Margulis and the endosymbiont hypothesis: 50 years later.}, journal = {Molecular biology of the cell}, volume = {28}, number = {10}, pages = {1285-1287}, pmid = {28495966}, issn = {1939-4586}, mesh = {Bacteria ; *Biological Evolution ; Cilia ; Eukaryotic Cells ; Mitochondria ; Phylogeny ; Plastids ; *Symbiosis ; }, abstract = {The 1967 article "On the Origin of Mitosing Cells" in the Journal of Theoretical Biology by Lynn Margulis (then Lynn Sagan) is widely regarded as stimulating renewed interest in the long-dormant endosymbiont hypothesis of organelle origins. In her article, not only did Margulis champion an endosymbiotic origin of mitochondria and plastids from bacterial ancestors, but she also posited that the eukaryotic flagellum (undulipodium in her usage) and mitotic apparatus originated from an endosymbiotic, spirochete-like organism. In essence, she presented a comprehensive symbiotic view of eukaryotic cell evolution (eukaryogenesis). Not all of the ideas in her article have been accepted, for want of compelling evidence, but her vigorous promotion of the role of symbiosis in cell evolution unquestionably had a major influence on how subsequent investigators have viewed the origin and evolution of mitochondria and plastids and the eukaryotic cell per se.}, } @article {pmid28478110, year = {2017}, author = {Harish, A and Kurland, CG}, title = {Empirical genome evolution models root the tree of life.}, journal = {Biochimie}, volume = {138}, number = {}, pages = {137-155}, doi = {10.1016/j.biochi.2017.04.014}, pmid = {28478110}, issn = {1638-6183}, mesh = {Archaea/genetics ; Bacteria/genetics ; Bayes Theorem ; Eukaryota/genetics ; *Evolution, Molecular ; *Genome ; *Models, Genetic ; *Phylogeny ; }, abstract = {A reliable phylogenetic reconstruction of the evolutionary history of contemporary species depends on a robust identification of the universal common ancestor (UCA) at the root of the Tree of Life (ToL). That root polarizes the tree so that the evolutionary succession of ancestors to descendants is discernable. In effect, the root determines the branching order and the direction of character evolution. Typically, conventional phylogenetic analyses implement time-reversible models of evolution for which character evolution is un-polarized. Such practices leave the root and the direction of character evolution undefined by the data used to construct such trees. In such cases, rooting relies on theoretic assumptions and/or the use of external data to interpret unrooted trees. The most common rooting method, the outgroup method is clearly inapplicable to the ToL, which has no outgroup. Both here and in the accompanying paper (Harish and Kurland, 2017) we have explored the theoretical and technical issues related to several rooting methods. We demonstrate (1) that Genome-level characters and evolution models are necessary for species phylogeny reconstructions. By the same token, standard practices exploiting sequence-based methods that implement gene-scale substitution models do not root species trees; (2) Modeling evolution of complex genomic characters and processes that are non-reversible and non-stationary is required to reconstruct the polarized evolution of the ToL; (3) Rooting experiments and Bayesian model selection tests overwhelmingly support the earlier finding that akaryotes and eukaryotes are sister clades that descend independently from UCA (Harish and Kurland, 2013); (4) Consistent ancestral state reconstructions from independent genome samplings confirm the previous finding that UCA features three fourths of the unique protein domain-superfamilies encoded by extant genomes.}, } @article {pmid28471691, year = {2017}, author = {Rout, MP and Field, MC}, title = {The Evolution of Organellar Coat Complexes and Organization of the Eukaryotic Cell.}, journal = {Annual review of biochemistry}, volume = {86}, number = {}, pages = {637-657}, doi = {10.1146/annurev-biochem-061516-044643}, pmid = {28471691}, issn = {1545-4509}, support = {R21 AI096069/AI/NIAID NIH HHS/United States ; U54 GM103511/GM/NIGMS NIH HHS/United States ; MR/K008749/1/MRC_/Medical Research Council/United Kingdom ; R01 GM112108/GM/NIGMS NIH HHS/United States ; 204697/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; U01 GM098256/GM/NIGMS NIH HHS/United States ; MR/P009018/1/MRC_/Medical Research Council/United Kingdom ; P41 GM109824/GM/NIGMS NIH HHS/United States ; MR/N010558/1/MRC_/Medical Research Council/United Kingdom ; 203134/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Active Transport, Cell Nucleus ; Cell Membrane/chemistry/metabolism/*ultrastructure ; Clathrin/*chemistry/genetics/metabolism ; Coat Protein Complex I/*chemistry/genetics/metabolism ; Coated Vesicles/chemistry/metabolism/*ultrastructure ; Eukaryotic Cells/chemistry/metabolism/*ultrastructure ; Evolution, Molecular ; Flagella/chemistry/metabolism/ultrastructure ; Gene Expression ; Models, Molecular ; Monomeric GTP-Binding Proteins/*chemistry/genetics/metabolism ; Nuclear Pore/chemistry/metabolism/ultrastructure ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Domains ; }, abstract = {Eukaryotic cells possess a remarkably diverse range of organelles that provide compartmentalization for distinct cellular functions and are likely responsible for the remarkable success of these organisms. The origins and subsequent elaboration of these compartments represent a key aspect in the transition between prokaryotic and eukaryotic cellular forms. The protein machinery required to build, maintain, and define many membrane-bound compartments is encoded by several paralog families, including small GTPases, coiled-bundle proteins, and proteins with β-propeller and α-solenoid secondary structures. Together these proteins provide the membrane coats and control systems to structure and coordinate the endomembrane system. Mechanistically and evolutionarily, they unite not only secretory and endocytic organelles but also the flagellum and nucleus. The ancient origins for these families have been revealed by recent findings, providing new perspectives on the deep evolutionary processes and relationships that underlie eukaryotic cell structure.}, } @article {pmid28463551, year = {2017}, author = {Obado, SO and Field, MC and Rout, MP}, title = {Comparative interactomics provides evidence for functional specialization of the nuclear pore complex.}, journal = {Nucleus (Austin, Tex.)}, volume = {8}, number = {4}, pages = {340-352}, pmid = {28463551}, issn = {1949-1042}, support = {203134/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MR/N010558/1/MRC_/Medical Research Council/United Kingdom ; P41 GM109824/GM/NIGMS NIH HHS/United States ; R01 GM112108/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Evolution, Molecular ; Humans ; Models, Biological ; Nuclear Pore Complex Proteins/*chemistry/*metabolism ; Opisthorchis/*chemistry ; Protein Folding ; *Proteomics ; Trypanosoma/chemistry/*metabolism ; }, abstract = {The core architecture of the eukaryotic cell was established well over one billion years ago, and is largely retained in all extant lineages. However, eukaryotic cells also possess lineage-specific features, frequently keyed to specific functional requirements. One quintessential core eukaryotic structure is the nuclear pore complex (NPC), responsible for regulating exchange of macromolecules between the nucleus and cytoplasm as well as acting as a nuclear organizational hub. NPC architecture has been best documented in one eukaryotic supergroup, the Opisthokonts (e.g. Saccharomyces cerevisiae and Homo sapiens), which although compositionally similar, have significant variations in certain NPC subcomplex structures. The variation of NPC structure across other taxa in the eukaryotic kingdom however, remains poorly understood. We explored trypanosomes, highly divergent organisms, and mapped and assigned their NPC proteins to specific substructures to reveal their NPC architecture. We showed that the NPC central structural scaffold is conserved, likely across all eukaryotes, but more peripheral elements can exhibit very significant lineage-specific losses, duplications or other alterations in their components. Amazingly, trypanosomes lack the major components of the mRNA export platform that are asymmetrically localized within yeast and vertebrate NPCs. Concomitant with this, the trypanosome NPC is ALMOST completely symmetric with the nuclear basket being the only major source of asymmetry. We suggest these features point toward a stepwise evolution of the NPC in which a coating scaffold first stabilized the pore after which selective gating emerged and expanded, leading to the addition of peripheral remodeling machineries on the nucleoplasmic and cytoplasmic sides of the pore.}, } @article {pmid28461155, year = {2017}, author = {Harish, A and Kurland, CG}, title = {Akaryotes and Eukaryotes are independent descendants of a universal common ancestor.}, journal = {Biochimie}, volume = {138}, number = {}, pages = {168-183}, doi = {10.1016/j.biochi.2017.04.013}, pmid = {28461155}, issn = {1638-6183}, mesh = {Archaea/genetics ; Bacteria/genetics ; Bayes Theorem ; Eukaryota/genetics ; *Evolution, Molecular ; *Genome ; Mitochondria ; *Models, Genetic ; *Phylogeny ; *Proteome ; }, abstract = {We reconstructed a global tree of life (ToL) with non-reversible and non-stationary models of genome evolution that root trees intrinsically. We implemented Bayesian model selection tests and compared the statistical support for four conflicting ToL hypotheses. We show that reconstructions obtained with a Bayesian implementation (Klopfstein et al., 2015) are consistent with reconstructions obtained with an empirical Sankoff parsimony (ESP) implementation (Harish et al., 2013). Both are based on the genome contents of coding sequences for protein domains (superfamilies) from hundreds of genomes. Thus, we conclude that the independent descent of Eukaryotes and Akaryotes (archaea and bacteria) from the universal common ancestor (UCA) is the most probable as well as the most parsimonious hypothesis for the evolutionary origins of extant genomes. Reconstructions of ancestral proteomes by both Bayesian and ESP methods suggest that at least 70% of unique domain-superfamilies known in extant species were present in the UCA. In addition, identification of a vast majority (96%) of the mitochondrial superfamilies in the UCA proteome precludes a symbiotic hypothesis for the origin of eukaryotes. Accordingly, neither the archaeal origin of eukaryotes nor the bacterial origin of mitochondria is supported by the data. The proteomic complexity of the UCA suggests that the evolution of cellular phenotypes in the two primordial lineages, Akaryotes and Eukaryotes, was driven largely by duplication of common superfamilies as well as by loss of unique superfamilies. Finally, innovation of novel superfamilies has played a surprisingly small role in the evolution of Akaryotes and only a marginal role in the evolution of Eukaryotes.}, } @article {pmid28338801, year = {2017}, author = {Omura, T and Gotoh, O}, title = {Evolutionary origin of mitochondrial cytochrome P450.}, journal = {Journal of biochemistry}, volume = {161}, number = {5}, pages = {399-407}, doi = {10.1093/jb/mvx011}, pmid = {28338801}, issn = {1756-2651}, mesh = {Animals ; Cytochrome P-450 Enzyme System/*metabolism ; Fungi/metabolism ; Mitochondria/enzymology/*metabolism ; Plants/metabolism ; }, abstract = {Different molecular species of cytochrome P450 (P450) are distributed between endoplasmic reticulum (microsomes) and mitochondria in animal cells. Plants and fungi have many microsomal P450s, but no mitochondrial P450 has so far been reported. To elucidate the evolutionary origin of mitochondrial P450s in animal cells, available evidence is examined, and the virtual absence of mitochondrial P450 in plants and fungi is confirmed. It is also suggested that a microsomal P450 is the ancestor of animal mitochondrial P450s. It is likely that the endoplasmic reticulum-targeting sequence at the amino-terminus of a microsomal P450 was converted to a mitochondria-targeting sequence possibly by point mutations of a few amino acid residues or by an exon-shuffling/moving event shortly after animal lineage diverged from plants and fungi in the course of evolution of eukaryotes. It is suggested that the microsome-type P450 first imported into mitochondria utilized the existing ferredoxin in the matrix to receive electrons from NADPH, retained its oxygenase activity in the mitochondria, and gradually diversified to several P450s with different substrate specificities in the course of the evolution of animals.}, } @article {pmid28265765, year = {2017}, author = {Martin, WF and Cerff, R}, title = {Physiology, phylogeny, early evolution, and GAPDH.}, journal = {Protoplasma}, volume = {254}, number = {5}, pages = {1823-1834}, pmid = {28265765}, issn = {1615-6102}, support = {666053//European Research Council/International ; }, mesh = {Animals ; Glyceraldehyde-3-Phosphate Dehydrogenases/genetics/*metabolism ; Humans ; Mitochondria/genetics/metabolism ; Phylogeny ; Plastids/enzymology ; Symbiosis/genetics/physiology ; }, abstract = {The chloroplast and cytosol of plant cells harbor a number of parallel biochemical reactions germane to the Calvin cycle and glycolysis, respectively. These reactions are catalyzed by nuclear encoded, compartment-specific isoenzymes that differ in their physiochemical properties. The chloroplast cytosol isoenzymes of D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) harbor evidence of major events in the history of life: the origin of the first genes, the bacterial-archaeal split, the origin of eukaryotes, the evolution of protein compartmentation during eukaryote evolution, the origin of plastids, and the secondary endosymbiosis among the algae with complex plastids. The reaction mechanism of GAPDH entails phosphorolysis of a thioester to yield an energy-rich acyl phosphate bond, a chemistry that points to primitive pathways of energy conservation that existed even before the origin of the first free-living cells. Here, we recount the main insights that chloroplast and cytosolic GAPDH provided into endosymbiosis and physiological evolution.}, } @article {pmid28254477, year = {2017}, author = {López-García, P and Eme, L and Moreira, D}, title = {Symbiosis in eukaryotic evolution.}, journal = {Journal of theoretical biology}, volume = {434}, number = {}, pages = {20-33}, pmid = {28254477}, issn = {1095-8541}, support = {322669/ERC_/European Research Council/International ; }, mesh = {*Biological Evolution ; Ecosystem ; Eukaryota/*cytology/ultrastructure ; Eukaryotic Cells/ultrastructure ; Microbiota ; *Symbiosis ; }, abstract = {Fifty years ago, Lynn Margulis, inspiring in early twentieth-century ideas that put forward a symbiotic origin for some eukaryotic organelles, proposed a unified theory for the origin of the eukaryotic cell based on symbiosis as evolutionary mechanism. Margulis was profoundly aware of the importance of symbiosis in the natural microbial world and anticipated the evolutionary significance that integrated cooperative interactions might have as mechanism to increase cellular complexity. Today, we have started fully appreciating the vast extent of microbial diversity and the importance of syntrophic metabolic cooperation in natural ecosystems, especially in sediments and microbial mats. Also, not only the symbiogenetic origin of mitochondria and chloroplasts has been clearly demonstrated, but improvement in phylogenomic methods combined with recent discoveries of archaeal lineages more closely related to eukaryotes further support the symbiogenetic origin of the eukaryotic cell. Margulis left us in legacy the idea of 'eukaryogenesis by symbiogenesis'. Although this has been largely verified, when, where, and specifically how eukaryotic cells evolved are yet unclear. Here, we shortly review current knowledge about symbiotic interactions in the microbial world and their evolutionary impact, the status of eukaryogenetic models and the current challenges and perspectives ahead to reconstruct the evolutionary path to eukaryotes.}, } @article {pmid28245058, year = {2017}, author = {Duanmu, D and Rockwell, NC and Lagarias, JC}, title = {Algal light sensing and photoacclimation in aquatic environments.}, journal = {Plant, cell & environment}, volume = {40}, number = {11}, pages = {2558-2570}, pmid = {28245058}, issn = {1365-3040}, support = {R01 GM068552/GM/NIGMS NIH HHS/United States ; }, mesh = {Acclimatization/*radiation effects ; Aquatic Organisms/*physiology/*radiation effects ; Eukaryota/*physiology/*radiation effects ; *Light ; Models, Biological ; Photosynthesis/radiation effects ; }, abstract = {Anoxygenic photosynthetic prokaryotes arose in ancient oceans ~3.5 billion years ago. The evolution of oxygenic photosynthesis by cyanobacteria followed soon after, enabling eukaryogenesis and the evolution of complex life. The Archaeplastida lineage dates back ~1.5 billion years to the domestication of a cyanobacterium. Eukaryotic algae have subsequently radiated throughout oceanic/freshwater/terrestrial environments, adopting distinctive morphological and developmental strategies for adaptation to diverse light environments. Descendants of the ancestral photosynthetic alga remain challenged by a typical diurnally fluctuating light supply ranging from ~0 to ~2000 μE m[-2] s[-1] . Such extreme changes in light intensity and variations in light quality have driven the evolution of novel photoreceptors, light-harvesting complexes and photoprotective mechanisms in photosynthetic eukaryotes. This minireview focuses on algal light sensors, highlighting the unexpected roles for linear tetrapyrroles (bilins) in the maintenance of functional chloroplasts in chlorophytes, sister species to streptophyte algae and land plants.}, } @article {pmid28111289, year = {2017}, author = {Staley, JT and Fuerst, JA}, title = {Ancient, highly conserved proteins from a LUCA with complex cell biology provide evidence in support of the nuclear compartment commonality (NuCom) hypothesis.}, journal = {Research in microbiology}, volume = {168}, number = {5}, pages = {395-412}, doi = {10.1016/j.resmic.2017.01.001}, pmid = {28111289}, issn = {1769-7123}, mesh = {Bacterial Proteins/metabolism ; Cell Compartmentation/*genetics ; Chlamydia/genetics ; Eukaryota/genetics ; *Evolution, Molecular ; *Nuclear Envelope ; Phylogeny ; Tubulin/genetics/metabolism ; Ubiquitin/genetics/metabolism ; Verrucomicrobia/genetics ; }, abstract = {The nuclear compartment commonality (NuCom) hypothesis posits a complex last common ancestor (LUCA) with membranous compartments including a nuclear membrane. Such a LUCA then evolved to produce two nucleated lineages of the tree of life: the Planctomycetes-Verrucomicrobia-Chlamydia superphylum (PVC) within the Bacteria, and the Eukarya. We propose that a group of ancient essential protokaryotic signature proteins (PSPs) originating in LUCA were incorporated into ancestors of PVC Bacteria and Eukarya. Tubulins, ubiquitin system enzymes and sterol-synthesizing enzymes are consistent with early origins of these features shared between the PVC superphylum and Eukarya.}, } @article {pmid28096055, year = {2017}, author = {Wells, ML and Perera, L and Blackshear, PJ}, title = {An Ancient Family of RNA-Binding Proteins: Still Important!.}, journal = {Trends in biochemical sciences}, volume = {42}, number = {4}, pages = {285-296}, pmid = {28096055}, issn = {0968-0004}, support = {Z01 ES090080-11//Intramural NIH HHS/United States ; }, mesh = {Animals ; Humans ; RNA-Binding Proteins/*chemistry/*metabolism ; }, abstract = {RNA-binding proteins are important modulators of mRNA stability, a crucial process that determines the ultimate cellular levels of mRNAs and their encoded proteins. The tristetraprolin (TTP) family of RNA-binding proteins appeared early in the evolution of eukaryotes, and has persisted in modern eukaryotes. The domain structures and biochemical functions of family members from widely divergent lineages are remarkably similar, but their mRNA 'targets' can be very different, even in closely related species. Recent gene knockout studies in species as distantly related as plants, flies, yeasts, and mice have demonstrated crucial roles for these proteins in a wide variety of physiological processes. Inflammatory and hematopoietic phenotypes in mice have suggested potential therapeutic approaches for analogous human disorders.}, } @article {pmid28087778, year = {2017}, author = {Domazet-Lošo, T and Carvunis, AR and Albà, MM and Šestak, MS and Bakaric, R and Neme, R and Tautz, D}, title = {No Evidence for Phylostratigraphic Bias Impacting Inferences on Patterns of Gene Emergence and Evolution.}, journal = {Molecular biology and evolution}, volume = {34}, number = {4}, pages = {843-856}, pmid = {28087778}, issn = {1537-1719}, support = {322564/ERC_/European Research Council/International ; K99 GM108865/GM/NIGMS NIH HHS/United States ; R00 GM108865/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bias ; Biological Evolution ; Computational Biology/*methods ; Computer Simulation ; Drosophila ; Evolution, Molecular ; Genome ; Models, Genetic ; Phylogeny ; Sequence Analysis, DNA/*methods ; Sequence Analysis, Protein/*methods ; Time Factors ; }, abstract = {Phylostratigraphy is a computational framework for dating the emergence of DNA and protein sequences in a phylogeny. It has been extensively applied to make inferences on patterns of genome evolution, including patterns of disease gene evolution, ontogeny and de novo gene origination. Phylostratigraphy typically relies on BLAST searches along a species tree, but new simulation studies have raised concerns about the ability of BLAST to detect remote homologues and its impact on phylostratigraphic inferences. Here, we re-assessed these simulations. We found that, even with a possible overall BLAST false negative rate between 11-15%, the large majority of sequences assigned to a recent evolutionary origin by phylostratigraphy is unaffected by technical concerns about BLAST. Where the results of the simulations did cast doubt on previously reported findings, we repeated the original analyses but now excluded all questionable sequences. The originally described patterns remained essentially unchanged. These new analyses strongly support phylostratigraphic inferences, including: genes that emerged after the origin of eukaryotes are more likely to be expressed in the ectoderm than in the endoderm or mesoderm in Drosophila, and the de novo emergence of protein-coding genes from non-genic sequences occurs through proto-gene intermediates in yeast. We conclude that BLAST is an appropriate and sufficiently sensitive tool in phylostratigraphic analysis that does not appear to introduce significant biases into evolutionary pattern inferences.}, } @article {pmid28050162, year = {2016}, author = {Nasir, A and Kim, KM and Da Cunha, V and Caetano-Anollés, G}, title = {Arguments Reinforcing the Three-Domain View of Diversified Cellular Life.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2016}, number = {}, pages = {1851865}, pmid = {28050162}, issn = {1472-3654}, support = {340440/ERC_/European Research Council/International ; }, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; }, abstract = {The archaeal ancestor scenario (AAS) for the origin of eukaryotes implies the emergence of a new kind of organism from the fusion of ancestral archaeal and bacterial cells. Equipped with this "chimeric" molecular arsenal, the resulting cell would gradually accumulate unique genes and develop the complex molecular machineries and cellular compartments that are hallmarks of modern eukaryotes. In this regard, proteins related to phagocytosis and cell movement should be present in the archaeal ancestor, thus identifying the recently described candidate archaeal phylum "Lokiarchaeota" as resembling a possible candidate ancestor of eukaryotes. Despite its appeal, AAS seems incompatible with the genomic, molecular, and biochemical differences that exist between Archaea and Eukarya. In particular, the distribution of conserved protein domain structures in the proteomes of cellular organisms and viruses appears hard to reconcile with the AAS. In addition, concerns related to taxon and character sampling, presupposing bacterial outgroups in phylogenies, and nonuniform effects of protein domain structure rearrangement and gain/loss in concatenated alignments of protein sequences cast further doubt on AAS-supporting phylogenies. Here, we evaluate AAS against the traditional "three-domain" world of cellular organisms and propose that the discovery of Lokiarchaeota could be better reconciled under the latter view, especially in light of several additional biological and technical considerations.}, } @article {pmid27940473, year = {2017}, author = {Favarato, RM and Ribeiro, LB and Feldberg, E and Matoso, DA}, title = {Chromosomal Mapping of Transposable Elements of the Rex Family in the Bristlenose Catfish, Ancistrus (Siluriformes, Loricariidae), from the Amazonian Region.}, journal = {The Journal of heredity}, volume = {108}, number = {3}, pages = {254-261}, doi = {10.1093/jhered/esw084}, pmid = {27940473}, issn = {1465-7333}, mesh = {Animals ; Brazil ; Catfishes/classification/*genetics ; *Chromosome Mapping ; *DNA Transposable Elements ; Female ; In Situ Hybridization, Fluorescence ; Karyotype ; Male ; Retroelements ; }, abstract = {Repetitive DNA sequences are present in the genome of basically every known organism, and transposable elements (TE) are one of the most representative sequences involved in chromosomal rearrangements and the genomic evolution of eukaryotes. In fish, the non-LTR retrotransposon TEs, Rex1, Rex3, and Rex6, are widely distributed in fish genomes and are the best-characterized TEs in several species. In the current study, three of these retroelements were physically mapped, through fluorescent in situ hybridization (FISH), in 7 species (71 specimens) of the genus Ancistrus, known as bristlenose catfish: Ancistrus ranunculus, Ancistrus sp. 1 "Purus," Ancistrus sp. 2 "Catalão," Ancistrus dolichopterus, Ancistrus maximus, Ancistrus aff. dolichopterus, and Ancistrus dubius. Rex1, Rex3, and Rex6 showed a cluster distribution, mainly in the terminal and pericentromeric portions, in heterochromatic and euchromatic regions, and did not occur in sexual chromosomes; however, the number and position of the clusters varied between species. This TE distribution suggests its implication in the karyotypic evolution of these species, without affecting the rise of sexual chromosome systems in Ancistrus, in view of their chromosomal variation.}, } @article {pmid27880711, year = {2016}, author = {Kollmar, M}, title = {Fine-Tuning Motile Cilia and Flagella: Evolution of the Dynein Motor Proteins from Plants to Humans at High Resolution.}, journal = {Molecular biology and evolution}, volume = {33}, number = {12}, pages = {3249-3267}, pmid = {27880711}, issn = {1537-1719}, mesh = {Amino Acid Sequence ; Animals ; Axoneme/genetics/metabolism ; Base Sequence ; Cilia/*genetics/metabolism ; Dyneins/*genetics/metabolism ; Evolution, Molecular ; Flagella/*genetics/metabolism ; Humans ; Kinesins/genetics ; Myosins/genetics/metabolism ; Phylogeny ; Plants/genetics ; Protein Isoforms ; }, abstract = {The flagellum is a key innovation linked to eukaryogenesis. It provides motility by regulated cycles of bending and bend propagation, which are thought to be controlled by a complex arrangement of seven distinct dyneins in repeated patterns of outer- (OAD) and inner-arm dynein (IAD) complexes. Electron tomography showed high similarity of this axonemal repeat pattern across ciliates, algae, and animals, but the diversity of dynein sequences across the eukaryotes has not yet comprehensively been resolved and correlated with structural data. To shed light on the evolution of the axoneme I performed an exhaustive analysis of dyneins using the available sequenced genome data. Evidence from motor domain phylogeny allowed expanding the current set of nine dynein subtypes by eight additional isoforms with, however, restricted taxonomic distributions. I confirmed the presence of the nine dyneins in all eukaryotic super-groups indicating their origin predating the last eukaryotic common ancestor. The comparison of the N-terminal tail domains revealed a most likely axonemal dynein origin of the new classes, a group of chimeric dyneins in plants/algae and Stramenopiles, and the unique domain architecture and origin of the outermost OADs present in green algae and ciliates but not animals. The correlation of sequence and structural data suggests the single-headed class-8 and class-9 dyneins to localize to the distal end of the axonemal repeat and the class-7 dyneins filling the region up to the proximal heterodimeric IAD. Tracing dynein gene duplications across the eukaryotes indicated ongoing diversification and fine-tuning of flagellar functions in extant taxa and species.}, } @article {pmid27827352, year = {2016}, author = {Eisenreichova, A and Klima, M and Boura, E}, title = {Crystal structures of a yeast 14-3-3 protein from Lachancea thermotolerans in the unliganded form and bound to a human lipid kinase PI4KB-derived peptide reveal high evolutionary conservation.}, journal = {Acta crystallographica. Section F, Structural biology communications}, volume = {72}, number = {Pt 11}, pages = {799-803}, pmid = {27827352}, issn = {2053-230X}, mesh = {1-Phosphatidylinositol 4-Kinase/*chemistry/genetics/metabolism ; 14-3-3 Proteins/*chemistry/genetics/metabolism ; Amino Acid Sequence ; Binding Sites ; Cloning, Molecular ; Conserved Sequence ; Crystallography, X-Ray ; Escherichia coli/genetics/metabolism ; Evolution, Molecular ; Fungal Proteins/*chemistry/genetics/metabolism ; Gene Expression ; Humans ; Ligands ; Models, Molecular ; Phosphoproteins/*chemistry/genetics/metabolism ; Plasmids/chemistry/metabolism ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Isoforms/chemistry/genetics/metabolism ; Recombinant Proteins/chemistry/genetics/metabolism ; Saccharomycetales/*chemistry/metabolism ; Sequence Alignment ; Structural Homology, Protein ; }, abstract = {14-3-3 proteins bind phosphorylated binding partners to regulate several of their properties, including enzymatic activity, stability and subcellular localization. Here, two crystal structures are presented: the crystal structures of the 14-3-3 protein (also known as Bmh1) from the yeast Lachancea thermotolerans in the unliganded form and bound to a phosphopeptide derived from human PI4KB (phosphatidylinositol 4-kinase B). The structures demonstrate the high evolutionary conservation of ligand recognition by 14-3-3 proteins. The structural analysis suggests that ligand recognition by 14-3-3 proteins evolved very early in the evolution of eukaryotes and remained conserved, underlying the importance of 14-3-3 proteins in physiology.}, } @article {pmid27756227, year = {2016}, author = {Kienle, N and Kloepper, TH and Fasshauer, D}, title = {Shedding light on the expansion and diversification of the Cdc48 protein family during the rise of the eukaryotic cell.}, journal = {BMC evolutionary biology}, volume = {16}, number = {1}, pages = {215}, pmid = {27756227}, issn = {1471-2148}, mesh = {Adenosine Triphosphatases/*chemistry/genetics ; Biological Evolution ; Cell Cycle Proteins/*chemistry/genetics ; Eukaryotic Cells/cytology/*metabolism/ultrastructure ; *Evolution, Molecular ; Markov Chains ; Phylogeny ; Prokaryotic Cells/cytology/metabolism/ultrastructure ; Protein Domains ; Valosin Containing Protein ; }, abstract = {BACKGROUND: A defining feature of eukaryotic cells is the presence of various distinct membrane-bound compartments with different metabolic roles. Material exchange between most compartments occurs via a sophisticated vesicle trafficking system. This intricate cellular architecture of eukaryotes appears to have emerged suddenly, about 2 billion years ago, from much less complex ancestors. How the eukaryotic cell acquired its internal complexity is poorly understood, partly because no prokaryotic precursors have been found for many key factors involved in compartmentalization. One exception is the Cdc48 protein family, which consists of several distinct classical ATPases associated with various cellular activities (AAA+) proteins with two consecutive AAA domains.

RESULTS: Here, we have classified the Cdc48 family through iterative use of hidden Markov models and tree building. We found only one type, Cdc48, in prokaryotes, although a set of eight diverged members that function at distinct subcellular compartments were retrieved from eukaryotes and were probably present in the last eukaryotic common ancestor (LECA). Pronounced changes in sequence and domain structure during the radiation into the LECA set are delineated. Moreover, our analysis brings to light lineage-specific losses and duplications that often reflect important biological changes. Remarkably, we also found evidence for internal duplications within the LECA set that probably occurred during the rise of the eukaryotic cell.

CONCLUSIONS: Our analysis corroborates the idea that the diversification of the Cdc48 family is closely intertwined with the development of the compartments of the eukaryotic cell.}, } @article {pmid27703691, year = {2016}, author = {Tekle, YI and Williams, JR}, title = {Cytoskeletal architecture and its evolutionary significance in amoeboid eukaryotes and their mode of locomotion.}, journal = {Royal Society open science}, volume = {3}, number = {9}, pages = {160283}, pmid = {27703691}, issn = {2054-5703}, abstract = {The cytoskeleton is the hallmark of eukaryotic evolution. The molecular and architectural aspects of the cytoskeleton have been playing a prominent role in our understanding of the origin and evolution of eukaryotes. In this study, we seek to investigate the cytoskeleton architecture and its evolutionary significance in understudied amoeboid lineages belonging to Amoebozoa. These amoebae primarily use cytoplasmic extensions supported by the cytoskeleton to perform important cellular processes such as movement and feeding. Amoeboid structure has important taxonomic significance, but, owing to techniques used, its potential significance in understanding diversity of the group has been seriously compromised, leading to an under-appreciation of its value. Here, we used immunocytochemistry and confocal microscopy to study the architecture of microtubules (MTs) and F-actin in diverse groups of amoebae. Our results demonstrate that all Amoebozoa examined are characterized by a complex cytoskeletal array, unlike what has been previously thought to exist. Our results not only conclusively demonstrate that all amoebozoans possess complex cytoplasmic MTs, but also provide, for the first time, a potential synapomorphy for the molecularly defined Amoebozoa clade. Based on this evidence, the last common ancestor of amoebozoans is hypothesized to have had a complex interwoven MT architecture limited within the granular cell body. We also generate several cytoskeleton characters related to MT and F-actin, which are found to be robust for defining groups in deep and shallow nodes of Amoebozoa.}, } @article {pmid27672020, year = {2016}, author = {Dacks, JB and Field, MC and Buick, R and Eme, L and Gribaldo, S and Roger, AJ and Brochier-Armanet, C and Devos, DP}, title = {The changing view of eukaryogenesis - fossils, cells, lineages and how they all come together.}, journal = {Journal of cell science}, volume = {129}, number = {20}, pages = {3695-3703}, doi = {10.1242/jcs.178566}, pmid = {27672020}, issn = {1477-9137}, mesh = {Archaea/metabolism ; Eukaryotic Cells/*metabolism ; *Fossils ; *Phylogeny ; Prokaryotic Cells ; Time Factors ; }, abstract = {Eukaryogenesis - the emergence of eukaryotic cells - represents a pivotal evolutionary event. With a fundamentally more complex cellular plan compared to prokaryotes, eukaryotes are major contributors to most aspects of life on Earth. For decades, we have understood that eukaryotic origins lie within both the Archaea domain and α-Proteobacteria. However, it is much less clear when, and from which precise ancestors, eukaryotes originated, or the order of emergence of distinctive eukaryotic cellular features. Many competing models for eukaryogenesis have been proposed, but until recently, the absence of discriminatory data meant that a consensus was elusive. Recent advances in paleogeology, phylogenetics, cell biology and microbial diversity, particularly the discovery of the 'Candidatus Lokiarcheaota' phylum, are now providing new insights into these aspects of eukaryogenesis. The new data have allowed the time frame during which eukaryogenesis occurred to be finessed, a more precise identification of the contributing lineages and the biological features of the contributors to be clarified. Considerable advances have now been used to pinpoint the prokaryotic origins of key eukaryotic cellular processes, such as intracellular compartmentalisation, with major implications for models of eukaryogenesis.}, } @article {pmid27604877, year = {2016}, author = {Nishimura, Y and Tanifuji, G and Kamikawa, R and Yabuki, A and Hashimoto, T and Inagaki, Y}, title = {Mitochondrial Genome of Palpitomonas bilix: Derived Genome Structure and Ancestral System for Cytochrome c Maturation.}, journal = {Genome biology and evolution}, volume = {8}, number = {10}, pages = {3090-3098}, pmid = {27604877}, issn = {1759-6653}, mesh = {Archaea/classification/*genetics ; Archaeal Proteins/*genetics ; Cytochromes c/*genetics ; DNA Copy Number Variations ; *Evolution, Molecular ; *Genome, Archaeal ; *Genome, Mitochondrial ; Phylogeny ; }, abstract = {We here reported the mitochondrial (mt) genome of one of the heterotrophic microeukaryotes related to cryptophytes, Palpitomonas bilix The P. bilix mt genome was found to be a linear molecule composed of "single copy region" (∼16 kb) and repeat regions (∼30 kb) arranged in an inverse manner at both ends of the genome. Linear mt genomes with large inverted repeats are known for three distantly related eukaryotes (including P. bilix), suggesting that this particular mt genome structure has emerged at least three times in the eukaryotic tree of life. The P. bilix mt genome contains 47 protein-coding genes including ccmA, ccmB, ccmC, and ccmF, which encode protein subunits involved in the system for cytochrome c maturation inherited from a bacterium (System I). We present data indicating that the phylogenetic relatives of P. bilix, namely, cryptophytes, goniomonads, and kathablepharids, utilize an alternative system for cytochrome c maturation, which has most likely emerged during the evolution of eukaryotes (System III). To explain the distribution of Systems I and III in P. bilix and its phylogenetic relatives, two scenarios are possible: (i) System I was replaced by System III on the branch leading to the common ancestor of cryptophytes, goniomonads, and kathablepharids, and (ii) the two systems co-existed in their common ancestor, and lost differentially among the four descendants.}, } @article {pmid27573115, year = {2016}, author = {Kutschera, U}, title = {Haeckel's 1866 tree of life and the origin of eukaryotes.}, journal = {Nature microbiology}, volume = {1}, number = {8}, pages = {16114}, pmid = {27573115}, issn = {2058-5276}, mesh = {*Biological Evolution ; *Eukaryota ; Evolution, Molecular ; Germany ; History, 19th Century ; Life ; Models, Biological ; Origin of Life ; Phylogeny ; }, } @article {pmid27492357, year = {2016}, author = {Lombard, J}, title = {The multiple evolutionary origins of the eukaryotic N-glycosylation pathway.}, journal = {Biology direct}, volume = {11}, number = {}, pages = {36}, pmid = {27492357}, issn = {1745-6150}, mesh = {Eukaryota/*classification/*metabolism ; *Evolution, Molecular ; *Glycosylation ; *Metabolic Networks and Pathways ; Phylogeny ; }, abstract = {BACKGROUND: The N-glycosylation is an essential protein modification taking place in the membranes of the endoplasmic reticulum (ER) in eukaryotes and the plasma membranes in archaea. It shares mechanistic similarities based on the use of polyisoprenol lipid carriers with other glycosylation pathways involved in the synthesis of bacterial cell wall components (e.g. peptidoglycan and teichoic acids). Here, a phylogenomic analysis was carried out to examine the validity of rival hypotheses suggesting alternative archaeal or bacterial origins to the eukaryotic N-glycosylation pathway.

RESULTS: The comparison of several polyisoprenol-based glycosylation pathways from the three domains of life shows that most of the implicated proteins belong to a limited number of superfamilies. The N-glycosylation pathway enzymes are ancestral to the eukaryotes, but their origins are mixed: Alg7, Dpm and maybe also one gene of the glycosyltransferase 1 (GT1) superfamily and Stt3 have proteoarchaeal (TACK superphylum) origins; alg2/alg11 may have resulted from the duplication of the original GT1 gene; the lumen glycosyltransferases were probably co-opted and multiplied through several gene duplications during eukaryogenesis; Alg13/Alg14 are more similar to their bacterial homologues; and Alg1, Alg5 and a putative flippase have unknown origins.

CONCLUSIONS: The origin of the eukaryotic N-glycosylation pathway is not unique and less straightforward than previously thought: some basic components likely have proteoarchaeal origins, but the pathway was extensively developed before the eukaryotic diversification through multiple gene duplications, protein co-options, neofunctionalizations and even possible horizontal gene transfers from bacteria. These results may have important implications for our understanding of the ER evolution and eukaryogenesis.

REVIEWERS: This article was reviewed by Pr. Patrick Forterre and Dr. Sergei Mekhedov (nominated by Editorial Board member Michael Galperin).}, } @article {pmid27473689, year = {2016}, author = {Degli Esposti, M and Cortez, D and Lozano, L and Rasmussen, S and Nielsen, HB and Martinez Romero, E}, title = {Alpha proteobacterial ancestry of the [Fe-Fe]-hydrogenases in anaerobic eukaryotes.}, journal = {Biology direct}, volume = {11}, number = {}, pages = {34}, pmid = {27473689}, issn = {1745-6150}, mesh = {Alphaproteobacteria/*genetics ; Amino Acid Sequence ; Bacterial Proteins/*genetics ; Evolution, Molecular ; Gastrointestinal Microbiome/*genetics ; Humans ; Hydrogenase/*genetics ; Phylogeny ; Rhodospirillaceae/genetics ; }, abstract = {UNLABELLED: Eukaryogenesis, a major transition in evolution of life, originated from the symbiogenic fusion of an archaea with a metabolically versatile bacterium. By general consensus, the latter organism belonged to α proteobacteria, subsequently evolving into the mitochondrial organelle of our cells. The consensus is based upon genetic and metabolic similarities between mitochondria and aerobic α proteobacteria but fails to explain the origin of several enzymes found in the mitochondria-derived organelles of anaerobic eukaryotes such as Trichomonas and Entamoeba. These enzymes are thought to derive from bacterial lineages other than α proteobacteria, e.g., Clostridium - an obligate anaerobe. [FeFe]-hydrogenase constitues the characteristic enzyme of this anaerobic metabolism and is present in different types also in Entamoeba and other anaerobic eukaryotes. Here we show that α proteobacteria derived from metagenomic studies possess both the cytosolic and organellar type of [FeFe]-hydrogenase, as well as all the proteins required for hydrogenase maturation. These organisms are related to cultivated members of the Rhodospirillales order previously suggested to be close relatives of mitochondrial ancestors. For the first time, our evidence supports an α proteobacterial ancestry for both the anaerobic and the aerobic metabolism of eukaryotes.

REVIEWERS: This article was reviewed by William Martin and Nick Lane, both suggested by the Authors.}, } @article {pmid27411857, year = {2016}, author = {Hu, YB and Sosso, D and Qu, XQ and Chen, LQ and Ma, L and Chermak, D and Zhang, DC and Frommer, WB}, title = {Phylogenetic evidence for a fusion of archaeal and bacterial SemiSWEETs to form eukaryotic SWEETs and identification of SWEET hexose transporters in the amphibian chytrid pathogen Batrachochytrium dendrobatidis.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {30}, number = {10}, pages = {3644-3654}, doi = {10.1096/fj.201600576R}, pmid = {27411857}, issn = {1530-6860}, mesh = {Animals ; Biological Transport ; Chytridiomycota/isolation & purification/*pathogenicity ; Eukaryota/*metabolism ; Membrane Transport Proteins/*metabolism ; Monosaccharide Transport Proteins/*metabolism ; Structure-Activity Relationship ; }, abstract = {SWEETs represent a new class of sugar transporters first described in plants, animals, and humans and later in prokaryotes. Plant SWEETs play key roles in phloem loading, seed filling, and nectar secretion, whereas the role of archaeal, bacterial, and animal transporters remains elusive. Structural analyses show that eukaryotic SWEETs are composed of 2 triple-helix bundles (THBs) fused via an inversion linker helix, whereas prokaryotic SemiSWEETs contain only a single THB and require homodimerization to form transport pores. This study indicates that SWEETs retained sugar transport activity in all kingdoms of life, and that SemiSWEETs are likely their ancestral units. Fusion of oligomeric subunits into single polypeptides during evolution of eukaryotes is commonly found for transporters. Phylogenetic analyses indicate that THBs of eukaryotic SWEETs may not have evolved by tandem duplication of an open reading frame, but rather originated by fusion between an archaeal and a bacterial SemiSWEET, which potentially explains the asymmetry of eukaryotic SWEETs. Moreover, despite the ancient ancestry, SWEETs had not been identified in fungi or oomycetes. Here, we report the identification of SWEETs in oomycetes as well as SWEETs and a potential SemiSWEET in primitive fungi. BdSWEET1 and BdSWEET2 from Batrachochytrium dendrobatidis, a nonhyphal zoosporic fungus that causes global decline in amphibians, showed glucose and fructose transport activities.-Hu, Y.-B., Sosso, D., Qu, X.-Q., Chen, L.-Q., Ma, L., Chermak, D., Zhang, D.-C., Frommer, W. B. Phylogenetic evidence for a fusion of archaeal and bacterial SemiSWEETs to form eukaryotic SWEETs and identification of SWEET hexose transporters in the amphibian chytrid pathogen Batrachochytrium dendrobatidis.}, } @article {pmid27398800, year = {2016}, author = {Slijepcevic, P}, title = {Mechanisms of the Evolutionary Chromosome Plasticity: Integrating the 'Centromere-from-Telomere' Hypothesis with Telomere Length Regulation.}, journal = {Cytogenetic and genome research}, volume = {148}, number = {4}, pages = {268-278}, doi = {10.1159/000447415}, pmid = {27398800}, issn = {1424-859X}, mesh = {Animals ; Centromere/*genetics ; *Evolution, Molecular ; Genomic Instability/*genetics ; Humans ; Karyotype ; *Models, Genetic ; Symbiosis/genetics ; Telomere/*genetics ; *Telomere Homeostasis ; }, abstract = {The 'centromere-from-telomere' hypothesis proposed by Villasante et al. [2007a] aims to explain the evolutionary origin of the eukaryotic chromosome. The hypothesis is based on the notion that the process of eukaryogenesis was initiated by adaptive responses of the symbiont eubacterium and its archaeal host to their new conditions. The adaptive responses included fragmentation of the circular genome of the host into multiple linear fragments with free DNA ends. The action of mobile genetic elements stabilized the free DNA ends resulting in the formation of proto-telomeres. Sequences next to the proto-telomeres, the subtelomeric sequences, were immediately targeted as the new cargo by the tubulin-based cytoskeleton, thus becoming proto-centromeres. A period of genomic instability followed. Eventually, functioning centromeres and telomeres emerged heralding the arrival of the eukaryotic chromosome in the evolution. This paper expands the 'centromere-from-telomere' hypothesis by integrating it with 2 sets of data: chromosome-specific telomere length distribution and chromomere size gradient. The integration adds a new dimension to the hypothesis but also provides an insight into the mechanisms of chromosome plasticity underlying karyotype evolution.}, } @article {pmid27345956, year = {2016}, author = {Garg, SG and Martin, WF}, title = {Mitochondria, the Cell Cycle, and the Origin of Sex via a Syncytial Eukaryote Common Ancestor.}, journal = {Genome biology and evolution}, volume = {8}, number = {6}, pages = {1950-1970}, pmid = {27345956}, issn = {1759-6653}, mesh = {Adenosine Triphosphate/*genetics/metabolism ; Archaea/genetics/physiology ; Biological Evolution ; Cell Cycle/genetics ; Cytosol/physiology ; Eukaryotic Cells/physiology ; *Evolution, Molecular ; Meiosis/genetics ; Mitochondria/*genetics ; Mitosis/genetics ; Prokaryotic Cells/physiology ; Protein Interaction Maps/genetics ; *Recombination, Genetic ; }, abstract = {Theories for the origin of sex traditionally start with an asexual mitosing cell and add recombination, thereby deriving meiosis from mitosis. Though sex was clearly present in the eukaryote common ancestor, the order of events linking the origin of sex and the origin of mitosis is unknown. Here, we present an evolutionary inference for the origin of sex starting with a bacterial ancestor of mitochondria in the cytosol of its archaeal host. We posit that symbiotic association led to the origin of mitochondria and gene transfer to host's genome, generating a nucleus and a dedicated translational compartment, the eukaryotic cytosol, in which-by virtue of mitochondria-metabolic energy was not limiting. Spontaneous protein aggregation (monomer polymerization) and Adenosine Tri-phosphate (ATP)-dependent macromolecular movement in the cytosol thereby became selectable, giving rise to continuous microtubule-dependent chromosome separation (reduction division). We propose that eukaryotic chromosome division arose in a filamentous, syncytial, multinucleated ancestor, in which nuclei with insufficient chromosome numbers could complement each other through mRNA in the cytosol and generate new chromosome combinations through karyogamy. A syncytial (or coenocytic, a synonym) eukaryote ancestor, or Coeca, would account for the observation that the process of eukaryotic chromosome separation is more conserved than the process of eukaryotic cell division. The first progeny of such a syncytial ancestor were likely equivalent to meiospores, released into the environment by the host's vesicle secretion machinery. The natural ability of archaea (the host) to fuse and recombine brought forth reciprocal recombination among fusing (syngamy and karyogamy) progeny-sex-in an ancestrally meiotic cell cycle, from which the simpler haploid and diploid mitotic cell cycles arose. The origin of eukaryotes was the origin of vertical lineage inheritance, and sex was required to keep vertically evolving lineages viable by rescuing the incipient eukaryotic lineage from Muller's ratchet. The origin of mitochondria was, in this view, the decisive incident that precipitated symbiosis-specific cell biological problems, the solutions to which were the salient features that distinguish eukaryotes from prokaryotes: A nuclear membrane, energetically affordable ATP-dependent protein-protein interactions in the cytosol, and a cell cycle involving reduction division and reciprocal recombination (sex).}, } @article {pmid27319280, year = {2016}, author = {Dey, G and Thattai, M and Baum, B}, title = {On the Archaeal Origins of Eukaryotes and the Challenges of Inferring Phenotype from Genotype.}, journal = {Trends in cell biology}, volume = {26}, number = {7}, pages = {476-485}, pmid = {27319280}, issn = {1879-3088}, support = {//Wellcome Trust/United Kingdom ; //Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; Genome ; Genotype ; Phenotype ; Phylogeny ; }, abstract = {If eukaryotes arose through a merger between archaea and bacteria, what did the first true eukaryotic cell look like? A major step toward an answer came with the discovery of Lokiarchaeum, an archaeon whose genome encodes small GTPases related to those used by eukaryotes to regulate membrane traffic. Although 'Loki' cells have yet to be seen, their existence has prompted the suggestion that the archaeal ancestor of eukaryotes engulfed the future mitochondrion by phagocytosis. We propose instead that the archaeal ancestor was a relatively simple cell, and that eukaryotic cellular organization arose as the result of a gradual transfer of bacterial genes and membranes driven by an ever-closer symbiotic partnership between a bacterium and an archaeon.}, } @article {pmid27289097, year = {2016}, author = {Degli Esposti, M}, title = {Late Mitochondrial Acquisition, Really?.}, journal = {Genome biology and evolution}, volume = {8}, number = {6}, pages = {2031-2035}, pmid = {27289097}, issn = {1759-6653}, mesh = {Eukaryota/*genetics ; *Evolution, Molecular ; Mitochondria/*genetics ; Proteobacteria/genetics ; }, abstract = {This article provides a timely critique of a recent Nature paper by Pittis and Gabaldón that has suggested a late origin of mitochondria in eukaryote evolution. It shows that the inferred ancestry of many mitochondrial proteins has been incorrectly assigned by Pittis and Gabaldón to bacteria other than the aerobic proteobacteria from which the ancestor of mitochondria originates, thereby questioning the validity of their suggestion that mitochondrial acquisition may be a late event in eukaryote evolution. The analysis and approach presented here may guide future studies to resolve the true ancestry of mitochondria.}, } @article {pmid27277956, year = {2016}, author = {Markov, AV and Kaznacheev, IS}, title = {Evolutionary consequences of polyploidy in prokaryotes and the origin of mitosis and meiosis.}, journal = {Biology direct}, volume = {11}, number = {}, pages = {28}, pmid = {27277956}, issn = {1745-6150}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Computer Simulation ; *Evolution, Molecular ; *Meiosis ; *Mitosis ; Models, Genetic ; *Polyploidy ; }, abstract = {BACKGROUND: The origin of eukaryote-specific traits such as mitosis and sexual reproduction remains disputable. There is growing evidence that both mitosis and eukaryotic sex (i.e., the alternation of syngamy and meiosis) may have already existed in the basal eukaryotes. The mating system of the halophilic archaeon Haloferax volcanii probably represents an intermediate stage between typical prokaryotic and eukaryotic sex. H. volcanii is highly polyploid, as well as many other Archaea. Here, we use computer simulation to explore genetic and evolutionary outcomes of polyploidy in amitotic prokaryotes and its possible role in the origin of mitosis, meiosis and eukaryotic sex.

RESULTS: Modeling suggests that polyploidy can confer strong short-term evolutionary advantage to amitotic prokaryotes. However, it also promotes the accumulation of recessive deleterious mutations and the risk of extinction in the long term, especially in highly mutagenic environment. There are several possible strategies that amitotic polyploids can use in order to reduce the genetic costs of polyploidy while retaining its benefits. Interestingly, most of these strategies resemble different components or aspects of eukaryotic sex. They include asexual ploidy cycles, equalization of genome copies by gene conversion, high-frequency lateral gene transfer between relatives, chromosome exchange coupled with homologous recombination, and the evolution of more accurate chromosome distribution during cell division (mitosis). Acquisition of mitosis by an amitotic polyploid results in chromosome diversification and specialization. Ultimately, it transforms a polyploid cell into a functionally monoploid one with multiple unique, highly redundant chromosomes. Specialization of chromosomes makes the previously evolved modes of promiscuous chromosome shuffling deleterious. This can result in selective pressure to develop accurate mechanisms of homolog pairing, and, ultimately, meiosis.

CONCLUSION: Emergence of mitosis and the first evolutionary steps towards eukaryotic sex could have taken place in the ancestral polyploid, amitotic proto-eukaryotes, as they were struggling to survive in the highly mutagenic environment of the Early Proterozoic shallow water microbial communities, through the succession of the following stages: (1) acquisition of high-frequency between-individual genetic exchange coupled with homologous recombination; (2) acquisition of mitosis, followed by rapid chromosome diversification and specialization; (3) evolution of homolog synapsis and meiosis. Additional evidence compatible with this scenario includes mass acquisition of new families of paralogous genes by the basal eukaryotes, and recently discovered correlation between polyploidy and the presence of histones in Archaea.

REVIEWER: This article was reviewed by Eugene Koonin, Uri Gophna and Armen Mulkidjanian. For the full reviews, please go to the Reviewers' comments section.}, } @article {pmid27266671, year = {2016}, author = {Radzvilavicius, AL}, title = {Evolutionary dynamics of cytoplasmic segregation and fusion: Mitochondrial mixing facilitated the evolution of sex at the origin of eukaryotes.}, journal = {Journal of theoretical biology}, volume = {404}, number = {}, pages = {160-168}, doi = {10.1016/j.jtbi.2016.05.037}, pmid = {27266671}, issn = {1095-8541}, mesh = {Alleles ; Animals ; *Biological Evolution ; Cell Fusion ; Cell Nucleus/metabolism ; Eukaryota/*metabolism ; Female ; Genetic Fitness ; Male ; Mitochondria/*metabolism ; Models, Biological ; Mutation/genetics ; *Sex Characteristics ; }, abstract = {Sexual reproduction is a trait shared by all complex life, but the complete account of its origin is missing. Virtually all theoretical work on the evolution of sex has been centered around the benefits of reciprocal recombination among nuclear genes, paying little attention to the evolutionary dynamics of multi-copy mitochondrial genomes. Here I develop a mathematical model to study the evolution of nuclear alleles inducing cell fusion in an ancestral population of clonal proto-eukaryotes. Segregational drift maintains high mitochondrial variance between clonally reproducing hosts, but the effect of segregation is opposed by cytoplasmic mixing which tends to reduce variation between cells in favor of higher heterogeneity within the cell. Despite the reduced long-term population fitness, alleles responsible for sexual cell fusion can spread to fixation. The evolution of sex requires negative epistatic interactions between mitochondrial mutations under strong purifying selection, low mutation load and weak mitochondrial-nuclear associations. I argue that similar conditions could have been maintained during the late stages of eukaryogenesis, facilitating the evolution of sexual cell fusion and meiotic recombination without compromising the stability of the emerging complex cell.}, } @article {pmid27259501, year = {2016}, author = {Olejniczak, SA and Łojewska, E and Kowalczyk, T and Sakowicz, T}, title = {Chloroplasts: state of research and practical applications of plastome sequencing.}, journal = {Planta}, volume = {244}, number = {3}, pages = {517-527}, pmid = {27259501}, issn = {1432-2048}, mesh = {Chloroplasts/*genetics ; Gene Expression ; Genetic Engineering ; *Genome, Chloroplast ; Sequence Analysis, DNA ; }, abstract = {This review presents origins, structure and expression of chloroplast genomes. It also describes their sequencing, analysis and modification, focusing on potential practical uses and biggest challenges of chloroplast genome modification. During the evolution of eukaryotes, cyanobacteria are believed to have merged with host heterotrophic cell. Afterward, most of cyanobacterial genes from cyanobacteria were transferred to cell nucleus or lost in the process of endosymbiosis. As a result of these changes, a primary plastid was established. Nowadays, plastid genome (plastome) is almost always circular, has a size of 100-200 kbp (120-160 in land plants), and harbors 100-120 highly conserved unique genes. Plastids have their own gene expression system, which is similar to one of their cyanobacterial ancestors. Two different polymerases, plastid-derived PEP and nucleus-derived NEP, participate in transcription. Translation is similar to the one observed in cyanobacteria, but it also utilizes protein translation factors and positive regulatory mRNA elements absent from bacteria. Plastoms play an important role in genetic transformation. Transgenes are introduced into them either via gene gun (in undamaged tissues) or polyethylene glycol treatment (when protoplasts are targeted). Antibiotic resistance markers are the most common tool used for selection of transformed plants. In recent years, plastome transformation emerged as a promising alternative to nuclear transformation because of (1) high yield of target protein, (2) removing the risk of outcrossing with weeds, (3) lack of silencing mechanisms, and (4) ability to engineer the entire metabolic pathways rather than single gene traits. Currently, the main directions of such research regard: developing efficient enzyme, vaccine antigen, and biopharmaceutical protein production methods in plant cells and improving crops by increasing their resistance to a wide array of biotic and abiotic stresses. Because of that, the detailed knowledge of plastome structure and mechanism of functioning started to play a major role.}, } @article {pmid27189989, year = {2016}, author = {Koreny, L and Field, MC}, title = {Ancient Eukaryotic Origin and Evolutionary Plasticity of Nuclear Lamina.}, journal = {Genome biology and evolution}, volume = {8}, number = {9}, pages = {2663-2671}, pmid = {27189989}, issn = {1759-6653}, support = {//Wellcome Trust/United Kingdom ; 082813//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Dictyosteliida/classification/genetics ; *Evolution, Molecular ; HEK293 Cells ; Humans ; Lamins/chemistry/*genetics ; Nuclear Lamina/*genetics/metabolism ; Phylogeny ; Phytophthora infestans/classification/genetics ; Polymorphism, Genetic ; Protozoan Proteins/chemistry/genetics ; }, abstract = {The emergence of the nucleus was a major event of eukaryogenesis. How the nuclear envelope (NE) arose and acquired functions governing chromatin organization and epigenetic control has direct bearing on origins of developmental/stage-specific expression programs. The configuration of the NE and the associated lamina in the last eukaryotic common ancestor (LECA) is of major significance and can provide insight into activities within the LECA nucleus. Subsequent lamina evolution, alterations, and adaptations inform on the variation and selection of distinct mechanisms that subtend gene expression in distinct taxa. Understanding lamina evolution has been difficult due to the diversity and limited taxonomic distributions of the three currently known highly distinct nuclear lamina. We rigorously searched available sequence data for an expanded view of the distribution of known lamina and lamina-associated proteins. While the lamina proteins of plants and trypanosomes are indeed taxonomically restricted, homologs of metazoan lamins and key lamin-binding proteins have significantly broader distributions, and a lamin gene tree supports vertical evolution from the LECA. Two protist lamins from highly divergent taxa target the nucleus in mammalian cells and polymerize into filamentous structures, suggesting functional conservation of distant lamin homologs. Significantly, a high level of divergence of lamin homologs within certain eukaryotic groups and the apparent absence of lamins and/or the presence of seemingly different lamina proteins in many eukaryotes suggests great evolutionary plasticity in structures at the NE, and hence mechanisms of chromatin tethering and epigenetic gene control.}, } @article {pmid27128953, year = {2016}, author = {Blackstone, NW}, title = {An Evolutionary Framework for Understanding the Origin of Eukaryotes.}, journal = {Biology}, volume = {5}, number = {2}, pages = {}, pmid = {27128953}, issn = {2079-7737}, abstract = {Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real-the endosymbiosis that led to the mitochondrion is often described as "non-Darwinian" because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious-all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes.}, } @article {pmid27034425, year = {2016}, author = {Surkont, J and Pereira-Leal, JB}, title = {Are There Rab GTPases in Archaea?.}, journal = {Molecular biology and evolution}, volume = {33}, number = {7}, pages = {1833-1842}, pmid = {27034425}, issn = {1537-1719}, mesh = {Archaea/*enzymology/genetics/metabolism ; Biological Evolution ; Eukaryotic Cells/metabolism ; Evolution, Molecular ; Guanine Nucleotide Dissociation Inhibitors/genetics/metabolism ; Phylogeny ; Protein Binding ; Protein Transport ; Sequence Analysis, Protein/methods ; rab GTP-Binding Proteins/genetics/*metabolism ; }, abstract = {A complex endomembrane system is one of the hallmarks of Eukaryotes. Vesicle trafficking between compartments is controlled by a diverse protein repertoire, including Rab GTPases. These small GTP-binding proteins contribute identity and specificity to the system, and by working as molecular switches, trigger multiple events in vesicle budding, transport, and fusion. A diverse collection of Rab GTPases already existed in the ancestral Eukaryote, yet, it is unclear how such elaborate repertoire emerged. A novel archaeal phylum, the Lokiarchaeota, revealed that several eukaryotic-like protein systems, including small GTPases, are present in Archaea. Here, we test the hypothesis that the Rab family of small GTPases predates the origin of Eukaryotes. Our bioinformatic pipeline detected multiple putative Rab-like proteins in several archaeal species. Our analyses revealed the presence and strict conservation of sequence features that distinguish eukaryotic Rabs from other small GTPases (Rab family motifs), mapping to the same regions in the structure as in eukaryotic Rabs. These mediate Rab-specific interactions with regulators of the REP/GDI (Rab Escort Protein/GDP dissociation Inhibitor) family. Sensitive structure-based methods further revealed the existence of REP/GDI-like genes in Archaea, involved in isoprenyl metabolism. Our analysis supports a scenario where Rabs differentiated into an independent family in Archaea, interacting with proteins involved in membrane biogenesis. These results further support the archaeal nature of the eukaryotic ancestor and provide a new insight into the intermediate stages and the evolutionary path toward the complex membrane-associated signaling circuits that characterize the Ras superfamily of small GTPases, and specifically Rab proteins.}, } @article {pmid26976593, year = {2016}, author = {Méheust, R and Zelzion, E and Bhattacharya, D and Lopez, P and Bapteste, E}, title = {Protein networks identify novel symbiogenetic genes resulting from plastid endosymbiosis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {13}, pages = {3579-3584}, pmid = {26976593}, issn = {1091-6490}, mesh = {Eukaryota/genetics ; *Evolution, Molecular ; Gene Fusion ; Genome, Plant ; Models, Genetic ; Multigene Family ; Oxidation-Reduction ; Photosynthesis/genetics ; Phylogeny ; Plants/genetics ; Plastids/*genetics ; Proteins/*genetics ; Sequence Homology, Amino Acid ; Symbiosis/*genetics ; }, abstract = {The integration of foreign genetic information is central to the evolution of eukaryotes, as has been demonstrated for the origin of the Calvin cycle and of the heme and carotenoid biosynthesis pathways in algae and plants. For photosynthetic lineages, this coordination involved three genomes of divergent phylogenetic origins (the nucleus, plastid, and mitochondrion). Major hurdles overcome by the ancestor of these lineages were harnessing the oxygen-evolving organelle, optimizing the use of light, and stabilizing the partnership between the plastid endosymbiont and host through retargeting of proteins to the nascent organelle. Here we used protein similarity networks that can disentangle reticulate gene histories to explore how these significant challenges were met. We discovered a previously hidden component of algal and plant nuclear genomes that originated from the plastid endosymbiont: symbiogenetic genes (S genes). These composite proteins, exclusive to photosynthetic eukaryotes, encode a cyanobacterium-derived domain fused to one of cyanobacterial or another prokaryotic origin and have emerged multiple, independent times during evolution. Transcriptome data demonstrate the existence and expression of S genes across a wide swath of algae and plants, and functional data indicate their involvement in tolerance to oxidative stress, phototropism, and adaptation to nitrogen limitation. Our research demonstrates the "recycling" of genetic information by photosynthetic eukaryotes to generate novel composite genes, many of which function in plastid maintenance.}, } @article {pmid26894379, year = {2016}, author = {Forterre, P and Gaïa, M}, title = {Giant viruses and the origin of modern eukaryotes.}, journal = {Current opinion in microbiology}, volume = {31}, number = {}, pages = {44-49}, doi = {10.1016/j.mib.2016.02.001}, pmid = {26894379}, issn = {1879-0364}, mesh = {Archaea/genetics ; Bacteria/genetics ; Cell Nucleus/*genetics ; Eukaryota/*cytology/*genetics ; *Evolution, Molecular ; Giant Viruses/classification/*genetics ; Phylogeny ; }, abstract = {Several authors have suggested that viruses from the NucleoCytoplasmic Large DNA Viruses group (NCLDV) have played an important role in the origin of modern eukaryotes. Notably, the viral eukaryogenesis theory posits that the nucleus originated from an ancient NCLDV-related virus. Focusing on the viral factory instead of the virion adds credit to this hypothesis, but also suggests alternative scenarios. Beside a role in the emergence of the nucleus, ancient NCLDV may have provided new genes and/or chromosomes to the proto-eukaryotic lineage. Phylogenetic analyses suggest that NCLDV informational proteins, related to those of Archaea and Eukarya, were either recruited by ancient NCLDV from proto-eukaryotes and/or transferred to proto-eukaryotes, in agreement with the antiquity of NCLDV and their possible role in eukaryogenesis.}, } @article {pmid26893300, year = {2016}, author = {Klinger, CM and Spang, A and Dacks, JB and Ettema, TJ}, title = {Tracing the Archaeal Origins of Eukaryotic Membrane-Trafficking System Building Blocks.}, journal = {Molecular biology and evolution}, volume = {33}, number = {6}, pages = {1528-1541}, doi = {10.1093/molbev/msw034}, pmid = {26893300}, issn = {1537-1719}, mesh = {Amino Acid Sequence ; Archaea/*genetics/*metabolism ; Biological Evolution ; Eukaryota/*genetics/*metabolism ; Evolution, Molecular ; Genes, Archaeal ; Membrane Transport Proteins/*genetics/*metabolism ; Monomeric GTP-Binding Proteins/genetics/metabolism ; Phylogeny ; Protein Transport ; Sequence Analysis, Protein/methods ; }, abstract = {In contrast to prokaryotes, eukaryotic cells are characterized by a complex set of internal membrane-bound compartments. A subset of these, and the protein machineries that move material between them, define the membrane-trafficking system (MTS), the emergence of which represents a landmark in eukaryotic evolution. Unlike mitochondria and plastids, MTS organelles have autogenous origins. Much of the MTS machinery is composed of building blocks, including small GTPase, coiled-coil, beta-propeller + alpha-solenoid, and longin domains. Despite the identification of prokaryotic proteins containing these domains, only few represent direct orthologues, leaving the origins and early evolution of the MTS poorly understood. Here, we present an in-depth analysis of MTS building block homologues in the composite genome of Lokiarchaeum, the recently discovered archaeal sister clade of eukaryotes, yielding several key insights. We identify two previously unreported Eukaryotic Signature Proteins; orthologues of the Gtr/Rag family GTPases, involved in target of rapamycin complex signaling, and of the RLC7 dynein component. We could not identify golgin or SNARE (coiled-coil) or beta-propeller + alpha-solenoid orthologues, nor typical MTS domain fusions, suggesting that these either were lost from Lokiarchaeum or emerged later in eukaryotic evolution. Furthermore, our phylogenetic analyses of lokiarchaeal GTPases support a split into Ras-like and Arf-like superfamilies, with different prokaryotic antecedents, before the advent of eukaryotes. While no GTPase activating proteins or exchange factors were identified, we show that Lokiarchaeum encodes numerous roadblock domain proteins and putative longin domain proteins, confirming the latter's origin from Archaea. Altogether, our study provides new insights into the emergence and early evolution of the eukaryotic membrane-trafficking system.}, } @article {pmid26840490, year = {2016}, author = {Pittis, AA and Gabaldón, T}, title = {Late acquisition of mitochondria by a host with chimaeric prokaryotic ancestry.}, journal = {Nature}, volume = {531}, number = {7592}, pages = {101-104}, pmid = {26840490}, issn = {1476-4687}, support = {310325/ERC_/European Research Council/International ; }, mesh = {Eukaryotic Cells/*cytology/metabolism ; Genes, Bacterial/*genetics ; Genes, Mitochondrial/*genetics ; Genomics ; Mitochondria/*genetics/metabolism ; Mitochondrial Proteins/genetics/metabolism ; Models, Biological ; *Phylogeny ; Prokaryotic Cells/*cytology/metabolism ; Symbiosis/*genetics ; }, abstract = {The origin of eukaryotes stands as a major conundrum in biology. Current evidence indicates that the last eukaryotic common ancestor already possessed many eukaryotic hallmarks, including a complex subcellular organization. In addition, the lack of evolutionary intermediates challenges the elucidation of the relative order of emergence of eukaryotic traits. Mitochondria are ubiquitous organelles derived from an alphaproteobacterial endosymbiont. Different hypotheses disagree on whether mitochondria were acquired early or late during eukaryogenesis. Similarly, the nature and complexity of the receiving host are debated, with models ranging from a simple prokaryotic host to an already complex proto-eukaryote. Most competing scenarios can be roughly grouped into either mito-early, which consider the driving force of eukaryogenesis to be mitochondrial endosymbiosis into a simple host, or mito-late, which postulate that a significant complexity predated mitochondrial endosymbiosis. Here we provide evidence for late mitochondrial endosymbiosis. We use phylogenomics to directly test whether proto-mitochondrial proteins were acquired earlier or later than other proteins of the last eukaryotic common ancestor. We find that last eukaryotic common ancestor protein families of alphaproteobacterial ancestry and of mitochondrial localization show the shortest phylogenetic distances to their closest prokaryotic relatives, compared with proteins of different prokaryotic origin or cellular localization. Altogether, our results shed new light on a long-standing question and provide compelling support for the late acquisition of mitochondria into a host that already had a proteome of chimaeric phylogenetic origin. We argue that mitochondrial endosymbiosis was one of the ultimate steps in eukaryogenesis and that it provided the definitive selective advantage to mitochondria-bearing eukaryotes over less complex forms.}, } @article {pmid26742849, year = {2016}, author = {Lai, S and Safaei, J and Pelech, S}, title = {Evolutionary Ancestry of Eukaryotic Protein Kinases and Choline Kinases.}, journal = {The Journal of biological chemistry}, volume = {291}, number = {10}, pages = {5199-5205}, pmid = {26742849}, issn = {1083-351X}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Amino Acyl-tRNA Synthetases/chemistry/*genetics ; Animals ; Bacterial Proteins/chemistry/genetics ; Choline Kinase/chemistry/*genetics ; *Consensus Sequence ; *Evolution, Molecular ; Humans ; Molecular Sequence Data ; Protein Kinases/chemistry/*genetics ; Protein Structure, Tertiary ; Sequence Alignment ; }, abstract = {The reversible phosphorylation of proteins catalyzed by protein kinases in eukaryotes supports an important role for eukaryotic protein kinases (ePKs) in the emergence of nucleated cells in the third superkingdom of life. Choline kinases (ChKs) could also be critical in the early evolution of eukaryotes, because of their function in the biosynthesis of phosphatidylcholine, which is unique to eukaryotic membranes. However, the genomic origins of ePKs and ChKs are unclear. The high degeneracy of protein sequences and broad expansion of ePK families have made this fundamental question difficult to answer. In this study, we identified two class-I aminoacyl-tRNA synthetases with high similarities to consensus amino acid sequences of human protein-serine/threonine kinases. Comparisons of primary and tertiary structures supported that ePKs and ChKs evolved from a common ancestor related to glutaminyl aminoacyl-tRNA synthetases, which may have been one of the key factors in the successful of emergence of ancient eukaryotic cells from bacterial colonies.}, } @article {pmid26734499, year = {2015}, author = {Lahr, DJ and Bosak, T and Lara, E and Mitchell, EA}, title = {The Phanerozoic diversification of silica-cycling testate amoebae and its possible links to changes in terrestrial ecosystems.}, journal = {PeerJ}, volume = {3}, number = {}, pages = {e1234}, pmid = {26734499}, issn = {2167-8359}, abstract = {The terrestrial cycling of Si is thought to have a large influence on the terrestrial and marine primary production, as well as the coupled biogeochemical cycles of Si and C. Biomineralization of silica is widespread among terrestrial eukaryotes such as plants, soil diatoms, freshwater sponges, silicifying flagellates and testate amoebae. Two major groups of testate (shelled) amoebae, arcellinids and euglyphids, produce their own silica particles to construct shells. The two are unrelated phylogenetically and acquired biomineralizing capabilities independently. Hyalosphenids, a group within arcellinids, are predators of euglyphids. We demonstrate that hyalosphenids can construct shells using silica scales mineralized by the euglyphids. Parsimony analyses of the current hyalosphenid phylogeny indicate that the ability to "steal" euglyphid scales is most likely ancestral in hyalosphenids, implying that euglyphids should be older than hyalosphenids. However, exactly when euglyphids arose is uncertain. Current fossil record contains unambiguous euglyphid fossils that are as old as 50 million years, but older fossils are scarce and difficult to interpret. Poor taxon sampling of euglyphids has also prevented the development of molecular clocks. Here, we present a novel molecular clock reconstruction for arcellinids and consider the uncertainties due to various previously used calibration points. The new molecular clock puts the origin of hyalosphenids in the early Carboniferous (∼370 mya). Notably, this estimate coincides with the widespread colonization of land by Si-accumulating plants, suggesting possible links between the evolution of Arcellinid testate amoebae and the expansion of terrestrial habitats rich in organic matter and bioavailable Si.}, } @article {pmid26621739, year = {2015}, author = {Casanova, JL}, title = {Human genetic basis of interindividual variability in the course of infection.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {51}, pages = {E7118-27}, pmid = {26621739}, issn = {1091-6490}, mesh = {Animals ; Carrier State ; Ecosystem ; Genetic Predisposition to Disease ; Genetics, Medical ; Humans ; Immunologic Deficiency Syndromes/etiology ; Infections/*genetics/immunology ; Malaria/genetics/prevention & control ; Models, Genetic ; Models, Immunological ; Plants/genetics/microbiology ; Sickle Cell Trait/genetics ; }, abstract = {The key problem in human infectious diseases was posed at the turn of the 20th century: their pathogenesis. For almost any given virus, bacterium, fungus, or parasite, life-threatening clinical disease develops in only a small minority of infected individuals. Solving this infection enigma is important clinically, for diagnosis, prognosis, prevention, and treatment. Some microbes will inevitably remain refractory to, or escape vaccination, or chemotherapy, or both. The solution also is important biologically, because the emergence and evolution of eukaryotes alongside more rapidly evolving prokaryotes, archaea, and viruses posed immunological challenges of an ecological and evolutionary nature. We need to study these challenges in natural, as opposed to experimental, conditions, and also at the molecular and cellular levels. According to the human genetic theory of infectious diseases, inborn variants underlie life-threatening infectious diseases. Here I review the history of the field of human genetics of infectious diseases from the turn of the 19th century to the second half of the 20th century. This paper thus sets the scene, providing the background information required to understand and appreciate the more recently described monogenic forms of resistance or predisposition to specific infections discussed in a second paper in this issue.}, } @article {pmid26577075, year = {2015}, author = {Speijer, D}, title = {Birth of the eukaryotes by a set of reactive innovations: New insights force us to relinquish gradual models.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {37}, number = {12}, pages = {1268-1276}, doi = {10.1002/bies.201500107}, pmid = {26577075}, issn = {1521-1878}, mesh = {Adenosine Triphosphate/metabolism ; Archaea/metabolism ; Eukaryota/*metabolism/*physiology ; Mitochondria/metabolism ; Proteome/metabolism ; Reactive Oxygen Species/metabolism ; }, abstract = {Of two contending models for eukaryotic evolution the "archezoan" has an amitochondriate eukaryote take up an endosymbiont, while "symbiogenesis" states that an Archaeon became a eukaryote as the result of this uptake. If so, organelle formation resulting from new engulfments is simplified by the primordial symbiogenesis, and less informative regarding the bacterium-to-mitochondrion conversion. Gradualist archezoan visions still permeate evolutionary thinking, but are much less likely than symbiogenesis. Genuine amitochondriate eukaryotes have never been found and rapid, explosive adaptive periods characteristic of symbiogenetic models explain this. Mitochondrial proteomes, encoded by genes of "eukaryotic origin" not easily linked to host or endosymbiont, can be understood in light of rapid adjustments to new evolutionary pressures. Symbiogenesis allows "expensive" eukaryotic inventions via efficient ATP generation by nascent mitochondria. However, efficient ATP production equals enhanced toxic internal ROS formation. The synergistic combination of these two driving forces gave rise to the rapid evolution of eukaryotes. Also watch the Video Abstract.}, } @article {pmid26556480, year = {2015}, author = {Kojima, KK and Jurka, J}, title = {Ancient Origin of the U2 Small Nuclear RNA Gene-Targeting Non-LTR Retrotransposons Utopia.}, journal = {PloS one}, volume = {10}, number = {11}, pages = {e0140084}, pmid = {26556480}, issn = {1932-6203}, support = {P41 LM006252/LM/NLM NIH HHS/United States ; P41LM006252/LM/NLM NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; *Biological Evolution ; Eukaryota/*genetics ; Gene Dosage ; Molecular Sequence Data ; Oomycetes/genetics ; Phylogeny ; RNA, Small Nuclear/*genetics ; Retroelements/*genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {Most non-long terminal repeat (non-LTR) retrotransposons encoding a restriction-like endonuclease show target-specific integration into repetitive sequences such as ribosomal RNA genes and microsatellites. However, only a few target-specific lineages of non-LTR retrotransposons are distributed widely and no lineage is found across the eukaryotic kingdoms. Here we report the most widely distributed lineage of target sequence-specific non-LTR retrotransposons, designated Utopia. Utopia is found in three supergroups of eukaryotes: Amoebozoa, SAR, and Opisthokonta. Utopia is inserted into a specific site of U2 small nuclear RNA genes with different strength of specificity for each family. Utopia families from oomycetes and wasps show strong target specificity while only a small number of Utopia copies from reptiles are flanked with U2 snRNA genes. Oomycete Utopia families contain an "archaeal" RNase H domain upstream of reverse transcriptase (RT), which likely originated from a plant RNase H gene. Analysis of Utopia from oomycetes indicates that multiple lineages of Utopia have been maintained inside of U2 genes with few copy numbers. Phylogenetic analysis of RT suggests the monophyly of Utopia, and it likely dates back to the early evolution of eukaryotes.}, } @article {pmid26475454, year = {2015}, author = {Durzyńska, J and Goździcka-Józefiak, A}, title = {Viruses and cells intertwined since the dawn of evolution.}, journal = {Virology journal}, volume = {12}, number = {}, pages = {169}, pmid = {26475454}, issn = {1743-422X}, mesh = {*Biological Evolution ; Eukaryotic Cells/*physiology/*virology ; Viruses/genetics/*growth & development ; }, abstract = {Many attempts have been made to define nature of viruses and to uncover their origin. Our aim within this work was to show that there are different perceptions of viruses and many concepts to explain their emergence: the virus-first concept (also called co-evolution), the escape and the reduction theories. Moreover, a relatively new concept of polyphyletic virus origin called "three RNA cells, three DNA viruses" proposed by Forterre is described herein. In this paper, not only is each thesis supported by a body of evidence but also counter-argued in the light of various findings to give more insightful considerations to the readers. As the origin of viruses and that of living cells are most probably interdependent, we decided to reveal ideas concerning nature of cellular last universal common ancestor (LUCA). Furthermore, we discuss monophyletic ancestry of cellular domains and their relationships at the molecular level of membrane lipids and replication strategies of these three types of cells. In this review, we also present the emergence of DNA viruses requiring an evolutionary transition from RNA to DNA and recently discovered giant DNA viruses possibly involved in eukaryogenesis. In the course of evolution viruses emerged many times. They have always played a key role through horizontal gene transfer in evolutionary events and in formation of the tree of life or netlike routes of evolution providing a great deal of genetic diversity. In our opinion, future findings are crucial to better understand past relations between viruses and cells and the origin of both.}, } @article {pmid26474847, year = {2016}, author = {Mani, J and Meisinger, C and Schneider, A}, title = {Peeping at TOMs-Diverse Entry Gates to Mitochondria Provide Insights into the Evolution of Eukaryotes.}, journal = {Molecular biology and evolution}, volume = {33}, number = {2}, pages = {337-351}, doi = {10.1093/molbev/msv219}, pmid = {26474847}, issn = {1537-1719}, mesh = {*Biological Evolution ; Eukaryota/classification/*genetics ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins/chemistry/*metabolism ; Mitochondrial Proteins/metabolism ; Multigene Family ; Multiprotein Complexes ; Plants/metabolism ; Porins/chemistry/metabolism ; Protein Binding ; Protein Subunits/metabolism ; Protein Transport ; Receptors, Cell Surface/chemistry/metabolism ; Symbiosis ; Trypanosoma/metabolism ; Yeasts/metabolism ; }, abstract = {Mitochondria are essential for eukaryotic life and more than 95% of their proteins are imported as precursors from the cytosol. The targeting signals for this posttranslational import are conserved in all eukaryotes. However, this conservation does not hold true for the protein translocase of the mitochondrial outer membrane that serves as entry gate for essentially all precursor proteins. Only two of its subunits, Tom40 and Tom22, are conserved and thus likely were present in the last eukaryotic common ancestor. Tom7 is found in representatives of all supergroups except the Excavates. This suggests that it was added to the core of the translocase after the Excavates segregated from all other eukaryotes. A comparative analysis of the biochemically and functionally characterized outer membrane translocases of yeast, plants, and trypanosomes, which represent three eukaryotic supergroups, shows that the receptors that recognize the conserved import signals differ strongly between the different systems. They present a remarkable example of convergent evolution at the molecular level. The structural diversity of the functionally conserved import receptors therefore provides insight into the early evolutionary history of mitochondria.}, } @article {pmid26468067, year = {2015}, author = {Radzvilavicius, AL and Blackstone, NW}, title = {Conflict and cooperation in eukaryogenesis: implications for the timing of endosymbiosis and the evolution of sex.}, journal = {Journal of the Royal Society, Interface}, volume = {12}, number = {111}, pages = {20150584}, pmid = {26468067}, issn = {1742-5662}, mesh = {Adenylyl Cyclases/metabolism ; Alleles ; *Biological Evolution ; Calcium/metabolism ; Cytoplasm/metabolism ; Cytosol/metabolism ; Electron Transport ; Eukaryotic Cells/*physiology ; Genome ; Mitochondrial ADP, ATP Translocases/metabolism ; Models, Biological ; Oxidation-Reduction ; Phylogeny ; *Reproduction ; Signal Transduction ; *Symbiosis ; }, abstract = {Roughly 1.5-2.0 Gya, the eukaryotic cell evolved from an endosymbiosis of an archaeal host and proteobacterial symbionts. The timing of this endosymbiosis relative to the evolution of eukaryotic features remains subject to considerable debate, yet the evolutionary process itself constrains the timing of these events. Endosymbiosis entailed levels-of-selection conflicts, and mechanisms of conflict mediation had to evolve for eukaryogenesis to proceed. The initial mechanisms of conflict mediation (e.g. signalling with calcium and soluble adenylyl cyclase, substrate carriers, adenine nucleotide translocase, uncouplers) led to metabolic homeostasis in the eukaryotic cell. Later mechanisms (e.g. mitochondrial gene loss) contributed to the chimeric eukaryotic genome. These integral features of eukaryotes were derived because of, and therefore subsequent to, endosymbiosis. Perhaps the greatest opportunity for conflict arose with the emergence of eukaryotic sex, involving whole-cell fusion. A simple model demonstrates that competition on the lower level severely hinders the evolution of sex. Cytoplasmic mixing, however, is beneficial for non-cooperative endosymbionts, which could have used their aerobic metabolism to manipulate the life history of the host. While early evolution of sex may have facilitated symbiont acquisition, sex would have also destabilized the subsequent endosymbiosis. More plausibly, the evolution of sex and the true nucleus concluded the transition.}, } @article {pmid26455774, year = {2015}, author = {López-García, P and Moreira, D}, title = {Open Questions on the Origin of Eukaryotes.}, journal = {Trends in ecology & evolution}, volume = {30}, number = {11}, pages = {697-708}, pmid = {26455774}, issn = {1872-8383}, support = {322669/ERC_/European Research Council/International ; }, mesh = {Archaea ; *Biological Evolution ; Eukaryota/*classification ; Eukaryotic Cells ; Mitochondria ; *Phylogeny ; Symbiosis ; }, abstract = {Despite recent progress, the origin of the eukaryotic cell remains enigmatic. It is now known that the last eukaryotic common ancestor was complex and that endosymbiosis played a crucial role in eukaryogenesis at least via the acquisition of the alphaproteobacterial ancestor of mitochondria. However, the nature of the mitochondrial host is controversial, although the recent discovery of an archaeal lineage phylogenetically close to eukaryotes reinforces models proposing archaea-derived hosts. We argue that, in addition to improved phylogenomic analyses with more comprehensive taxon sampling to pinpoint the closest prokaryotic relatives of eukaryotes, determining plausible mechanisms and selective forces at the origin of key eukaryotic features, such as the nucleus or the bacterial-like eukaryotic membrane system, is essential to constrain existing models.}, } @article {pmid26437773, year = {2015}, author = {Koonin, EV}, title = {Archaeal ancestors of eukaryotes: not so elusive any more.}, journal = {BMC biology}, volume = {13}, number = {}, pages = {84}, pmid = {26437773}, issn = {1741-7007}, support = {//Intramural NIH HHS/United States ; }, mesh = {Archaea/*genetics ; Biological Evolution ; Eukaryota/classification/*genetics ; *Genome ; Genome, Archaeal ; *Phylogeny ; }, abstract = {The origin of eukaryotes is one of the hardest problems in evolutionary biology and sometimes raises the ominous specter of irreducible complexity. Reconstruction of the gene repertoire of the last eukaryotic common ancestor (LECA) has revealed a highly complex organism with a variety of advanced features but no detectable evolutionary intermediates to explain their origin. Recently, however, genome analysis of diverse archaea led to the discovery of apparent ancestral versions of several signature eukaryotic systems, such as the actin cytoskeleton and the ubiquitin network, that are scattered among archaea. These findings inspired the hypothesis that the archaeal ancestor of eukaryotes was an unusually complex form with an elaborate intracellular organization. The latest striking discovery made by deep metagenomic sequencing vindicates this hypothesis by showing that in phylogenetic trees eukaryotes fall within a newly identified archaeal group, the Lokiarchaeota, which combine several eukaryotic signatures previously identified in different archaea. The discovery of complex archaea that are the closest living relatives of eukaryotes is most compatible with the symbiogenetic scenario for eukaryogenesis.}, } @article {pmid26374538, year = {2015}, author = {Scheid, P}, title = {Viruses in close associations with free-living amoebae.}, journal = {Parasitology research}, volume = {114}, number = {11}, pages = {3959-3967}, pmid = {26374538}, issn = {1432-1955}, mesh = {Amoeba/ultrastructure/*virology ; Biological Evolution ; Cytoplasm/virology ; DNA Viruses/*genetics/ultrastructure ; Genome, Viral/*genetics ; Mimiviridae/genetics ; Phylogeny ; }, abstract = {As both groups of organisms, free-living amoebae (FLA) and viruses, can be found in aquatic environments side by side, it appears obvious that there are multiple interactions with respect to host-endocytobiont relationships. Several relationships between viruses and protozoan hosts are described and it was the discovery of the so called "giant viruses," associated with amoebae, which gave another dimension to these interactions. Mimiviruses, Pandoraviruses and Pithoviruses are examples for interesting viral endocytobionts within FLA. In the Mimivirus viral factories, viral DNA undergoes replication and transcription, and the DNA is prepared to be packed in procapsids. Theses Mimivirus factories can be considered as efficient "production lines" where, at any given moment, all stages of viral generation including membrane biogenesis, capsid assembly and genome encapsidation, are occurring concomitantly. There are some hints that similar replication factories are involved as well during the Pandoravirus development. Some scientists favour the assumption that the giant viruses have received many of their genes from their hosts or from sympatric occurring endocytobionts via lateral gene transfer. This hypothesis would mean that this type of transfer has been an important process in the evolution of genomes in the context of the intracellular parasitic or endocytobiotic lifestyle. In turn, that would migitate against hypothesizing development of a new branch in the tree of life. Based on the described scenarios to explain the presence of genes related to translation, it is also possible that earlier ancestors of today's DNA viruses were involved in the origin of eukaryotes. That possibly could in turn support the idea that cellular organisms could have evolved from viruses with growing autarkic properties. In future we expect the discovery of further (giant) viruses within free-living amoebae and other protozoa through genomic, transcriptomic and proteomic analyses.}, } @article {pmid26323767, year = {2015}, author = {Akanni, WA and Siu-Ting, K and Creevey, CJ and McInerney, JO and Wilkinson, M and Foster, PG and Pisani, D}, title = {Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1678}, pages = {20140337}, pmid = {26323767}, issn = {1471-2970}, support = {BB/G024707/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/K007440//BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/*genetics ; *Biological Evolution ; *Gene Flow ; Genome, Bacterial ; Models, Genetic ; }, abstract = {The origin of the eukaryotic cell is considered one of the major evolutionary transitions in the history of life. Current evidence strongly supports a scenario of eukaryotic origin in which two prokaryotes, an archaebacterial host and an α-proteobacterium (the free-living ancestor of the mitochondrion), entered a stable symbiotic relationship. The establishment of this relationship was associated with a process of chimerization, whereby a large number of genes from the α-proteobacterial symbiont were transferred to the host nucleus. A general framework allowing the conceptualization of eukaryogenesis from a genomic perspective has long been lacking. Recent studies suggest that the origins of several archaebacterial phyla were coincident with massive imports of eubacterial genes. Although this does not indicate that these phyla originated through the same process that led to the origin of Eukaryota, it suggests that Archaebacteria might have had a general propensity to integrate into their genomes large amounts of eubacterial DNA. We suggest that this propensity provides a framework in which eukaryogenesis can be understood and studied in the light of archaebacterial ecology. We applied a recently developed supertree method to a genomic dataset composed of 392 eubacterial and 51 archaebacterial genera to test whether large numbers of genes flowing from Eubacteria are indeed coincident with the origin of major archaebacterial clades. In addition, we identified two potential large-scale transfers of uncertain directionality at the base of the archaebacterial tree. Our results are consistent with previous findings and seem to indicate that eubacterial gene imports (particularly from δ-Proteobacteria, Clostridia and Actinobacteria) were an important factor in archaebacterial history. Archaebacteria seem to have long relied on Eubacteria as a source of genetic diversity, and while the precise mechanism that allowed these imports is unknown, we suggest that our results support the view that processes comparable to those through which eukaryotes emerged might have been common in archaebacterial history.}, } @article {pmid26323764, year = {2015}, author = {Koonin, EV}, title = {Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier?.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1678}, pages = {20140333}, pmid = {26323764}, issn = {1471-2970}, mesh = {Archaea/*genetics ; *Biological Evolution ; Eukaryota/genetics ; *Eukaryotic Cells ; *Genome, Archaeal ; }, abstract = {The origin of eukaryotes is a fundamental, forbidding evolutionary puzzle. Comparative genomic analysis clearly shows that the last eukaryotic common ancestor (LECA) possessed most of the signature complex features of modern eukaryotic cells, in particular the mitochondria, the endomembrane system including the nucleus, an advanced cytoskeleton and the ubiquitin network. Numerous duplications of ancestral genes, e.g. DNA polymerases, RNA polymerases and proteasome subunits, also can be traced back to the LECA. Thus, the LECA was not a primitive organism and its emergence must have resulted from extensive evolution towards cellular complexity. However, the scenario of eukaryogenesis, and in particular the relationship between endosymbiosis and the origin of eukaryotes, is far from being clear. Four recent developments provide new clues to the likely routes of eukaryogenesis. First, evolutionary reconstructions suggest complex ancestors for most of the major groups of archaea, with the subsequent evolution dominated by gene loss. Second, homologues of signature eukaryotic proteins, such as actin and tubulin that form the core of the cytoskeleton or the ubiquitin system, have been detected in diverse archaea. The discovery of this 'dispersed eukaryome' implies that the archaeal ancestor of eukaryotes was a complex cell that might have been capable of a primitive form of phagocytosis and thus conducive to endosymbiont capture. Third, phylogenomic analyses converge on the origin of most eukaryotic genes of archaeal descent from within the archaeal evolutionary tree, specifically, the TACK superphylum. Fourth, evidence has been presented that the origin of the major archaeal phyla involved massive acquisition of bacterial genes. Taken together, these findings make the symbiogenetic scenario for the origin of eukaryotes considerably more plausible and the origin of the organizational complexity of eukaryotic cells more readily explainable than they appeared until recently.}, } @article {pmid26323761, year = {2015}, author = {Martin, WF and Garg, S and Zimorski, V}, title = {Endosymbiotic theories for eukaryote origin.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1678}, pages = {20140330}, pmid = {26323761}, issn = {1471-2970}, mesh = {*Biological Evolution ; Eukaryotic Cells/*classification/*cytology ; Organelles/genetics/physiology ; Symbiosis/*genetics/*physiology ; }, abstract = {For over 100 years, endosymbiotic theories have figured in thoughts about the differences between prokaryotic and eukaryotic cells. More than 20 different versions of endosymbiotic theory have been presented in the literature to explain the origin of eukaryotes and their mitochondria. Very few of those models account for eukaryotic anaerobes. The role of energy and the energetic constraints that prokaryotic cell organization placed on evolutionary innovation in cell history has recently come to bear on endosymbiotic theory. Only cells that possessed mitochondria had the bioenergetic means to attain eukaryotic cell complexity, which is why there are no true intermediates in the prokaryote-to-eukaryote transition. Current versions of endosymbiotic theory have it that the host was an archaeon (an archaebacterium), not a eukaryote. Hence the evolutionary history and biology of archaea increasingly comes to bear on eukaryotic origins, more than ever before. Here, we have compiled a survey of endosymbiotic theories for the origin of eukaryotes and mitochondria, and for the origin of the eukaryotic nucleus, summarizing the essentials of each and contrasting some of their predictions to the observations. A new aspect of endosymbiosis in eukaryote evolution comes into focus from these considerations: the host for the origin of plastids was a facultative anaerobe.}, } @article {pmid26323760, year = {2015}, author = {Gouy, R and Baurain, D and Philippe, H}, title = {Rooting the tree of life: the phylogenetic jury is still out.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1678}, pages = {20140329}, pmid = {26323760}, issn = {1471-2970}, mesh = {Animals ; Eukaryotic Cells/*classification/cytology ; Models, Genetic ; *Phylogeny ; Prokaryotic Cells/*classification/cytology ; }, abstract = {This article aims to shed light on difficulties in rooting the tree of life (ToL) and to explore the (sociological) reasons underlying the limited interest in accurately addressing this fundamental issue. First, we briefly review the difficulties plaguing phylogenetic inference and the ways to improve the modelling of the substitution process, which is highly heterogeneous, both across sites and over time. We further observe that enriched taxon samplings, better gene samplings and clever data removal strategies have led to numerous revisions of the ToL, and that these improved shallow phylogenies nearly always relocate simple organisms higher in the ToL provided that long-branch attraction artefacts are kept at bay. Then, we note that, despite the flood of genomic data available since 2000, there has been a surprisingly low interest in inferring the root of the ToL. Furthermore, the rare studies dealing with this question were almost always based on methods dating from the 1990s that have been shown to be inaccurate for much more shallow issues! This leads us to argue that the current consensus about a bacterial root for the ToL can be traced back to the prejudice of Aristotle's Great Chain of Beings, in which simple organisms are ancestors of more complex life forms. Finally, we demonstrate that even the best models cannot yet handle the complexity of the evolutionary process encountered both at shallow depth, when the outgroup is too distant, and at the level of the inter-domain relationships. Altogether, we conclude that the commonly accepted bacterial root is still unproven and that the root of the ToL should be revisited using phylogenomic supermatrices to ensure that new evidence for eukaryogenesis, such as the recently described Lokiarcheota, is interpreted in a sound phylogenetic framework.}, } @article {pmid26323759, year = {2015}, author = {Saw, JH and Spang, A and Zaremba-Niedzwiedzka, K and Juzokaite, L and Dodsworth, JA and Murugapiran, SK and Colman, DR and Takacs-Vesbach, C and Hedlund, BP and Guy, L and Ettema, TJ}, title = {Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1678}, pages = {20140328}, pmid = {26323759}, issn = {1471-2970}, support = {310039/ERC_/European Research Council/International ; }, mesh = {Archaea/classification/*genetics ; Eukaryotic Cells/*classification/*cytology ; Gene Expression Regulation, Archaeal/physiology ; Genetic Variation ; Genome, Archaeal ; Metagenomics/*methods ; *Phylogeny ; RNA, Archaeal/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The origin of eukaryotes represents an enigmatic puzzle, which is still lacking a number of essential pieces. Whereas it is currently accepted that the process of eukaryogenesis involved an interplay between a host cell and an alphaproteobacterial endosymbiont, we currently lack detailed information regarding the identity and nature of these players. A number of studies have provided increasing support for the emergence of the eukaryotic host cell from within the archaeal domain of life, displaying a specific affiliation with the archaeal TACK superphylum. Recent studies have shown that genomic exploration of yet-uncultivated archaea, the so-called archaeal 'dark matter', is able to provide unprecedented insights into the process of eukaryogenesis. Here, we provide an overview of state-of-the-art cultivation-independent approaches, and demonstrate how these methods were used to obtain draft genome sequences of several novel members of the TACK superphylum, including Lokiarchaeum, two representatives of the Miscellaneous Crenarchaeotal Group (Bathyarchaeota), and a Korarchaeum-related lineage. The maturation of cultivation-independent genomics approaches, as well as future developments in next-generation sequencing technologies, will revolutionize our current view of microbial evolution and diversity, and provide profound new insights into the early evolution of life, including the enigmatic origin of the eukaryotic cell.}, } @article {pmid26323758, year = {2015}, author = {Moreira, D and López-García, P}, title = {Evolution of viruses and cells: do we need a fourth domain of life to explain the origin of eukaryotes?.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1678}, pages = {20140327}, pmid = {26323758}, issn = {1471-2970}, support = {322669/ERC_/European Research Council/International ; }, mesh = {*Biological Evolution ; Eukaryotic Cells/*classification/*cytology ; Gene Transfer, Horizontal ; Genome, Viral ; Viruses/*classification/*genetics ; }, abstract = {The recent discovery of diverse very large viruses, such as the mimivirus, has fostered a profusion of hypotheses positing that these viruses define a new domain of life together with the three cellular ones (Archaea, Bacteria and Eucarya). It has also been speculated that they have played a key role in the origin of eukaryotes as donors of important genes or even as the structures at the origin of the nucleus. Thanks to the increasing availability of genome sequences for these giant viruses, those hypotheses are amenable to testing via comparative genomic and phylogenetic analyses. This task is made very difficult by the high evolutionary rate of viruses, which induces phylogenetic artefacts, such as long branch attraction, when inadequate methods are applied. It can be demonstrated that phylogenetic trees supporting viruses as a fourth domain of life are artefactual. In most cases, the presence of homologues of cellular genes in viruses is best explained by recurrent horizontal gene transfer from cellular hosts to their infecting viruses and not the opposite. Today, there is no solid evidence for the existence of a viral domain of life or for a significant implication of viruses in the origin of the cellular domains.}, } @article {pmid26323755, year = {2015}, author = {McInerney, J and Pisani, D and O'Connell, MJ}, title = {The ring of life hypothesis for eukaryote origins is supported by multiple kinds of data.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1678}, pages = {20140323}, pmid = {26323755}, issn = {1471-2970}, mesh = {Archaea/genetics ; Bacteria/genetics ; *Eukaryotic Cells ; *Evolution, Molecular ; *Phylogeny ; }, abstract = {The literature is replete with manuscripts describing the origin of eukaryotic cells. Most of the models for eukaryogenesis are either autogenous (sometimes called slow-drip), or symbiogenic (sometimes called big-bang). In this article, we use large and diverse suites of 'Omics' and other data to make the inference that autogeneous hypotheses are a very poor fit to the data and the origin of eukaryotic cells occurred in a single symbiosis.}, } @article {pmid26299945, year = {2015}, author = {Jadhav, B and Wild, K and Pool, MR and Sinning, I}, title = {Structure and Switch Cycle of SRβ as Ancestral Eukaryotic GTPase Associated with Secretory Membranes.}, journal = {Structure (London, England : 1993)}, volume = {23}, number = {10}, pages = {1838-1847}, doi = {10.1016/j.str.2015.07.010}, pmid = {26299945}, issn = {1878-4186}, mesh = {ADP-Ribosylation Factors/chemistry/genetics/metabolism ; Amino Acid Sequence ; Binding Sites ; Biological Evolution ; Chaetomium/genetics/*metabolism ; Crystallography, X-Ray ; Endoplasmic Reticulum/chemistry/*metabolism ; Escherichia coli/genetics/metabolism ; Fungal Proteins/*chemistry/genetics/metabolism ; Gene Expression ; Guanosine Diphosphate/chemistry/metabolism ; Guanosine Triphosphate/chemistry/metabolism ; Intracellular Membranes/chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Binding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/*chemistry/genetics/metabolism ; Recombinant Proteins/chemistry/genetics/metabolism ; Ribosomes/chemistry/metabolism ; Sequence Alignment ; Signal Recognition Particle/*chemistry/genetics/metabolism ; Vesicular Transport Proteins/chemistry/genetics/metabolism ; }, abstract = {G proteins of the Ras-family of small GTPases trace the evolution of eukaryotes. The earliest branching involves the closely related Arf, Sar1, and SRβ GTPases associated with secretory membranes. SRβ is an integral membrane component of the signal recognition particle (SRP) receptor that targets ribosome-nascent chain complexes to the ER. How SRβ integrates into the regulation of SRP-dependent membrane protein biogenesis is not known. Here we show that SRβ-GTP interacts with ribosomes only in presence of SRα and present crystal structures of SRβ in complex with the SRX domain of SRα in the GTP-bound state at 3.2 Å, and of GDP- and GDP · Mg(2+)-bound SRβ at 1.9 Å and 2.4 Å, respectively. We define the GTPase switch cycle of SRβ and identify specific differences to the Arf and Sar1 families with implications for GTPase regulation. Our data allow a better integration of SRβ into the scheme of protein targeting.}, } @article {pmid26299654, year = {2016}, author = {Tangphatsornruang, S and Ruang-Areerate, P and Sangsrakru, D and Rujirawat, T and Lohnoo, T and Kittichotirat, W and Patumcharoenpol, P and Grenville-Briggs, LJ and Krajaejun, T}, title = {Comparative mitochondrial genome analysis of Pythium insidiosum and related oomycete species provides new insights into genetic variation and phylogenetic relationships.}, journal = {Gene}, volume = {575}, number = {1}, pages = {34-41}, doi = {10.1016/j.gene.2015.08.036}, pmid = {26299654}, issn = {1879-0038}, mesh = {*Evolution, Molecular ; *Genetic Variation ; *Genome, Mitochondrial ; *Phylogeny ; Pythium/*genetics ; }, abstract = {Oomycetes are eukaryotic microorganisms, which are phylogenetically distinct from the true-fungi, which they resemble morphologically. While many oomycetes are pathogenic to plants, Pythium insidiosum is capable of infecting humans and animals. Mitochondrial (mt) genomes are valuable genetic resources for exploring the evolution of eukaryotes. During the course of 454-based nuclear genome sequencing, we identified a complete 54.9 kb mt genome sequence, containing 2 large inverted repeats, from P. insidiosum. It contains 65 different genes (including 2 ribosomal RNA genes, 25 transfer RNA genes and 38 genes encoding NADH dehydrogenases, cytochrome b, cytochrome c oxidases, ATP synthases, and ribosomal proteins). Thirty-nine of the 65 genes have two copies, giving a total of 104 genes. A set of 30 conserved protein-coding genes from the mt genomes of P. insidiosum, 11 other oomycetes, and 2 diatoms (outgroup) were used for phylogenetic analyses. The oomycetes can be classified into 2 phylogenetic groups, in relation to their taxonomic lineages: Saprolegnialean and Peronosporalean. P. insidiosum is more closely related to Pythium ultimum than other oomycetes. In conclusion, the complete mt genome of P. insidiosum was successfully sequenced, assembled, and annotated, providing a useful genetic resource for exploring the biology and evolution of P. insidiosum and other oomycetes.}, } @article {pmid26234735, year = {2015}, author = {Kurland, CG and Harish, A}, title = {The phylogenomics of protein structures: The backstory.}, journal = {Biochimie}, volume = {119}, number = {}, pages = {284-302}, doi = {10.1016/j.biochi.2015.07.027}, pmid = {26234735}, issn = {1638-6183}, mesh = {Amino Acid Sequence ; Animals ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome ; Humans ; *Models, Genetic ; Mutation ; *Phylogeny ; Protein Conformation ; Protein Isoforms/chemistry/genetics/metabolism ; Protein Structure, Tertiary ; Proteome/*chemistry/genetics/metabolism ; }, abstract = {In this introductory retrospective, evolution as viewed through gene trees is inspected through a lens compounded from its founding operational assumptions. The four assumptions of the gene tree culture that are singularly important to evolutionary interpretations are: a. that protein-coding sequences are molecular fossils; b. that gene trees are equivalent to species trees; c. that the tree of life is assumed to be rooted in a simple akaryote cell implying that akaryotes are primitive, and d. that the notion that all or most incongruities between alignment-based gene trees are due to horizontal gene transfer (HGT), which includes the endosymbiotic models postulated for the origins of eukaryotes. What has been unusual about these particular assumptions is that though each was taken on board explicitly, they are defended in the face of factual challenge by a stolid disregard for the conflicting observations. The factual challenges to the mainstream gene tree-inspired evolutionary view are numerous and most convincingly summarized as: Genome trees tell a very different story. Phylogeny inferred from genomic assortments of homologous protein structural-domains does not support any one of the four principle evolutionary interpretations of gene trees: a. 3D protein domain structures are the molecular fossils of evolution, while coding sequences are transients; b. Species trees are very different from gene trees; c. The ToL is rooted in a surprisingly complex universal common ancestor (UCA) that is distinct from any specific modern descendant and d. HGT including endosymbiosis is a negligible player in genome evolution from UCA to the present.}, } @article {pmid26213149, year = {2015}, author = {Goncearenco, A and Shaytan, AK and Shoemaker, BA and Panchenko, AR}, title = {Structural Perspectives on the Evolutionary Expansion of Unique Protein-Protein Binding Sites.}, journal = {Biophysical journal}, volume = {109}, number = {6}, pages = {1295-1306}, pmid = {26213149}, issn = {1542-0086}, support = {//Intramural NIH HHS/United States ; }, mesh = {Animals ; Binding Sites/*genetics ; *Evolution, Molecular ; Humans ; Models, Molecular ; Protein Binding/*genetics ; Proteins/*genetics/*metabolism ; }, abstract = {Structures of protein complexes provide atomistic insights into protein interactions. Human proteins represent a quarter of all structures in the Protein Data Bank; however, available protein complexes cover less than 10% of the human proteome. Although it is theoretically possible to infer interactions in human proteins based on structures of homologous protein complexes, it is still unclear to what extent protein interactions and binding sites are conserved, and whether protein complexes from remotely related species can be used to infer interactions and binding sites. We considered biological units of protein complexes and clustered protein-protein binding sites into similarity groups based on their structure and sequence, which allowed us to identify unique binding sites. We showed that the growth rate of the number of unique binding sites in the Protein Data Bank was much slower than the growth rate of the number of structural complexes. Next, we investigated the evolutionary roots of unique binding sites and identified the major phyletic branches with the largest expansion in the number of novel binding sites. We found that many binding sites could be traced to the universal common ancestor of all cellular organisms, whereas relatively few binding sites emerged at the major evolutionary branching points. We analyzed the physicochemical properties of unique binding sites and found that the most ancient sites were the largest in size, involved many salt bridges, and were the most compact and least planar. In contrast, binding sites that appeared more recently in the evolution of eukaryotes were characterized by a larger fraction of polar and aromatic residues, and were less compact and more planar, possibly due to their more transient nature and roles in signaling processes.}, } @article {pmid26112912, year = {2015}, author = {Nasir, A and Kim, KM and Caetano-Anollés, G}, title = {Lokiarchaeota: eukaryote-like missing links from microbial dark matter?.}, journal = {Trends in microbiology}, volume = {23}, number = {8}, pages = {448-450}, doi = {10.1016/j.tim.2015.06.001}, pmid = {26112912}, issn = {1878-4380}, mesh = {Archaea/classification/*genetics ; *Evolution, Molecular ; *Genome, Archaeal ; }, abstract = {Identification and genome sequencing of novel organismal groups can reduce the gap between the sequenced minority and the unexplored majority. The recent discovery of phylum Lokiarchaeota promises understanding of biological history. Here we inquire if Lokiarchaeota truly represent ancient eukaryotic ancestors or just microbial dark matter of expanding archaeal diversity.}, } @article {pmid26104693, year = {2015}, author = {Poulter, RTM and Butler, MI}, title = {Tyrosine Recombinase Retrotransposons and Transposons.}, journal = {Microbiology spectrum}, volume = {3}, number = {2}, pages = {MDNA3-0036-2014}, doi = {10.1128/microbiolspec.MDNA3-0036-2014}, pmid = {26104693}, issn = {2165-0497}, mesh = {DNA Replication ; Eukaryota/*genetics ; Evolution, Molecular ; Genetic Variation ; Phylogeny ; Recombinases/*metabolism ; Recombination, Genetic ; *Retroelements ; }, abstract = {Retrotransposons carrying tyrosine recombinases (YR) are widespread in eukaryotes. The first described tyrosine recombinase mobile element, DIRS1, is a retroelement from the slime mold Dictyostelium discoideum. The YR elements are bordered by terminal repeats related to their replication via free circular dsDNA intermediates. Site-specific recombination is believed to integrate the circle without creating duplications of the target sites. Recently a large number of YR retrotransposons have been described, including elements from fungi (mucorales and basidiomycetes), plants (green algae) and a wide range of animals including nematodes, insects, sea urchins, fish, amphibia and reptiles. YR retrotransposons can be divided into three major groups: the DIRS elements, PAT-like and the Ngaro elements. The three groups form distinct clades on phylogenetic trees based on alignments of reverse transcriptase/ribonuclease H (RT/RH) and YR sequences, and also having some structural distinctions. A group of eukaryote DNA transposons, cryptons, also carry tyrosine recombinases. These DNA transposons do not encode a reverse transcriptase. They have been detected in several pathogenic fungi and oomycetes. Sequence comparisons suggest that the crypton YRs are related to those of the YR retrotransposons. We suggest that the YR retrotransposons arose from the combination of a crypton-like YR DNA transposon and the RT/RH encoding sequence of a retrotransposon. This acquisition must have occurred at a very early point in the evolution of eukaryotes.}, } @article {pmid26099175, year = {2015}, author = {Lill, R and Dutkiewicz, R and Freibert, SA and Heidenreich, T and Mascarenhas, J and Netz, DJ and Paul, VD and Pierik, AJ and Richter, N and Stümpfig, M and Srinivasan, V and Stehling, O and Mühlenhoff, U}, title = {The role of mitochondria and the CIA machinery in the maturation of cytosolic and nuclear iron-sulfur proteins.}, journal = {European journal of cell biology}, volume = {94}, number = {7-9}, pages = {280-291}, doi = {10.1016/j.ejcb.2015.05.002}, pmid = {26099175}, issn = {1618-1298}, mesh = {ATP-Binding Cassette Transporters/*metabolism ; Cell Nucleus/metabolism ; Cytosol/*metabolism ; Humans ; Iron-Sulfur Proteins/*metabolism ; Membrane Transport Proteins/metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/*metabolism ; Protein Transport/physiology ; }, abstract = {Mitochondria have been derived from alpha-bacterial endosymbionts during the evolution of eukaryotes. Numerous bacterial functions have been maintained inside the organelles including fatty acid degradation, citric acid cycle, oxidative phosphorylation, and the synthesis of heme or lipoic acid cofactors. Additionally, mitochondria have inherited the bacterial iron-sulfur cluster assembly (ISC) machinery. Many of the ISC components are essential for cell viability because they generate a still unknown, sulfur-containing compound for the assembly of cytosolic and nuclear Fe/S proteins that perform important functions in, e.g., protein translation, DNA synthesis and repair, and chromosome segregation. The sulfur-containing compound is exported by the mitochondrial ABC transporter Atm1 (human ABCB7) and utilized by components of the cytosolic iron-sulfur protein assembly (CIA) machinery. An appealing minimal model for the striking compartmentation of eukaryotic Fe/S protein biogenesis is provided by organisms that contain mitosomes instead of mitochondria. Mitosomes have been derived from mitochondria by reductive evolution, during which they have lost virtually all classical mitochondrial tasks. Nevertheless, mitosomes harbor all core ISC components which presumably have been maintained for assisting the maturation of cytosolic-nuclear Fe/S proteins. The current review is centered around the Atm1 export process. We present an overview on the mitochondrial requirements for the export reaction, summarize recent insights into the 3D structure and potential mechanism of Atm1, and explain how the CIA machinery uses the mitochondrial export product for the assembly of cytosolic and nuclear Fe/S proteins.}, } @article {pmid25976611, year = {2015}, author = {Burroughs, AM and Zhang, D and Aravind, L}, title = {The eukaryotic translation initiation regulator CDC123 defines a divergent clade of ATP-grasp enzymes with a predicted role in novel protein modifications.}, journal = {Biology direct}, volume = {10}, number = {}, pages = {21}, pmid = {25976611}, issn = {1745-6150}, support = {//Intramural NIH HHS/United States ; }, mesh = {Adenosine Triphosphate/*chemistry ; Algorithms ; Amino Acid Sequence ; Bacterial Proteins/genetics ; Cell Cycle Proteins/*genetics ; Computational Biology ; DNA Viruses/genetics ; Eukaryotic Initiation Factor-2/metabolism ; Evolution, Molecular ; Lysine/chemistry ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; Saccharomyces cerevisiae Proteins/*genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Viral Proteins/genetics ; }, abstract = {Deciphering the origin of uniquely eukaryotic features of sub-cellular systems, such as the translation apparatus, is critical in reconstructing eukaryogenesis. One such feature is the highly conserved, but poorly understood, eukaryotic protein CDC123, which regulates the abundance of the eukaryotic translation initiation eIF2 complex and binds one of its components eIF2γ. We show that the eukaryotic protein CDC123 defines a novel clade of ATP-grasp enzymes distinguished from all other members of the superfamily by a RAGNYA domain with two conserved lysines (henceforth the R2K clade). Combining the available biochemical and genetic data on CDC123 with the inferred enzymatic function, we propose that the eukaryotic CDC123 proteins are likely to function as ATP-dependent protein-peptide ligases which modify proteins by ribosome-independent addition of an oligopeptide tag. We also show that the CDC123 family emerged first in bacteria where it appears to have diversified along with the two other families of the R2K clade. The bacterial CDC123 family members are of two distinct types, one found as part of type VI secretion systems which deliver polymorphic toxins and the other functioning as potential effectors delivered to amoeboid eukaryotic hosts. Representatives of the latter type have also been independently transferred to phylogenetically unrelated amoeboid eukaryotes and their nucleo-cytoplasmic large DNA viruses. Similarly, the two other prokaryotic R2K clade families are also proposed to participate in biological conflicts between bacteriophages and their hosts. These findings add further evidence to the recently proposed hypothesis that the horizontal transfer of enzymatic effectors from the bacterial endosymbionts of the stem eukaryotes played a fundamental role in the emergence of the characteristically eukaryotic regulatory systems and sub-cellular structures.}, } @article {pmid25888113, year = {2015}, author = {Hooper, SL and Burstein, HJ}, title = {Erratum to: Minimization of extracellular space as a driving force in prokaryote association and the origin of eukaryotes.}, journal = {Biology direct}, volume = {10}, number = {}, pages = {11}, pmid = {25888113}, issn = {1745-6150}, abstract = {Following the publication of this article [1] it was noticed that, due to an error on the part of the publisher, the 2nd round of comments submitted by Reviewer 1, Dr. López-García, were unintentionally omitted during the peer review process. As a consequence of this error, the authors were unable to reply to Dr. López-García's comments and subsequently revise their manuscript accordingly (where appropriate).In fairness to both the authors and reviewer, Dr. López-García's (Reviewer 1) 2nd round of comments are now included below and Scott L Hooper and Helaine J Burstein (author) were given the opportunity to reply. Any consequent amendments to the research article [1] are outlined in the author's replies.}, } @article {pmid25883268, year = {2015}, author = {O'Malley, MA}, title = {Endosymbiosis and its implications for evolutionary theory.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {33}, pages = {10270-10277}, pmid = {25883268}, issn = {1091-6490}, mesh = {Animals ; Bacteria ; *Biological Evolution ; Environment ; Evolution, Molecular ; Genetics, Population ; Models, Theoretical ; Mutation ; Origin of Life ; Phenotype ; Phylogeny ; Plants ; Symbiosis/*physiology ; }, abstract = {Historically, conceptualizations of symbiosis and endosymbiosis have been pitted against Darwinian or neo-Darwinian evolutionary theory. In more recent times, Lynn Margulis has argued vigorously along these lines. However, there are only shallow grounds for finding Darwinian concepts or population genetic theory incompatible with endosymbiosis. But is population genetics sufficiently explanatory of endosymbiosis and its role in evolution? Population genetics "follows" genes, is replication-centric, and is concerned with vertically consistent genetic lineages. It may also have explanatory limitations with regard to macroevolution. Even so, asking whether population genetics explains endosymbiosis may have the question the wrong way around. We should instead be asking how explanatory of evolution endosymbiosis is, and exactly which features of evolution it might be explaining. This paper will discuss how metabolic innovations associated with endosymbioses can drive evolution and thus provide an explanatory account of important episodes in the history of life. Metabolic explanations are both proximate and ultimate, in the same way genetic explanations are. Endosymbioses, therefore, point evolutionary biology toward an important dimension of evolutionary explanation.}, } @article {pmid25883267, year = {2015}, author = {Booth, A and Doolittle, WF}, title = {Eukaryogenesis, how special really?.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {33}, pages = {10278-10285}, pmid = {25883267}, issn = {1091-6490}, mesh = {Animals ; *Biological Evolution ; Energy Metabolism ; Escherichia coli/metabolism ; Eukaryota/*metabolism ; Eukaryotic Cells/cytology ; Evolution, Molecular ; Genome, Bacterial ; Humans ; Introns ; Mitochondria/metabolism/physiology ; *Origin of Life ; Phenotype ; Phylogeny ; Plants ; Prokaryotic Cells/cytology ; Spliceosomes/physiology ; }, abstract = {Eukaryogenesis is widely viewed as an improbable evolutionary transition uniquely affecting the evolution of life on this planet. However, scientific and popular rhetoric extolling this event as a singularity lacks rigorous evidential and statistical support. Here, we question several of the usual claims about the specialness of eukaryogenesis, focusing on both eukaryogenesis as a process and its outcome, the eukaryotic cell. We argue in favor of four ideas. First, the criteria by which we judge eukaryogenesis to have required a genuinely unlikely series of events 2 billion years in the making are being eroded by discoveries that fill in the gaps of the prokaryote:eukaryote "discontinuity." Second, eukaryogenesis confronts evolutionary theory in ways not different from other evolutionary transitions in individuality; parallel systems can be found at several hierarchical levels. Third, identifying which of several complex cellular features confer on eukaryotes a putative richer evolutionary potential remains an area of speculation: various keys to success have been proposed and rejected over the five-decade history of research in this area. Fourth, and perhaps most importantly, it is difficult and may be impossible to eliminate eukaryocentric bias from the measures by which eukaryotes as a whole are judged to have achieved greater success than prokaryotes as a whole. Overall, we question whether premises of existing theories about the uniqueness of eukaryogenesis and the greater evolutionary potential of eukaryotes have been objectively formulated and whether, despite widespread acceptance that eukaryogenesis was "special," any such notion has more than rhetorical value.}, } @article {pmid25868533, year = {2015}, author = {Henry, LM and Maiden, MC and Ferrari, J and Godfray, HC}, title = {Insect life history and the evolution of bacterial mutualism.}, journal = {Ecology letters}, volume = {18}, number = {6}, pages = {516-525}, doi = {10.1111/ele.12425}, pmid = {25868533}, issn = {1461-0248}, support = {087622//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Ants ; Aphids/classification/*microbiology ; Bacteria/*classification ; Bayes Theorem ; *Biological Evolution ; Markov Chains ; Models, Genetic ; Monte Carlo Method ; Phylogeny ; Plants ; *Symbiosis ; }, abstract = {Bacterial symbiosis has played a fundamental role in the evolution of eukaryotes. However, we still know little about how cooperative relationships with bacteria originate, and why they form in some host species but not others. Facultative symbionts that are beneficial, but not essential, provide unique insights into these processes. We use data from over a hundred aphid species to test if host life history is associated with the presence of facultative symbionts. We find that aphid species that have mutualistic associations with ants that protect them from natural enemies are less likely to carry symbionts that provide similar benefits. We also find one symbiont species occurs more frequently in unrelated aphid species that specialise on certain plant genera. In addition, aphid species that attack multiple plants often carry different symbiont complements. Our findings provide evidence of the ecological conditions that facilitate stable, mutually beneficial relationships between microbes and eukaryotic hosts.}, } @article {pmid25601290, year = {2015}, author = {Méheust, R and Lopez, P and Bapteste, E}, title = {Metabolic bacterial genes and the construction of high-level composite lineages of life.}, journal = {Trends in ecology & evolution}, volume = {30}, number = {3}, pages = {127-129}, pmid = {25601290}, issn = {1872-8383}, mesh = {Archaea/*classification/*genetics ; Bacteria/*genetics ; Euryarchaeota/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genes, Archaeal/*genetics ; Genes, Bacterial/*genetics ; }, abstract = {Understanding how major organismal lineages originated is fundamental for understanding processes by which life evolved. Major evolutionary transitions, like eukaryogenesis, merging genetic material from distantly related organisms, are rare events, hence difficult ones to explain causally. If most archaeal lineages emerged after massive acquisitions of bacterial genes, a rule however arises: metabolic bacterial genes contributed to all major evolutionary transitions.}, } @article {pmid28357258, year = {2015}, author = {Djuika, CF and Huerta-Cepas, J and Przyborski, JM and Deil, S and Sanchez, CP and Doerks, T and Bork, P and Lanzer, M and Deponte, M}, title = {Prokaryotic ancestry and gene fusion of a dual localized peroxiredoxin in malaria parasites.}, journal = {Microbial cell (Graz, Austria)}, volume = {2}, number = {1}, pages = {5-13}, pmid = {28357258}, issn = {2311-2638}, abstract = {Horizontal gene transfer has emerged as a crucial driving force for the evolution of eukaryotes. This also includes Plasmodium falciparum and related economically and clinically relevant apicomplexan parasites, whose rather small genomes have been shaped not only by natural selection in different host populations but also by horizontal gene transfer following endosymbiosis. However, there is rather little reliable data on horizontal gene transfer between animal hosts or bacteria and apicomplexan parasites. Here we show that apicomplexan homologues of peroxiredoxin 5 (Prx5) have a prokaryotic ancestry and therefore represent a special subclass of Prx5 isoforms in eukaryotes. Using two different immunobiochemical approaches, we found that the P. falciparum Prx5 homologue is dually localized to the parasite plastid and cytosol. This dual localization is reflected by a modular Plasmodium-specific gene architecture consisting of two exons. Despite the plastid localization, our phylogenetic analyses contradict an acquisition by secondary endosymbiosis and support a gene fusion event following a horizontal prokaryote-to-eukaryote gene transfer in early apicomplexans. The results provide unexpected insights into the evolution of apicomplexan parasites as well as the molecular evolution of peroxiredoxins, an important family of ubiquitous, usually highly concentrated thiol-dependent hydroperoxidases that exert functions as detoxifying enzymes, redox sensors and chaperones.}, } @article {pmid25525215, year = {2015}, author = {Grau-Bové, X and Sebé-Pedrós, A and Ruiz-Trillo, I}, title = {The eukaryotic ancestor had a complex ubiquitin signaling system of archaeal origin.}, journal = {Molecular biology and evolution}, volume = {32}, number = {3}, pages = {726-739}, pmid = {25525215}, issn = {1537-1719}, support = {206883/ERC_/European Research Council/International ; }, mesh = {Cluster Analysis ; Eukaryota/*genetics ; *Evolution, Molecular ; Genes/genetics ; Genes, Archaeal/*genetics ; Phylogeny ; Small Ubiquitin-Related Modifier Proteins/*genetics ; Ubiquitin/*genetics ; }, abstract = {The origin of the eukaryotic cell is one of the most important transitions in the history of life. However, the emergence and early evolution of eukaryotes remains poorly understood. Recent data have shown that the last eukaryotic common ancestor (LECA) was much more complex than previously thought. The LECA already had the genetic machinery encoding the endomembrane apparatus, spliceosome, nuclear pore, and myosin and kinesin cytoskeletal motors. It is unclear, however, when the functional regulation of these cellular components evolved. Here, we address this question by analyzing the origin and evolution of the ubiquitin (Ub) signaling system, one of the most important regulatory layers in eukaryotes. We delineated the evolution of the whole Ub, Small-Ub-related MOdifier (SUMO), and Ub-fold modifier 1 (Ufm1) signaling networks by analyzing representatives from all major eukaryotic, bacterial, and archaeal lineages. We found that the Ub toolkit had a pre-eukaryotic origin and is present in three extant archaeal groups. The pre-eukaryotic Ub toolkit greatly expanded during eukaryogenesis, through massive gene innovation and diversification of protein domain architectures. This resulted in a LECA with essentially all of the Ub-related genes, including the SUMO and Ufm1 Ub-like systems. Ub and SUMO signaling further expanded during eukaryotic evolution, especially labeling and delabeling enzymes responsible for substrate selection. Additionally, we analyzed protein domain architecture evolution and found that multicellular lineages have the most complex Ub systems in terms of domain architectures. Together, we demonstrate that the Ub system predates the origin of eukaryotes and that a burst of innovation during eukaryogenesis led to a LECA with complex posttranslational regulation.}, } @article {pmid25483189, year = {2014}, author = {Tian, T and Harding, A}, title = {How MAP kinase modules function as robust, yet adaptable, circuits.}, journal = {Cell cycle (Georgetown, Tex.)}, volume = {13}, number = {15}, pages = {2379-2390}, pmid = {25483189}, issn = {1551-4005}, mesh = {Biological Evolution ; Computer Simulation ; Humans ; MAP Kinase Signaling System/*physiology ; *Models, Biological ; Saccharomyces cerevisiae ; }, abstract = {Genetic and biochemical studies have revealed that the diversity of cell types and developmental patterns evident within the animal kingdom is generated by a handful of conserved, core modules. Core biological modules must be robust, able to maintain functionality despite perturbations, and yet sufficiently adaptable for random mutations to generate phenotypic variation during evolution. Understanding how robust, adaptable modules have influenced the evolution of eukaryotes will inform both evolutionary and synthetic biology. One such system is the MAP kinase module, which consists of a 3-tiered kinase circuit configuration that has been evolutionarily conserved from yeast to man. MAP kinase signal transduction pathways are used across eukaryotic phyla to drive biological functions that are crucial for life. Here we ask the fundamental question, why do MAPK modules follow a conserved 3-tiered topology rather than some other number? Using computational simulations, we identify a fundamental 2-tiered circuit topology that can be readily reconfigured by feedback loops and scaffolds to generate diverse signal outputs. When this 2-kinase circuit is connected to proximal input kinases, a 3-tiered modular configuration is created that is both robust and adaptable, providing a biological circuit that can regulate multiple phenotypes and maintain functionality in an uncertain world. We propose that the 3-tiered signal transduction module has been conserved through positive selection, because it facilitated the generation of phenotypic variation during eukaryotic evolution.}, } @article {pmid25481706, year = {2015}, author = {Blackstone, NW}, title = {The impact of mitochondrial endosymbiosis on the evolution of calcium signaling.}, journal = {Cell calcium}, volume = {57}, number = {3}, pages = {133-139}, doi = {10.1016/j.ceca.2014.11.006}, pmid = {25481706}, issn = {1532-1991}, mesh = {Animals ; *Biological Evolution ; Calcium Signaling/*physiology ; Eukaryotic Cells/metabolism ; Humans ; Mitochondria/*metabolism ; Prokaryotic Cells/metabolism ; Symbiosis/*physiology ; }, abstract = {At high concentrations, calcium has detrimental effects on biological systems. Life likely arose in a low calcium environment, and the first cells evolved mechanisms to maintain this environment internally. Bursts of calcium influx followed by efflux or sequestration thus developed in a functional context. For example, in proto-cells with exterior energy-converting membranes, such bursts could be used to depolarize the membrane. In this way, proto-cells could maintain maximal phosphorylation (metabolic state 3) and moderate levels of reactive oxygen species (ROS), while avoiding the resting state (metabolic state 4) and high levels of ROS. This trait is likely a shared primitive characteristic of prokaryotes. When eukaryotes evolved, the α-proteobacteria that gave rise to proto-mitochondria inhabited a novel environment, the interior of the proto-eukaryote that had a low calcium concentration. In this environment, metabolic homeostasis was difficult to maintain, and there were inherent risks from ROS, yet depolarizing the proto-mitochondrial membrane by calcium influx was challenging. To maintain metabolic state 3, proto-mitochondria were required to congregate near calcium influx points in the proto-eukaryotic membrane. This behavior, resulting in embryonic forms of calcium signaling, may have occurred immediately after the initiation of the endosymbiosis. Along with ROS, calcium may have served as one of the key forms of crosstalk among the community of prokaryotes that led to the eukaryotic cell.}, } @article {pmid25421434, year = {2014}, author = {Kannan, S and Rogozin, IB and Koonin, EV}, title = {MitoCOGs: clusters of orthologous genes from mitochondria and implications for the evolution of eukaryotes.}, journal = {BMC evolutionary biology}, volume = {14}, number = {}, pages = {237}, pmid = {25421434}, issn = {1471-2148}, support = {//Intramural NIH HHS/United States ; }, mesh = {Alphaproteobacteria/genetics/physiology ; Biological Evolution ; Cell Nucleus/genetics ; Eukaryota/*cytology/*genetics/physiology ; *Evolution, Molecular ; Genes, Mitochondrial ; Introns ; Mitochondria/genetics/physiology ; Symbiosis ; }, abstract = {BACKGROUND: Mitochondria are ubiquitous membranous organelles of eukaryotic cells that evolved from an alpha-proteobacterial endosymbiont and possess a small genome that encompasses from 3 to 106 genes. Accumulation of thousands of mitochondrial genomes from diverse groups of eukaryotes provides an opportunity for a comprehensive reconstruction of the evolution of the mitochondrial gene repertoire.

RESULTS: Clusters of orthologous mitochondrial protein-coding genes (MitoCOGs) were constructed from all available mitochondrial genomes and complemented with nuclear orthologs of mitochondrial genes. With minimal exceptions, the mitochondrial gene complements of eukaryotes are subsets of the superset of 66 genes found in jakobids. Reconstruction of the evolution of mitochondrial genomes indicates that the mitochondrial gene set of the last common ancestor of the extant eukaryotes was slightly larger than that of jakobids. This superset of mitochondrial genes likely represents an intermediate stage following the loss and transfer to the nucleus of most of the endosymbiont genes early in eukaryote evolution. Subsequent evolution in different lineages involved largely parallel transfer of ancestral endosymbiont genes to the nuclear genome. The intron density in nuclear orthologs of mitochondrial genes typically is nearly the same as in the rest of the genes in the respective genomes. However, in land plants, the intron density in nuclear orthologs of mitochondrial genes is almost 1.5-fold lower than the genomic mean, suggestive of ongoing transfer of functional genes from mitochondria to the nucleus.

CONCLUSIONS: The MitoCOGs are expected to become an important resource for the study of mitochondrial evolution. The nearly complete superset of mitochondrial genes in jakobids likely represents an intermediate stage in the evolution of eukaryotes after the initial, extensive loss and transfer of the endosymbiont genes. In addition, the bacterial multi-subunit RNA polymerase that is encoded in the jakobid mitochondrial genomes was replaced by a single-subunit phage-type RNA polymerase in the rest of the eukaryotes. These results are best compatible with the rooting of the eukaryotic tree between jakobids and the rest of the eukaryotes. The land plants are the only eukaryotic branch in which the gene transfer from the mitochondrial to the nuclear genome appears to be an active, ongoing process.}, } @article {pmid25406691, year = {2014}, author = {Hooper, SL and Burstein, HJ}, title = {Minimization of extracellular space as a driving force in prokaryote association and the origin of eukaryotes.}, journal = {Biology direct}, volume = {9}, number = {1}, pages = {24}, pmid = {25406691}, issn = {1745-6150}, mesh = {Biofilms ; *Biological Evolution ; Eukaryotic Cells/*physiology ; Genetic Variation ; *Microbial Interactions ; *Models, Biological ; Prokaryotic Cells/*physiology ; }, abstract = {BACKGROUND: Internalization-based hypotheses of eukaryotic origin require close physical association of host and symbiont. Prior hypotheses of how these associations arose include chance, specific metabolic couplings between partners, and prey-predator/parasite interactions. Since these hypotheses were proposed, it has become apparent that mixed-species, close-association assemblages (biofilms) are widespread and predominant components of prokaryotic ecology. Which forces drove prokaryotes to evolve the ability to form these assemblages are uncertain. Bacteria and archaea have also been found to form membrane-lined interconnections (nanotubes) through which proteins and RNA pass. These observations, combined with the structure of the nuclear envelope and an energetic benefit of close association (see below), lead us to propose a novel hypothesis of the driving force underlying prokaryotic close association and the origin of eukaryotes.

RESULTS: Respiratory proton transport does not alter external pH when external volume is effectively infinite. Close physical association decreases external volume. For small external volumes, proton transport decreases external pH, resulting in each transported proton increasing proton motor force to a greater extent. We calculate here that in biofilms this effect could substantially decrease how many protons need to be transported to achieve a given proton motor force. Based as it is solely on geometry, this energetic benefit would occur for all prokaryotes using proton-based respiration.

CONCLUSIONS: This benefit may be a driving force in biofilm formation. Under this hypothesis a very wide range of prokaryotic species combinations could serve as eukaryotic progenitors. We use this observation and the discovery of prokaryotic nanotubes to propose that eukaryotes arose from physically distinct, functionally specialized (energy factory, protein factory, DNA repository/RNA factory), obligatorily symbiotic prokaryotes in which the protein factory and DNA repository/RNA factory cells were coupled by nanotubes and the protein factory ultimately internalized the other two. This hypothesis naturally explains many aspects of eukaryotic physiology, including the nuclear envelope being a folded single membrane repeatedly pierced by membrane-bound tubules (the nuclear pores), suggests that species analogous or homologous to eukaryotic progenitors are likely unculturable as monocultures, and makes a large number of testable predictions.

REVIEWERS: This article was reviewed by Purificación López-García and Toni Gabaldón.}, } @article {pmid25274701, year = {2014}, author = {Schlacht, A and Herman, EK and Klute, MJ and Field, MC and Dacks, JB}, title = {Missing pieces of an ancient puzzle: evolution of the eukaryotic membrane-trafficking system.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {6}, number = {10}, pages = {a016048}, pmid = {25274701}, issn = {1943-0264}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/K008749/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Biological Transport/*physiology ; Cell Membrane/*metabolism ; Eukaryotic Cells/*metabolism ; Evolution, Molecular ; Membrane Transport Proteins/physiology ; *Models, Biological ; }, abstract = {The membrane-trafficking system underpins cellular trafficking of material in eukaryotes and its evolution would have been a watershed in eukaryogenesis. Evolutionary cell biological studies have been unraveling the history of proteins responsible for vesicle transport and organelle identity revealing both highly conserved components and lineage-specific innovations. Recently, endomembrane components with a broad, but patchy, distribution have been observed as well, pieces that are missing from our cell biological and evolutionary models of membrane trafficking. These data together allow for new insights into the history and forces that shape the evolution of this critical cell biological system.}, } @article {pmid25183828, year = {2014}, author = {Cavalier-Smith, T}, title = {The neomuran revolution and phagotrophic origin of eukaryotes and cilia in the light of intracellular coevolution and a revised tree of life.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {6}, number = {9}, pages = {a016006}, pmid = {25183828}, issn = {1943-0264}, mesh = {Animals ; Archaea/genetics ; *Biological Evolution ; Cell Membrane/metabolism ; Cilia/metabolism ; Cytoplasm/metabolism ; Cytoskeleton/metabolism ; DNA/analysis ; DNA Repair ; Eukaryota ; Eukaryotic Cells/cytology ; Origin of Life ; Peptidoglycan/chemistry ; Phylogeny ; }, abstract = {Three kinds of cells exist with increasingly complex membrane-protein targeting: Unibacteria (Archaebacteria, Posibacteria) with one cytoplasmic membrane (CM); Negibacteria with a two-membrane envelope (inner CM; outer membrane [OM]); eukaryotes with a plasma membrane and topologically distinct endomembranes and peroxisomes. I combine evidence from multigene trees, palaeontology, and cell biology to show that eukaryotes and archaebacteria are sisters, forming the clade neomura that evolved ~1.2 Gy ago from a posibacterium, whose DNA segregation and cell division were destabilized by murein wall loss and rescued by the evolving novel neomuran endoskeleton, histones, cytokinesis, and glycoproteins. Phagotrophy then induced coevolving serial major changes making eukaryote cells, culminating in two dissimilar cilia via a novel gliding-fishing-swimming scenario. I transfer Chloroflexi to Posibacteria, root the universal tree between them and Heliobacteria, and argue that Negibacteria are a clade whose OM, evolving in a green posibacterium, was never lost.}, } @article {pmid25138576, year = {2015}, author = {Wang, X and Jin, D and Wang, Z and Guo, H and Zhang, L and Wang, L and Li, J and Paterson, AH}, title = {Telomere-centric genome repatterning determines recurring chromosome number reductions during the evolution of eukaryotes.}, journal = {The New phytologist}, volume = {205}, number = {1}, pages = {378-389}, doi = {10.1111/nph.12985}, pmid = {25138576}, issn = {1469-8137}, mesh = {Arabidopsis/genetics ; *Biological Evolution ; Chromosomes, Plant/*genetics ; Computer Simulation ; Eukaryota/*genetics ; *Genome, Plant ; Karyotyping ; Models, Genetic ; Musa/genetics ; Oryza/genetics ; Poaceae/genetics ; Telomere/*genetics ; }, abstract = {Whole-genome duplication (WGD) is central to the evolution of many eukaryotic genomes, in particular rendering angiosperm (flowering plant) genomes much less stable than those of animals. Following repeated duplication/triplication(s), angiosperm chromosome numbers have usually been restored to a narrow range, as one element in a 'diploidization' process that re-establishes diploid heredity. In several angiosperms affected by WGD, we show that chromosome number reduction (CNR) is best explained by intra- and/or inter-chromosomal crossovers to form new chromosomes that utilize the existing telomeres of 'invaded' and centromeres of 'invading' chromosomes, the alternative centromeres and telomeres being lost. Comparison with the banana (Musa acuminata) genome supports a 'fusion model' for the evolution of rice (Oryza sativa) chromosomes 2 and 3, implying that the grass common ancestor had seven chromosomes rather than the five implied by a 'fission model.' The 'invading' and 'invaded' chromosomes are frequently homoeologs, originating from duplication of a common ancestral chromosome and with greater-than-average DNA-level correspondence to one another. Telomere-centric CNR following recursive WGD in plants is also important in mammals and yeast, and may be a general mechanism of restoring small linear chromosome numbers in higher eukaryotes.}, } @article {pmid25038049, year = {2014}, author = {Poole, AM and Gribaldo, S}, title = {Eukaryotic origins: How and when was the mitochondrion acquired?.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {6}, number = {12}, pages = {a015990}, pmid = {25038049}, issn = {1943-0264}, mesh = {*Biological Evolution ; Eukaryota/*cytology ; Mitochondria/*physiology ; *Models, Biological ; Phagocytosis/*physiology ; *Phylogeny ; *Symbiosis ; }, abstract = {Comparative genomics has revealed that the last eukaryotic common ancestor possessed the hallmark cellular architecture of modern eukaryotes. However, the remarkable success of such analyses has created a dilemma. If key eukaryotic features are ancestral to this group, then establishing the relative timing of their origins becomes difficult. In discussions of eukaryote origins, special significance has been placed on the timing of mitochondrial acquisition. In one view, mitochondrial acquisition was the trigger for eukaryogenesis. Others argue that development of phagocytosis was a prerequisite to acquisition. Results from comparative genomics and molecular phylogeny are often invoked to support one or the other scenario. We show here that the associations between specific cell biological models of eukaryogenesis and evolutionary genomic data are not as strong as many suppose. Disentangling these eliminates many of the arguments that polarize current debate.}, } @article {pmid24984775, year = {2014}, author = {Aravind, L and Burroughs, AM and Zhang, D and Iyer, LM}, title = {Protein and DNA modifications: evolutionary imprints of bacterial biochemical diversification and geochemistry on the provenance of eukaryotic epigenetics.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {6}, number = {7}, pages = {a016063}, pmid = {24984775}, issn = {1943-0264}, support = {//Intramural NIH HHS/United States ; }, mesh = {*Biodiversity ; DNA Methylation ; DNA, Bacterial/*chemistry/metabolism ; *Epigenomics ; Eukaryota/*genetics ; *Evolution, Molecular ; Histones/metabolism ; Models, Molecular ; Phosphorylation ; Phylogeny ; Protein Processing, Post-Translational ; Protein Structure, Tertiary ; Proteins/chemistry/metabolism ; Ubiquitination ; }, abstract = {Epigenetic information, which plays a major role in eukaryotic biology, is transmitted by covalent modifications of nuclear proteins (e.g., histones) and DNA, along with poorly understood processes involving cytoplasmic/secreted proteins and RNAs. The origin of eukaryotes was accompanied by emergence of a highly developed biochemical apparatus for encoding, resetting, and reading covalent epigenetic marks in proteins such as histones and tubulins. The provenance of this apparatus remained unclear until recently. Developments in comparative genomics show that key components of eukaryotic epigenetics emerged as part of the extensive biochemical innovation of secondary metabolism and intergenomic/interorganismal conflict systems in prokaryotes, particularly bacteria. These supplied not only enzymatic components for encoding and removing epigenetic modifications, but also readers of some of these marks. Diversification of these prokaryotic systems and subsequently eukaryotic epigenetics appear to have been considerably influenced by the great oxygenation event in the Earth's history.}, } @article {pmid24907565, year = {2014}, author = {Blackstone, NW}, title = {sAC as a model for understanding the impact of endosymbiosis on cell signaling.}, journal = {Biochimica et biophysica acta}, volume = {1842}, number = {12 Pt B}, pages = {2548-2554}, doi = {10.1016/j.bbadis.2014.05.037}, pmid = {24907565}, issn = {0006-3002}, mesh = {Adenylyl Cyclases/*metabolism ; Biological Evolution ; Humans ; *Signal Transduction ; *Symbiosis ; }, abstract = {As signaling pathways evolve, selection for new functions guides the co-option of existing material. Major transitions in the history of life, including the evolution of eukaryotes and multicellularity, exemplify this process. These transitions provided both strong selection and a plenitude of available material for the evolution of signaling pathways. Mechanisms that evolved to mediate conflict during the evolution of eukaryotes may subsequently have been co-opted during the many independent derivations of multicellularity. The soluble adenylyl cyclase (sAC) signaling pathway illustrates this hypothesis. Class III adenylyl cyclases, which include sAC, are found in bacteria, including the α-proteobacteria. These adenylyl cyclases are the only ones present in eukaryotes but appear to be absent in archaeans. This pattern suggests that the mitochondrial endosymbiosis brought sAC signaling to eukaryotes as part of an intact module. After transfer to the proto-nuclear genome, this module was then co-opted into numerous new functions. In the evolution of eukaryotes, sAC signaling may have mediated conflicts by maintaining metabolic homeostasis. In the evolution of multicellularity, in different lineages sAC may have been co-opted into parallel tasks originally related to conflict mediation. Elucidating the history of the sAC pathway may be relatively straightforward because it is ubiquitous and linked to near universal metabolic by-products (CO2/HCO(3)(-)). Other signaling pathways (e.g., those involving STAT and VEGF) present a greater challenge but may suggest a complementary pattern. The impact of the mitochondrial endosymbiosis on cell signaling may thus have been profound. This article is part of a Special Issue entitled: The role of soluble adenylyl cyclase in health and disease.}, } @article {pmid24906191, year = {2014}, author = {Chatre, L and Ricchetti, M}, title = {Are mitochondria the Achilles' heel of the Kingdom Fungi?.}, journal = {Current opinion in microbiology}, volume = {20}, number = {}, pages = {49-54}, doi = {10.1016/j.mib.2014.05.001}, pmid = {24906191}, issn = {1879-0364}, mesh = {*Energy Metabolism ; Fungi/metabolism/pathogenicity/*physiology ; Microbial Viability ; Mitochondria/*metabolism ; }, abstract = {A founding event in the origin of eukaryotes is the acquisition of an extraordinary organelle, the mitochondrion, which contains its own genome. Being linked to energy metabolism, oxidative stress, cell signalling, and cell death, the mitochondrion to a certain extent controls life and death in eukaryotic cells. The large metabolic diversity and living strategies of the Kingdom Fungi make their mitochondria of particular evolutionary interest. The review focuses first on the characteristics of mitochondria in the Kingdom Fungi, then on their implications in the organism survival, pathogenicity and resistance, and finally on proposing unconventional strategies to investigate the biology of fungal mitochondria, unveiling the possibility that mitochondria play as the Achilles' heel of this kingdom.}, } @article {pmid24890509, year = {2014}, author = {Irimia, M and Roy, SW}, title = {Origin of spliceosomal introns and alternative splicing.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {6}, number = {6}, pages = {}, pmid = {24890509}, issn = {1943-0264}, mesh = {*Alternative Splicing ; Exons ; *Introns ; *Spliceosomes ; }, abstract = {In this work we review the current knowledge on the prehistory, origins, and evolution of spliceosomal introns. First, we briefly outline the major features of the different types of introns, with particular emphasis on the nonspliceosomal self-splicing group II introns, which are widely thought to be the ancestors of spliceosomal introns. Next, we discuss the main scenarios proposed for the origin and proliferation of spliceosomal introns, an event intimately linked to eukaryogenesis. We then summarize the evidence that suggests that the last eukaryotic common ancestor (LECA) had remarkably high intron densities and many associated characteristics resembling modern intron-rich genomes. From this intron-rich LECA, the different eukaryotic lineages have taken very distinct evolutionary paths leading to profoundly diverged modern genome structures. Finally, we discuss the origins of alternative splicing and the qualitative differences in alternative splicing forms and functions across lineages.}, } @article {pmid24814066, year = {2014}, author = {McInerney, JO and O'Connell, MJ and Pisani, D}, title = {The hybrid nature of the Eukaryota and a consilient view of life on Earth.}, journal = {Nature reviews. Microbiology}, volume = {12}, number = {6}, pages = {449-455}, pmid = {24814066}, issn = {1740-1534}, mesh = {*Biological Evolution ; Eukaryota/*genetics ; Prokaryotic Cells/*physiology ; }, abstract = {The origin of the eukaryotic cell, which is known as eukaryogenesis, has puzzled scientists for more than 100 years, and many hypotheses have been proposed. Recent analyses of new data enable the safe elimination of some of these hypotheses, whereas support for other hypotheses has increased. In this Opinion article, we evaluate the available theories for their compatibility with empirical observations and conclude that cellular life consists of two primary, paraphyletic prokaryotic groups and one secondary, monophyletic group that has symbiogenic origins - the eukaryotes.}, } @article {pmid24682152, year = {2014}, author = {Tsaousis, AD and Nyvltová, E and Sutak, R and Hrdy, I and Tachezy, J}, title = {A nonmitochondrial hydrogen production in Naegleria gruberi.}, journal = {Genome biology and evolution}, volume = {6}, number = {4}, pages = {792-799}, pmid = {24682152}, issn = {1759-6653}, mesh = {Cytosol/*enzymology ; Hydrogen/*metabolism ; Hydrogenase/genetics/*metabolism ; Mitochondria/genetics/metabolism ; Naegleria/*enzymology/genetics ; Protozoan Proteins/genetics/*metabolism ; }, abstract = {Naegleria gruberi is a free-living heterotrophic aerobic amoeba well known for its ability to transform from an amoeba to a flagellate form. The genome of N. gruberi has been recently published, and in silico predictions demonstrated that Naegleria has the capacity for both aerobic respiration and anaerobic biochemistry to produce molecular hydrogen in its mitochondria. This finding was considered to have fundamental implications on the evolution of mitochondrial metabolism and of the last eukaryotic common ancestor. However, no actual experimental data have been shown to support this hypothesis. For this reason, we have decided to investigate the anaerobic metabolism of the mitochondrion of N. gruberi. Using in vivo biochemical assays, we have demonstrated that N. gruberi has indeed a functional [FeFe]-hydrogenase, an enzyme that is attributed to anaerobic organisms. Surprisingly, in contrast to the published predictions, we have demonstrated that hydrogenase is localized exclusively in the cytosol, while no hydrogenase activity was associated with mitochondria of the organism. In addition, cytosolic localization displayed for HydE, a marker component of hydrogenase maturases. Naegleria gruberi, an obligate aerobic organism and one of the earliest eukaryotes, is producing hydrogen, a function that raises questions on the purpose of this pathway for the lifestyle of the organism and potentially on the evolution of eukaryotes.}, } @article {pmid24646792, year = {2014}, author = {Gomaa, F and Kosakyan, A and Heger, TJ and Corsaro, D and Mitchell, EA and Lara, E}, title = {One alga to rule them all: unrelated mixotrophic testate amoebae (amoebozoa, rhizaria and stramenopiles) share the same symbiont (trebouxiophyceae).}, journal = {Protist}, volume = {165}, number = {2}, pages = {161-176}, doi = {10.1016/j.protis.2014.01.002}, pmid = {24646792}, issn = {1618-0941}, mesh = {Amoebozoa/*parasitology ; Chlorophyta/*classification/enzymology/genetics/*physiology ; Electron Transport Complex IV/genetics ; Molecular Sequence Data ; Rhizaria/*parasitology ; Ribulose-Bisphosphate Carboxylase/genetics ; Sequence Analysis, DNA ; Stramenopiles/*parasitology ; *Symbiosis ; }, abstract = {Endosymbiosis is a central and much studied process in the evolution of eukaryotes. While plastid evolution in eukaryotic algae has been extensively studied, much less is known about the evolution of mixotrophy in amoeboid protists, which has been found in three of the five super groups of Eukaryotes. We identified the green endosymbionts in four obligate mixotrophic testate amoeba species belonging to three major eukaryotic clades, Hyalosphenia papilio and Heleopera sphagni (Amoebozoa: Arcellinida), Placocista spinosa (Rhizaria: Euglyphida), and Archerella flavum (Stramenopiles: Labyrinthulomycetes) based on rbcL (ribulose-1,5-diphosphate carboxylase/oxygenase large subunit) gene sequences. We further investigated whether there were different phylotypes of algal endosymbionts within single H. papilio cells and the degree of host-symbiont specificity by amplifying two genes: COI (mitochondrial cytochrome oxydase subunit 1) from the testate amoeba host, and rbcL from the endosymbiont. Results show that all studied endosymbionts belong to genus Chlorella sensu stricto, closely related to Paramecium bursaria Chlorella symbionts, some lichen symbionts and also several free-living algae. Most rbcL gene sequences derived from symbionts from all testate amoeba species were almost identical (at most 3 silent nucleotides difference out of 780 bp) and were assigned to a new Trebouxiophyceae taxon we named TACS (Testate Amoeba Chlorella Symbionts). This "one alga fits all mixotrophic testate amoeba" pattern suggests that photosynthetic symbionts have pre-adaptations to endosymbiosis and colonise diverse hosts from a free-living stage.}, } @article {pmid24596261, year = {2014}, author = {Villanueva, L and Rijpstra, WI and Schouten, S and Damsté, JS}, title = {Genetic biomarkers of the sterol-biosynthetic pathway in microalgae.}, journal = {Environmental microbiology reports}, volume = {6}, number = {1}, pages = {35-44}, doi = {10.1111/1758-2229.12106}, pmid = {24596261}, issn = {1758-2229}, mesh = {*Biosynthetic Pathways ; Diatoms/classification/enzymology/genetics/*metabolism ; Genetic Markers ; Intramolecular Transferases/chemistry/*genetics/metabolism ; Microalgae/enzymology/genetics/*metabolism ; Phylogeny ; Ribulose-Bisphosphate Carboxylase/chemistry/genetics/metabolism ; Sequence Homology, Amino Acid ; Sterols/*biosynthesis ; }, abstract = {Sterols are cyclic isoprenoid lipids present in all eukaryotes. These compounds have been used to determine the composition of algal communities in marine and lake environments, and because of their preservation potential have been used to reconstruct the evolution of eukaryotes. In the last years, there have been major advances in understanding the sterol biosynthetic pathways and the enzymes involved. Here, we have explored the diversity and phylogenetic distribution of the gene coding the cycloartenol synthase (CS), a key enzyme of the phytosterol biosynthetic pathway. We propose a gene-based approach that can be used to assess the sterol-forming potential of algal groups. CS coding gene was annotated in genomes of microalgae using protein homology with previously annotated CS sequences. Primers for the detection of CS gene sequences of diatoms, one of the most dominant groups of microalgae, were designed and evaluated in cultures and environmental samples. A comparison of the phylogeny of the recovered CS sequences in combination with sequence data of the gene rbcL coding for the large subunit of the ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) demonstrates the potential of the CS gene as phylogenetic marker, as well as an indicator for the identity of sterol-producing organisms in the environment.}, } @article {pmid24572480, year = {2014}, author = {Koonin, EV}, title = {Carl Woese's vision of cellular evolution and the domains of life.}, journal = {RNA biology}, volume = {11}, number = {3}, pages = {197-204}, pmid = {24572480}, issn = {1555-8584}, support = {//Intramural NIH HHS/United States ; }, mesh = {*Biological Evolution ; Gene Transfer, Horizontal ; Genomics ; Phylogeny ; RNA, Ribosomal ; }, abstract = {In a series of conceptual articles published around the millennium, Carl Woese emphasized that evolution of cells is the central problem of evolutionary biology, that the three-domain ribosomal tree of life is an essential framework for reconstructing cellular evolution, and that the evolutionary dynamics of functionally distinct cellular systems are fundamentally different, with the information processing systems "crystallizing" earlier than operational systems. The advances of evolutionary genomics over the last decade vindicate major aspects of Woese's vision. Despite the observations of pervasive horizontal gene transfer among bacteria and archaea, the ribosomal tree of life comes across as a central statistical trend in the "forest" of phylogenetic trees of individual genes, and hence, an appropriate scaffold for evolutionary reconstruction. The evolutionary stability of information processing systems, primarily translation, becomes ever more striking with the accumulation of comparative genomic data indicating that nearly all of the few universal genes encode translation system components. Woese's view on the fundamental distinctions between the three domains of cellular life also withstand the test of comparative genomics, although his non-acceptance of symbiogenetic scenarios for the origin of eukaryotes might not. Above all, Woese's key prediction that understanding evolution of microbes will be the core of the new evolutionary biology appears to be materializing.}, } @article {pmid24532674, year = {2014}, author = {Williams, TA and Embley, TM}, title = {Archaeal "dark matter" and the origin of eukaryotes.}, journal = {Genome biology and evolution}, volume = {6}, number = {3}, pages = {474-481}, pmid = {24532674}, issn = {1759-6653}, support = {268701/ERC_/European Research Council/International ; }, mesh = {Archaea/*genetics ; *Biological Evolution ; Eukaryota/*genetics ; Genome, Archaeal ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; Sequence Alignment ; }, abstract = {Current hypotheses about the history of cellular life are mainly based on analyses of cultivated organisms, but these represent only a small fraction of extant biodiversity. The sequencing of new environmental lineages therefore provides an opportunity to test, revise, or reject existing ideas about the tree of life and the origin of eukaryotes. According to the textbook three domains hypothesis, the eukaryotes emerge as the sister group to a monophyletic Archaea. However, recent analyses incorporating better phylogenetic models and an improved sampling of the archaeal domain have generally supported the competing eocyte hypothesis, in which core genes of eukaryotic cells originated from within the Archaea, with important implications for eukaryogenesis. Given this trend, it was surprising that a recent analysis incorporating new genomes from uncultivated Archaea recovered a strongly supported three domains tree. Here, we show that this result was due in part to the use of a poorly fitting phylogenetic model and also to the inclusion by an automated pipeline of genes of putative bacterial origin rather than nucleocytosolic versions for some of the eukaryotes analyzed. When these issues were resolved, analyses including the new archaeal lineages placed core eukaryotic genes within the Archaea. These results are consistent with a number of recent studies in which improved archaeal sampling and better phylogenetic models agree in supporting the eocyte tree over the three domains hypothesis.}, } @article {pmid24492708, year = {2014}, author = {Keeling, PJ}, title = {The impact of history on our perception of evolutionary events: endosymbiosis and the origin of eukaryotic complexity.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {6}, number = {2}, pages = {}, pmid = {24492708}, issn = {1943-0264}, mesh = {Eukaryota/*genetics ; *Evolution, Molecular ; Mitochondria/genetics ; Plastids/genetics ; Symbiosis/*genetics ; }, abstract = {Evolutionary hypotheses are correctly interpreted as products of the data they set out to explain, but they are less often recognized as being heavily influenced by other factors. One of these is the history of preceding thought, and here I look back on historically important changes in our thinking about the role of endosymbiosis in the origin of eukaryotic cells. Specifically, the modern emphasis on endosymbiotic explanations for numerous eukaryotic features, including the cell itself (the so-called chimeric hypotheses), can be seen not only as resulting from the advent of molecular and genomic data, but also from the intellectual acceptance of the endosymbiotic origin of mitochondria and plastids. This transformative idea may have unduly affected how other aspects of the eukaryotic cell are explained, in effect priming us to accept endosymbiotic explanations for endogenous processes. Molecular and genomic data, which were originally harnessed to answer questions about cell evolution, now so dominate our thinking that they largely define the question, and the original questions about how eukaryotic cellular architecture evolved have been neglected. This is unfortunate because, as Roger Stanier pointed out, these cellular changes represent life's "greatest single evolutionary discontinuity," and on this basis I advocate a return to emphasizing evolutionary cell biology when thinking about the origin of eukaryotes, and suggest that endogenous explanations will prevail when we refocus on the evolution of the cell.}, } @article {pmid24489782, year = {2014}, author = {Guo, M and Zhou, Q and Zhou, Y and Yang, L and Liu, T and Yang, J and Chen, Y and Su, L and Xu, J and Chen, J and Liu, F and Chen, J and Dai, W and Ni, P and Fang, C and Yang, R}, title = {Genomic evolution of 11 type strains within family Planctomycetaceae.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e86752}, pmid = {24489782}, issn = {1932-6203}, mesh = {*Biological Evolution ; *Genome, Bacterial ; Genomic Islands ; Metabolic Networks and Pathways ; Multigene Family ; *Phylogeny ; Planctomycetales/*classification/*genetics/metabolism/ultrastructure ; Plasmids ; }, abstract = {The species in family Planctomycetaceae are ideal groups for investigating the origin of eukaryotes. Their cells are divided by a lipidic intracytoplasmic membrane and they share a number of eukaryote-like molecular characteristics. However, their genomic structures, potential abilities, and evolutionary status are still unknown. In this study, we searched for common protein families and a core genome/pan genome based on 11 sequenced species in family Planctomycetaceae. Then, we constructed phylogenetic tree based on their 832 common protein families. We also annotated the 11 genomes using the Clusters of Orthologous Groups database. Moreover, we predicted and reconstructed their core/pan metabolic pathways using the KEGG (Kyoto Encyclopedia of Genes and Genomes) orthology system. Subsequently, we identified genomic islands (GIs) and structural variations (SVs) among the five complete genomes and we specifically investigated the integration of two Planctomycetaceae plasmids in all 11 genomes. The results indicate that Planctomycetaceae species share diverse genomic variations and unique genomic characteristics, as well as have huge potential for human applications.}, } @article {pmid24443438, year = {2014}, author = {Sebé-Pedrós, A and Grau-Bové, X and Richards, TA and Ruiz-Trillo, I}, title = {Evolution and classification of myosins, a paneukaryotic whole-genome approach.}, journal = {Genome biology and evolution}, volume = {6}, number = {2}, pages = {290-305}, pmid = {24443438}, issn = {1759-6653}, support = {206883/ERC_/European Research Council/International ; BB/G00885X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/G00885X/2/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Eukaryota/chemistry/*classification/*genetics ; *Evolution, Molecular ; *Genome ; Myosins/chemistry/*genetics ; Phylogeny ; Protein Structure, Tertiary ; }, abstract = {Myosins are key components of the eukaryotic cytoskeleton, providing motility for a broad diversity of cargoes. Therefore, understanding the origin and evolutionary history of myosin classes is crucial to address the evolution of eukaryote cell biology. Here, we revise the classification of myosins using an updated taxon sampling that includes newly or recently sequenced genomes and transcriptomes from key taxa. We performed a survey of eukaryotic genomes and phylogenetic analyses of the myosin gene family, reconstructing the myosin toolkit at different key nodes in the eukaryotic tree of life. We also identified the phylogenetic distribution of myosin diversity in terms of number of genes, associated protein domains and number of classes in each taxa. Our analyses show that new classes (i.e., paralogs) and domain architectures were continuously generated throughout eukaryote evolution, with a significant expansion of myosin abundance and domain architectural diversity at the stem of Holozoa, predating the origin of animal multicellularity. Indeed, single-celled holozoans have the most complex myosin complement among eukaryotes, with paralogs of most myosins previously considered animal specific. We recover a dynamic evolutionary history, with several lineage-specific expansions (e.g., the myosin III-like gene family diversification in choanoflagellates), convergence in protein domain architectures (e.g., fungal and animal chitin synthase myosins), and important secondary losses. Overall, our evolutionary scheme demonstrates that the ancestral eukaryote likely had a complex myosin repertoire that included six genes with different protein domain architectures. Finally, we provide an integrative and robust classification, useful for future genomic and functional studies on this crucial eukaryotic gene family.}, } @article {pmid24398320, year = {2014}, author = {Rochette, NC and Brochier-Armanet, C and Gouy, M}, title = {Phylogenomic test of the hypotheses for the evolutionary origin of eukaryotes.}, journal = {Molecular biology and evolution}, volume = {31}, number = {4}, pages = {832-845}, pmid = {24398320}, issn = {1537-1719}, mesh = {Archaea/genetics ; Bacteria/genetics ; Biological Evolution ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Speciation ; Genome, Human ; Humans ; *Models, Genetic ; Phylogeny ; Symbiosis/genetics ; Yeasts/genetics ; }, abstract = {The evolutionary origin of eukaryotes is a question of great interest for which many different hypotheses have been proposed. These hypotheses predict distinct patterns of evolutionary relationships for individual genes of the ancestral eukaryotic genome. The availability of numerous completely sequenced genomes covering the three domains of life makes it possible to contrast these predictions with empirical data. We performed a systematic analysis of the phylogenetic relationships of ancestral eukaryotic genes with archaeal and bacterial genes. In contrast with previous studies, we emphasize the critical importance of methods accounting for statistical support, horizontal gene transfer, and gene loss, and we disentangle the processes underlying the phylogenomic pattern we observe. We first recover a clear signal indicating that a fraction of the bacteria-like eukaryotic genes are of alphaproteobacterial origin. Then, we show that the majority of bacteria-related eukaryotic genes actually do not point to a relationship with a specific bacterial taxonomic group. We also provide evidence that eukaryotes branch close to the last archaeal common ancestor. Our results demonstrate that there is no phylogenetic support for hypotheses involving a fusion with a bacterium other than the ancestor of mitochondria. Overall, they leave only two possible interpretations, respectively, based on the early-mitochondria hypotheses, which suppose an early endosymbiosis of an alphaproteobacterium in an archaeal host and on the slow-drip autogenous hypothesis, in which early eukaryotic ancestors were particularly prone to horizontal gene transfers.}, } @article {pmid24348094, year = {2013}, author = {Forterre, P}, title = {The common ancestor of archaea and eukarya was not an archaeon.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2013}, number = {}, pages = {372396}, pmid = {24348094}, issn = {1472-3654}, mesh = {Archaea/*classification/genetics ; Bacteria/classification/genetics ; Biological Evolution ; Cell Lineage/*genetics ; DNA, Archaeal/*genetics ; DNA, Bacterial/genetics ; Eukaryota/*classification/genetics ; Evolution, Molecular ; Phylogeny ; }, abstract = {It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea. Here, I argue that these analyses are not reliable, and I critically discuss archaeal ancestor scenarios, as well as fusion scenarios for the origin of eukaryotes. Based on recognized evolutionary trends toward reduction in archaea and toward complexity in eukarya, I suggest that their last common ancestor was more complex than modern archaea but simpler than modern eukaryotes (the bug in-between scenario). I propose that the ancestors of archaea (and bacteria) escaped protoeukaryotic predators by invading high temperature biotopes, triggering their reductive evolution toward the "prokaryotic" phenotype (the thermoreduction hypothesis). Intriguingly, whereas archaea and eukarya share many basic features at the molecular level, the archaeal mobilome resembles more the bacterial than the eukaryotic one. I suggest that selection of different parts of the ancestral virosphere at the onset of the three domains played a critical role in shaping their respective biology. Eukarya probably evolved toward complexity with the help of retroviruses and large DNA viruses, whereas similar selection pressure (thermoreduction) could explain why the archaeal and bacterial mobilomes somehow resemble each other.}, } @article {pmid24336283, year = {2013}, author = {Williams, TA and Foster, PG and Cox, CJ and Embley, TM}, title = {An archaeal origin of eukaryotes supports only two primary domains of life.}, journal = {Nature}, volume = {504}, number = {7479}, pages = {231-236}, pmid = {24336283}, issn = {1476-4687}, support = {BB/C006143/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/C508777/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Archaea/*classification/cytology/genetics ; Bacteria/classification/genetics ; Cell Membrane/metabolism ; Eukaryota/*classification/cytology/genetics ; Mitochondria/genetics ; *Models, Biological ; *Phylogeny ; RNA, Ribosomal/genetics ; Symbiosis ; }, abstract = {The discovery of the Archaea and the proposal of the three-domains 'universal' tree, based on ribosomal RNA and core genes mainly involved in protein translation, catalysed new ideas for cellular evolution and eukaryotic origins. However, accumulating evidence suggests that the three-domains tree may be incorrect: evolutionary trees made using newer methods place eukaryotic core genes within the Archaea, supporting hypotheses in which an archaeon participated in eukaryotic origins by founding the host lineage for the mitochondrial endosymbiont. These results provide support for only two primary domains of life--Archaea and Bacteria--because eukaryotes arose through partnership between them.}, } @article {pmid24323918, year = {2014}, author = {Schönknecht, G and Weber, AP and Lercher, MJ}, title = {Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {36}, number = {1}, pages = {9-20}, doi = {10.1002/bies.201300095}, pmid = {24323918}, issn = {1521-1878}, mesh = {Adaptation, Physiological/*genetics ; Animals ; Biological Evolution ; Eukaryota/*genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Phylogeny ; }, abstract = {In contrast to vertical gene transfer from parent to offspring, horizontal (or lateral) gene transfer moves genetic information between different species. Bacteria and archaea often adapt through horizontal gene transfer. Recent analyses indicate that eukaryotic genomes, too, have acquired numerous genes via horizontal transfer from prokaryotes and other lineages. Based on this we raise the hypothesis that horizontally acquired genes may have contributed more to adaptive evolution of eukaryotes than previously assumed. Current candidate sets of horizontally acquired eukaryotic genes may just be the tip of an iceberg. We have recently shown that adaptation of the thermoacidophilic red alga Galdieria sulphuraria to its hot, acid, toxic-metal laden, volcanic environment was facilitated by the acquisition of numerous genes from extremophile bacteria and archaea. Other recently published examples of horizontal acquisitions involved in adaptation include ice-binding proteins in marine algae, enzymes for carotenoid biosynthesis in aphids, and genes involved in fungal metabolism. Editor's suggested further reading in BioEssays Jumping the fine LINE between species: Horizontal transfer of transposable elements in animals catalyses genome evolution Abstract.}, } @article {pmid24316280, year = {2014}, author = {Makiuchi, T and Nozaki, T}, title = {Highly divergent mitochondrion-related organelles in anaerobic parasitic protozoa.}, journal = {Biochimie}, volume = {100}, number = {}, pages = {3-17}, doi = {10.1016/j.biochi.2013.11.018}, pmid = {24316280}, issn = {1638-6183}, mesh = {Alveolata/physiology/ultrastructure ; Amoebozoa/physiology/ultrastructure ; Anaerobiosis ; Biodiversity ; *Biological Evolution ; Cryptophyta/physiology/ultrastructure ; Diplomonadida/physiology/ultrastructure ; Gene Expression Regulation ; Genome, Mitochondrial ; Humans ; Mitochondria/*genetics/*metabolism/ultrastructure ; Mitochondrial Proteins/genetics/*metabolism ; Neocallimastix/physiology/ultrastructure ; Phylogeny ; Protein Transport ; }, abstract = {The mitochondria have arisen as a consequence of endosymbiosis of an ancestral α-proteobacterium with a methane-producing archae. The main function of the canonical aerobic mitochondria include ATP generation via oxidative phosphorylation, heme and phospholipid synthesis, calcium homeostasis, programmed cell death, and the formation of iron-sulfur clusters. Under oxygen-restricted conditions, the mitochondrion has often undergone remarkable reductive alterations of its content and function, leading to the generation of mitochondrion-related organelles (MROs), such as mitosomes, hydrogenosomes, and mithochondrion-like organelles, which are found in a wide range of anaerobic/microaerophilic eukaryotes that include several medically important parasitic protists such as Entamoeba histolytica, Giardia intestinalis, Trichomonas vaginalis, Cryptosporidium parvum, Blastocystis hominis, and Encephalitozoon cuniculi, as well as free-living protists such as Sawyeria marylandensis, Neocallimastix patriciarum, and Mastigamoeba balamuthi. The transformation from canonical aerobic mitochondria to MROs apparently have occurred in independent lineages, and resulted in the diversity of their components and functions. Due to medical and veterinary importance of the MRO-possessing human- and animal-pathogenic protozoa, their genomic, transcriptomic, proteomic, and biochemical evidence has been accumulated. Detailed analyses of the constituents and functions of the MROs in such anaerobic pathogenic protozoa, which reside oxygen-deprived or oxygen-poor environments such as the mammalian intestine and the genital organs, should illuminate the current evolutionary status of the MROs in these organisms, and give insight to environmental constraints that drive the evolution of eukaryotes and their organelles. In this review, we summarize and discuss the diverse metabolic functions and protein transport systems of the MROs from anaerobic parasitic protozoa.}, } @article {pmid24279500, year = {2014}, author = {Field, MC and Koreny, L and Rout, MP}, title = {Enriching the pore: splendid complexity from humble origins.}, journal = {Traffic (Copenhagen, Denmark)}, volume = {15}, number = {2}, pages = {141-156}, pmid = {24279500}, issn = {1600-0854}, support = {U54 GM103511/GM/NIGMS NIH HHS/United States ; R21 AI096069/AI/NIAID NIH HHS/United States ; 090007/Z/09/Z/WT_/Wellcome Trust/United Kingdom ; U01 GM098256/GM/NIGMS NIH HHS/United States ; MR/K008749/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Active Transport, Cell Nucleus ; Animals ; *Evolution, Molecular ; Humans ; Nuclear Pore/genetics/*metabolism ; Nuclear Pore Complex Proteins/chemistry/genetics/metabolism ; }, abstract = {The nucleus is the defining intracellular organelle of eukaryotic cells and represents a major structural innovation that differentiates the eukaryotic and prokaryotic cellular form. The presence of a nuclear envelope (NE) encapsulating the nucleus necessitates a mechanism for interchange between the contents of the nuclear interior and the cytoplasm, which is mediated via the nuclear pore complex (NPC), a large protein assembly residing in nuclear pores in the NE. Recent advances have begun to map the structure and functions of the NPC in multiple organisms, and to allow reconstruction of some of the evolutionary events that underpin the modern NPC form, highlighting common and differential NPC features across the eukaryotes. Here we discuss some of these advances and the questions being pursued, consider how the evolution of the NPC has been constrained, and finally propose a model for how the NPC evolved.}, } @article {pmid24214024, year = {2013}, author = {Feng, JM and Tian, HF and Wen, JF}, title = {Origin and evolution of the eukaryotic SSU processome revealed by a comprehensive genomic analysis and implications for the origin of the nucleolus.}, journal = {Genome biology and evolution}, volume = {5}, number = {12}, pages = {2255-2267}, pmid = {24214024}, issn = {1759-6653}, mesh = {Base Sequence ; Biological Evolution ; Databases, Nucleic Acid ; Eukaryota/*genetics ; Eukaryotic Cells/cytology ; Evolution, Molecular ; Nuclear Proteins/genetics ; Nucleolus Organizer Region/*genetics ; Phylogeny ; RNA Splicing/genetics ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 18S/genetics ; Ribosomal Proteins ; Ribosome Subunits, Small, Eukaryotic/*genetics ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/genetics ; Sequence Alignment ; }, abstract = {As a nucleolar complex for small-subunit (SSU) ribosomal RNA processing, SSU processome has been extensively studied mainly in Saccharomyces cerevisiae but not in diverse organisms, leaving open the question of whether it is a ubiquitous mechanism across eukaryotes and how it evolved in the course of the evolution of eukaryotes. Genome-wide survey and identification of SSU processome components showed that the majority of all 77 yeast SSU processome proteins possess homologs in almost all of the main eukaryotic lineages, and 14 of them have homologs in archaea but few in bacteria, suggesting that the complex is ubiquitous in eukaryotes, and its evolutionary history began with abundant protein homologs being present in archaea and then a fairly complete form of the complex emerged in the last eukaryotic common ancestor (LECA). Phylogenetic analysis indicated that ancient gene duplication and functional divergence of the protein components of the complex occurred frequently during the evolutionary origin of the LECA from prokaryotes. We found that such duplications not only increased the complex's components but also produced some new functional proteins involved in other nucleolar functions, such as ribosome biogenesis and even some nonnucleolar (but nuclear) proteins participating in pre-mRNA splicing, implying the evolutionary emergence of the subnuclear compartment-the nucleolus-has occurred in the LECA. Therefore, the LECA harbored not only complicated SSU processomes but also a nucleolus. Our analysis also revealed that gene duplication, innovation, and loss, caused further divergence of the complex during the divergence of eukaryotes.}, } @article {pmid24188869, year = {2014}, author = {Bogumil, D and Alvarez-Ponce, D and Landan, G and McInerney, JO and Dagan, T}, title = {Integration of two ancestral chaperone systems into one: the evolution of eukaryotic molecular chaperones in light of eukaryogenesis.}, journal = {Molecular biology and evolution}, volume = {31}, number = {2}, pages = {410-418}, pmid = {24188869}, issn = {1537-1719}, support = {281357/ERC_/European Research Council/International ; }, mesh = {Archaea/*genetics/metabolism ; Bacteria/*genetics/metabolism ; *Biological Evolution ; Eukaryota/*genetics/metabolism ; Histone Chaperones/*genetics ; Models, Molecular ; Phylogeny ; Protein Folding ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Symbiosis ; }, abstract = {Eukaryotic genomes are mosaics of genes acquired from their prokaryotic ancestors, the eubacterial endosymbiont that gave rise to the mitochondrion and its archaebacterial host. Genomic footprints of the prokaryotic merger at the origin of eukaryotes are still discernable in eukaryotic genomes, where gene expression and function correlate with their prokaryotic ancestry. Molecular chaperones are essential in all domains of life as they assist the functional folding of their substrate proteins and protect the cell against the cytotoxic effects of protein misfolding. Eubacteria and archaebacteria code for slightly different chaperones, comprising distinct protein folding pathways. Here we study the evolution of the eukaryotic protein folding pathways following the endosymbiosis event. A phylogenetic analysis of all 64 chaperones encoded in the Saccharomyces cerevisiae genome revealed 25 chaperones of eubacterial ancestry, 11 of archaebacterial ancestry, 10 of ambiguous prokaryotic ancestry, and 18 that may represent eukaryotic innovations. Several chaperone families (e.g., Hsp90 and Prefoldin) trace their ancestry to only one prokaryote group, while others, such as Hsp40 and Hsp70, are of mixed ancestry, with members contributed from both prokaryotic ancestors. Analysis of the yeast chaperone-substrate interaction network revealed no preference for interaction between chaperones and substrates of the same origin. Our results suggest that the archaebacterial and eubacterial protein folding pathways have been reorganized and integrated into the present eukaryotic pathway. The highly integrated chaperone system of yeast is a manifestation of the central role of chaperone-mediated folding in maintaining cellular fitness. Most likely, both archaebacterial and eubacterial chaperone systems were essential at the very early stages of eukaryogenesis, and the retention of both may have offered new opportunities for expanding the scope of chaperone-mediated folding.}, } @article {pmid24170805, year = {2014}, author = {Yoshida, T and Furihata, HY and Kawabe, A}, title = {Patterns of genomic integration of nuclear chloroplast DNA fragments in plant species.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {21}, number = {2}, pages = {127-140}, pmid = {24170805}, issn = {1756-1663}, mesh = {Cell Nucleus/*genetics/metabolism ; Chloroplasts/*genetics/metabolism ; DNA, Plant/*genetics/metabolism ; Evolution, Molecular ; *Genome, Plant ; Plants/*genetics/metabolism ; Plastids/genetics/metabolism ; }, abstract = {The transfer of organelle DNA fragments to the nuclear genome is frequently observed in eukaryotes. These transfers are thought to play an important role in gene and genome evolution of eukaryotes. In plants, such transfers occur from plastid to nuclear [nuclear plastid DNAs (NUPTs)] and mitochondrial to nuclear (nuclear mitochondrial DNAs) genomes. The amount and genomic organization of organelle DNA fragments have been studied in model plant species, such as Arabidopsis thaliana and rice. At present, publicly available genomic data can be used to conduct such studies in non-model plants. In this study, we analysed the amount and genomic organization of NUPTs in 17 plant species for which genome sequences are available. The amount and distribution of NUPTs varied among the species. We also estimated the distribution of NUPTs according to the time of integration (relative age) by conducting sequence similarity analysis between NUPTs and the plastid genome. The age distributions suggested that the present genomic constitutions of NUPTs could be explained by the combination of the rapidly eliminated deleterious parts and few but constantly existing less deleterious parts.}, } @article {pmid24103012, year = {2013}, author = {Lloyd, JP and Davies, B}, title = {SMG1 is an ancient nonsense-mediated mRNA decay effector.}, journal = {The Plant journal : for cell and molecular biology}, volume = {76}, number = {5}, pages = {800-810}, doi = {10.1111/tpj.12329}, pmid = {24103012}, issn = {1365-313X}, support = {BB/H00775X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Arabidopsis/genetics ; Bryopsida/*genetics ; Conserved Sequence ; Evolution, Molecular ; Gene Knockout Techniques ; *Genes, Plant ; *Nonsense Mediated mRNA Decay ; Phosphatidylinositol 3-Kinases/*genetics ; Phosphorylation ; Phylogeny ; Protein Isoforms/genetics ; }, abstract = {Nonsense-mediated mRNA decay (NMD) is a eukaryotic process that targets selected mRNAs for destruction, for both quality control and gene regulatory purposes. SMG1, the core kinase of the NMD machinery in animals, phosphorylates the highly conserved UPF1 effector protein to activate NMD. However, SMG1 is missing from the genomes of fungi and the model flowering plant Arabidopsis thaliana, leading to the conclusion that SMG1 is animal-specific and questioning the mechanistic conservation of the pathway. Here we show that SMG1 is not animal-specific, by identifying SMG1 in a range of eukaryotes, including all examined green plants with the exception of A. thaliana. Knockout of SMG1 by homologous recombination in the basal land plant Physcomitrella patens reveals that SMG1 has a conserved role in the NMD pathway across kingdoms. SMG1 has been lost at various points during the evolution of eukaryotes from multiple lineages, including an early loss in the fungal lineage and a very recent observable gene loss in A. thaliana. These findings suggest that the SMG1 kinase functioned in the NMD pathway of the last common eukaryotic ancestor.}, } @article {pmid24043313, year = {2013}, author = {Aich, A and Shaha, C}, title = {Novel role of calmodulin in regulating protein transport to mitochondria in a unicellular eukaryote.}, journal = {Molecular and cellular biology}, volume = {33}, number = {22}, pages = {4579-4593}, pmid = {24043313}, issn = {1098-5549}, mesh = {Amino Acid Sequence ; Binding Sites ; Calmodulin/*metabolism ; Humans ; Leishmania donovani/chemistry/genetics/*metabolism ; Leishmaniasis, Visceral/parasitology ; Mitochondria/*metabolism ; Molecular Sequence Data ; Mutation ; Peroxidases/analysis/genetics/*metabolism ; Protein Sorting Signals ; Protein Transport ; Protozoan Proteins/analysis/genetics/*metabolism ; }, abstract = {Lower eukaryotes like the kinetoplastid parasites are good models to study evolution of cellular pathways during steps to eukaryogenesis. In this study, a kinetoplastid parasite, Leishmania donovani, was used to understand the process of mitochondrial translocation of a nucleus-encoded mitochondrial protein, the mitochondrial tryparedoxin peroxidase (mTXNPx). We report the presence of an N-terminal cleavable mitochondrial targeting signal (MTS) validated through deletion and grafting experiments. We also establish a novel finding of calmodulin (CaM) binding to the MTS of mTXNPx through specific residues. Mutation of CaM binding residues, keeping intact the residues involved in mitochondrial targeting and biochemical inhibition of CaM activity both in vitro and in vivo, prevented mitochondrial translocation. Through reconstituted import assays, we demonstrate obstruction of mitochondrial translocation either in the absence of CaM or Ca(2+) or in the presence of CaM inhibitors. We also demonstrate the prevention of temperature-driven mTXNPx aggregation in the presence of CaM. These findings establish the idea that CaM is required for the transport of the protein to mitochondria through maintenance of translocation competence posttranslation.}, } @article {pmid23968920, year = {2013}, author = {van der Giezen, M}, title = {Evolution: one thread to unite them all.}, journal = {Current biology : CB}, volume = {23}, number = {16}, pages = {R679-81}, doi = {10.1016/j.cub.2013.06.048}, pmid = {23968920}, issn = {1879-0445}, mesh = {Animals ; Chytridiomycota/*genetics ; DNA, Fungal/*genetics ; DNA, Protozoan/*genetics ; *Genome, Fungal ; *Genome, Protozoan ; Microsporidia/*genetics ; *Phylogeny ; Rhizaria/*genetics ; }, abstract = {Mitochondria play import roles in the overall metabolism of eukaryotes. Traditionally, they have played a secondary role to the nucleus in the origin of eukaryotes. However, their relative positions in this crucial event for eukaryotic evolution might be reversed.}, } @article {pmid23895660, year = {2013}, author = {Koumandou, VL and Wickstead, B and Ginger, ML and van der Giezen, M and Dacks, JB and Field, MC}, title = {Molecular paleontology and complexity in the last eukaryotic common ancestor.}, journal = {Critical reviews in biochemistry and molecular biology}, volume = {48}, number = {4}, pages = {373-396}, pmid = {23895660}, issn = {1549-7798}, support = {082813//Wellcome Trust/United Kingdom ; //Biotechnology and Biological Sciences Research Council/United Kingdom ; //Medical Research Council/United Kingdom ; }, mesh = {Biological Evolution ; Eukaryotic Cells/classification/*cytology/*metabolism ; Paleontology/*methods ; Phylogeny ; }, abstract = {Eukaryogenesis, the origin of the eukaryotic cell, represents one of the fundamental evolutionary transitions in the history of life on earth. This event, which is estimated to have occurred over one billion years ago, remains rather poorly understood. While some well-validated examples of fossil microbial eukaryotes for this time frame have been described, these can provide only basic morphology and the molecular machinery present in these organisms has remained unknown. Complete and partial genomic information has begun to fill this gap, and is being used to trace proteins and cellular traits to their roots and to provide unprecedented levels of resolution of structures, metabolic pathways and capabilities of organisms at these earliest points within the eukaryotic lineage. This is essentially allowing a molecular paleontology. What has emerged from these studies is spectacular cellular complexity prior to expansion of the eukaryotic lineages. Multiple reconstructed cellular systems indicate a very sophisticated biology, which by implication arose following the initial eukaryogenesis event but prior to eukaryotic radiation and provides a challenge in terms of explaining how these early eukaryotes arose and in understanding how they lived. Here, we provide brief overviews of several cellular systems and the major emerging conclusions, together with predictions for subsequent directions in evolution leading to extant taxa. We also consider what these reconstructions suggest about the life styles and capabilities of these earliest eukaryotes and the period of evolution between the radiation of eukaryotes and the eukaryogenesis event itself.}, } @article {pmid23885060, year = {2013}, author = {Blackstone, NW}, title = {Evolution and cell physiology. 2. The evolution of cell signaling: from mitochondria to Metazoa.}, journal = {American journal of physiology. Cell physiology}, volume = {305}, number = {9}, pages = {C909-15}, doi = {10.1152/ajpcell.00216.2013}, pmid = {23885060}, issn = {1522-1563}, mesh = {Animals ; *Biological Evolution ; Cell Physiological Phenomena/*physiology ; Humans ; Mitochondria/*physiology ; Signal Transduction/*physiology ; }, abstract = {The history of life is a history of levels-of-selection transitions. Each transition requires mechanisms that mediate conflict among the lower-level units. In the origins of multicellular eukaryotes, cell signaling is one such mechanism. The roots of cell signaling, however, may extend to the previous major transition, the origin of eukaryotes. Energy-converting protomitochondria within a larger cell allowed eukaryotes to transcend the surface-to-volume constraints inherent in the design of prokaryotes. At the same time, however, protomitochondria can selfishly allocate energy to their own replication. Metabolic signaling may have mediated this principal conflict in several ways. Variation of the protomitochondria was constrained by stoichiometry and strong metabolic demand (state 3) exerted by the protoeukaryote. Variation among protoeukaryotes was increased by the sexual stage of the life cycle, triggered by weak metabolic demand (state 4), resulting in stochastic allocation of protomitochondria to daughter cells. Coupled with selection, many selfish protomitochondria could thus be removed from the population. Hence, regulation of states 3 and 4, as, for instance, provided by the CO2/soluble adenylyl cyclase/cAMP pathway in mitochondria, was critical for conflict mediation. Subsequently, as multicellular eukaryotes evolved, metabolic signaling pathways employed by eukaryotes to mediate conflict within cells could now be co-opted into conflict mediation between cells. For example, in some fungi, the CO2/soluble adenylyl cyclase/cAMP pathway regulates the transition from yeast to forms with hyphae. In animals, this pathway regulates the maturation of sperm. While the particular features (sperm and hyphae) are distinct, both may involve between-cell conflicts that required mediation.}, } @article {pmid23856158, year = {2013}, author = {Jones, BL and VanLoozen, J and Kim, MH and Miles, SJ and Dunham, CM and Williams, LD and Snell, TW}, title = {Stress granules form in Brachionus manjavacas (Rotifera) in response to a variety of stressors.}, journal = {Comparative biochemistry and physiology. Part A, Molecular & integrative physiology}, volume = {166}, number = {2}, pages = {375-384}, doi = {10.1016/j.cbpa.2013.07.009}, pmid = {23856158}, issn = {1531-4332}, mesh = {Adaptation, Physiological ; Animals ; Cycloheximide/pharmacology ; Cytoplasmic Granules/*metabolism ; Eukaryotic Initiation Factor-3/metabolism ; Eukaryotic Initiation Factor-4E/metabolism ; Helminth Proteins/*metabolism ; Poly(A)-Binding Proteins/metabolism ; Protein Synthesis Inhibitors/pharmacology ; Protein Transport ; Puromycin/pharmacology ; Ribosome Subunits, Large/metabolism ; Rotifera/*metabolism/physiology ; Stress, Physiological ; }, abstract = {Many eukaryotes share a common response to environmental stresses. The responses include reorganization of cellular organelles and proteins. Similar stress responses between divergent species suggest that these protective mechanisms may have evolved early and been retained from the earliest eukaryotic ancestors. Many eukaryotic cells have the capacity to sequester proteins and mRNAs into transient stress granules (SGs) that protect most cellular mRNAs (Anderson and Kedersha, 2008). Our observations extend the phylogenetic range of SGs from trypanosomatids, insects, yeast and mammalian cells, where they were first described, to a species of the lophotrochozoan animal phylum Rotifera. We focus on the distribution of three proteins known to be associated with both ribosomes and SG formation: eukaryotic initiation factors eIF3B, eIF4E and T-cell-restricted intracellular antigen 1. We found that these three proteins co-localize to SGs in rotifers in response to temperature stress, osmotic stress and nutrient deprivation as has been described in other eukaryotes. We have also found that the large ribosomal subunit fails to localize to the SGs in rotifers. Furthermore, the SGs in rotifers disperse once the environmental stress is removed as demonstrated in yeast and mammalian cells. These results are consistent with SG formation in trypanosomatids, insects, yeast and mammalian cells, further supporting the presence of this protective mechanism early in the evolution of eukaryotes.}, } @article {pmid23754817, year = {2013}, author = {Blackstone, NW}, title = {Why did eukaryotes evolve only once? Genetic and energetic aspects of conflict and conflict mediation.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {368}, number = {1622}, pages = {20120266}, pmid = {23754817}, issn = {1471-2970}, mesh = {*Biological Evolution ; *Energy Metabolism ; Eukaryota/*genetics/*physiology ; Genetic Variation ; Genome ; Mitochondria ; }, abstract = {According to multi-level theory, evolutionary transitions require mediating conflicts between lower-level units in favour of the higher-level unit. By this view, the origin of eukaryotes and the origin of multicellularity would seem largely equivalent. Yet, eukaryotes evolved only once in the history of life, whereas multicellular eukaryotes have evolved many times. Examining conflicts between evolutionary units and mechanisms that mediate these conflicts can illuminate these differences. Energy-converting endosymbionts that allow eukaryotes to transcend surface-to-volume constraints also can allocate energy into their own selfish replication. This principal conflict in the origin of eukaryotes can be mediated by genetic or energetic mechanisms. Genome transfer diminishes the heritable variation of the symbiont, but requires the de novo evolution of the protein-import apparatus and was opposed by selection for selfish symbionts. By contrast, metabolic signalling is a shared primitive feature of all cells. Redox state of the cytosol is an emergent feature that cannot be subverted by an individual symbiont. Hypothetical scenarios illustrate how metabolic regulation may have mediated the conflicts inherent at different stages in the origin of eukaryotes. Aspects of metabolic regulation may have subsequently been coopted from within-cell to between-cell pathways, allowing multicellularity to emerge repeatedly.}, } @article {pmid23754807, year = {2013}, author = {Lane, N and Martin, WF and Raven, JA and Allen, JF}, title = {Energy, genes and evolution: introduction to an evolutionary synthesis.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {368}, number = {1622}, pages = {20120253}, pmid = {23754807}, issn = {1471-2970}, mesh = {Animals ; *Biological Evolution ; Energy Metabolism/*genetics/*physiology ; Gene Expression Regulation/*physiology ; Genome ; }, abstract = {Life is the harnessing of chemical energy in such a way that the energy-harnessing device makes a copy of itself. No energy, no evolution. The 'modern synthesis' of the past century explained evolution in terms of genes, but this is only part of the story. While the mechanisms of natural selection are correct, and increasingly well understood, they do little to explain the actual trajectories taken by life on Earth. From a cosmic perspective-what is the probability of life elsewhere in the Universe, and what are its probable traits?-a gene-based view of evolution says almost nothing. Irresistible geological and environmental changes affected eukaryotes and prokaryotes in very different ways, ones that do not relate to specific genes or niches. Questions such as the early emergence of life, the morphological and genomic constraints on prokaryotes, the singular origin of eukaryotes, and the unique and perplexing traits shared by all eukaryotes but not found in any prokaryote, are instead illuminated by bioenergetics. If nothing in biology makes sense except in the light of evolution, nothing in evolution makes sense except in the light of energetics. This Special Issue of Philosophical Transactions examines the interplay between energy transduction and genome function in the major transitions of evolution, with implications ranging from planetary habitability to human health. We hope that these papers will contribute to a new evolutionary synthesis of energetics and genetics.}, } @article {pmid23699225, year = {2013}, author = {Garavís, M and González, C and Villasante, A}, title = {On the origin of the eukaryotic chromosome: the role of noncanonical DNA structures in telomere evolution.}, journal = {Genome biology and evolution}, volume = {5}, number = {6}, pages = {1142-1150}, pmid = {23699225}, issn = {1759-6653}, mesh = {Animals ; Centromere/genetics ; Chromosomes/*genetics ; *Evolution, Molecular ; *G-Quadruplexes ; Humans ; Retroelements ; Telomerase/metabolism ; Telomere/*genetics/metabolism ; }, abstract = {The transition of an ancestral circular genome to multiple linear chromosomes was crucial for eukaryogenesis because it allowed rapid adaptive evolution through aneuploidy. Here, we propose that the ends of nascent linear chromosomes should have had a dual function in chromosome end protection (capping) and chromosome segregation to give rise to the "proto-telomeres." Later on, proper centromeres evolved at subtelomeric regions. We also propose that both noncanonical structures based on guanine-guanine interactions and the end-protection proteins recruited by the emergent telomeric heterochromatin have been required for telomere maintenance through evolution. We further suggest that the origin of Drosophila telomeres may be reminiscent of how the first telomeres arose.}, } @article {pmid23576716, year = {2013}, author = {Alvarez-Ponce, D and Lopez, P and Bapteste, E and McInerney, JO}, title = {Gene similarity networks provide tools for understanding eukaryote origins and evolution.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {17}, pages = {E1594-603}, pmid = {23576716}, issn = {1091-6490}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Biological Evolution ; Computational Biology ; Eukaryota/*genetics ; Genes/*genetics ; *Phylogeny ; Plasmids/genetics ; Proteome/genetics ; *Sequence Homology, Nucleic Acid ; Viruses/*genetics ; }, abstract = {The complexity and depth of the relationships between the three domains of life challenge the reliability of phylogenetic methods, encouraging the use of alternative analytical tools. We reconstructed a gene similarity network comprising the proteomes of 14 eukaryotes, 104 prokaryotes, 2,389 viruses and 1,044 plasmids. This network contains multiple signatures of the chimerical origin of Eukaryotes as a fusion of an archaebacterium and a eubacterium that could not have been observed using phylogenetic trees. A number of connected components (gene sets with stronger similarities than expected by chance) contain pairs of eukaryotic sequences exhibiting no direct detectable similarity. Instead, many eukaryotic sequences were indirectly connected through a "eukaryote-archaebacterium-eubacterium-eukaryote" similarity path. Furthermore, eukaryotic genes highly connected to prokaryotic genes from one domain tend not to be connected to genes from the other prokaryotic domain. Genes of archaebacterial and eubacterial ancestry tend to perform different functions and to act at different subcellular compartments, but in such an intertwined way that suggests an early rather than late integration of both gene repertoires. The archaebacterial repertoire has a similar size in all eukaryotic genomes whereas the number of eubacterium-derived genes is much more variable, suggesting a higher plasticity of this gene repertoire. Consequently, highly reduced eukaryotic genomes contain more genes of archaebacterial than eubacterial affinity. Connected components with prokaryotic and eukaryotic genes tend to include viral and plasmid genes, compatible with a role of gene mobility in the origin of Eukaryotes. Our analyses highlight the power of network approaches to study deep evolutionary events.}, } @article {pmid23455615, year = {2013}, author = {Iida, H and Ota, S and Inouye, I}, title = {Cleavage, incomplete inversion, and cytoplasmic bridges in Gonium pectorale (Volvocales, Chlorophyta).}, journal = {Journal of plant research}, volume = {126}, number = {5}, pages = {699-707}, pmid = {23455615}, issn = {1618-0860}, mesh = {Biological Evolution ; *Cell Division ; Chlorophyta/*embryology/ultrastructure ; Cytoplasm/ultrastructure ; Microscopy, Electron, Scanning ; Microscopy, Fluorescence ; Species Specificity ; Time-Lapse Imaging ; }, abstract = {Multicellularity arose several times in evolution of eukaryotes. The volvocine algae have full range of colonial organization from unicellular to colonies, and thus these algae are well-known models for examining the evolution and mechanisms of multicellularity. Gonium pectorale is a multicellular species of Volvocales and is thought to be one of the first small colonial organisms among the volvocine algae. In these algae, a cytoplasmic bridge is one of the key traits that arose during the evolution of multicellularity. Here, we observed the inversion process and the cytoplasmic bridges in G. pectorale using time-lapse, fluorescence, and electron microscopy. The cytoplasmic bridges were located in the middle region of the cell in 2-, 4-, 8-, and 16-celled stages and in inversion stages. However, there were no cytoplasmic bridges in the mature adult stage. Cytoplasmic bridges and cortical microtubules in G. pectorale suggest that a mechanism of kinesin-microtubule machinery similar to that in other volvocine algae is responsible for inversion in this species.}, } @article {pmid23397796, year = {2012}, author = {Chapman, M and Alliegro, MC}, title = {The karyomastigont as an evolutionary seme.}, journal = {The Quarterly review of biology}, volume = {87}, number = {4}, pages = {315-324}, doi = {10.1086/668165}, pmid = {23397796}, issn = {0033-5770}, mesh = {Animals ; *Biological Evolution ; *Eukaryotic Cells ; }, abstract = {The problem of eukaryogenesis--the evolutionary mechanism whereby eukaryotic cells evolved from prokaryotes--remains one of the great unsolved mysteries of cell biology, possibly due to the reductionist tendency of most scientists to work only within their subdisciplines. Communication between biologists who conduct research on the nucleus and those working on the cytoskeleton or endomembrane system are sometimes wanting, and yet, all of these quintessentially eukaryotic elements of the cell are interdependent, and are physically associated in many protists as the karyomastigont organellar system: nucleus, one or more basal bodies and flagella, nuclear connector, and Golgi apparatus. Here we suggest a more holistic view of the karyomastigont as not simply an organellar system, but an evolutionary seme, the archaic state of the eukaryotic cell. We also present a scheme whereby the karyomastigont may have dissociated, giving rise in more derived cells to one or more free nuclei and discrete flagellar apparati (akaryomastigonts).}, } @article {pmid23356327, year = {2013}, author = {Martijn, J and Ettema, TJ}, title = {From archaeon to eukaryote: the evolutionary dark ages of the eukaryotic cell.}, journal = {Biochemical Society transactions}, volume = {41}, number = {1}, pages = {451-457}, doi = {10.1042/BST20120292}, pmid = {23356327}, issn = {1470-8752}, mesh = {Archaea/classification/*genetics ; *Eukaryotic Cells ; *Evolution, Molecular ; Gene Duplication ; Genes, Archaeal ; Phagocytosis ; Phylogeny ; }, abstract = {The evolutionary origin of the eukaryotic cell represents an enigmatic, yet largely incomplete, puzzle. Several mutually incompatible scenarios have been proposed to explain how the eukaryotic domain of life could have emerged. To date, convincing evidence for these scenarios in the form of intermediate stages of the proposed eukaryogenesis trajectories is lacking, presenting the emergence of the complex features of the eukaryotic cell as an evolutionary deus ex machina. However, recent advances in the field of phylogenomics have started to lend support for a model that places a cellular fusion event at the basis of the origin of eukaryotes (symbiogenesis), involving the merger of an as yet unknown archaeal lineage that most probably belongs to the recently proposed 'TACK superphylum' (comprising Thaumarchaeota, Aigarchaeota, Crenarchaeota and Korarchaeota) with an alphaproteobacterium (the protomitochondrion). Interestingly, an increasing number of so-called ESPs (eukaryotic signature proteins) is being discovered in recently sequenced archaeal genomes, indicating that the archaeal ancestor of the eukaryotic cell might have been more eukaryotic in nature than presumed previously, and might, for example, have comprised primitive phagocytotic capabilities. In the present paper, we review the evolutionary transition from archaeon to eukaryote, and propose a new model for the emergence of the eukaryotic cell, the 'PhAT (phagocytosing archaeon theory)', which explains the emergence of the cellular and genomic features of eukaryotes in the light of a transiently complex phagocytosing archaeon.}, } @article {pmid23348003, year = {2013}, author = {Kokošar, J and Kordiš, D}, title = {Genesis and regulatory wiring of retroelement-derived domesticated genes: a phylogenomic perspective.}, journal = {Molecular biology and evolution}, volume = {30}, number = {5}, pages = {1015-1031}, pmid = {23348003}, issn = {1537-1719}, mesh = {Animals ; Evolution, Molecular ; Gene Duplication/genetics ; Genomics/*methods ; Mammals/genetics ; *Phylogeny ; Retroelements/*genetics ; }, abstract = {Molecular domestications of transposable elements have occurred repeatedly during the evolution of eukaryotes. Vertebrates, especially mammals, possess numerous single copy domesticated genes (DGs) that have originated from the intronless multicopy transposable elements. However, the origin and evolution of the retroelement-derived DGs (RDDGs) that originated from Metaviridae has been only partially elucidated, due to absence of genome data or to limited analysis of a single family of DGs. We traced the genesis and regulatory wiring of the Metaviridae-derived DGs through phylogenomic analysis, using whole-genome information from more than 90 chordate genomes. Phylogenomic analysis of these DGs in chordate genomes provided direct evidence that major diversification has occurred in the ancestor of placental mammals. Mammalian RDDGs have been shown to originate in several steps by independent domestication events and to diversify later by gene duplications. Analysis of syntenic loci has shown that diverse RDDGs and their chromosomal positions were fully established in the ancestor of placental mammals. By analysis of active Metaviridae lineages in amniotes, we have demonstrated that RDDGs originated from retroelement remains. The chromosomal gene movements of RDDGs were highly dynamic only in the ancestor of placental mammals. During the domestication process, de novo acquisition of regulatory regions is shown to be a prerequisite for the survival of the DGs. The origin and evolution of de novo acquired promoters and untranslated regions in diverse mammalian RDDGs have been explained by comparative analysis of orthologous gene loci. The origin of placental mammal-specific innovations and adaptations, such as placenta and newly evolved brain functions, was most probably connected to the regulatory wiring of DGs and their rapid fixation in the ancestor of placental mammals.}, } @article {pmid23315654, year = {2013}, author = {Parfrey, LW and Lahr, DJ}, title = {Multicellularity arose several times in the evolution of eukaryotes (response to DOI 10.1002/bies.201100187).}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {35}, number = {4}, pages = {339-347}, doi = {10.1002/bies.201200143}, pmid = {23315654}, issn = {1521-1878}, mesh = {Animals ; *Cell Polarity ; Dictyostelium/*cytology ; Epithelial Cells/*physiology ; Humans ; }, abstract = {The cellular slime mold Dictyostelium has cell-cell connections similar in structure, function, and underlying molecular mechanisms to animal epithelial cells. These similarities form the basis for the proposal that multicellularity is ancestral to the clade containing animals, fungi, and Amoebozoa (including Dictyostelium): Amorphea (formerly "unikonts"). This hypothesis is intriguing and if true could precipitate a paradigm shift. However, phylogenetic analyses of two key genes reveal patterns inconsistent with a single origin of multicellularity. A single origin in Amorphea would also require loss of multicellularity in each of the many unicellular lineages within this clade. Further, there are numerous other origins of multicellularity within eukaryotes, including three within Amorphea, that are not characterized by these structural and mechanistic similarities. Instead, convergent evolution resulting from similar selective pressures for forming multicellular structures with motile and differentiated cells is the most likely explanation for the observed similarities between animal and dictyostelid cell-cell connections.}, } @article {pmid23085998, year = {2013}, author = {Rodríguez de la Vega Otazo, M and Lorenzo, J and Tort, O and Avilés, FX and Bautista, JM}, title = {Functional segregation and emerging role of cilia-related cytosolic carboxypeptidases (CCPs).}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {27}, number = {2}, pages = {424-431}, doi = {10.1096/fj.12-209080}, pmid = {23085998}, issn = {1530-6860}, mesh = {Animals ; Carboxypeptidases/classification/*genetics/*metabolism ; Cilia/*enzymology ; Cytosol/enzymology ; Eukaryota/enzymology/genetics ; *Evolution, Molecular ; HeLa Cells ; Humans ; Mice ; Models, Biological ; NIH 3T3 Cells ; Phylogeny ; }, abstract = {Recent experimental data indicating axonal regeneration, axogenesis, dendritogenesis, and ciliary axoneme assembly and wellness have linked the role of cytosolic metallocarboxypeptidase 1 (CCP1/AGTPBP1/Nna1) to the microtubule network. In addition, 5 of the 6 mammalian ccp genes have been shown to participate in post-translational modifications of tubulin, which occur in the microtubules of neurons, mitotic spindles, cilia, and basal bodies. Here, we compile evidence for the idea that the occurrence of CCPs strongly correlates with the presence of cilia, suggesting that CCP functions might be primarily related to cilia and basal bodies (CBBs). In agreement with this hypothesis, CCPs were localized in centrioles, basal bodies, and mitotic spindles in HeLa cells by confocal microscopy. By reconstructing the evolutionary history of CCPs, we show their presence in the last eukaryotic common ancestor and relate each group of CCP orthologs to specific roles in CBBs. The clues presented in this study suggest that during the evolution of eukaryotes, mechanisms mediated by CCPs through tubulin post-translational modifications controlling assembly, trafficking, and signaling in the microtubules, were transferred from cilia to cell and axon microtubules.}, } @article {pmid23020305, year = {2012}, author = {Zhao, S and Liang, Z and Demko, V and Wilson, R and Johansen, W and Olsen, OA and Shalchian-Tabrizi, K}, title = {Massive expansion of the calpain gene family in unicellular eukaryotes.}, journal = {BMC evolutionary biology}, volume = {12}, number = {}, pages = {193}, pmid = {23020305}, issn = {1471-2148}, mesh = {Bayes Theorem ; Binding Sites/genetics ; Calpain/classification/*genetics ; Chlamydomonas reinhardtii/enzymology/genetics ; Entamoeba histolytica/enzymology/genetics ; Eukaryotic Cells/cytology/enzymology/*metabolism ; Evolution, Molecular ; *Genetic Variation ; Models, Genetic ; *Phylogeny ; Species Specificity ; Trichomonas vaginalis/enzymology/genetics ; }, abstract = {BACKGROUND: Calpains are Ca2+-dependent cysteine proteases that participate in a range of crucial cellular processes. Dysfunction of these enzymes may cause, for instance, life-threatening diseases in humans, the loss of sex determination in nematodes and embryo lethality in plants. Although the calpain family is well characterized in animal and plant model organisms, there is a great lack of knowledge about these genes in unicellular eukaryote species (i.e. protists). Here, we study the distribution and evolution of calpain genes in a wide range of eukaryote genomes from major branches in the tree of life.

RESULTS: Our investigations reveal 24 types of protein domains that are combined with the calpain-specific catalytic domain CysPc. In total we identify 41 different calpain domain architectures, 28 of these domain combinations have not been previously described. Based on our phylogenetic inferences, we propose that at least four calpain variants were established in the early evolution of eukaryotes, most likely before the radiation of all the major supergroups of eukaryotes. Many domains associated with eukaryotic calpain genes can be found among eubacteria or archaebacteria but never in combination with the CysPc domain.

CONCLUSIONS: The analyses presented here show that ancient modules present in prokaryotes, and a few de novo eukaryote domains, have been assembled into many novel domain combinations along the evolutionary history of eukaryotes. Some of the new calpain genes show a narrow distribution in a few branches in the tree of life, likely representing lineage-specific innovations. Hence, the functionally important classical calpain genes found among humans and vertebrates make up only a tiny fraction of the calpain family. In fact, a massive expansion of the calpain family occurred by domain shuffling among unicellular eukaryotes and contributed to a wealth of functionally different genes.}, } @article {pmid22992703, year = {2012}, author = {Field, MC and Horn, D and Alsford, S and Koreny, L and Rout, MP}, title = {Telomeres, tethers and trypanosomes.}, journal = {Nucleus (Austin, Tex.)}, volume = {3}, number = {6}, pages = {478-486}, pmid = {22992703}, issn = {1949-1042}, support = {U54 RR022220/RR/NCRR NIH HHS/United States ; U54 GM103511/GM/NIGMS NIH HHS/United States ; R21 AI096069/AI/NIAID NIH HHS/United States ; 082813/WT_/Wellcome Trust/United Kingdom ; 093010/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Cell Nucleus/metabolism ; Chromosomes/metabolism ; Fungi/metabolism ; Gene Silencing ; Heterochromatin/metabolism ; Histones/metabolism ; Lamins/metabolism ; Nuclear Envelope/metabolism ; Nuclear Pore Complex Proteins/metabolism ; Telomere/*metabolism ; Trypanosoma/*metabolism ; }, abstract = {Temporal and spatial organization of the nucleus is critical for the control of transcription, mRNA processing and the assembly of ribosomes. This includes the occupancy of specific territories by mammalian chromosomes, the presence of subnuclear compartments such as the nucleolus and Cajal bodies and the division of chromatin between active and inactive states. These latter are commonly associated with the location of DNA within euchromatin and heterochromatin respectively; critically these distinctions arise through modifications to chromatin-associated proteins, including histones, as well as the preferential localization of heterochromatin at the nuclear periphery. Most research on nuclear organization has focused on metazoa and fungi; however, recent technical advances have made more divergent eukaryotes accessible to study, with some surprising results. For example, the organization of heterochromatin is mediated in metazoan nuclei in large part by lamins, the prototypical intermediate filament proteins. Despite the presence of heterochromatin, detected both biochemically and by EM in most eukaryotic organisms, until this year lamins were thought to be restricted to metazoan taxa, and the proteins comprising the lamina in other lineages were unknown. Recent work indicates the presence of lamin orthologs in amoeba, while trypanosomatids possess a large coiled-coil protein, NUP-1, that performs functions analogous to lamins. These data indicate that the presence of a nuclear lamina is substantially more widespread than previously thought, with major implications for the evolution of eukaryotic gene expression mechanisms. We discuss these and other recent findings on the organization of nuclei in diverse organisms, and the implications of these findings for the evolutionary origin of eukaryotes.}, } @article {pmid22919680, year = {2012}, author = {Aravind, L and Anantharaman, V and Zhang, D and de Souza, RF and Iyer, LM}, title = {Gene flow and biological conflict systems in the origin and evolution of eukaryotes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {2}, number = {}, pages = {89}, pmid = {22919680}, issn = {2235-2988}, mesh = {Adaptation, Biological ; Eukaryota/*genetics ; *Evolution, Molecular ; *Gene Flow ; Gene Transfer, Horizontal ; *Symbiosis ; }, abstract = {The endosymbiotic origin of eukaryotes brought together two disparate genomes in the cell. Additionally, eukaryotic natural history has included other endosymbiotic events, phagotrophic consumption of organisms, and intimate interactions with viruses and endoparasites. These phenomena facilitated large-scale lateral gene transfer and biological conflicts. We synthesize information from nearly two decades of genomics to illustrate how the interplay between lateral gene transfer and biological conflicts has impacted the emergence of new adaptations in eukaryotes. Using apicomplexans as example, we illustrate how lateral transfer from animals has contributed to unique parasite-host interfaces comprised of adhesion- and O-linked glycosylation-related domains. Adaptations, emerging due to intense selection for diversity in the molecular participants in organismal and genomic conflicts, being dispersed by lateral transfer, were subsequently exapted for eukaryote-specific innovations. We illustrate this using examples relating to eukaryotic chromatin, RNAi and RNA-processing systems, signaling pathways, apoptosis and immunity. We highlight the major contributions from catalytic domains of bacterial toxin systems to the origin of signaling enzymes (e.g., ADP-ribosylation and small molecule messenger synthesis), mutagenic enzymes for immune receptor diversification and RNA-processing. Similarly, we discuss contributions of bacterial antibiotic/siderophore synthesis systems and intra-genomic and intra-cellular selfish elements (e.g., restriction-modification, mobile elements and lysogenic phages) in the emergence of chromatin remodeling/modifying enzymes and RNA-based regulation. We develop the concept that biological conflict systems served as evolutionary "nurseries" for innovations in the protein world, which were delivered to eukaryotes via lateral gene flow to spur key evolutionary innovations all the way from nucleogenesis to lineage-specific adaptations.}, } @article {pmid22913376, year = {2012}, author = {Godde, JS}, title = {Breaking through a phylogenetic impasse: a pair of associated archaea might have played host in the endosymbiotic origin of eukaryotes.}, journal = {Cell & bioscience}, volume = {2}, number = {1}, pages = {29}, pmid = {22913376}, issn = {2045-3701}, abstract = {For over a century, the origin of eukaryotes has been a topic of intense debate among scientists. Although it has become widely accepted that organelles such as the mitochondria and chloroplasts arose via endosymbiosis, the origin of the eukaryotic nucleus remains enigmatic. Numerous models for the origin of the nucleus have been proposed over the years, many of which use endosymbiosis to explain its existence. Proposals of microbes whose ancestors may have served as either a host or a guest in various endosymbiotic scenarios abound, none of which have been able to sufficiently incorporate the cell biological as well as phylogenetic data which links these organisms to the nucleus. While it is generally agreed that eukaryotic nuclei share more features in common with archaea rather than with bacteria, different studies have identified either one or the other of the two major groups of archaea as potential ancestors, leading to somewhat of a stalemate. This paper seeks to resolve this impasse by presenting evidence that not just one, but a pair of archaea might have served as host to the bacterial ancestor of the mitochondria. This pair may have consisted of ancestors of both Ignicoccus hospitalis as well as its ectosymbiont/ectoparasite 'Nanoarchaeum equitans'.}, } @article {pmid22908957, year = {2012}, author = {Ito, M and Tohsato, Y and Sugisawa, H and Kohara, S and Fukuchi, S and Nishikawa, I and Nishikawa, K}, title = {Intrinsically disordered proteins in human mitochondria.}, journal = {Genes to cells : devoted to molecular & cellular mechanisms}, volume = {17}, number = {10}, pages = {817-825}, doi = {10.1111/gtc.12000}, pmid = {22908957}, issn = {1365-2443}, mesh = {Computational Biology/methods ; Databases, Protein ; Enzymes/chemistry/metabolism ; Humans ; Mitochondria/*metabolism ; Mitochondrial Proteins/chemistry/classification/*metabolism ; Protein Sorting Signals ; Protein Transport ; }, abstract = {Intrinsically disordered (ID) proteins (IDPs) are abundant in eukaryotes but are scarce in prokaryotes. Mitochondria, cellular organelles that descended from Rickettsia-like α-proteobacteria, are at the intersection between prokaryotes and eukaryotes. Although IDPs are reportedly as rare in mitochondria as in bacteria, these details remained to be clarified. Human mitochondrial proteins (n = 706) were obtained from the UniProt database, and information on ID regions of all human proteins was extracted from the DICHOT database. A BLAST search carried out against all α-proteobacterial proteins identified two types of mitochondrial proteins: those with (B) and without (E) bacterial homologues. The B-type proteins (n = 387) descended from a bacterial ancestor, whereas the E-type proteins (n = 319) were more recently added to the mitochondria via the host cell during the early evolution of eukaryotes. The average ID ratios of B-type/E-type proteins are 10.3% and 21.4%, respectively. The 706 proteins were further classified into four groups based on the mitochondrial subcompartment, namely, the matrix, intermembrane space, inner membrane, or outer membrane. The ID ratios in these different locations suggest that the frequency of IDPs in mitochondria might be due to the evolutionary origin (B-type/E-type) of the protein, rather than differences in its functional environment.}, } @article {pmid22803798, year = {2012}, author = {Katz, LA}, title = {Origin and diversification of eukaryotes.}, journal = {Annual review of microbiology}, volume = {66}, number = {}, pages = {411-427}, doi = {10.1146/annurev-micro-090110-102808}, pmid = {22803798}, issn = {1545-3251}, support = {1R15GM081865-01/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biodiversity ; *Biological Evolution ; Eukaryota/*classification/*genetics ; }, abstract = {The bulk of the diversity of eukaryotic life is microbial. Although the larger eukaryotes-namely plants, animals, and fungi-dominate our visual landscapes, microbial lineages compose the greater part of both genetic diversity and biomass, and contain many evolutionary innovations. Our understanding of the origin and diversification of eukaryotes has improved substantially with analyses of molecular data from diverse lineages. These data have provided insight into the nature of the genome of the last eukaryotic common ancestor (LECA). Yet, the origin of key eukaryotic features, namely the nucleus and cytoskeleton, remains poorly understood. In contrast, the past decades have seen considerable refinement in hypotheses on the major branching events in the evolution of eukaryotic diversity. New insights have also emerged, including evidence for the acquisition of mitochondria at the time of the origin of eukaryotes and data supporting the dynamic nature of genomes in LECA.}, } @article {pmid22796299, year = {2012}, author = {Lodé, T}, title = {For quite a few chromosomes more: the origin of eukaryotes….}, journal = {Journal of molecular biology}, volume = {423}, number = {2}, pages = {135-142}, doi = {10.1016/j.jmb.2012.07.005}, pmid = {22796299}, issn = {1089-8638}, mesh = {Cell Nucleus/metabolism ; Chromosomes/*genetics ; DNA/chemistry ; Eukaryota/*genetics ; Eukaryotic Cells/chemistry/metabolism ; Evolution, Molecular ; Genome ; Nuclear Envelope/metabolism ; Phylogeny ; }, abstract = {The evolution of eukaryotes addresses an enigmatic question: what are the evolutionary advantages of having a nucleus? The nucleus is traditionally thought to act as protection for DNA, but eukaryotes are more fragile than bacteria. The compartmentalization of the eukaryotic cell might stem from invaginations of the plasma membrane, and I argue that this autogenous origin of the nucleus constituted a selective innovation caused by cellular constraints due to a large genome. The protoeukaryotic nucleus appears to be a physical and chemical solution to the problem of large amounts of DNA in the form of many linear chromosomes. The selective advantages of having a nuclear envelope are to house a large genome in a stabilized structure and to decouple gene translation from transcription. Supporting the karyogenic model, this new hypothesis opens an original perspective to help in understanding the very ancient origin of eukaryotes.}, } @article {pmid22748146, year = {2012}, author = {De Craene, JO and Ripp, R and Lecompte, O and Thompson, JD and Poch, O and Friant, S}, title = {Evolutionary analysis of the ENTH/ANTH/VHS protein superfamily reveals a coevolution between membrane trafficking and metabolism.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {297}, pmid = {22748146}, issn = {1471-2164}, mesh = {Biological Evolution ; Cell Membrane/*metabolism ; Cytokinesis/physiology ; Genomics/*methods ; Phylogeny ; Protein Transport/*physiology ; Proteins/chemistry/classification/*metabolism ; }, abstract = {BACKGROUND: Membrane trafficking involves the complex regulation of proteins and lipids intracellular localization and is required for metabolic uptake, cell growth and development. Different trafficking pathways passing through the endosomes are coordinated by the ENTH/ANTH/VHS adaptor protein superfamily. The endosomes are crucial for eukaryotes since the acquisition of the endomembrane system was a central process in eukaryogenesis.

RESULTS: Our in silico analysis of this ENTH/ANTH/VHS superfamily, consisting of proteins gathered from 84 complete genomes representative of the different eukaryotic taxa, revealed that genomic distribution of this superfamily allows to discriminate Fungi and Metazoa from Plantae and Protists. Next, in a four way genome wide comparison, we showed that this discriminative feature is observed not only for other membrane trafficking effectors, but also for proteins involved in metabolism and in cytokinesis, suggesting that metabolism, cytokinesis and intracellular trafficking pathways co-evolved. Moreover, some of the proteins identified were implicated in multiple functions, in either trafficking and metabolism or trafficking and cytokinesis, suggesting that membrane trafficking is central to this co-evolution process.

CONCLUSIONS: Our study suggests that membrane trafficking and compartmentalization were not only key features for the emergence of eukaryotic cells but also drove the separation of the eukaryotes in the different taxa.}, } @article {pmid22507701, year = {2012}, author = {Rogozin, IB and Carmel, L and Csuros, M and Koonin, EV}, title = {Origin and evolution of spliceosomal introns.}, journal = {Biology direct}, volume = {7}, number = {}, pages = {11}, pmid = {22507701}, issn = {1745-6150}, support = {Z01LM000073-12/LM/NLM NIH HHS/United States ; //Intramural NIH HHS/United States ; }, mesh = {Alternative Splicing ; Animals ; Base Sequence ; Conserved Sequence ; Eukaryota/chemistry/classification/genetics ; *Evolution, Molecular ; Exons ; Genetics, Population ; Genome ; *Introns ; Phylogeny ; RNA Splice Sites ; Selection, Genetic ; Spliceosomes/chemistry/*genetics ; Untranslated Regions ; }, abstract = {Evolution of exon-intron structure of eukaryotic genes has been a matter of long-standing, intensive debate. The introns-early concept, later rebranded 'introns first' held that protein-coding genes were interrupted by numerous introns even at the earliest stages of life's evolution and that introns played a major role in the origin of proteins by facilitating recombination of sequences coding for small protein/peptide modules. The introns-late concept held that introns emerged only in eukaryotes and new introns have been accumulating continuously throughout eukaryotic evolution. Analysis of orthologous genes from completely sequenced eukaryotic genomes revealed numerous shared intron positions in orthologous genes from animals and plants and even between animals, plants and protists, suggesting that many ancestral introns have persisted since the last eukaryotic common ancestor (LECA). Reconstructions of intron gain and loss using the growing collection of genomes of diverse eukaryotes and increasingly advanced probabilistic models convincingly show that the LECA and the ancestors of each eukaryotic supergroup had intron-rich genes, with intron densities comparable to those in the most intron-rich modern genomes such as those of vertebrates. The subsequent evolution in most lineages of eukaryotes involved primarily loss of introns, with only a few episodes of substantial intron gain that might have accompanied major evolutionary innovations such as the origin of metazoa. The original invasion of self-splicing Group II introns, presumably originating from the mitochondrial endosymbiont, into the genome of the emerging eukaryote might have been a key factor of eukaryogenesis that in particular triggered the origin of endomembranes and the nucleus. Conversely, splicing errors gave rise to alternative splicing, a major contribution to the biological complexity of multicellular eukaryotes. There is no indication that any prokaryote has ever possessed a spliceosome or introns in protein-coding genes, other than relatively rare mobile self-splicing introns. Thus, the introns-first scenario is not supported by any evidence but exon-intron structure of protein-coding genes appears to have evolved concomitantly with the eukaryotic cell, and introns were a major factor of evolution throughout the history of eukaryotes.}, } @article {pmid22446522, year = {2011}, author = {Bernander, R and Lind, AE and Ettema, TJ}, title = {An archaeal origin for the actin cytoskeleton: Implications for eukaryogenesis.}, journal = {Communicative & integrative biology}, volume = {4}, number = {6}, pages = {664-667}, pmid = {22446522}, issn = {1942-0889}, abstract = {A hallmark of the eukaryotic cell is the actin cytoskeleton, involved in a wide array of processes ranging from shape determination and phagocytosis to intracellular transport and cytokinesis. Recently, we reported the discovery of an actin-based cytoskeleton also in Archaea. The archaeal actin ortholog, Crenactin, was shown to belong to a conserved operon, Arcade (actin-related cytoskeleton in Archaea involved in shape determination), encoding an additional set of cytoskeleton-associated proteins. Here, we elaborate on the implications of these findings for the evolutionary relation between archaea and eukaryotes, with particular focus on the possibility that eukaryotic actin and actin-related proteins have evolved from an ancestral archaeal actin gene. Archaeal actin could thus have played an important role in cellular processes essential for the origin and early evolution of the eukaryotic lineage. Further exploration of uncharacterized archaeal lineages is necessary to find additional missing pieces in the evolutionary trajectory that ultimately gave rise to present-day organisms.}, } @article {pmid22409430, year = {2012}, author = {Tian, HF and Feng, JM and Wen, JF}, title = {The evolution of cardiolipin biosynthesis and maturation pathways and its implications for the evolution of eukaryotes.}, journal = {BMC evolutionary biology}, volume = {12}, number = {}, pages = {32}, pmid = {22409430}, issn = {1471-2148}, mesh = {Base Sequence ; Bayes Theorem ; Biosynthetic Pathways/*physiology ; Cardiolipins/*biosynthesis/*metabolism ; Eukaryota/*enzymology/genetics/metabolism ; *Evolution, Molecular ; Likelihood Functions ; Membrane Proteins/metabolism/*physiology ; Models, Genetic ; Molecular Sequence Data ; Phospholipases A2, Calcium-Independent/genetics/metabolism ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Transferases (Other Substituted Phosphate Groups)/metabolism/*physiology ; }, abstract = {BACKGROUND: Cardiolipin (CL) is an important component in mitochondrial inner and bacterial membranes. Its appearance in these two biomembranes has been considered as evidence of the endosymbiotic origin of mitochondria. But CL was reported to be synthesized through two distinct enzymes--CLS_cap and CLS_pld in eukaryotes and bacteria. Therefore, how the CL biosynthesis pathway evolved is an interesting question.

RESULTS: Phylogenetic distribution investigation of CL synthase (CLS) showed: most bacteria have CLS_pld pathway, but in partial bacteria including proteobacteria and actinobacteria CLS_cap pathway has already appeared; in eukaryotes, Supergroup Opisthokonta and Archaeplastida, and Subgroup Stramenopiles, which all contain multicellular organisms, possess CLS_cap pathway, while Supergroup Amoebozoa and Excavata and Subgroup Alveolata, which all consist exclusively of unicellular eukaryotes, bear CLS_pld pathway; amitochondriate protists in any supergroups have neither. Phylogenetic analysis indicated the CLS_cap in eukaryotes have the closest relationship with those of alpha proteobacteria, while the CLS_pld in eukaryotes share a common ancestor but have no close correlation with those of any particular bacteria.

CONCLUSIONS: The first eukaryote common ancestor (FECA) inherited the CLS_pld from its bacterial ancestor (e. g. the bacterial partner according to any of the hypotheses about eukaryote evolution); later, when the FECA evolved into the last eukaryote common ancestor (LECA), the endosymbiotic mitochondria (alpha proteobacteria) brought in CLS_cap, and then in some LECA individuals the CLS_cap substituted the CLS_pld, and these LECAs would evolve into the protist lineages from which multicellular eukaryotes could arise, while in the other LECAs the CLS_pld was retained and the CLS_cap was lost, and these LECAs would evolve into the protist lineages possessing CLS_pld. Besides, our work indicated CL maturation pathway arose after the emergence of eukaryotes probably through mechanisms such as duplication of other genes, and gene duplication and loss occurred frequently at different lineage levels, increasing the pathway diversity probably to fit the complicated cellular process in various cells. Our work also implies the classification putting Stramenopiles and Alveolata together to form Chromalveolata may be unreasonable; the absence of CL synthesis and maturation pathways in amitochondriate protists is most probably due to secondary loss.}, } @article {pmid22399849, year = {2012}, author = {Syamaladevi, DP and Spudich, JA and Sowdhamini, R}, title = {Structural and functional insights on the Myosin superfamily.}, journal = {Bioinformatics and biology insights}, volume = {6}, number = {}, pages = {11-21}, pmid = {22399849}, issn = {1177-9322}, support = {R01 GM033289/GM/NIGMS NIH HHS/United States ; }, abstract = {The myosin superfamily is a versatile group of molecular motors involved in the transport of specific biomolecules, vesicles and organelles in eukaryotic cells. The processivity of myosins along an actin filament and transport of intracellular 'cargo' are achieved by generating physical force from chemical energy of ATP followed by appropriate conformational changes. The typical myosin has a head domain, which harbors an ATP binding site, an actin binding site, and a light-chain bound 'lever arm', followed often by a coiled coil domain and a cargo binding domain. Evolution of myosins started at the point of evolution of eukaryotes, S. cerevisiae being the simplest one known to contain these molecular motors. The coiled coil domain of the myosin classes II, V and VI in whole genomes of several model organisms display differences in the length and the strength of interactions at the coiled coil interface. Myosin II sequences have long-length coiled coil regions that are predicted to have a highly stable dimeric interface. These are interrupted, however, by regions that are predicted to be unstable, indicating possibilities of alternate conformations, associations to make thick filaments, and interactions with other molecules. Myosin V sequences retain intermittent regions of strong and weak interactions, whereas myosin VI sequences are relatively devoid of strong coiled coil motifs. Structural deviations at coiled coil regions could be important for carrying out normal biological function of these proteins.}, } @article {pmid22355196, year = {2012}, author = {Thiergart, T and Landan, G and Schenk, M and Dagan, T and Martin, WF}, title = {An evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin.}, journal = {Genome biology and evolution}, volume = {4}, number = {4}, pages = {466-485}, pmid = {22355196}, issn = {1759-6653}, support = {232975/ERC_/European Research Council/International ; }, mesh = {Archaea/genetics ; Bacteria/genetics ; Eukaryota/classification/*genetics ; *Evolution, Molecular ; *Genome ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {To test the predictions of competing and mutually exclusive hypotheses for the origin of eukaryotes, we identified from a sample of 27 sequenced eukaryotic and 994 sequenced prokaryotic genomes 571 genes that were present in the eukaryote common ancestor and that have homologues among eubacterial and archaebacterial genomes. Maximum-likelihood trees identified the prokaryotic genomes that most frequently contained genes branching as the sister to the eukaryotic nuclear homologues. Among the archaebacteria, euryarchaeote genomes most frequently harbored the sister to the eukaryotic nuclear gene, whereas among eubacteria, the α-proteobacteria were most frequently represented within the sister group. Only 3 genes out of 571 gave a 3-domain tree. Homologues from α-proteobacterial genomes that branched as the sister to nuclear genes were found more frequently in genomes of facultatively anaerobic members of the rhiozobiales and rhodospirilliales than in obligate intracellular ricketttsial parasites. Following α-proteobacteria, the most frequent eubacterial sister lineages were γ-proteobacteria, δ-proteobacteria, and firmicutes, which were also the prokaryote genomes least frequently found as monophyletic groups in our trees. Although all 22 higher prokaryotic taxa sampled (crenarchaeotes, γ-proteobacteria, spirochaetes, chlamydias, etc.) harbor genes that branch as the sister to homologues present in the eukaryotic common ancestor, that is not evidence of 22 different prokaryotic cells participating at eukaryote origins because prokaryotic "lineages" have laterally acquired genes for more than 1.5 billion years since eukaryote origins. The data underscore the archaebacterial (host) nature of the eukaryotic informational genes and the eubacterial (mitochondrial) nature of eukaryotic energy metabolism. The network linking genes of the eukaryote ancestor to contemporary homologues distributed across prokaryotic genomes elucidates eukaryote gene origins in a dialect cognizant of gene transfer in nature.}, } @article {pmid22247777, year = {2012}, author = {Xie, Q and Wang, Y and Lin, J and Qin, Y and Wang, Y and Bu, W}, title = {Potential key bases of ribosomal RNA to kingdom-specific spectra of antibiotic susceptibility and the possible archaeal origin of eukaryotes.}, journal = {PloS one}, volume = {7}, number = {1}, pages = {e29468}, pmid = {22247777}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/*metabolism ; Archaea/*genetics ; Base Pairing ; Base Sequence ; Binding Sites ; Escherichia coli/genetics/metabolism ; Eukaryota/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Peptidyl Transferases/metabolism ; RNA, Ribosomal/*genetics/*metabolism ; Ribosomes/*metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; Structure-Activity Relationship ; }, abstract = {In support of the hypothesis of the endosymbiotic origin of eukaryotes, much evidence has been found to support the idea that some organelles of eukaryotic cells originated from bacterial ancestors. Less attention has been paid to the identity of the host cell, although some biochemical and molecular genetic properties shared by archaea and eukaryotes have been documented. Through comparing 507 taxa of 16S-18S rDNA and 347 taxa of 23S-28S rDNA, we found that archaea and eukaryotes share twenty-six nucleotides signatures in ribosomal DNA. These signatures exist in all living eukaryotic organisms, whether protist, green plant, fungus, or animal. This evidence explicitly supports the archaeal origin of eukaryotes. In the ribosomal RNA, besides A2058 in Escherichia coli vs. G2400 in Saccharomyces cerevisiae, there still exist other twenties of sites, in which the bases are kingdom-specific. Some of these sites concentrate in the peptidyl transferase centre (PTC) of the 23S-28S rRNA. The results suggest potential key sites to explain the kingdom-specific spectra of drug resistance of ribosomes.}, } @article {pmid25382122, year = {2012}, author = {Egel, R}, title = {Primal eukaryogenesis: on the communal nature of precellular States, ancestral to modern life.}, journal = {Life (Basel, Switzerland)}, volume = {2}, number = {1}, pages = {170-212}, pmid = {25382122}, issn = {2075-1729}, abstract = {This problem-oriented, exploratory and hypothesis-driven discourse toward the unknown combines several basic tenets: (i) a photo-active metal sulfide scenario of primal biogenesis in the porespace of shallow sedimentary flats, in contrast to hot deep-sea hydrothermal vent conditions; (ii) an inherently complex communal system at the common root of present life forms; (iii) a high degree of internal compartmentalization at this communal root, progressively resembling coenocytic (syncytial) super-cells; (iv) a direct connection from such communal super-cells to proto-eukaryotic macro-cell organization; and (v) multiple rounds of micro-cellular escape with streamlined reductive evolution-leading to the major prokaryotic cell lines, as well as to megaviruses and other viral lineages. Hopefully, such nontraditional concepts and approaches will contribute to coherent and plausible views about the origins and early life on Earth. In particular, the coevolutionary emergence from a communal system at the common root can most naturally explain the vast discrepancy in subcellular organization between modern eukaryotes on the one hand and both archaea and bacteria on the other.}, } @article {pmid22185365, year = {2011}, author = {Diévart, A and Gilbert, N and Droc, G and Attard, A and Gourgues, M and Guiderdoni, E and Périn, C}, title = {Leucine-rich repeat receptor kinases are sporadically distributed in eukaryotic genomes.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {367}, pmid = {22185365}, issn = {1471-2148}, mesh = {Eukaryota/*genetics ; *Evolution, Molecular ; Genome ; Genome, Plant ; Oomycetes/genetics ; *Phylogeny ; Plants/genetics ; Protein Kinases/*genetics ; Sequence Alignment ; Sequence Analysis, Protein ; }, abstract = {BACKGROUND: Plant leucine-rich repeat receptor-like kinases (LRR-RLKs) are receptor kinases that contain LRRs in their extracellular domain. In the last 15 years, many research groups have demonstrated major roles played by LRR-RLKs in plants during almost all developmental processes throughout the life of the plant and in defense/resistance against a large range of pathogens. Recently, a breakthrough has been made in this field that challenges the dogma of the specificity of plant LRR-RLKs.

RESULTS: We analyzed ~1000 complete genomes and show that LRR-RK genes have now been identified in 8 non-plant genomes. We performed an exhaustive phylogenetic analysis of all of these receptors, revealing that all of the LRR-containing receptor subfamilies form lineage-specific clades. Our results suggest that the association of LRRs with RKs appeared independently at least four times in eukaryotic evolutionary history. Moreover, the molecular evolutionary history of the LRR-RKs found in oomycetes is reminiscent of the pattern observed in plants: expansion with amplification/deletion and evolution of the domain organization leading to the functional diversification of members of the gene family. Finally, the expression data suggest that oomycete LRR-RKs may play a role in several stages of the oomycete life cycle.

CONCLUSIONS: In view of the key roles that LRR-RLKs play throughout the entire lifetime of plants and plant-environment interactions, the emergence and expansion of this type of receptor in several phyla along the evolution of eukaryotes, and particularly in oomycete genomes, questions their intrinsic functions in mimicry and/or in the coevolution of receptors between hosts and pathogens.}, } @article {pmid22018741, year = {2011}, author = {Guy, L and Ettema, TJ}, title = {The archaeal 'TACK' superphylum and the origin of eukaryotes.}, journal = {Trends in microbiology}, volume = {19}, number = {12}, pages = {580-587}, doi = {10.1016/j.tim.2011.09.002}, pmid = {22018741}, issn = {1878-4380}, mesh = {Archaea/*classification/*genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; *Phylogeny ; }, abstract = {Although most hypotheses to explain the emergence of the eukaryotic lineage are conflicting, some consensus exists concerning the requirement of a genomic fusion between archaeal and bacterial components. Recent phylogenomic studies have provided support for eocyte-like scenarios in which the alleged 'archaeal parent' of the eukaryotic cell emerged from the Crenarchaeota/Thaumarchaeota. Here, we provide evidence for a scenario in which this archaeal parent emerged from within the 'TACK' superphylum that comprises the Thaumarchaeota, Crenarchaeota and Korarchaeota, as well as the recently proposed phylum 'Aigarchaeota'. In support of this view, functional and comparative genomics studies have unearthed an increasing number of features that are uniquely shared by the TACK superphylum and eukaryotes, including proteins involved in cytokinesis, membrane remodeling, cell shape determination and protein recycling.}, } @article {pmid22008946, year = {2011}, author = {Vesteg, M and Krajčovič, J}, title = {The falsifiability of the models for the origin of eukaryotes.}, journal = {Current genetics}, volume = {57}, number = {6}, pages = {367-390}, pmid = {22008946}, issn = {1432-0983}, mesh = {Archaea/genetics ; Bacteria/genetics ; *Biological Evolution ; *Eukaryotic Cells ; Models, Biological ; Phylogeny ; Symbiosis ; }, abstract = {One group of hypotheses suggests archaeal and/or bacterial ancestry of eukaryotes, while the second group suggests that the ancestor of eukaryotes was different. Especially, the followers of the first group of hypotheses should ask the following: is the replacement of archaeal lipids by bacterial (or vice versa) possible? Do the phylogenies support the origin of one domain from another (or the others)? Can we consider the nutritional mode to resolve the problems of cell origin(s)? Is there any evidence that the ancestor of eukaryotes was intron-free? Would the symbiosis of α-proteobacterial ancestors of mitochondria be successful in an asexual host? Is there evidence that the last universal common ancestor (LUCA) or the last eukaryotic common ancestor was bounded by one membrane only? With respect to the current knowledge about cells and their molecular components, the answer to most of these questions is: No! A model for the origins of domains is briefly presented which cannot be assigned as false through the current scientific data, and is rather consistent with the assumption that eukaryotes are direct descendants of neither archaea nor bacteria. It is proposed that the domain Bacteria arose the first, and that the last common ancestor of Archaea and Eukarya was a pre-cell or a progenote similar to LUCA. The pre-karyote (the host entity for α-proteobacterial ancestors of mitochondria) was probably bounded by two membranes, possessed spliceosomal introns and spliceosomes, was sexual, and α-proteobacterial ancestors of mitochondria were most likely parasites of the pre-karyote periplasm (intermembrane space).}, } @article {pmid21963440, year = {2012}, author = {Suvorova, ES and Lehmann, MM and Kratzer, S and White, MW}, title = {Nuclear actin-related protein is required for chromosome segregation in Toxoplasma gondii.}, journal = {Molecular and biochemical parasitology}, volume = {181}, number = {1}, pages = {7-16}, pmid = {21963440}, issn = {1872-9428}, support = {R01 AI077662/AI/NIAID NIH HHS/United States ; R01-AI077662/AI/NIAID NIH HHS/United States ; R01 AI077662-03/AI/NIAID NIH HHS/United States ; R01-AI089885/AI/NIAID NIH HHS/United States ; R01 AI089885/AI/NIAID NIH HHS/United States ; R01 AI089885-01A1/AI/NIAID NIH HHS/United States ; R01 AI077662-02/AI/NIAID NIH HHS/United States ; }, mesh = {Actins/chemistry/genetics/*metabolism ; Amino Acid Substitution ; Chromosome Mapping ; *Chromosome Segregation ; Genetic Complementation Test ; *Mitosis ; Mutant Proteins/chemistry/genetics/metabolism ; Mutation ; Nuclear Proteins/chemistry/genetics/*metabolism ; Protein Stability ; Temperature ; Toxoplasma/growth & development/*physiology ; }, abstract = {Apicomplexa parasites use complex cell cycles to replicate that are not well understood mechanistically. We have established a robust forward genetic strategy to identify the essential components of parasite cell division. Here we describe a novel temperature sensitive Toxoplasma strain, mutant 13-20C2, which growth arrests due to a defect in mitosis. The primary phenotype is the mis-segregation of duplicated chromosomes with chromosome loss during nuclear division. This defect is conditional-lethal with respect to temperature, although relatively mild in regard to the preservation of the major microtubule organizing centers. Despite severe DNA loss many of the physical structures associated with daughter budding and the assembly of invasion structures formed and operated normally at the non-permissive temperature before completely arresting. These results suggest there are coordinating mechanisms that govern the timing of these events in the parasite cell cycle. The defect in mutant 13-20C2 was mapped by genetic complementation to Toxoplasma chromosome III and to a specific mutation in the gene encoding an ortholog of nuclear actin-related protein 4. A change in a conserved isoleucine to threonine in the helical structure of this nuclear actin related protein leads to protein instability and cellular mis-localization at the higher temperature. Given the age of this protist family, the results indicate a key role for nuclear actin-related proteins in chromosome segregation was established very early in the evolution of eukaryotes.}, } @article {pmid21920985, year = {2011}, author = {Reynaud, EG and Devos, DP}, title = {Transitional forms between the three domains of life and evolutionary implications.}, journal = {Proceedings. Biological sciences}, volume = {278}, number = {1723}, pages = {3321-3328}, pmid = {21920985}, issn = {1471-2954}, mesh = {Archaea/cytology/*genetics/metabolism ; Bacteria/cytology/*genetics/metabolism ; *Biological Evolution ; Eukaryota/cytology/*genetics/metabolism ; *Models, Genetic ; *Phylogeny ; }, abstract = {The question as to the origin and relationship between the three domains of life is lodged in a phylogenetic impasse. The dominant paradigm is to see the three domains as separated. However, the recently characterized bacterial species have suggested continuity between the three domains. Here, we review the evidence in support of this hypothesis and evaluate the implications for and against the models of the origin of the three domains of life. The existence of intermediate steps between the three domains discards the need for fusion to explain eukaryogenesis and suggests that the last universal common ancestor was complex. We propose a scenario in which the ancestor of the current bacterial Planctomycetes, Verrucomicrobiae and Chlamydiae superphylum was related to the last archaeal and eukaryotic common ancestor, thus providing a way out of the phylogenetic impasse.}, } @article {pmid21900601, year = {2011}, author = {Zhou, R and Moshgabadi, N and Adams, KL}, title = {Extensive changes to alternative splicing patterns following allopolyploidy in natural and resynthesized polyploids.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {38}, pages = {16122-16127}, pmid = {21900601}, issn = {1091-6490}, mesh = {Alternative Splicing/*genetics ; Base Sequence ; Brassica/classification/*genetics ; Brassica napus/genetics ; Brassica rapa/genetics ; Cotyledon/genetics ; *Evolution, Molecular ; Gene Expression Regulation, Plant ; Genes, Duplicate/genetics ; Genes, Plant/genetics ; Plant Leaves/genetics ; *Polyploidy ; Reverse Transcriptase Polymerase Chain Reaction ; Species Specificity ; Temperature ; }, abstract = {Polyploidy has been a common process during the evolution of eukaryotes, especially plants, leading to speciation and the evolution of new gene functions. Gene expression levels and patterns can change, and gene silencing can occur in allopolyploids--phenomena sometimes referred to as "transcriptome shock." Alternative splicing (AS) creates multiple mature mRNAs from a single type of precursor mRNA. Here we examined the evolution of AS patterns after polyploidy, with natural and two resynthesized allotetraploid Brassica napus lines, using RT-PCR and sequencing assays of 82 AS events in duplicated gene pairs (homeologs). Comparing the AS patterns between the two homeologs in natural B. napus revealed that many of the gene pairs show different AS patterns, with a few showing variation that was organ specific or induced by abiotic stress treatments. In the resynthesized allotetraploids, 26-30% of the duplicated genes showed changes in AS compared with the parents, including many cases of AS event loss after polyploidy. Parallel losses of many AS events after allopolyploidy were detected in the two independently resynthesized lines. More changes occurred in parallel between the two lines than changes specific to each line. The PASTICCINO gene showed partitioning of two AS events between the two homeologs in the resynthesized allopolyploids. AS changes after allopolyploidy were much more common than homeolog silencing. Our findings indicate that AS patterns can change rapidly after polyploidy, that many genes are affected, and that AS changes are an important component of the transcriptome shock experienced by new allopolyploids.}, } @article {pmid21859859, year = {2011}, author = {Wickstead, B and Gull, K}, title = {The evolution of the cytoskeleton.}, journal = {The Journal of cell biology}, volume = {194}, number = {4}, pages = {513-525}, pmid = {21859859}, issn = {1540-8140}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Cytoskeletal Proteins/chemistry/genetics/*metabolism ; Cytoskeleton/genetics/*physiology ; Eukaryotic Cells/*physiology ; *Evolution, Molecular ; Gene Expression Regulation ; Humans ; Phylogeny ; Prokaryotic Cells/*physiology ; }, abstract = {The cytoskeleton is a system of intracellular filaments crucial for cell shape, division, and function in all three domains of life. The simple cytoskeletons of prokaryotes show surprising plasticity in composition, with none of the core filament-forming proteins conserved in all lineages. In contrast, eukaryotic cytoskeletal function has been hugely elaborated by the addition of accessory proteins and extensive gene duplication and specialization. Much of this complexity evolved before the last common ancestor of eukaryotes. The distribution of cytoskeletal filaments puts constraints on the likely prokaryotic line that made this leap of eukaryogenesis.}, } @article {pmid21849086, year = {2011}, author = {Xie, X and Jin, J and Mao, Y}, title = {Evolutionary versatility of eukaryotic protein domains revealed by their bigram networks.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {242}, pmid = {21849086}, issn = {1471-2148}, mesh = {Adaptation, Biological/*genetics ; Cluster Analysis ; Computational Biology/*methods ; Eukaryota/*genetics ; *Evolution, Molecular ; Humans ; *Models, Genetic ; Protein Structure, Tertiary/*genetics ; Proteins/*genetics ; }, abstract = {BACKGROUND: Protein domains are globular structures of independently folded polypeptides that exert catalytic or binding activities. Their sequences are recognized as evolutionary units that, through genome recombination, constitute protein repertoires of linkage patterns. Via mutations, domains acquire modified functions that contribute to the fitness of cells and organisms. Recent studies have addressed the evolutionary selection that may have shaped the functions of individual domains and the emergence of particular domain combinations, which led to new cellular functions in multi-cellular animals. This study focuses on modeling domain linkage globally and investigates evolutionary implications that may be revealed by novel computational analysis.

RESULTS: A survey of 77 completely sequenced eukaryotic genomes implies a potential hierarchical and modular organization of biological functions in most living organisms. Domains in a genome or multiple genomes are modeled as a network of hetero-duplex covalent linkages, termed bigrams. A novel computational technique is introduced to decompose such networks, whereby the notion of domain "networking versatility" is derived and measured. The most and least "versatile" domains (termed "core domains" and "peripheral domains" respectively) are examined both computationally via sequence conservation measures and experimentally using selected domains. Our study suggests that such a versatility measure extracted from the bigram networks correlates with the adaptivity of domains during evolution, where the network core domains are highly adaptive, significantly contrasting the network peripheral domains.

CONCLUSIONS: Domain recombination has played a major part in the evolution of eukaryotes attributing to genome complexity. From a system point of view, as the results of selection and constant refinement, networks of domain linkage are structured in a hierarchical modular fashion. Domains with high degree of networking versatility appear to be evolutionary adaptive, potentially through functional innovations. Domain bigram networks are informative as a model of biological functions. The networking versatility indices extracted from such networks for individual domains reflect the strength of evolutionary selection that the domains have experienced.}, } @article {pmid21810989, year = {2011}, author = {Parfrey, LW and Lahr, DJ and Knoll, AH and Katz, LA}, title = {Estimating the timing of early eukaryotic diversification with multigene molecular clocks.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {33}, pages = {13624-13629}, pmid = {21810989}, issn = {1091-6490}, mesh = {*Biological Evolution ; Eukaryotic Cells/*classification ; Fossils ; Oceans and Seas ; *Phylogeny ; *Time ; }, abstract = {Although macroscopic plants, animals, and fungi are the most familiar eukaryotes, the bulk of eukaryotic diversity is microbial. Elucidating the timing of diversification among the more than 70 lineages is key to understanding the evolution of eukaryotes. Here, we use taxon-rich multigene data combined with diverse fossils and a relaxed molecular clock framework to estimate the timing of the last common ancestor of extant eukaryotes and the divergence of major clades. Overall, these analyses suggest that the last common ancestor lived between 1866 and 1679 Ma, consistent with the earliest microfossils interpreted with confidence as eukaryotic. During this interval, the Earth's surface differed markedly from today; for example, the oceans were incompletely ventilated, with ferruginous and, after about 1800 Ma, sulfidic water masses commonly lying beneath moderately oxygenated surface waters. Our time estimates also indicate that the major clades of eukaryotes diverged before 1000 Ma, with most or all probably diverging before 1200 Ma. Fossils, however, suggest that diversity within major extant clades expanded later, beginning about 800 Ma, when the oceans began their transition to a more modern chemical state. In combination, paleontological and molecular approaches indicate that long stems preceded diversification in the major eukaryotic lineages.}, } @article {pmid21795752, year = {2011}, author = {Alvarez-Ponce, D and McInerney, JO}, title = {The human genome retains relics of its prokaryotic ancestry: human genes of archaebacterial and eubacterial origin exhibit remarkable differences.}, journal = {Genome biology and evolution}, volume = {3}, number = {}, pages = {782-790}, pmid = {21795752}, issn = {1759-6653}, mesh = {Animals ; Archaea/*genetics ; Bacteria/*genetics ; Computational Biology ; *Evolution, Molecular ; Genes, Bacterial/genetics ; Genes, Lethal ; Genetic Diseases, Inborn/genetics ; Genome, Human/*genetics ; Humans ; Mice ; Symbiosis/genetics ; }, abstract = {Eukaryotes are generally thought to stem from a fusion event involving an archaebacterium and a eubacterium. As a result of this event, contemporaneous eukaryotic genomes are chimeras of genes inherited from both endosymbiotic partners. These two coexisting gene repertoires have been shown to differ in a number of ways in yeast. Here we combine genomic and functional data in order to determine if and how human genes that have been inherited from both prokaryotic ancestors remain distinguishable. We show that, despite being fewer in number, human genes of archaebacterial origin are more highly and broadly expressed across tissues, are more likely to have lethal mouse orthologs, tend to be involved in informational processes, are more selectively constrained, and encode shorter and more central proteins in the protein-protein interaction network than eubacterium-like genes. Furthermore, consistent with endosymbiotic theory, we show that proteins tend to interact with those encoded by genes of the same ancestry. Most interestingly from a human health perspective, archaebacterial genes are less likely to be involved in heritable human disease. Taken together, these results show that more than 2 billion years after eukaryogenesis, the human genome retains at least two somewhat distinct communities of genes.}, } @article {pmid21760940, year = {2011}, author = {Schlüter, A and Ruiz-Trillo, I and Pujol, A}, title = {Phylogenomic evidence for a myxococcal contribution to the mitochondrial fatty acid beta-oxidation.}, journal = {PloS one}, volume = {6}, number = {7}, pages = {e21989}, pmid = {21760940}, issn = {1932-6203}, mesh = {Acyl Coenzyme A/metabolism ; Eukaryota/metabolism ; Fatty Acids/*metabolism ; *Genomics ; Metabolic Networks and Pathways ; Mitochondria/*genetics ; Models, Biological ; Myxococcales/*genetics ; Oxidation-Reduction ; *Phylogeny ; Proteins/genetics ; }, abstract = {BACKGROUND: The origin of eukaryotes remains a fundamental question in evolutionary biology. Although it is clear that eukaryotic genomes are a chimeric combination of genes of eubacterial and archaebacterial ancestry, the specific ancestry of most eubacterial genes is still unknown. The growing availability of microbial genomes offers the possibility of analyzing the ancestry of eukaryotic genomes and testing previous hypotheses on their origins.

Here, we have applied a phylogenomic analysis to investigate a possible contribution of the Myxococcales to the first eukaryotes. We conducted a conservative pipeline with homologous sequence searches against a genomic sampling of 40 eukaryotic and 357 prokaryotic genomes. The phylogenetic reconstruction showed that several eukaryotic proteins traced to Myxococcales. Most of these proteins were associated with mitochondrial lipid intermediate pathways, particularly enzymes generating reducing equivalents with pivotal roles in fatty acid β-oxidation metabolism. Our data suggest that myxococcal species with the ability to oxidize fatty acids transferred several genes to eubacteria that eventually gave rise to the mitochondrial ancestor. Later, the eukaryotic nucleocytoplasmic lineage acquired those metabolic genes through endosymbiotic gene transfer.

CONCLUSIONS/SIGNIFICANCE: Our results support a prokaryotic origin, different from α-proteobacteria, for several mitochondrial genes. Our data reinforce a fluid prokaryotic chromosome model in which the mitochondrion appears to be an important entry point for myxococcal genes to enter eukaryotes.}, } @article {pmid21749854, year = {2011}, author = {Cardol, P}, title = {Mitochondrial NADH:ubiquinone oxidoreductase (complex I) in eukaryotes: a highly conserved subunit composition highlighted by mining of protein databases.}, journal = {Biochimica et biophysica acta}, volume = {1807}, number = {11}, pages = {1390-1397}, doi = {10.1016/j.bbabio.2011.06.015}, pmid = {21749854}, issn = {0006-3002}, mesh = {Amino Acid Sequence ; Animals ; Data Mining ; *Databases, Protein ; Electron Transport Complex I/chemistry/*genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Protein Subunits/chemistry/*genetics ; Sequence Alignment ; }, abstract = {Complex I (NADH:ubiquinone oxidoreductase) is the largest enzyme of the mitochondrial respiratory chain. Compared to its bacterial counterpart which encompasses 14-17 subunits, mitochondrial complex I has almost tripled its subunit composition during evolution of eukaryotes, by recruitment of so-called accessory subunits, part of them being specific to distinct evolutionary lineages. The increasing availability of numerous broadly sampled eukaryotic genomes now enables the reconstruction of the evolutionary history of this large protein complex. Here, a combination of profile-based sequence comparisons and basic structural properties analyses at the protein level enabled to pinpoint homology relationships between complex I subunits from fungi, mammals or green plants, previously identified as "lineage-specific" subunits. In addition, homologs of at least 40 mammalian complex I subunits are present in representatives of all major eukaryote assemblages, half of them having not been investigated so far (Excavates, Chromalveolates, Amoebozoa). This analysis revealed that complex I was subject to a phenomenal increase in size that predated the diversification of extant eukaryotes, followed by very few lineage-specific additions/losses of subunits. The implications of this subunit conservation for studies of complex I are discussed.}, } @article {pmid21714941, year = {2011}, author = {Lane, N}, title = {Energetics and genetics across the prokaryote-eukaryote divide.}, journal = {Biology direct}, volume = {6}, number = {}, pages = {35}, pmid = {21714941}, issn = {1745-6150}, mesh = {Adenosine Triphosphate/metabolism ; *Biological Evolution ; Cell Cycle ; Cell Membrane/physiology ; Cell Nucleus/genetics ; Cytoplasm/genetics/physiology ; *Energy Metabolism ; Eukaryotic Cells/*cytology/physiology ; Gene Transfer, Horizontal ; Genes, Mitochondrial ; Introns ; Mitochondria/genetics/physiology ; Mutation ; Oxidative Phosphorylation ; Phylogeny ; Prokaryotic Cells/*cytology/physiology ; Selection, Genetic ; *Symbiosis ; }, abstract = {BACKGROUND: All complex life on Earth is eukaryotic. All eukaryotic cells share a common ancestor that arose just once in four billion years of evolution. Prokaryotes show no tendency to evolve greater morphological complexity, despite their metabolic virtuosity. Here I argue that the eukaryotic cell originated in a unique prokaryotic endosymbiosis, a singular event that transformed the selection pressures acting on both host and endosymbiont.

RESULTS: The reductive evolution and specialisation of endosymbionts to mitochondria resulted in an extreme genomic asymmetry, in which the residual mitochondrial genomes enabled the expansion of bioenergetic membranes over several orders of magnitude, overcoming the energetic constraints on prokaryotic genome size, and permitting the host cell genome to expand (in principle) over 200,000-fold. This energetic transformation was permissive, not prescriptive; I suggest that the actual increase in early eukaryotic genome size was driven by a heavy early bombardment of genes and introns from the endosymbiont to the host cell, producing a high mutation rate. Unlike prokaryotes, with lower mutation rates and heavy selection pressure to lose genes, early eukaryotes without genome-size limitations could mask mutations by cell fusion and genome duplication, as in allopolyploidy, giving rise to a proto-sexual cell cycle. The side effect was that a large number of shared eukaryotic basal traits accumulated in the same population, a sexual eukaryotic common ancestor, radically different to any known prokaryote.

CONCLUSIONS: The combination of massive bioenergetic expansion, release from genome-size constraints, and high mutation rate favoured a protosexual cell cycle and the accumulation of eukaryotic traits. These factors explain the unique origin of eukaryotes, the absence of true evolutionary intermediates, and the evolution of sex in eukaryotes but not prokaryotes.

REVIEWERS: This article was reviewed by: Eugene Koonin, William Martin, Ford Doolittle and Mark van der Giezen. For complete reports see the Reviewers' Comments section.}, } @article {pmid21690562, year = {2011}, author = {Sassera, D and Lo, N and Epis, S and D'Auria, G and Montagna, M and Comandatore, F and Horner, D and Peretó, J and Luciano, AM and Franciosi, F and Ferri, E and Crotti, E and Bazzocchi, C and Daffonchio, D and Sacchi, L and Moya, A and Latorre, A and Bandi, C}, title = {Phylogenomic evidence for the presence of a flagellum and cbb(3) oxidase in the free-living mitochondrial ancestor.}, journal = {Molecular biology and evolution}, volume = {28}, number = {12}, pages = {3285-3296}, doi = {10.1093/molbev/msr159}, pmid = {21690562}, issn = {1537-1719}, mesh = {Base Sequence ; *Biological Evolution ; Electron Transport Complex IV/*genetics ; Eukaryotic Cells ; Evolution, Molecular ; Flagella/*genetics ; Genome, Bacterial ; Mitochondria/*genetics/*physiology/*ultrastructure ; Oxidative Phosphorylation ; Phylogeny ; Rickettsieae/*genetics ; Sequence Analysis, DNA ; *Symbiosis/genetics ; }, abstract = {The initiation of the intracellular symbiosis that would give rise to mitochondria and eukaryotes was a major event in the history of life on earth. Hypotheses to explain eukaryogenesis fall into two broad and competing categories: those proposing that the host was a phagocytotic proto-eukaryote that preyed upon the free-living mitochondrial ancestor (hereafter FMA), and those proposing that the host was an archaebacterium that engaged in syntrophy with the FMA. Of key importance to these hypotheses are whether the FMA was motile or nonmotile, and the atmospheric conditions under which the FMA thrived. Reconstructions of the FMA based on genome content of Rickettsiales representatives-generally considered to be the closest living relatives of mitochondria-indicate that it was nonmotile and aerobic. We have sequenced the genome of Candidatus Midichloria mitochondrii, a novel and phylogenetically divergent member of the Rickettsiales. We found that it possesses unique gene sets found in no other Rickettsiales, including 26 genes associated with flagellar assembly, and a cbb(3)-type cytochrome oxidase. Phylogenomic analyses show that these genes were inherited in a vertical fashion from an ancestral α-proteobacterium, and indicate that the FMA possessed a flagellum, and could undergo oxidative phosphorylation under both aerobic and microoxic conditions. These results indicate that the FMA played a more active and potentially parasitic role in eukaryogenesis than currently appreciated and provide an explanation for how the symbiosis could have evolved under low levels of oxygen.}, } @article {pmid21664808, year = {2011}, author = {Brodsky, JL and Skach, WR}, title = {Protein folding and quality control in the endoplasmic reticulum: Recent lessons from yeast and mammalian cell systems.}, journal = {Current opinion in cell biology}, volume = {23}, number = {4}, pages = {464-475}, pmid = {21664808}, issn = {1879-0410}, support = {P30 DK079307-04/DK/NIDDK NIH HHS/United States ; GM75061/GM/NIGMS NIH HHS/United States ; GM53457/GM/NIGMS NIH HHS/United States ; P30 DK079307/DK/NIDDK NIH HHS/United States ; DK79307/DK/NIDDK NIH HHS/United States ; DK51818/DK/NIDDK NIH HHS/United States ; R01 GM075061/GM/NIGMS NIH HHS/United States ; K01 DK078734/DK/NIDDK NIH HHS/United States ; R01 GM075061-06/GM/NIGMS NIH HHS/United States ; R01 DK051818/DK/NIDDK NIH HHS/United States ; R01 GM053457/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Endoplasmic Reticulum/enzymology/*metabolism ; Humans ; Mammals/*metabolism ; Membrane Proteins/metabolism ; *Protein Folding ; Proteins/*metabolism ; Yeasts/cytology/*metabolism ; }, abstract = {The evolution of eukaryotes was accompanied by an increased need for intracellular communication and cellular specialization. Thus, a more complex collection of secreted and membrane proteins had to be synthesized, modified, and folded. The endoplasmic reticulum (ER) thereby became equipped with devoted enzymes and associated factors that both catalyze the production of secreted proteins and remove damaged proteins. A means to modify ER function to accommodate and destroy misfolded proteins also evolved. Not surprisingly, a growing number of human diseases are linked to various facets of ER function. Each of these topics will be discussed in this article, with an emphasis on recent reports in the literature that employed diverse models.}, } @article {pmid21595937, year = {2011}, author = {Chernikova, D and Motamedi, S and Csürös, M and Koonin, EV and Rogozin, IB}, title = {A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes.}, journal = {Biology direct}, volume = {6}, number = {}, pages = {26}, pmid = {21595937}, issn = {1745-6150}, support = {//Intramural NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; *Amino Acid Substitution ; Biological Evolution ; Conserved Sequence ; Eukaryota/*genetics ; *Evolution, Molecular ; Fossils ; Genetic Speciation ; *Genome ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; }, abstract = {BACKGROUND: Accurate estimation of the divergence time of the extant eukaryotes is a fundamentally important but extremely difficult problem owing primarily to gross violations of the molecular clock at long evolutionary distances and the lack of appropriate calibration points close to the date of interest. These difficulties are intrinsic to the dating of ancient divergence events and are reflected in the large discrepancies between estimates obtained with different approaches. Estimates of the age of Last Eukaryotic Common Ancestor (LECA) vary approximately twofold, from ~1,100 million years ago (Mya) to ~2,300 Mya.

RESULTS: We applied the genome-wide analysis of rare genomic changes associated with conserved amino acids (RGC_CAs) and used several independent techniques to obtain date estimates for the divergence of the major lineages of eukaryotes with calibration intervals for insects, land plants and vertebrates. The results suggest an early divergence of monocot and dicot plants, approximately 340 Mya, raising the possibility of plant-insect coevolution. The divergence of bilaterian animal phyla is estimated at ~400-700 Mya, a range of dates that is consistent with cladogenesis immediately preceding the Cambrian explosion. The origin of opisthokonts (the supergroup of eukaryotes that includes metazoa and fungi) is estimated at ~700-1,000 Mya, and the age of LECA at ~1,000-1,300 Mya. We separately analyzed the red algal calibration interval which is based on single fossil. This analysis produced time estimates that were systematically older compared to the other estimates. Nevertheless, the majority of the estimates for the age of the LECA using the red algal data fell within the 1,200-1,400 Mya interval.

CONCLUSION: The inference of a "young LECA" is compatible with the latest of previously estimated dates and has substantial biological implications. If these estimates are valid, the approximately 1 to 1.4 billion years of evolution of eukaryotes that is open to comparative-genomic study probably was preceded by hundreds of millions years of evolution that might have included extinct diversity inaccessible to comparative approaches.

REVIEWERS: This article was reviewed by William Martin, Herve Philippe (nominated by I. King Jordan), and Romain Derelle.}, } @article {pmid21512129, year = {2011}, author = {Xiong, Z and Gaeta, RT and Pires, JC}, title = {Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {19}, pages = {7908-7913}, pmid = {21512129}, issn = {1091-6490}, mesh = {Aneuploidy ; Base Sequence ; Brassica napus/*genetics ; Chromosomal Instability ; Chromosomes, Plant/genetics ; Cytogenetic Analysis ; DNA Shuffling ; DNA, Plant/genetics ; DNA, Ribosomal/genetics ; Dosage Compensation, Genetic ; Gene Rearrangement ; Genome, Plant ; In Situ Hybridization, Fluorescence ; Karyotyping ; *Polyploidy ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 5S/genetics ; }, abstract = {Polyploidy has contributed to the evolution of eukaryotes, particularly flowering plants. The genomic consequences of polyploidy have been extensively studied, but the mechanisms for chromosome stability and diploidization in polyploids remain largely unknown. By using new cytogenetic tools to identify all of the homoeologous chromosomes, we conducted a cytological investigation of 50 resynthesized Brassica napus allopolyploids across generations S(0:1) to S(5:6) and in the S(10:11) generation. Changes in copy number of individual chromosomes were detected in the S(0:1) generation and increased in subsequent generations, despite the fact that the mean chromosome number among lines was approximately 38. The chromosome complement of individual plants (segregants) ranged from 36 to 42, with a bias toward the accumulation of extra chromosomes. Karyotype analysis of the S(10:11) generation detected aneuploidy and inter- and intragenomic rearrangements, chromosome breakage and fusion, rDNA changes, and loss of repeat sequences. Chromosome sets with extensive homoeology showed the greatest instability. Dosage balance requirements maintained chromosome numbers at or near the tetraploid level, and the loss and gain of chromosomes frequently involved homoeologous chromosome replacement and compensation. These data indicate that early generations of resynthesized B. napus involved aneuploidy and gross chromosomal rearrangements, and that dosage balance mechanisms enforced chromosome number stability. Seed yield and pollen viability were inversely correlated with increasing aneuploidy, and the greatest fertility was observed in two lines that were additive for parental chromosomes. These data on resynthesized B. napus and the correlation of fertility with additive karyotypes cast light on the origins and establishment of natural B. napus.}, } @article {pmid21337482, year = {2011}, author = {Paleos, CM and Tsiourvas, D and Sideratou, Z}, title = {Interaction of vesicles: adhesion, fusion and multicompartment systems formation.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {12}, number = {4}, pages = {510-521}, doi = {10.1002/cbic.201000614}, pmid = {21337482}, issn = {1439-7633}, mesh = {Cell Adhesion ; *Cell Compartmentation ; Microscopy, Electron, Transmission ; Molecular Structure ; Transport Vesicles/*chemistry ; }, abstract = {In this review, interactions of selected vesicles, induced either by molecular recognition or by electrostatic interactions, for the simulation of cell-cell and cell-drug interaction processes are discussed. In order of increasing complexity, examples of vesicles adhesion are presented at first, followed by recognition experiments in which fusion takes place. This differentiation in behavior was primarily attributed to the structural features of interacting vesicular pairs primarily affected by concentration and lateral phase separation of the anchored recognizable groups. In certain cases, fusion is accompanied by multicompartmentalization of the obtained aggregates. In connection with the formation of these multicompartment systems, it was proposed that an analogous mechanism could be operating in the evolution of eukaryotes during the symbiosis of prokaryotes.}, } @article {pmid21232122, year = {2011}, author = {Mayer, WE and Schuster, LN and Bartelmes, G and Dieterich, C and Sommer, RJ}, title = {Horizontal gene transfer of microbial cellulases into nematode genomes is associated with functional assimilation and gene turnover.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {13}, pmid = {21232122}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Animals ; Cellulase/chemistry/*genetics/*metabolism ; *Gene Transfer, Horizontal ; *Genome, Helminth ; Helminth Proteins/chemistry/*genetics/*metabolism ; Molecular Sequence Data ; Nematoda/classification/*enzymology/genetics ; Sequence Alignment ; }, abstract = {BACKGROUND: Natural acquisition of novel genes from other organisms by horizontal or lateral gene transfer is well established for microorganisms. There is now growing evidence that horizontal gene transfer also plays important roles in the evolution of eukaryotes. Genome-sequencing and EST projects of plant and animal associated nematodes such as Brugia, Meloidogyne, Bursaphelenchus and Pristionchus indicate horizontal gene transfer as a key adaptation towards parasitism and pathogenicity. However, little is known about the functional activity and evolutionary longevity of genes acquired by horizontal gene transfer and the mechanisms favoring such processes.

RESULTS: We examine the transfer of cellulase genes to the free-living and beetle-associated nematode Pristionchus pacificus, for which detailed phylogenetic knowledge is available, to address predictions by evolutionary theory for successful gene transfer. We used transcriptomics in seven Pristionchus species and three other related diplogastrid nematodes with a well-defined phylogenetic framework to study the evolution of ancestral cellulase genes acquired by horizontal gene transfer. We performed intra-species, inter-species and inter-genic analysis by comparing the transcriptomes of these ten species and tested for cellulase activity in each species. Species with cellulase genes in their transcriptome always exhibited cellulase activity indicating functional integration into the host's genome and biology. The phylogenetic profile of cellulase genes was congruent with the species phylogeny demonstrating gene longevity. Cellulase genes show notable turnover with elevated birth and death rates. Comparison by sequencing of three selected cellulase genes in 24 natural isolates of Pristionchus pacificus suggests these high evolutionary dynamics to be associated with copy number variations and positive selection.

CONCLUSION: We could demonstrate functional integration of acquired cellulase genes into the nematode's biology as predicted by theory. Thus, functional assimilation, remarkable gene turnover and selection might represent key features of horizontal gene transfer events in nematodes.}, } @article {pmid21223572, year = {2011}, author = {Serpeloni, M and Vidal, NM and Goldenberg, S and Avila, AR and Hoffmann, FG}, title = {Comparative genomics of proteins involved in RNA nucleocytoplasmic export.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {7}, pmid = {21223572}, issn = {1471-2148}, mesh = {Active Transport, Cell Nucleus ; Cell Nucleus/genetics/*metabolism ; Eukaryota/classification/*genetics/metabolism ; *Genomics ; Phylogeny ; Proteins/genetics/*metabolism ; RNA/genetics/*metabolism ; *RNA Transport ; }, abstract = {BACKGROUND: The establishment of the nuclear membrane resulted in the physical separation of transcription and translation, and presented early eukaryotes with a formidable challenge: how to shuttle RNA from the nucleus to the locus of protein synthesis. In prokaryotes, mRNA is translated as it is being synthesized, whereas in eukaryotes mRNA is synthesized and processed in the nucleus, and it is then exported to the cytoplasm. In metazoa and fungi, the different RNA species are exported from the nucleus by specialized pathways. For example, tRNA is exported by exportin-t in a RanGTP-dependent fashion. By contrast, mRNAs are associated to ribonucleoproteins (RNPs) and exported by an essential shuttling complex (TAP-p15 in human, Mex67-mtr2 in yeast) that transports them through the nuclear pore. The different RNA export pathways appear to be well conserved among members of Opisthokonta, the eukaryotic supergroup that includes Fungi and Metazoa. However, it is not known whether RNA export in the other eukaryotic supergroups follows the same export routes as in opisthokonts.

METHODS: Our objective was to reconstruct the evolutionary history of the different RNA export pathways across eukaryotes. To do so, we screened an array of eukaryotic genomes for the presence of homologs of the proteins involved in RNA export in Metazoa and Fungi, using human and yeast proteins as queries.

RESULTS: Our genomic comparisons indicate that the basic components of the RanGTP-dependent RNA pathways are conserved across eukaryotes, and thus we infer that these are traceable to the last eukaryotic common ancestor (LECA). On the other hand, several of the proteins involved in RanGTP-independent mRNA export pathways are less conserved, which would suggest that they represent innovations that appeared later in the evolution of eukaryotes.

CONCLUSIONS: Our analyses suggest that the LECA possessed the basic components of the different RNA export mechanisms found today in opisthokonts, and that these mechanisms became more specialized throughout eukaryotic evolution.}, } @article {pmid21190527, year = {2011}, author = {Basu, S}, title = {PP2A in the regulation of cell motility and invasion.}, journal = {Current protein & peptide science}, volume = {12}, number = {1}, pages = {3-11}, doi = {10.2174/138920311795659443}, pmid = {21190527}, issn = {1875-5550}, mesh = {Cell Movement/*physiology ; Humans ; Neoplasm Invasiveness/*pathology ; Protein Phosphatase 2/*metabolism ; Signal Transduction ; }, abstract = {Cell motility is a very critical phenomenon that plays an important role in the development of eukaryotic organisms. One of the well studied cell motility phenomena is chemotaxis, which is described as a directional movement of cell in response to changes in external chemotactic gradient. Numerous studies conducted both in unicellular organism and in mammalian cells have demonstrated the importance of phosphatidylionositol-3 kinase (PI3K) in this process. In addition, it is now well established that although PI3K plays an activation role in chemotaxis, the role of phosphatases is also critical to maintain this dynamic cyclical process. Protein phosphatase 2A (PP2A) is a major serine/threonine phosphatase that is a key player in regulating PI3K signaling. PP2A is abundantly and ubiquitously expressed and has been highly conserved during the evolution of eukaryotes. PP2A is composed of three protein subunits, A, B, and C. Subunit 'A' is a 60-65 kDa structural component, 'C' is a 36-38 kDa catalytic subunit, and 'B' is a 54-130 kDa regulatory subunit. The core complex of PP2A is comprised of the A and C subunits, which are tightly associated and this dimeric core complexes with the regulatory B subunit. The B subunit determines the substrate specificity as well as the spatial and temporal functions of PP2A. PP2A plays an important role in regulating multiple signal transduction pathways, including cell-cycle regulation, cell-growth and development, cytoskeleton dynamics, and cell motility. This review focuses on the role of PP2A in regulating motility of normal and transformed cells.}, } @article {pmid21126361, year = {2010}, author = {Burki, F and Kudryavtsev, A and Matz, MV and Aglyamova, GV and Bulman, S and Fiers, M and Keeling, PJ and Pawlowski, J}, title = {Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {377}, pmid = {21126361}, issn = {1471-2148}, mesh = {Actins/genetics ; Bayes Theorem ; *Biological Evolution ; Contig Mapping ; *Expressed Sequence Tags ; Gene Library ; Likelihood Functions ; Molecular Sequence Data ; *Phylogeny ; Polyubiquitin/genetics ; Rhizaria/classification/*genetics ; Ribosomal Proteins/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Recent phylogenomic analyses have revolutionized our view of eukaryote evolution by revealing unexpected relationships between and within the eukaryotic supergroups. However, for several groups of uncultivable protists, only the ribosomal RNA genes and a handful of proteins are available, often leading to unresolved evolutionary relationships. A striking example concerns the supergroup Rhizaria, which comprises several groups of uncultivable free-living protists such as radiolarians, foraminiferans and gromiids, as well as the parasitic plasmodiophorids and haplosporids. Thus far, the relationships within this supergroup have been inferred almost exclusively from rRNA, actin, and polyubiquitin genes, and remain poorly resolved. To address this, we have generated large Expressed Sequence Tag (EST) datasets for 5 species of Rhizaria belonging to 3 important groups: Acantharea (Astrolonche sp., Phyllostaurus sp.), Phytomyxea (Spongospora subterranea, Plasmodiophora brassicae) and Gromiida (Gromia sphaerica).

RESULTS: 167 genes were selected for phylogenetic analyses based on the representation of at least one rhizarian species for each gene. Concatenation of these genes produced a supermatrix composed of 36,735 amino acid positions, including 10 rhizarians, 9 stramenopiles, and 9 alveolates. Phylogenomic analyses of this large dataset revealed a strongly supported clade grouping Foraminifera and Acantharea. The position of this clade within Rhizaria was sensitive to the method employed and the taxon sampling: Maximum Likelihood (ML) and Bayesian analyses using empirical model of evolution favoured an early divergence, whereas the CAT model and ML analyses with fast-evolving sites or the foraminiferan species Reticulomyxa filosa removed suggested a derived position, closely related to Gromia and Phytomyxea. In contrast to what has been previously reported, our analyses also uncovered the presence of the rhizarian-specific polyubiquitin insertion in Acantharea. Finally, this work reveals another possible rhizarian signature in the 60S ribosomal protein L10a.

CONCLUSIONS: Our study provides new insights into the evolution of Rhizaria based on phylogenomic analyses of ESTs from three groups of previously under-sampled protists. It was enabled through the application of a recently developed method of transcriptome analysis, requiring very small amount of starting material. Our study illustrates the potential of this method to elucidate the early evolution of eukaryotes by providing large amount of data for uncultivable free-living and parasitic protists.}, } @article {pmid21115819, year = {2010}, author = {Jones, MA and Covington, MF and DiTacchio, L and Vollmers, C and Panda, S and Harmer, SL}, title = {Jumonji domain protein JMJD5 functions in both the plant and human circadian systems.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {50}, pages = {21623-21628}, pmid = {21115819}, issn = {1091-6490}, support = {R01 GM069418/GM/NIGMS NIH HHS/United States ; GM069418/GM/NIGMS NIH HHS/United States ; }, mesh = {Arabidopsis/*physiology ; Arabidopsis Proteins/genetics/metabolism ; Biological Clocks/*physiology ; Cell Line ; Circadian Rhythm/*physiology ; Gene Expression Regulation, Plant ; Humans ; Jumonji Domain-Containing Histone Demethylases/genetics/*metabolism ; Phenotype ; Photoperiod ; Protein Isoforms/genetics/*metabolism ; Seedlings/genetics/metabolism ; Transcription Factors/genetics/metabolism ; }, abstract = {Circadian clocks are near-ubiquitous molecular oscillators that coordinate biochemical, physiological, and behavioral processes with environmental cues, such as dawn and dusk. Circadian timing mechanisms are thought to have arisen multiple times throughout the evolution of eukaryotes but share a similar overall structure consisting of interlocking transcriptional and posttranslational feedback loops. Recent work in both plants and animals has also linked modification of histones to circadian clock function. Now, using data from published microarray experiments, we have identified a histone demethylase, jumonji domain containing 5 (JMJD5), as a previously undescribed participant in both the human and Arabidopsis circadian systems. Arabidopsis JMJD5 is coregulated with evening-phased clock components and positively affects expression of clock genes expressed at dawn. We found that both Arabidopsis jmjd5 mutant seedlings and mammalian cell cultures deficient for the human ortholog of this gene have similar fast-running circadian oscillations compared with WT. Remarkably, both the Arabidopsis and human JMJD5 orthologs retain sufficient commonality to rescue the circadian phenotype of the reciprocal system. Thus, JMJD5 plays an interchangeable role in the timing mechanisms of plants and animals despite their highly divergent evolutionary paths.}, } @article {pmid21104437, year = {2011}, author = {Li, Y and Wang, H and Xia, R and Wu, S and Shi, S and Su, J and Liu, Y and Qin, L and Wang, Z}, title = {Molecular cloning, expression pattern and phylogenetic analysis of the will die slowly gene from the Chinese oak silkworm, Antheraea pernyi.}, journal = {Molecular biology reports}, volume = {38}, number = {6}, pages = {3795-3803}, pmid = {21104437}, issn = {1573-4978}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; China ; Cloning, Molecular ; *Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Genes, Insect/*genetics ; Insect Proteins/chemistry/genetics/metabolism ; Molecular Sequence Data ; Moths/*genetics ; *Phylogeny ; Quercus/*parasitology ; Sequence Alignment ; Sequence Analysis, DNA ; Stress, Physiological/genetics ; Temperature ; }, abstract = {The will die slowly (wds) gene coding for a WD-repeat protein with seven repeats has been characterized in Drosophila melanogaster. In this paper, the wds gene was isolated and characterized from the Chinese oak silkworm, Antheraea pernyi (Lepidoptera: Saturniidae). The obtained 1733 bp cDNA sequence contains an open reading frame of 1041 bp encoding a polypeptide of 346 amino acids, with 85% sequence identity to that from D. melanogaster. RT-PCR analysis showed that the wds gene was transcribed during four developmental stages and in all the tissues tested, consistent with the result observed in Bombyx mori based on EST resources and genome-wide microarray information. The mRNA expression level of the A. pernyi wds gene was not significantly down- or up- regulated under temperature stress compared to the control, indicating that it may be not involved in temperature stress tolerance. In search of database, the wds protein homologues were found in various kinds of eukaryotes, including fungi, plants, invertebrates and vertebrates, with 50-93% amino acid sequence identities between them, suggesting that they are highly conserved during the evolution of eukaryotes. Phylogenetic analysis based on the wds protein homologue sequences clearly separated the known fungi, plants, invertebrates and vertebrates, consistent with the topology tree on the classical systematics, suggesting the potential value of wds protein in eukaryotic phylogenetic inference. In vertebrates, two apparent types of the wds proteins were also defined by sequence alignment and phylogenetic analysis.}, } @article {pmid21036663, year = {2010}, author = {Ginger, ML and Fritz-Laylin, LK and Fulton, C and Cande, WZ and Dawson, SC}, title = {Intermediary metabolism in protists: a sequence-based view of facultative anaerobic metabolism in evolutionarily diverse eukaryotes.}, journal = {Protist}, volume = {161}, number = {5}, pages = {642-671}, pmid = {21036663}, issn = {1618-0941}, support = {AI054693/AI/NIAID NIH HHS/United States ; R01 AI054693-01/AI/NIAID NIH HHS/United States ; 1R01AI77571-01A1/AI/NIAID NIH HHS/United States ; R01 AI077571/AI/NIAID NIH HHS/United States ; R01 AI077571-01A1/AI/NIAID NIH HHS/United States ; R01 AI054693/AI/NIAID NIH HHS/United States ; }, mesh = {Anaerobiosis ; *Energy Metabolism ; Eukaryota/classification/*metabolism ; Evolution, Molecular ; Phylogeny ; }, abstract = {Protists account for the bulk of eukaryotic diversity. Through studies of gene and especially genome sequences the molecular basis for this diversity can be determined. Evident from genome sequencing are examples of versatile metabolism that go far beyond the canonical pathways described for eukaryotes in textbooks. In the last 2-3 years, genome sequencing and transcript profiling has unveiled several examples of heterotrophic and phototrophic protists that are unexpectedly well-equipped for ATP production using a facultative anaerobic metabolism, including some protists that can (Chlamydomonas reinhardtii) or are predicted (Naegleria gruberi, Acanthamoeba castellanii, Amoebidium parasiticum) to produce H(2) in their metabolism. It is possible that some enzymes of anaerobic metabolism were acquired and distributed among eukaryotes by lateral transfer, but it is also likely that the common ancestor of eukaryotes already had far more metabolic versatility than was widely thought a few years ago. The discussion of core energy metabolism in unicellular eukaryotes is the subject of this review. Since genomic sequencing has so far only touched the surface of protist diversity, it is anticipated that sequences of additional protists may reveal an even wider range of metabolic capabilities, while simultaneously enriching our understanding of the early evolution of eukaryotes.}, } @article {pmid21034815, year = {2011}, author = {Desmond, E and Brochier-Armanet, C and Forterre, P and Gribaldo, S}, title = {On the last common ancestor and early evolution of eukaryotes: reconstructing the history of mitochondrial ribosomes.}, journal = {Research in microbiology}, volume = {162}, number = {1}, pages = {53-70}, doi = {10.1016/j.resmic.2010.10.004}, pmid = {21034815}, issn = {1769-7123}, mesh = {Eukaryota/*genetics ; *Evolution, Molecular ; Mitochondria/*genetics ; *Phylogeny ; Ribosomes/*genetics ; }, abstract = {Understanding early evolution is a major challenge for the post-genomic era. A promising way to tackle this issue is to analyze the evolutionary history of key cellular systems through phylogenomic approaches. The current availability of genomic data from representatives of diverse lineages (especially eukaryotes), together with the ever growing number of proteomic characterizations now provides ample material to apply this type of analyses to trace back the origin and evolution of the three domains of life. Here, we have reconstructed the composition of the ancestral mitochondrial ribosome in the Last Eukaryotic Common Ancestor (LECA) and investigated its subsequent evolution in six major eukaryotic supergroups. We infer that LECA possessed a mitochondrial ribosome that was already much larger than its bacterial ancestor, with 19 additional specific proteins, indicating that a certain amount of time occurred between initial endosymbiosis at the origin of the mitochondrion and the diversification of present-day eukaryotic supergroups. Subsequently, mitochondrial ribosomes appear to have undergone a very dynamic evolutionary history in the different eukaryotic lineages, involving the loss of different sets of ribosomal protein-coding genes, their transfer to the host genome, as well as the acquisition of many novel components. This chaotic history for a such fundamental cellular machinery is puzzling, especially when compared to cytosolic, bacterial or chloroplastic ribosomes, which are much more stable. Intriguingly, archaeal ribosomes also show a very dynamic nature, with multiple independent losses among lineages.}, } @article {pmid21034814, year = {2011}, author = {Poole, AM and Neumann, N}, title = {Reconciling an archaeal origin of eukaryotes with engulfment: a biologically plausible update of the Eocyte hypothesis.}, journal = {Research in microbiology}, volume = {162}, number = {1}, pages = {71-76}, doi = {10.1016/j.resmic.2010.10.002}, pmid = {21034814}, issn = {1769-7123}, mesh = {Archaea/*genetics/physiology ; Bacteria/genetics ; *Biological Evolution ; Eukaryota/*genetics ; Mitochondria/genetics ; Phagocytosis ; }, abstract = {An archaeal origin of eukaryotes is often equated with the engulfment of the bacterial ancestor of mitochondria by an archaeon. Such an event is problematic in that it is not supported by archaeal cell biology. We show that placing phylogenetic results within a stem-and-crown framework eliminates such incompatibilities, and that an archaeal origin for eukaryotes (as suggested from recent phylogenies) can be uncontroversially reconciled with phagocytosis as the mechanism for engulfment of the mitochondrial ancestor. This is significant because it eliminates a perceived problem with eukaryote origins: that an archaeal origin of eukaryotes (as under the Eocyte hypothesis) cannot be reconciled with existing cell biological mechanisms through which bacteria may take up residence inside eukaryote cells.}, } @article {pmid20934642, year = {2010}, author = {O'Malley, MA}, title = {The first eukaryote cell: an unfinished history of contestation.}, journal = {Studies in history and philosophy of biological and biomedical sciences}, volume = {41}, number = {3}, pages = {212-224}, doi = {10.1016/j.shpsc.2010.07.010}, pmid = {20934642}, issn = {1879-2499}, mesh = {*Biological Evolution ; Biology/history ; Cell Biology/*history ; Dissent and Disputes/history ; *Eukaryotic Cells ; History, 20th Century ; History, 21st Century ; Models, Biological ; Philosophy/history ; Symbiosis ; }, abstract = {The eukaryote cell is one of the most radical innovations in the history of life, and the circumstances of its emergence are still deeply contested. This paper will outline the recent history of attempts to reveal these origins, with special attention to the argumentative strategies used to support claims about the first eukaryote cell. I will focus on two general models of eukaryogenesis: the phagotrophy model and the syntrophy model. As their labels indicate, they are based on claims about metabolic relationships. The first foregrounds the ability to consume other organisms; the second the ability to enter into symbiotic metabolic arrangements. More importantly, however, the first model argues for the autogenous or self-generated origins of the eukaryote cell, and the second for its exogenous or externally generated origins. Framing cell evolution this way leads each model to assert different priorities in regard to cell-biological versus molecular evidence, cellular versus environmental influences, plausibility versus evolutionary probability, and irreducibility versus the continuity of cell types. My examination of these issues will conclude with broader reflections on the implications of eukaryogenesis studies for a philosophical understanding of scientific contestation.}, } @article {pmid20844558, year = {2010}, author = {Gribaldo, S and Poole, AM and Daubin, V and Forterre, P and Brochier-Armanet, C}, title = {The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?.}, journal = {Nature reviews. Microbiology}, volume = {8}, number = {10}, pages = {743-752}, pmid = {20844558}, issn = {1740-1534}, mesh = {Archaea/*classification/*genetics ; Bacteria/classification/genetics ; *Biological Evolution ; Classification/methods ; Eukaryota/*classification/*genetics ; Genome/*genetics ; }, abstract = {The origin of eukaryotes and their evolutionary relationship with the Archaea is a major biological question and the subject of intense debate. In the context of the classical view of the universal tree of life, the Archaea and the Eukarya have a common ancestor, the nature of which remains undetermined. Alternative views propose instead that the Eukarya evolved directly from a bona fide archaeal lineage. Several recent large-scale phylogenomic studies using an array of approaches are divided in supporting either one or the other scenario, despite analysing largely overlapping data sets of universal genes. We examine the reasons for such a lack of consensus and consider how alternative approaches may enable progress in answering this fascinating and as-yet-unresolved question.}, } @article {pmid20810725, year = {2010}, author = {Liu, H and Fu, Y and Jiang, D and Li, G and Xie, J and Cheng, J and Peng, Y and Ghabrial, SA and Yi, X}, title = {Widespread horizontal gene transfer from double-stranded RNA viruses to eukaryotic nuclear genomes.}, journal = {Journal of virology}, volume = {84}, number = {22}, pages = {11876-11887}, pmid = {20810725}, issn = {1098-5514}, mesh = {Amino Acid Sequence ; Animals ; Cell Nucleus/genetics/*virology ; Eukaryota/*genetics/*virology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome ; Molecular Sequence Data ; Phylogeny ; Plants/genetics/virology ; RNA Viruses/classification/*genetics/physiology ; RNA, Double-Stranded/genetics ; RNA, Viral/genetics ; Sequence Alignment ; }, abstract = {Horizontal gene transfer commonly occurs from cells to viruses but rarely occurs from viruses to their host cells, with the exception of retroviruses and some DNA viruses. However, extensive sequence similarity searches in public genome databases for various organisms showed that the capsid protein and RNA-dependent RNA polymerase genes from totiviruses and partitiviruses have widespread homologs in the nuclear genomes of eukaryotic organisms, including plants, arthropods, fungi, nematodes, and protozoa. PCR amplification and sequencing as well as comparative evidence of junction coverage between virus and host sequences support the conclusion that these viral homologs are real and occur in eukaryotic genomes. Sequence comparison and phylogenetic analysis suggest that these genes were likely transferred horizontally from viruses to eukaryotic genomes. Furthermore, we present evidence showing that some of the transferred genes are conserved and expressed in eukaryotic organisms and suggesting that these viral genes are also functional in the recipient genomes. Our findings imply that horizontal transfer of double-stranded RNA viral genes is widespread among eukaryotes and may give rise to functionally important new genes, thus entailing that RNA viruses may play significant roles in the evolution of eukaryotes.}, } @article {pmid20731852, year = {2010}, author = {Gross, J and Bhattacharya, D}, title = {Uniting sex and eukaryote origins in an emerging oxygenic world.}, journal = {Biology direct}, volume = {5}, number = {}, pages = {53}, pmid = {20731852}, issn = {1745-6150}, mesh = {Animals ; *Biological Evolution ; Eukaryotic Cells/*metabolism ; Oxygen/*metabolism ; Prokaryotic Cells/*metabolism ; Reactive Oxygen Species/metabolism ; }, abstract = {BACKGROUND: Theories about eukaryote origins (eukaryogenesis) need to provide unified explanations for the emergence of diverse complex features that define this lineage. Models that propose a prokaryote-to-eukaryote transition are gridlocked between the opposing "phagocytosis first" and "mitochondria as seed" paradigms, neither of which fully explain the origins of eukaryote cell complexity. Sex (outcrossing with meiosis) is an example of an elaborate trait not yet satisfactorily addressed in theories about eukaryogenesis. The ancestral nature of meiosis and its dependence on eukaryote cell biology suggest that the emergence of sex and eukaryogenesis were simultaneous and synergic and may be explained by a common selective pressure.

We propose that a local rise in oxygen levels, due to cyanobacterial photosynthesis in ancient Archean microenvironments, was highly toxic to the surrounding biota. This selective pressure drove the transformation of an archaeal (archaebacterial) lineage into the first eukaryotes. Key is that oxygen might have acted in synergy with environmental stresses such as ultraviolet (UV) radiation and/or desiccation that resulted in the accumulation of reactive oxygen species (ROS). The emergence of eukaryote features such as the endomembrane system and acquisition of the mitochondrion are posited as strategies to cope with a metabolic crisis in the cell plasma membrane and the accumulation of ROS, respectively. Selective pressure for efficient repair of ROS/UV-damaged DNA drove the evolution of sex, which required cell-cell fusions, cytoskeleton-mediated chromosome movement, and emergence of the nuclear envelope. Our model implies that evolution of sex and eukaryogenesis were inseparable processes.

TESTING THE HYPOTHESIS: Several types of data can be used to test our hypothesis. These include paleontological predictions, simulation of ancient oxygenic microenvironments, and cell biological experiments with Archaea exposed to ROS and UV stresses. Studies of archaeal conjugation, prokaryotic DNA recombination, and the universality of nuclear-mediated meiotic activities might corroborate the hypothesis that sex and the nucleus evolved to support DNA repair.

Oxygen tolerance emerges as an important principle to investigate eukaryogenesis. The evolution of eukaryotic complexity might be best understood as a synergic process between key evolutionary innovations, of which meiosis (sex) played a central role.

REVIEWERS: This manuscript was reviewed by Eugene V. Koonin, Anthony M. Poole, and Gáspár Jékely.}, } @article {pmid20691900, year = {2010}, author = {Ton-Hoang, B and Pasternak, C and Siguier, P and Guynet, C and Hickman, AB and Dyda, F and Sommer, S and Chandler, M}, title = {Single-stranded DNA transposition is coupled to host replication.}, journal = {Cell}, volume = {142}, number = {3}, pages = {398-408}, pmid = {20691900}, issn = {1097-4172}, support = {Z01 DK036154-01/ImNIH/Intramural NIH HHS/United States ; }, mesh = {DNA Helicases/metabolism ; DNA Primase/metabolism ; *DNA Replication ; *DNA Transposable Elements ; DNA, Single-Stranded/*metabolism ; Deinococcus/genetics/*metabolism ; Escherichia coli/genetics/*metabolism ; Escherichia coli Proteins/metabolism ; Trans-Activators/metabolism ; }, abstract = {DNA transposition has contributed significantly to evolution of eukaryotes and prokaryotes. Insertion sequences (ISs) are the simplest prokaryotic transposons and are divided into families on the basis of their organization and transposition mechanism. Here, we describe a link between transposition of IS608 and ISDra2, both members of the IS200/IS605 family, which uses obligatory single-stranded DNA intermediates, and the host replication fork. Replication direction through the IS plays a crucial role in excision: activity is maximal when the "top" IS strand is located on the lagging-strand template. Excision is stimulated upon transient inactivation of replicative helicase function or inhibition of Okazaki fragment synthesis. IS608 insertions also exhibit an orientation preference for the lagging-strand template and insertion can be specifically directed to stalled replication forks. An in silico genomic approach provides evidence that dissemination of other IS200/IS605 family members is also linked to host replication.}, } @article {pmid20551680, year = {2010}, author = {Koonin, EV and Yutin, N}, title = {Origin and evolution of eukaryotic large nucleo-cytoplasmic DNA viruses.}, journal = {Intervirology}, volume = {53}, number = {5}, pages = {284-292}, pmid = {20551680}, issn = {1423-0100}, support = {//Intramural NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Bacteriophages/genetics ; Cluster Analysis ; Computational Biology ; DNA Viruses/*genetics ; Eukaryota/*virology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Viral ; Interspersed Repetitive Sequences ; Phylogeny ; Recombination, Genetic ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND/AIMS: The nucleo-cytoplasmic large DNA viruses (NCLDV) constitute an apparently monophyletic group that consists of 6 families of viruses infecting a broad variety of eukaryotes. A comprehensive genome comparison and maximum-likelihood reconstruction of NCLDV evolution reveal a set of approximately 50 conserved genes that can be tentatively mapped to the genome of the common ancestor of this class of eukaryotic viruses. We address the origins and evolution of NCLDV.

RESULTS: Phylogenetic analysis indicates that some of the major clades of NCLDV infect diverse animals and protists, suggestive of early radiation of the NCLDV, possibly concomitant with eukaryogenesis. The core NCLDV genes seem to have originated from different sources including homologous genes of bacteriophages, bacteria and eukaryotes. These observations are compatible with a scenario of the origin of the NCLDV at an early stage of the evolution of eukaryotes through extensive mixing of genes from widely different genomes.

CONCLUSIONS: The common ancestor of the NCLDV probably evolved from a bacteriophage as a result of recruitment of numerous eukaryotic and some bacterial genes, and concomitant loss of the majority of phage genes except for a small core of genes coding for proteins essential for virus genome replication and virion formation.}, } @article {pmid20467212, year = {2010}, author = {Kuroiwa, T}, title = {Mechanisms of organelle division and inheritance and their implications regarding the origin of eukaryotic cells.}, journal = {Proceedings of the Japan Academy. Series B, Physical and biological sciences}, volume = {86}, number = {5}, pages = {455-471}, pmid = {20467212}, issn = {1349-2896}, mesh = {Animals ; Eukaryotic Cells/*cytology/metabolism/radiation effects ; Gene Targeting ; Genome/genetics ; Humans ; Light ; *Models, Biological ; Organelles/*genetics/*metabolism/radiation effects ; Reproduction, Asexual/genetics ; }, abstract = {Mitochondria and plastids have their own DNAs and are regarded as descendants of endosymbiotic prokaryotes. Organellar DNAs are not naked in vivo but are associated with basic proteins to form DNA-protein complexes (called organelle nuclei). The concept of organelle nuclei provides a new approach to explain the origin, division, and inheritance of organelles. Organelles divide using organelle division rings (machineries) after organelle-nuclear division. Organelle division machineries are a chimera of the FtsZ (filamentous temperature sensitive Z) ring of bacterial origin and the eukaryotic mechanochemical dynamin ring. Thus, organelle division machineries contain a key to solve the origin of organelles (eukaryotes). The maternal inheritance of organelles developed during sexual reproduction and it is also probably intimately related to the origin of organelles. The aims of this review are to describe the strategies used to reveal the dynamics of organelle division machineries, and the significance of the division machineries and maternal inheritance in the origin and evolution of eukaryotes.}, } @article {pmid20441612, year = {2010}, author = {Koonin, EV}, title = {The origin and early evolution of eukaryotes in the light of phylogenomics.}, journal = {Genome biology}, volume = {11}, number = {5}, pages = {209}, pmid = {20441612}, issn = {1474-760X}, support = {//Intramural NIH HHS/United States ; }, mesh = {Archaea/genetics ; Bacteria/genetics ; Eukaryota/*genetics ; *Genomics ; *Phylogeny ; }, abstract = {Phylogenomics of eukaryote supergroups suggest a highly complex last common ancestor of eukaryotes and a key role of mitochondrial endosymbiosis in the origin of eukaryotes.}, } @article {pmid20416272, year = {2010}, author = {Sørensen, DM and Buch-Pedersen, MJ and Palmgren, MG}, title = {Structural divergence between the two subgroups of P5 ATPases.}, journal = {Biochimica et biophysica acta}, volume = {1797}, number = {6-7}, pages = {846-855}, doi = {10.1016/j.bbabio.2010.04.010}, pmid = {20416272}, issn = {0006-3002}, mesh = {Adenosine Triphosphatases/chemistry/*classification/*genetics ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Catalytic Domain/genetics ; Computational Biology ; Databases, Protein ; Evolution, Molecular ; Humans ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Evolution of P5 type ATPases marks the origin of eukaryotes but still they remain the least characterized pumps in the superfamily of P-type ATPases. Phylogenetic analysis of available sequences suggests that P5 ATPases should be divided into at least two subgroups, P5A and P5B. P5A ATPases have been identified in the endoplasmic reticulum and seem to have basic functions in protein maturation and secretion. P5B ATPases localize to vacuolar/lysosomal or apical membranes and in animals play a role in hereditary neuronal diseases. Here we have used a bioinformatical approach to identify differences in the primary sequences between the two subgroups. P5A and P5B ATPases appear have a very different membrane topology from other P-type ATPases with two and one, respectively, additional transmembrane segments inserted in the N-terminal end. Based on conservation of residues in the transmembrane region, the two P5 subgroups most likely have different substrate specificities although these cannot be predicted from their sequences. Furthermore, sequence differences between P5A and P5B ATPases are identified in the catalytic domains that could influence key kinetic properties differentially. Together these findings indicate that P5A and P5B ATPases are structurally and functionally different.}, } @article {pmid20150890, year = {2010}, author = {Collins, AJ and Nyholm, SV}, title = {Obtaining hemocytes from the Hawaiian bobtail squid Euprymna scolopes and observing their adherence to symbiotic and non-symbiotic bacteria.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {36}, pages = {}, pmid = {20150890}, issn = {1940-087X}, mesh = {Animals ; Cell Adhesion/physiology ; Cell Separation/*methods ; Decapodiformes/*cytology/microbiology ; Hemocytes/*cytology/physiology ; Symbiosis ; Vibrio/*physiology ; }, abstract = {Studies concerning the role of the immune system in mediating molecular signaling between beneficial bacteria and their hosts have, in recent years, made significant contributions to our understanding of the co-evolution of eukaryotes with their microbiota. The symbiotic association between the Hawaiian bobtail squid, Euprymna scolopes and the bioluminescent bacterium Vibrio fischeri has been utilized as a model system for understanding the effects of beneficial bacteria on animal development. Recent studies have shown that macrophage-like hemocytes, the sole cellular component of the squid host's innate immune system, likely play an important role in mediating the establishment and maintenance of this association. This protocol will demonstrate how to obtain hemocytes from E. scolopes and then use these cells in bacterial binding assays. Adult squid are first anesthetized before hemolymph is collected by syringe from the main cephalic blood vessel. The host hemocytes, contained in the extracted hemolymph, are adhered to chambered glass coverslips and then exposed to green fluorescent protein-labeled symbiotic Vibrio fischeri and non-symbiotic Vibrio harveyi. The hemocytes are counterstained with a fluorescent dye (Cell Tracker Orange, Invitrogen) and then visualized using fluorescent microscopy.}, } @article {pmid20136503, year = {2010}, author = {Hakim, M and Fass, D}, title = {Cytosolic disulfide bond formation in cells infected with large nucleocytoplasmic DNA viruses.}, journal = {Antioxidants & redox signaling}, volume = {13}, number = {8}, pages = {1261-1271}, doi = {10.1089/ars.2010.3128}, pmid = {20136503}, issn = {1557-7716}, mesh = {Animals ; Biocatalysis ; Cytosol/enzymology/*metabolism/*virology ; DNA Viruses/classification/*physiology ; Disulfides/chemistry/*metabolism ; Eukaryotic Cells/cytology/enzymology/*metabolism/*virology ; Humans ; Mitochondrial Membrane Transport Proteins/chemistry/metabolism ; Oxidation-Reduction ; Protein Folding ; }, abstract = {Proteins that have evolved to contain stabilizing disulfide bonds generally fold in a membrane-delimited compartment in the cell [i.e., the endoplasmic reticulum (ER) or the mitochondrial intermembrane space (IMS)]. These compartments contain sulfhydryl oxidase enzymes that catalyze the pairing and oxidation of cysteine residues. In contrast, most proteins in a healthy cytosol are maintained in reduced form through surveillance by NADPH-dependent reductases and the lack of sulfhydryl oxidases. Nevertheless, one of the core functionalities that unify the broad and diverse set of nucleocytoplasmic large DNA viruses (NCLDVs) is the ability to catalyze disulfide formation in the cytosol. The substrates of this activity are proteins that contribute to the assembly, structure, and infectivity of the virions. If the last common ancestor of NCLDVs was present during eukaryogenesis as has been proposed, it is interesting to speculate that viral disulfide bond formation pathways may have predated oxidative protein folding in intracellular organelles.}, } @article {pmid20132544, year = {2010}, author = {Cavalier-Smith, T}, title = {Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution.}, journal = {Biology direct}, volume = {5}, number = {}, pages = {7}, pmid = {20132544}, issn = {1745-6150}, mesh = {Animals ; *Biological Evolution ; Cell Nucleus/genetics/*physiology ; Centrioles/metabolism ; Centromere/metabolism ; Eukaryotic Cells/metabolism ; Evolution, Molecular ; Heterochromatin/metabolism ; Intracellular Space/*metabolism ; Introns/genetics ; Mitosis/genetics/*physiology ; Nuclear Pore/metabolism ; Phagocytosis ; *Sex ; Spliceosomes/metabolism ; Telomere/metabolism ; }, abstract = {BACKGROUND: The transition from prokaryotes to eukaryotes was the most radical change in cell organisation since life began, with the largest ever burst of gene duplication and novelty. According to the coevolutionary theory of eukaryote origins, the fundamental innovations were the concerted origins of the endomembrane system and cytoskeleton, subsequently recruited to form the cell nucleus and coevolving mitotic apparatus, with numerous genetic eukaryotic novelties inevitable consequences of this compartmentation and novel DNA segregation mechanism. Physical and mutational mechanisms of origin of the nucleus are seldom considered beyond the long-standing assumption that it involved wrapping pre-existing endomembranes around chromatin. Discussions on the origin of sex typically overlook its association with protozoan entry into dormant walled cysts and the likely simultaneous coevolutionary, not sequential, origin of mitosis and meiosis.

RESULTS: I elucidate nuclear and mitotic coevolution, explaining the origins of dicer and small centromeric RNAs for positionally controlling centromeric heterochromatin, and how 27 major features of the cell nucleus evolved in four logical stages, making both mechanisms and selective advantages explicit: two initial stages (origin of 30 nm chromatin fibres, enabling DNA compaction; and firmer attachment of endomembranes to heterochromatin) protected DNA and nascent RNA from shearing by novel molecular motors mediating vesicle transport, division, and cytoplasmic motility. Then octagonal nuclear pore complexes (NPCs) arguably evolved from COPII coated vesicle proteins trapped in clumps by Ran GTPase-mediated cisternal fusion that generated the fenestrated nuclear envelope, preventing lethal complete cisternal fusion, and allowing passive protein and RNA exchange. Finally, plugging NPC lumens by an FG-nucleoporin meshwork and adopting karyopherins for nucleocytoplasmic exchange conferred compartmentation advantages. These successive changes took place in naked growing cells, probably as indirect consequences of the origin of phagotrophy. The first eukaryote had 1-2 cilia and also walled resting cysts; I outline how encystation may have promoted the origin of meiotic sex. I also explain why many alternative ideas are inadequate.

CONCLUSION: Nuclear pore complexes are evolutionary chimaeras of endomembrane- and mitosis-related chromatin-associated proteins. The keys to understanding eukaryogenesis are a proper phylogenetic context and understanding organelle coevolution: how innovations in one cell component caused repercussions on others.}, } @article {pmid20087413, year = {2010}, author = {Santarella-Mellwig, R and Franke, J and Jaedicke, A and Gorjánácz, M and Bauer, U and Budd, A and Mattaj, IW and Devos, DP}, title = {The compartmentalized bacteria of the planctomycetes-verrucomicrobia-chlamydiae superphylum have membrane coat-like proteins.}, journal = {PLoS biology}, volume = {8}, number = {1}, pages = {e1000281}, pmid = {20087413}, issn = {1545-7885}, support = {F32 GM082029/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/cytology/*genetics ; Bacterial Proteins/*chemistry/physiology ; Biological Evolution ; Cell Compartmentation ; Membrane Proteins/*chemistry/physiology ; Phylogeny ; Protein Structure, Tertiary ; Proteome ; Sequence Analysis, Protein ; }, abstract = {The development of the endomembrane system was a major step in eukaryotic evolution. Membrane coats, which exhibit a unique arrangement of beta-propeller and alpha-helical repeat domains, play key roles in shaping eukaryotic membranes. Such proteins are likely to have been present in the ancestral eukaryote but cannot be detected in prokaryotes using sequence-only searches. We have used a structure-based detection protocol to search all proteomes for proteins with this domain architecture. Apart from the eukaryotes, we identified this protein architecture only in the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) bacterial superphylum, many members of which share a compartmentalized cell plan. We determined that one such protein is partly localized at the membranes of vesicles formed inside the cells in the planctomycete Gemmata obscuriglobus. Our results demonstrate similarities between bacterial and eukaryotic compartmentalization machinery, suggesting that the bacterial PVC superphylum contributed significantly to eukaryogenesis.}, } @article {pmid20041159, year = {2009}, author = {de Castro, F and Gaedke, U and Boenigk, J}, title = {Reverse evolution: driving forces behind the loss of acquired photosynthetic traits.}, journal = {PloS one}, volume = {4}, number = {12}, pages = {e8465}, pmid = {20041159}, issn = {1932-6203}, support = {P 18315/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacteria ; *Biological Evolution ; Eukaryota/physiology ; Heterotrophic Processes/physiology ; *Models, Biological ; Photosynthesis/*genetics ; }, abstract = {BACKGROUND: The loss of photosynthesis has occurred often in eukaryotic evolution, even more than its acquisition, which occurred at least nine times independently and which generated the evolution of the supergroups Archaeplastida, Rhizaria, Chromalveolata and Excavata. This secondary loss of autotrophic capability is essential to explain the evolution of eukaryotes and the high diversity of protists, which has been severely underestimated until recently. However, the ecological and evolutionary scenarios behind this evolutionary "step back" are still largely unknown.

Using a dynamic model of heterotrophic and mixotrophic flagellates and two types of prey, large bacteria and ultramicrobacteria, we examine the influence of DOC concentration, mixotroph's photosynthetic growth rate, and external limitations of photosynthesis on the coexistence of both types of flagellates. Our key premises are: large bacteria grow faster than small ones at high DOC concentrations, and vice versa; and heterotrophic flagellates are more efficient than the mixotrophs grazing small bacteria (both empirically supported). We show that differential efficiency in bacteria grazing, which strongly depends on cell size, is a key factor to explain the loss of photosynthesis in mixotrophs (which combine photosynthesis and bacterivory) leading to purely heterotrophic lineages. Further, we show in what conditions an heterotroph mutant can coexist, or even out-compete, its mixotrophic ancestor, suggesting that bacterivory and cell size reduction may have been major triggers for the diversification of eukaryotes.

CONCLUSIONS/SIGNIFICANCE: Our results suggest that, provided the mixotroph's photosynthetic advantage is not too large, the (small) heterotroph will also dominate in nutrient-poor environments and will readily invade a community of mixotrophs and bacteria, due to its higher efficiency exploiting the ultramicrobacteria. As carbon-limited conditions were presumably widespread throughout Earth history, such a scenario may explain the numerous transitions from phototrophy to mixotrophy and further to heterotrophy within virtually all major algal lineages. We challenge prevailing concepts that affiliated the evolution of phagotrophy with eutrophic or strongly light-limited environments only.}, } @article {pmid20021668, year = {2009}, author = {Yutin, N and Koonin, EV}, title = {Evolution of DNA ligases of nucleo-cytoplasmic large DNA viruses of eukaryotes: a case of hidden complexity.}, journal = {Biology direct}, volume = {4}, number = {}, pages = {51}, pmid = {20021668}, issn = {1745-6150}, support = {//Intramural NIH HHS/United States ; }, mesh = {Asfarviridae/classification/enzymology/genetics ; *Biological Evolution ; Cell Nucleus/enzymology ; Cytoplasm/virology ; DNA Ligase ATP ; DNA Ligases/*genetics/metabolism ; DNA Viruses/classification/*enzymology/*genetics ; Eukaryota ; Genome, Viral ; Iridoviridae/classification/enzymology/genetics ; Phycodnaviridae/classification/enzymology/genetics ; Phylogeny ; Poxviridae/classification/enzymology/genetics ; }, abstract = {BACKGROUND: Eukaryotic Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) encode most if not all of the enzymes involved in their DNA replication. It has been inferred that genes for these enzymes were already present in the last common ancestor of the NCLDV. However, the details of the evolution of these genes that bear on the complexity of the putative ancestral NCLDV and on the evolutionary relationships between viruses and their hosts are not well understood.

RESULTS: Phylogenetic analysis of the ATP-dependent and NAD-dependent DNA ligases encoded by the NCLDV reveals an unexpectedly complex evolutionary history. The NAD-dependent ligases are encoded only by a minority of NCLDV (including mimiviruses, some iridoviruses and entomopoxviruses) but phylogenetic analysis clearly indicated that all viral NAD-dependent ligases are monophyletic. Combined with the topology of the NCLDV tree derived by consensus of trees for universally conserved genes suggests that this enzyme was represented in the ancestral NCLDV. Phylogenetic analysis of ATP-dependent ligases that are encoded by chordopoxviruses, most of the phycodnaviruses and Marseillevirus failed to demonstrate monophyly and instead revealed an unexpectedly complex evolutionary trajectory. The ligases of the majority of phycodnaviruses and Marseillevirus seem to have evolved from bacteriophage or bacterial homologs; the ligase of one phycodnavirus, Emiliana huxlei virus, belongs to the eukaryotic DNA ligase I branch; and ligases of chordopoxviruses unequivocally cluster with eukaryotic DNA ligase III.

CONCLUSIONS: Examination of phyletic patterns and phylogenetic analysis of DNA ligases of the NCLDV suggest that the common ancestor of the extant NCLDV encoded an NAD-dependent ligase that most likely was acquired from a bacteriophage at the early stages of evolution of eukaryotes. By contrast, ATP-dependent ligases from different prokaryotic and eukaryotic sources displaced the ancestral NAD-dependent ligase at different stages of subsequent evolution. These findings emphasize complex routes of viral evolution that become apparent through detailed phylogenomic analysis but not necessarily in reconstructions based on phyletic patterns of genes.

REVIEWERS: This article was reviewed by: Patrick Forterre, George V. Shpakovski, and Igor B. Zhulin.}, } @article {pmid19926289, year = {2010}, author = {Hernández, G and Altmann, M and Lasko, P}, title = {Origins and evolution of the mechanisms regulating translation initiation in eukaryotes.}, journal = {Trends in biochemical sciences}, volume = {35}, number = {2}, pages = {63-73}, doi = {10.1016/j.tibs.2009.10.009}, pmid = {19926289}, issn = {0968-0004}, mesh = {Animals ; Eukaryota/*metabolism ; Eukaryotic Initiation Factors/genetics/metabolism ; *Evolution, Molecular ; Humans ; *Peptide Chain Initiation, Translational ; }, abstract = {Translation in eukaryotes is a complex process that is closely regulated, mainly at the initiation step. Both universal and lineage-specific mechanisms regulate translation initiation. Considerable progress in our understanding of the regulation of translation has been achieved, but how these regulatory mechanisms evolved remains poorly understood. New discoveries in different fields suggest that the mechanisms that regulate translation emerged at different times during the evolution of eukaryotes, and that some initially evolved independently of the translation apparatus and were later incorporated into it. Overall, the emerging view suggests that 'tinkering' (i.e. co-opting and assembling molecules and regulatory mechanisms from other cellular processes) contributed importantly to the development of the mechanisms that regulate translation initiation during eukaryotic evolution.}, } @article {pmid19925652, year = {2009}, author = {Marín, I}, title = {Diversification of the cullin family.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {267}, pmid = {19925652}, issn = {1471-2148}, mesh = {*Comparative Genomic Hybridization ; Cullin Proteins/*genetics ; Databases, Protein ; Eukaryota/*genetics ; *Evolution, Molecular ; Humans ; Phylogeny ; Sequence Analysis, Protein ; }, abstract = {BACKGROUND: Cullins are proteins involved in ubiquitination through their participation in multisubunit ubiquitin ligase complexes. In this study, I use comparative genomic data to establish the pattern of emergence and diversification of cullins in eukaryotes.

RESULTS: The available data indicate that there were three cullin genes before the unikont/bikont split, which I have called Culalpha, Culbeta and Culgamma. Fungal species have quite strictly conserved these three ancestral genes, with only occasional lineage-specific duplications. On the contrary, several additional genes appeared in the animal or plant lineages. For example, the human genes Cul1, Cul2, Cul5, Cul7 and Parc all derive from the ancestral Culalpha gene. These results, together with the available functional data, suggest that three different types of ubiquitin ligase cullin-containing complexes were already present in early eukaryotic evolution: 1) SCF-like complexes with Culalpha proteins; 2) Culbeta/BTB complexes; and, 3) Complexes containing Culgamma and DDB1-like proteins. Complexes containing elongins have arisen more recently and perhaps twice independently in animals and fungi.

CONCLUSION: Most of the known types of cullin-containing ubiquitin ligase complexes are ancient. The available data suggest that, since the origin of eukaryotes, complex diversity has been mostly generated by combining closely related subunits, while radical innovations, giving rise to novel types of complexes, have been scarce. However, several protist groups not examined so far contain highly divergent cullins, indicating that additional types of complexes may exist.}, } @article {pmid19845630, year = {2009}, author = {Bell, PJ}, title = {The viral eukaryogenesis hypothesis: a key role for viruses in the emergence of eukaryotes from a prokaryotic world environment.}, journal = {Annals of the New York Academy of Sciences}, volume = {1178}, number = {}, pages = {91-105}, doi = {10.1111/j.1749-6632.2009.04994.x}, pmid = {19845630}, issn = {1749-6632}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Cell Nucleus/metabolism ; Cytoplasm/metabolism ; Eukaryotic Cells/cytology ; *Evolution, Molecular ; Meiosis ; Mitochondria/metabolism ; Prokaryotic Cells/cytology ; Viruses/*genetics ; }, abstract = {Understanding how the gulf between prokaryotic and eukaryotic cellular design arose is a major challenge. The viral eukaryogenesis (VE) hypothesis addresses the challenge of eukaryotic origins by suggesting the first eukaryotic cell was a multimember consortium consisting of a viral ancestor of the nucleus, an archaeal ancestor of the eukaryotic cytoplasm, and a bacterial ancestor of the mitochondria. Using only prokaryotes and their viruses, and invoking selective pressures observed in modern organisms, the VE hypothesis can explain the origins of the eukaryotic cell, sex, and meiosis. In the VE hypothesis, a cell wall-less archaeon and an alpha-proteobacterium established a syntrophic relationship, and then a complex DNA virus permanently lysogenized the archaeal syntroph to produce a consortium of three organisms that evolved into the eukaryotic cell. The mechanisms by which the virus replicated, controlled its copy number, and segregated to daughter cells led to the evolution of the asexual mitotic replication cycle and the sexual meiotic replication cycle. The VE hypothesis conceptually unifies prokaryotic and eukaryotic sex into variants of a single process.}, } @article {pmid19787059, year = {2009}, author = {Not, F and del Campo, J and Balagué, V and de Vargas, C and Massana, R}, title = {New insights into the diversity of marine picoeukaryotes.}, journal = {PloS one}, volume = {4}, number = {9}, pages = {e7143}, pmid = {19787059}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; Ciliophora/physiology ; Cloning, Molecular ; Computational Biology ; DNA, Ribosomal/analysis/*genetics ; Environment ; Eukaryota ; Genetic Variation ; Marine Biology/*methods ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 18S/*genetics ; Seawater ; Sequence Analysis, DNA ; }, abstract = {Over the last decade, culture-independent surveys of marine picoeukaryotic diversity based on 18S ribosomal DNA clone libraries have unveiled numerous sequences of novel high-rank taxa. This newfound diversity has significantly altered our understanding of marine microbial food webs and the evolution of eukaryotes. However, the current picture of marine eukaryotic biodiversity may be significantly skewed by PCR amplification biases, occurrence of rDNA genes in multiple copies within a single cell, and the capacity of DNA to persist as extracellular material. In this study we performed an analysis of the metagenomic dataset from the Global Ocean Survey (GOS) expedition, seeking eukaryotic ribosomal signatures. This PCR-free approach revealed similar phylogenetic patterns to clone library surveys, suggesting that PCR steps do not impose major biases in the exploration of environmental DNA. The different cell size fractions within the GOS dataset, however, displayed a distinct picture. High protistan diversity in the <0.8 microm size fraction, in particular sequences from radiolarians and ciliates (and their absence in the 0.8-3 microm fraction), suggest that most of the DNA in this fraction comes from extracellular material from larger cells. In addition, we compared the phylogenetic patterns from rDNA and reverse transcribed rRNA 18S clone libraries from the same sample harvested in the Mediterranean Sea. The libraries revealed major differences, with taxa such as pelagophytes or picobiliphytes only detected in the 18S rRNA library. MAST (Marine Stramenopiles) appeared as potentially prominent grazers and we observed a significant decrease in the contribution of alveolate and radiolarian sequences, which overwhelmingly dominated rDNA libraries. The rRNA approach appears to be less affected by taxon-specific rDNA copy number and likely better depicts the biogeochemical significance of marine protists.}, } @article {pmid19664694, year = {2009}, author = {Ying, M and Zhan, Z and Wang, W and Chen, D}, title = {Origin and evolution of ubiquitin-conjugating enzymes from Guillardia theta nucleomorph to hominoid.}, journal = {Gene}, volume = {447}, number = {2}, pages = {72-85}, doi = {10.1016/j.gene.2009.07.021}, pmid = {19664694}, issn = {1879-0038}, mesh = {Alternative Splicing ; Animals ; Base Sequence ; Cryptophyta/*enzymology/*genetics ; DNA/genetics ; DNA Transposable Elements ; *Evolution, Molecular ; Exons ; Gene Duplication ; Hominidae/*genetics/*metabolism ; Humans ; Multigene Family ; Phylogeny ; Primates/genetics/metabolism ; Time Factors ; Ubiquitin-Conjugating Enzymes/*genetics ; }, abstract = {The origin of eukaryotic ubiquitin-conjugating enzymes (E2s) can be traced back to the Guillardia theta nucleomorph about 2500 million years ago (Mya). E2s are largely vertically inherited over eukaryotic evolution [Lespinet, O., Wolf, Y.I., Koonin, E.V., Aravind, L., 2002. The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res. 1048-1059], while mammal E2s experienced evolution of multigene families by gene duplications which have been accompanied by the increase in the species complexity. Because of alternatively splicing, primate-specific expansions of E2s happened once again at a transcriptional level. Both of them resulted in increasing genomic complexity and diversity of primate E2 proteomic function. The evolutionary processes of human E2 gene structure during expansions were accompanied by exon duplication and exonization of intronic sequences. Exonizations of Transposable Elements (TEs) in UBE2D3, UBE2L3 and UBE2V1 genes from primates indicate that exaptation of TEs also plays important roles in the structural innovation of primate-specific E2s and may create alternative splicing isoforms at a transcriptional level. Estimates for the ratio of dN/dS suggest that a strong purifying selection had acted upon protein-coding sequences of their orthologous UBE2D2, UBE2A, UBE2N, UBE2I and Rbx1 genes from animals, plants and fungi. The similar rates of synonymous substitutions are in accordance with the neutral mutation-random drift hypothesis of molecular evolution. Systematic detection of the origin and evolution of E2s, analyzing the evolution of E2 multigene families by gene duplications and the evolutionary processes of E2s during expansions, and testing its evolutionary force using E2s from distant phylogenetic lineages may advance our distinguishing of ancestral E2s from created E2s, and reveal previously unknown relationships between E2s and metazoan complexity. Analysis of these conserved proteins provides strong support for a close relationship between social amoeba and eukaryote, choanoflagellate and metazoan, and for the central roles of social amoeba and choanoflagellate in the origin and evolution of eukaryote and metazoan. Retracing the different stages of primate E2 exonization by monitoring genomic events over 63 Myr of primate evolution will advance our understanding of how TEs dynamically modified primate transcriptome and proteome in the past, and continue to do so.}, } @article {pmid19664294, year = {2009}, author = {Maruyama, S and Matsuzaki, M and Misawa, K and Nozaki, H}, title = {Cyanobacterial contribution to the genomes of the plastid-lacking protists.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {197}, pmid = {19664294}, issn = {1471-2148}, mesh = {Animals ; Cyanobacteria/*genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; Fungi/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Fungal ; Genome, Protozoan ; Genomics/methods ; Multigene Family ; Phylogeny ; Plastids/genetics ; }, abstract = {BACKGROUND: Eukaryotic genes with cyanobacterial ancestry in plastid-lacking protists have been regarded as important evolutionary markers implicating the presence of plastids in the early evolution of eukaryotes. Although recent genomic surveys demonstrated the presence of cyanobacterial and algal ancestry genes in the genomes of plastid-lacking protists, comparative analyses on the origin and distribution of those genes are still limited.

RESULTS: We identified 12 gene families with cyanobacterial ancestry in the genomes of a taxonomically wide range of plastid-lacking eukaryotes (Phytophthora [Chromalveolata], Naegleria [Excavata], Dictyostelium [Amoebozoa], Saccharomyces and Monosiga [Opisthokonta]) using a novel phylogenetic pipeline. The eukaryotic gene clades with cyanobacterial ancestry were mostly composed of genes from bikonts (Archaeplastida, Chromalveolata, Rhizaria and Excavata). We failed to find genes with cyanobacterial ancestry in Saccharomyces and Dictyostelium, except for a photorespiratory enzyme conserved among fungi. Meanwhile, we found several Monosiga genes with cyanobacterial ancestry, which were unrelated to other Opisthokonta genes.

CONCLUSION: Our data demonstrate that a considerable number of genes with cyanobacterial ancestry have contributed to the genome composition of the plastid-lacking protists, especially bikonts. The origins of those genes might be due to lateral gene transfer events, or an ancient primary or secondary endosymbiosis before the diversification of bikonts. Our data also show that all genes identified in this study constitute multi-gene families with punctate distribution among eukaryotes, suggesting that the transferred genes could have survived through rounds of gene family expansion and differential reduction.}, } @article {pmid19661396, year = {2009}, author = {Zimmer, C}, title = {Origins. On the origin of eukaryotes.}, journal = {Science (New York, N.Y.)}, volume = {325}, number = {5941}, pages = {666-668}, doi = {10.1126/science.325_666}, pmid = {19661396}, issn = {1095-9203}, mesh = {Animals ; *Archaea/classification/genetics/physiology ; *Bacteria/classification/genetics ; Bacterial Physiological Phenomena ; *Biological Evolution ; Cell Nucleus/genetics/metabolism ; *Eukaryotic Cells/cytology/metabolism/physiology ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Genes, Mitochondrial ; *Genome ; Mitochondria/physiology ; Organelles/physiology ; *Prokaryotic Cells/cytology/metabolism/physiology ; Symbiosis ; }, } @article {pmid19619164, year = {2009}, author = {Nedelcu, AM and Blakney, AJ and Logue, KD}, title = {Functional replacement of a primary metabolic pathway via multiple independent eukaryote-to-eukaryote gene transfers and selective retention.}, journal = {Journal of evolutionary biology}, volume = {22}, number = {9}, pages = {1882-1894}, doi = {10.1111/j.1420-9101.2009.01797.x}, pmid = {19619164}, issn = {1420-9101}, mesh = {Animals ; *Biological Evolution ; Cation Transport Proteins/genetics ; Choanoflagellata/*genetics ; Eukaryota/genetics ; *Gene Transfer, Horizontal ; Glutamate Synthase/genetics ; Glutamate-Ammonia Ligase/genetics ; Metabolic Networks and Pathways/*genetics ; }, abstract = {Although lateral gene transfer (LGT) is now recognized as a major force in the evolution of prokaryotes, the contribution of LGT to the evolution and diversification of eukaryotes is less understood. Notably, transfers of complete pathways are believed to be less likely between eukaryotes, because the successful transfer of a pathway requires the physical clustering of functionally related genes. Here, we report that in one of the closest unicellular relatives of animals, the choanoflagellate, Monosiga, three genes whose products work together in the glutamate synthase cycle are of algal origin. The concerted retention of these three independently acquired genes is best explained as the consequence of a series of adaptive replacement events. More generally, this study argues that (i) eukaryote-to-eukaryote transfers of entire metabolic pathways are possible, (ii) adaptive functional replacements of primary pathways can occur, and (iii) functional replacements involving eukaryotic genes are likely to have also contributed to the evolution of eukaryotes. Lastly, these data underscore the potential contribution of algal genes to the evolution of nonphotosynthetic lineages.}, } @article {pmid19602080, year = {2009}, author = {Elias, M and Patron, NJ and Keeling, PJ}, title = {The RAB family GTPase Rab1A from Plasmodium falciparum defines a unique paralog shared by chromalveolates and rhizaria.}, journal = {The Journal of eukaryotic microbiology}, volume = {56}, number = {4}, pages = {348-356}, doi = {10.1111/j.1550-7408.2009.00408.x}, pmid = {19602080}, issn = {1550-7408}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Cryptophyta/*enzymology/genetics ; DNA, Algal/analysis/genetics ; DNA, Protozoan/analysis/genetics ; Evolution, Molecular ; Molecular Sequence Data ; Phylogeny ; Plasmodium falciparum/*enzymology/genetics ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Analysis, DNA ; rab1 GTP-Binding Proteins/chemistry/*genetics/metabolism ; }, abstract = {The RAB GTPases, which are involved in regulation of endomembrane trafficking, exhibit a complex but incompletely understood evolutionary history. We elucidated the evolution of the RAB1 subfamily ancestrally implicated in the endoplasmic reticulum-to-Golgi traffic. We found that RAB1 paralogs have been generated over the course of eukaryotic evolution, with some duplications coinciding with the advent of major eukaryotic lineages (e.g. Metazoa, haptophytes). We also identified a unique, derived RAB1 paralog, orthologous to the Plasmodium Rab1A, that occurs in stramenopiles, alveolates, and Rhizaria, represented by the chlorarachniophyte Gymnochlora stellata. This finding is consistent with the recently documented existence of a major eukaryotic clade ("SAR") comprising these three lineages. We further found a Rab1A-like protein in the cryptophyte Guillardia theta, but it exhibits unusual features among RAB proteins: absence of a C-terminal prenylation motif and an N-terminal extension with two MSP domains; and its phylogenetic relationships could not be established convincingly due to its divergent nature. Our results nevertheless point to a unique membrane trafficking pathway shared by at least some lineages of chromalveolates and Rhizaria, an insight that has implications towards interpreting the early evolution of eukaryotes and the endomembrane system.}, } @article {pmid19513207, year = {2008}, author = {Vesteg, M and Krajcovic, J}, title = {Origin of eukaryotic cells as a symbiosis of parasitic alpha-proteobacteria in the periplasm of two-membrane-bounded sexual pre-karyotes.}, journal = {Communicative & integrative biology}, volume = {1}, number = {1}, pages = {104-113}, pmid = {19513207}, issn = {1942-0889}, abstract = {The last universal common ancestor (LUCA) might have been either prokaryotic- or eukaryotic-like. Nevertheless, the universally distributed components suggest rather LUCA consistent with the pre-cell theory of Kandler. The hypotheses for the origin of eukaryotes are briefly summarized. The models under which prokaryotes or their chimeras were direct ancestors of eukaryotes are criticized. It is proposed that the pre-karyote (a host entity for alpha-proteobacteria) was a remnant of pre-cellular world, and was unlucky to have evolved fusion prohibiting cell surface, and thus could have evolved sex. The DNA damage checkpoint pathway could have represented the only pre-karyotic checkpoint control allowing division only when DNA was completely replicated without mistakes. The fusion of two partially diploid (in S-phase blocked) pre-karyotes might have represented another repair strategy. After completing replication of both haploid sets, DNA damage checkpoint would allow two subsequent rounds of fission. Alternatively, pre-karyote might have possessed two membranes inherited from LUCA. Under this hypothesis symbiotic alpha-proteobacterial ancestors of mitochondria might have ancestrally been selfish parasites of pre-karyote intermembrane space whose infection might have been analogous to infection of G(-)-bacterial periplasm by Bdellovibrio sp. It is suggested that eukaryotic plasma membrane might be derived from pre-karyote outer membrane and nuclear/ER membrane might be derived from pre-karyote inner membrane. Thus the nucleoplasm might be derived from pre-karyote cytoplasm and eukaryotic cytoplasm might be homologous to pre-karyote periplasm.}, } @article {pmid19506574, year = {2009}, author = {Gross, J and Bhattacharya, D}, title = {Mitochondrial and plastid evolution in eukaryotes: an outsiders' perspective.}, journal = {Nature reviews. Genetics}, volume = {10}, number = {7}, pages = {495-505}, pmid = {19506574}, issn = {1471-0064}, mesh = {Animals ; Eukaryotic Cells/*physiology ; *Evolution, Molecular ; Humans ; Plants ; Plastids/*physiology ; Protein Transport/physiology ; }, abstract = {The eukaryotic organelles mitochondrion and plastid originated from eubacterial endosymbionts. Here we propose that, in both cases, prokaryote-to-organelle conversion was driven by the internalization of host-encoded factors progressing from the outer membrane of the endosymbionts towards the intermembrane space, inner membrane and finally the organelle interior. This was made possible by an outside-to-inside establishment in the endosymbionts of host-controlled protein-sorting components, which enabled the gradual integration of organelle functions into the nuclear genome. Such a convergent trajectory for mitochondrion and plastid establishment suggests a novel paradigm for organelle evolution that affects theories of eukaryogenesis.}, } @article {pmid19492355, year = {2009}, author = {Davidov, Y and Jurkevitch, E}, title = {Predation between prokaryotes and the origin of eukaryotes.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {31}, number = {7}, pages = {748-757}, doi = {10.1002/bies.200900018}, pmid = {19492355}, issn = {1521-1878}, mesh = {*Biological Evolution ; Endocytosis ; Eukaryotic Cells/cytology/*metabolism ; Mitochondria/metabolism ; Phylogeny ; Prokaryotic Cells/cytology/*metabolism ; *Symbiosis ; }, abstract = {Accumulating data suggest that the eukaryotic cell originated from a merger of two prokaryotes, an archaeal host and a bacterial endosymbiont. However, since prokaryotes are unable to perform phagocytosis, the means by which the endosymbiont entered its host is an enigma. We suggest that a predatory or parasitic interaction between prokaryotes provides a reasonable explanation for this conundrum. According to the model presented here, the host in this interaction was an anaerobic archaeon with a periplasm-like space. The predator was a small (facultative) aerobic alpha-proteobacterium, which penetrated and replicated within the host periplasm, and later became the mitochondria. Plausible conditions under which this interaction took place and circumstances that may have led to the contemporary complex eukaryotic cell are discussed.}, } @article {pmid20842214, year = {2009}, author = {Tekle, YI and Parfrey, LW and Katz, LA}, title = {Molecular Data are Transforming Hypotheses on the Origin and Diversification of Eukaryotes.}, journal = {Bioscience}, volume = {59}, number = {6}, pages = {471-481}, pmid = {20842214}, issn = {0006-3568}, support = {R15 GM081865/GM/NIGMS NIH HHS/United States ; R15 GM081865-01/GM/NIGMS NIH HHS/United States ; }, abstract = {The explosion of molecular data has transformed hypotheses on both the origin of eukaryotes and the structure of the eukaryotic tree of life. Early ideas about the evolution of eukaryotes arose through analyses of morphology by light microscopy and later electron microscopy. Though such studies have proven powerful at resolving more recent events, theories on origins and diversification of eukaryotic life have been substantially revised in light of analyses of molecular data including gene and, increasingly, whole genome sequences. By combining these approaches, progress has been made in elucidating both the origin and diversification of eukaryotes. Yet many aspects of the evolution of eukaryotic life remain to be illuminated.}, } @article {pmid19296856, year = {2009}, author = {Tahirov, TH and Makarova, KS and Rogozin, IB and Pavlov, YI and Koonin, EV}, title = {Evolution of DNA polymerases: an inactivated polymerase-exonuclease module in Pol epsilon and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors.}, journal = {Biology direct}, volume = {4}, number = {}, pages = {11}, pmid = {19296856}, issn = {1745-6150}, support = {R01CA129925-01A2/CA/NCI NIH HHS/United States ; R01 GM082923/GM/NIGMS NIH HHS/United States ; R01 CA129925/CA/NCI NIH HHS/United States ; 1R01GM082923-01A2/GM/NIGMS NIH HHS/United States ; R01 CA129925-02/CA/NCI NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Archaea/classification/*enzymology ; Archaeal Proteins/chemistry/classification/genetics/metabolism ; Catalytic Domain ; Computer Simulation ; Conserved Sequence ; DNA Polymerase II/chemistry/classification/*genetics/*metabolism ; Enzyme Activation ; Eukaryotic Cells/classification/*enzymology ; *Evolution, Molecular ; Humans ; Molecular Sequence Data ; Phylogeny ; Recombinant Fusion Proteins/*chemistry/genetics/*metabolism ; Zinc Fingers ; }, abstract = {BACKGROUND: Evolution of DNA polymerases, the key enzymes of DNA replication and repair, is central to any reconstruction of the history of cellular life. However, the details of the evolutionary relationships between DNA polymerases of archaea and eukaryotes remain unresolved.

RESULTS: We performed a comparative analysis of archaeal, eukaryotic, and bacterial B-family DNA polymerases, which are the main replicative polymerases in archaea and eukaryotes, combined with an analysis of domain architectures. Surprisingly, we found that eukaryotic Polymerase epsilon consists of two tandem exonuclease-polymerase modules, the active N-terminal module and a C-terminal module in which both enzymatic domains are inactivated. The two modules are only distantly related to each other, an observation that suggests the possibility that Pol epsilon evolved as a result of insertion and subsequent inactivation of a distinct polymerase, possibly, of bacterial descent, upstream of the C-terminal Zn-fingers, rather than by tandem duplication. The presence of an inactivated exonuclease-polymerase module in Pol epsilon parallels a similar inactivation of both enzymatic domains in a distinct family of archaeal B-family polymerases. The results of phylogenetic analysis indicate that eukaryotic B-family polymerases, most likely, originate from two distantly related archaeal B-family polymerases, one form giving rise to Pol epsilon, and the other one to the common ancestor of Pol alpha, Pol delta, and Pol zeta. The C-terminal Zn-fingers that are present in all eukaryotic B-family polymerases, unexpectedly, are homologous to the Zn-finger of archaeal D-family DNA polymerases that are otherwise unrelated to the B family. The Zn-finger of Polepsilon shows a markedly greater similarity to the counterpart in archaeal PolD than the Zn-fingers of other eukaryotic B-family polymerases.

CONCLUSION: Evolution of eukaryotic DNA polymerases seems to have involved previously unnoticed complex events. We hypothesize that the archaeal ancestor of eukaryotes encoded three DNA polymerases, namely, two distinct B-family polymerases and a D-family polymerase all of which contributed to the evolution of the eukaryotic replication machinery. The Zn-finger might have been acquired from PolD by the B-family form that gave rise to Pol epsilon prior to or in the course of eukaryogenesis, and subsequently, was captured by the ancestor of the other B-family eukaryotic polymerases. The inactivated polymerase-exonuclease module of Pol epsilon might have evolved by fusion with a distinct polymerase, rather than by duplication of the active module of Pol epsilon, and is likely to play an important role in the assembly of eukaryotic replication and repair complexes.}, } @article {pmid19281955, year = {2009}, author = {Jaillon, O and Aury, JM and Wincker, P}, title = {"Changing by doubling", the impact of Whole Genome Duplications in the evolution of eukaryotes.}, journal = {Comptes rendus biologies}, volume = {332}, number = {2-3}, pages = {241-253}, doi = {10.1016/j.crvi.2008.07.007}, pmid = {19281955}, issn = {1768-3238}, mesh = {Animals ; *Biological Evolution ; Chromosomes/genetics ; DNA/genetics ; *Gene Duplication ; Genome/*genetics ; Humans ; Phylogeny ; }, abstract = {Species are usually defined by reproductive isolation and are characterized by their gene repertoire. These two aspects are consequences of events fixed during evolution, including whole genome duplications and other polyploidizations. Thanks to the recent progress in genome sequencing, new light has been shed on these events. In this review, we will summarize these findings and discuss the methodology involved. Evolutionary traces of such events have been evidenced in various lineages in plants, animals, fungi and protozoa. Comparative analysis of synteny is a powerful approach to unveil evolutionary footprints of these events. According to expectations, these events would facilitate speciation since some of them are thought to be at the base of major radiations such as teleostei or eudicotyledons. After an initial amplification, the gene repertoire would be shaped by constraints such as expression level and functional interactions that would tend to maintain only a tiny fraction of the duplicates over the long term. Functional innovation from duplication may be a secondary effect, enabled by these duplicate retention mechanisms.}, } @article {pmid19245710, year = {2009}, author = {Yutin, N and Wolf, MY and Wolf, YI and Koonin, EV}, title = {The origins of phagocytosis and eukaryogenesis.}, journal = {Biology direct}, volume = {4}, number = {}, pages = {9}, pmid = {19245710}, issn = {1745-6150}, support = {//Intramural NIH HHS/United States ; }, mesh = {Actins/chemistry ; Amino Acid Sequence ; Animals ; Archaea/genetics/metabolism ; Bacteria/enzymology ; Conserved Sequence ; Eukaryotic Cells/*cytology/enzymology ; Microfilament Proteins/chemistry ; Molecular Sequence Data ; Monomeric GTP-Binding Proteins/chemistry/genetics ; *Phagocytosis ; Phylogeny ; Proteomics ; Sequence Homology, Amino Acid ; Symbiosis ; ras Proteins/genetics ; }, abstract = {BACKGROUND: Phagocytosis, that is, engulfment of large particles by eukaryotic cells, is found in diverse organisms and is often thought to be central to the very origin of the eukaryotic cell, in particular, for the acquisition of bacterial endosymbionts including the ancestor of the mitochondrion.

RESULTS: Comparisons of the sets of proteins implicated in phagocytosis in different eukaryotes reveal extreme diversity, with very few highly conserved components that typically do not possess readily identifiable prokaryotic homologs. Nevertheless, phylogenetic analysis of those proteins for which such homologs do exist yields clues to the possible origin of phagocytosis. The central finding is that a subset of archaea encode actins that are not only monophyletic with eukaryotic actins but also share unique structural features with actin-related proteins (Arp) 2 and 3. All phagocytic processes are strictly dependent on remodeling of the actin cytoskeleton and the formation of branched filaments for which Arp2/3 are responsible. The presence of common structural features in Arp2/3 and the archaeal actins suggests that the common ancestors of the archaeal and eukaryotic actins were capable of forming branched filaments, like modern Arp2/3. The Rho family GTPases that are ubiquitous regulators of phagocytosis in eukaryotes appear to be of bacterial origin, so assuming that the host of the mitochondrial endosymbiont was an archaeon, the genes for these GTPases come via horizontal gene transfer from the endosymbiont or in an earlier event.

CONCLUSION: The present findings suggest a hypothetical scenario of eukaryogenesis under which the archaeal ancestor of eukaryotes had no cell wall (like modern Thermoplasma) but had an actin-based cytoskeleton including branched actin filaments that allowed this organism to produce actin-supported membrane protrusions. These protrusions would facilitate accidental, occasional engulfment of bacteria, one of which eventually became the mitochondrion. The acquisition of the endosymbiont triggered eukaryogenesis, in particular, the emergence of the endomembrane system that eventually led to the evolution of modern-type phagocytosis, independently in several eukaryotic lineages.}, } @article {pmid19209377, year = {2009}, author = {Nedelcu, AM}, title = {Comparative genomics of phylogenetically diverse unicellular eukaryotes provide new insights into the genetic basis for the evolution of the programmed cell death machinery.}, journal = {Journal of molecular evolution}, volume = {68}, number = {3}, pages = {256-268}, pmid = {19209377}, issn = {1432-1432}, mesh = {Amino Acid Sequence ; Animals ; Apoptosis Regulatory Proteins/*genetics ; Databases, Protein ; Eukaryotic Cells ; *Evolution, Molecular ; Fungi/genetics ; Genomics ; Molecular Sequence Data ; *Phylogeny ; Plants/genetics ; }, abstract = {Programmed cell death (PCD) represents a significant component of normal growth and development in multicellular organisms. Recently, PCD-like processes have been reported in single-celled eukaryotes, implying that some components of the PCD machinery existed early in eukaryotic evolution. This study provides a comparative analysis of PCD-related sequences across more than 50 unicellular genera from four eukaryotic supergroups: Unikonts, Excavata, Chromalveolata, and Plantae. A complex set of PCD-related sequences that correspond to domains or proteins associated with all main functional classes--from ligands and receptors to executors of PCD--was found in many unicellular lineages. Several PCD domains and proteins previously thought to be restricted to animals or land plants are also present in unicellular species. Noteworthy, the yeast, Saccharomyces cerevisiae--used as an experimental model system for PCD research, has a rather reduced set of PCD-related sequences relative to other unicellular species. The phylogenetic distribution of the PCD-related sequences identified in unicellular lineages suggests that the genetic basis for the evolution of the complex PCD machinery present in extant multicellular lineages has been established early in the evolution of eukaryotes. The shaping of the PCD machinery in multicellular lineages involved the duplication, co-option, recruitment, and shuffling of domains already present in their unicellular ancestors.}, } @article {pmid19185732, year = {2008}, author = {Picazarri, K and Nakada-Tsukui, K and Sato, D and Nozaki, T}, title = {Analysis of autophagy in the enteric protozoan parasite Entamoeba.}, journal = {Methods in enzymology}, volume = {451}, number = {}, pages = {359-371}, doi = {10.1016/S0076-6879(08)03224-2}, pmid = {19185732}, issn = {1557-7988}, mesh = {Animals ; Autophagy/*physiology ; Biological Assay/*methods ; Entamoeba histolytica/cytology/genetics/*physiology ; Entamoebiasis/*microbiology ; Humans ; Protozoan Proteins/genetics/metabolism ; Recombinant Fusion Proteins/genetics/metabolism ; }, abstract = {Entamoeba histolytica is the enteric protozoan parasite that causes human amoebiasis. We have previously shown that autophagy is involved in proliferation and differentiation in the related species Entamoeba invadens, which infects reptiles and develops similar clinical manifestations. Because this group of protists possesses only a limited set of genes known to participate in autophagy in other eukaryotes, it potentially represents a useful model for studying the core system of autophagy and provides tools to elucidate the evolution of eukaryotes and their organelles. Here we describe the methods to study autophagy in Entamoeba.}, } @article {pmid20409812, year = {2009}, author = {Rompolas, P and Patel-King, RS and King, SM}, title = {Schmidtea mediterranea: a model system for analysis of motile cilia.}, journal = {Methods in cell biology}, volume = {93}, number = {}, pages = {81-98}, doi = {10.1016/S0091-679X(08)93004-1}, pmid = {20409812}, issn = {0091-679X}, mesh = {Animals ; Cilia/*metabolism/ultrastructure ; Gene Expression ; Histocytological Preparation Techniques ; Humans ; Laboratory Animal Science/instrumentation/methods ; Mice ; Microscopy/methods ; *Models, Biological ; *Planarians/cytology/genetics/metabolism ; RNA Interference ; }, abstract = {Cilia are cellular organelles that appeared early in the evolution of eukaryotes. These structures and the pool of about 600genes involved in their assembly and function are highly conserved in organisms as distant as single-cell protists, like Chlamydomonas reinhardtti, and humans (Silflow and Lefebvre, 2001). A significant body of work on the biology of cilia has been produced over the years, with the help of powerful model organisms including C. reinhardtti, Caenorhabditis elegans, sea urchins, and mice. However, specific limitations of these systems, especially regarding the ability to efficiently study gene loss-of-function, warrant the search for a new model organism to study cilia and cilia-based motility. Schmidtea mediterranea is a species of planarian (Class: Tubellaria) with a well-defined monostratified ciliated epithelium, which contributes to the motility of the organism, in addition to other more specialized ciliary structures. The use of S. mediterranea as an experimental system to study stem cell biology and regeneration has led to a recently sequenced genome and to the development of a wide array of powerful tools including the ability to inhibit gene expression via RNA interference. In addition, we have developed and describe here a number of methods for analyzing motile cilia in S. mediterranea. Overall, S. mediterranea is a highly versatile, easy to maintain, and genetically tractable organism that provides a powerful alternative model system for the study of motile cilia.}, } @article {pmid19073919, year = {2008}, author = {Cox, CJ and Foster, PG and Hirt, RP and Harris, SR and Embley, TM}, title = {The archaebacterial origin of eukaryotes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {51}, pages = {20356-20361}, pmid = {19073919}, issn = {1091-6490}, support = {BB/C006143/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/C508777/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Archaea ; *Biological Evolution ; Crenarchaeota/*genetics ; *Eukaryotic Cells ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; Genomics ; *Models, Genetic ; Nucleic Acids/genetics ; *Phylogeny ; Protein Biosynthesis/genetics ; Transcription, Genetic/genetics ; }, abstract = {The origin of the eukaryotic genetic apparatus is thought to be central to understanding the evolution of the eukaryotic cell. Disagreement about the source of the relevant genes has spawned competing hypotheses for the origins of the eukaryote nuclear lineage. The iconic rooted 3-domains tree of life shows eukaryotes and archaebacteria as separate groups that share a common ancestor to the exclusion of eubacteria. By contrast, the eocyte hypothesis has eukaryotes originating within the archaebacteria and sharing a common ancestor with a particular group called the Crenarchaeota or eocytes. Here, we have investigated the relative support for each hypothesis from analysis of 53 genes spanning the 3 domains, including essential components of the eukaryotic nucleic acid replication, transcription, and translation apparatus. As an important component of our analysis, we investigated the fit between model and data with respect to composition. Compositional heterogeneity is a pervasive problem for reconstruction of ancient relationships, which, if ignored, can produce an incorrect tree with strong support. To mitigate its effects, we used phylogenetic models that allow for changing nucleotide or amino acid compositions over the tree and data. Our analyses favor a topology that supports the eocyte hypothesis rather than archaebacterial monophyly and the 3-domains tree of life.}, } @article {pmid18997823, year = {2008}, author = {Koonin, EV and Wolf, YI and Nagasaki, K and Dolja, VV}, title = {The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups.}, journal = {Nature reviews. Microbiology}, volume = {6}, number = {12}, pages = {925-939}, doi = {10.1038/nrmicro2030}, pmid = {18997823}, issn = {1740-1534}, support = {GM053190/GM/NIGMS NIH HHS/United States ; //Intramural NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Eukaryotic Cells/virology ; Genome, Viral ; Host-Pathogen Interactions/genetics ; Models, Biological ; Phylogeny ; Picornaviridae/*classification/enzymology/*genetics ; RNA Helicases/genetics ; RNA-Directed DNA Polymerase/genetics ; }, abstract = {The recent discovery of RNA viruses in diverse unicellular eukaryotes and developments in evolutionary genomics have provided the means for addressing the origin of eukaryotic RNA viruses. The phylogenetic analyses of RNA polymerases and helicases presented in this Analysis article reveal close evolutionary relationships between RNA viruses infecting hosts from the Chromalveolate and Excavate supergroups and distinct families of picorna-like viruses of plants and animals. Thus, diversification of picorna-like viruses probably occurred in a 'Big Bang' concomitant with key events of eukaryogenesis. The origins of the conserved genes of picorna-like viruses are traced to likely ancestors including bacterial group II retroelements, the family of HtrA proteases and DNA bacteriophages.}, } @article {pmid18935970, year = {2009}, author = {Cavalier-Smith, T}, title = {Predation and eukaryote cell origins: a coevolutionary perspective.}, journal = {The international journal of biochemistry & cell biology}, volume = {41}, number = {2}, pages = {307-322}, doi = {10.1016/j.biocel.2008.10.002}, pmid = {18935970}, issn = {1357-2725}, mesh = {Animals ; *Biological Evolution ; Eukaryotic Cells/cytology/*physiology ; Phylogeny ; }, abstract = {Cells are of only two kinds: bacteria, with DNA segregated by surface membrane motors, dating back approximately 3.5Gy; and eukaryotes, which evolved from bacteria, possibly as recently as 800-850My ago. The last common ancestor of eukaryotes was a sexual phagotrophic protozoan with mitochondria, one or two centrioles and cilia. Conversion of bacteria (=prokaryotes) into a eukaryote involved approximately 60 major innovations. Numerous contradictory ideas about eukaryogenesis fail to explain fundamental features of eukaryotic cell biology or conflict with phylogeny. Data are best explained by the intracellular coevolutionary theory, with three basic tenets: (1) the eukaryotic cytoskeleton and endomembrane system originated through cooperatively enabling the evolution of phagotrophy; (2) phagocytosis internalised DNA-membrane attachments, unavoidably disrupting bacterial division; recovery entailed the evolution of the nucleus and mitotic cycle; (3) the symbiogenetic origin of mitochondria immediately followed the perfection of phagotrophy and intracellular digestion, contributing greater energy efficiency and group II introns as precursors of spliceosomal introns. Eukaryotes plus their archaebacterial sisters form the clade neomura, which evolved from a radically modified derivative of an actinobacterial posibacterium that had replaced the ancestral eubacterial murein peptidoglycan by N-linked glycoproteins, radically modified its DNA-handling enzymes, and evolved cotranslational protein secretion, but not the isoprenoid-ether lipids of archaebacteria. I focus on this phylogenetic background and on explaining how in response to novel phagotrophic selective pressures and ensuing genome internalisation this prekaryote evolved efficient digestion of prey proteins by retrotranslocation and 26S proteasomes, then internal digestion by phagocytosis, lysosomes, and peroxisomes, and eukaryotic vesicle trafficking and intracellular compartmentation.}, } @article {pmid18931454, year = {2008}, author = {Saruhashi, S and Hamada, K and Miyata, D and Horiike, T and Shinozawa, T}, title = {Comprehensive analysis of the origin of eukaryotic genomes.}, journal = {Genes & genetic systems}, volume = {83}, number = {4}, pages = {285-291}, doi = {10.1266/ggs.83.285}, pmid = {18931454}, issn = {1341-7568}, mesh = {Animals ; Eukaryotic Cells/classification/metabolism/physiology ; *Evolution, Molecular ; *Genome/physiology ; Humans ; Phylogeny ; Prokaryotic Cells/metabolism ; }, abstract = {There is currently no consensus on the evolutionary origin of eukaryotes. In the search of the ancestors of eukaryotes, we analyzed the phylogeny of 46 genomes, including those of 2 eukaryotes, 8 archaea, and 36 eubacteria. To avoid the effects of gene duplications, we used inparalog pairs of genes with orthologous relationships. First, we grouped these inparalogs into the functional categories of the nucleus, cytoplasm, and mitochondria. Next, we counted the sister groups of eukaryotes in prokaryotic phyla and plotted them on a standard phylogenetic tree. Finally, we used Pearson's chi-square test to estimate the origin of the genomes from specific prokaryotic ancestors. The results suggest the eukaryotic nuclear genome descends from an archaea that was neither euryarchaeota nor crenarchaeota and that the mitochondrial genome descends from alpha-proteobacteria. In contrast, genes related to the cytoplasm do not appear to originate from a specific group of prokaryotes.}, } @article {pmid18687770, year = {2008}, author = {Scofield, DG and Lynch, M}, title = {Evolutionary diversification of the Sm family of RNA-associated proteins.}, journal = {Molecular biology and evolution}, volume = {25}, number = {11}, pages = {2255-2267}, pmid = {18687770}, issn = {1537-1719}, support = {R01 GM036827/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; DNA ; Eukaryotic Cells ; *Evolution, Molecular ; Genetic Variation ; Humans ; Molecular Sequence Data ; Phylogeny ; Protein Conformation ; Protein Structure, Tertiary ; Ribonucleoproteins, Small Nuclear/chemistry/classification/*genetics ; }, abstract = {The Sm family of proteins is closely associated with RNA metabolism throughout all life. These proteins form homomorphic and heteromorphic rings consisting of six or seven subunits with a characteristic central pore, the presence of which is critical for binding U-rich regions of single-stranded RNA. Eubacteria and Archaea typically carry one or two forms of Sm proteins and assemble one homomorphic ring per Sm protein. Eukaryotes typically carry 16 or more Sm proteins that assemble to form heteromorphic rings which lie at the center of a number of critical RNA-associated small nuclear ribonucleoproteins (snRNPs). High Sm protein diversity and heteromorphic Sm rings are features stretching back to the origin of eukaryotes; very deep phylogenetic divisions among existing Sm proteins indicate simultaneous evolution across essentially all existing eukaryotic life. Two basic forms of heteromorphic Sm rings are found in eukaryotes. Fixed Sm rings are highly stable and static and are assembled around an RNA cofactor. Flexible Sm rings also stabilize and chaperone RNA but assemble in the absence of an RNA substrate and, more significantly, associate with and dissociate from RNA substrates more freely than fixed rings. This suggests that the conformation of flexible Sm rings might be modified in some specific manner to facilitate association and dissociation with RNA. Diversification of eukaryotic Sm proteins may have been initiated by gene transfers and/or genome clashes that accompanied the origin of the eukaryotic cell itself, with further diversification driven by a greater need for steric specificity within increasingly complex snRNPs.}, } @article {pmid18665247, year = {2008}, author = {Chen, L and Zheng, S}, title = {Identify alternative splicing events based on position-specific evolutionary conservation.}, journal = {PloS one}, volume = {3}, number = {7}, pages = {e2806}, pmid = {18665247}, issn = {1932-6203}, mesh = {Algorithms ; *Alternative Splicing ; Computational Biology/*methods ; Databases, Genetic ; *Evolution, Molecular ; Exons ; Expressed Sequence Tags ; Gene Expression Profiling ; Genome ; Genome, Human ; HeLa Cells ; Humans ; Introns ; Models, Biological ; Models, Statistical ; }, abstract = {The evolution of eukaryotes is accompanied by the increased complexity of alternative splicing which greatly expands genome information. One of the greatest challenges in the post-genome era is a complete revelation of human transcriptome with consideration of alternative splicing. Here, we introduce a comparative genomics approach to systemically identify alternative splicing events based on the differential evolutionary conservation between exons and introns and the high-quality annotation of the ENCODE regions. Specifically, we focus on exons that are included in some transcripts but are completely spliced out for others and we call them conditional exons. First, we characterize distinguishing features among conditional exons, constitutive exons and introns. One of the most important features is the position-specific conservation score. There are dramatic differences in conservation scores between conditional exons and constitutive exons. More importantly, the differences are position-specific. For flanking intronic regions, the differences between conditional exons and constitutive exons are also position-specific. Using the Random Forests algorithm, we can classify conditional exons with high specificities (97% for the identification of conditional exons from intron regions and 95% for the classification of known exons) and fair sensitivities (64% and 32% respectively). We applied the method to the human genome and identified 39,640 introns that actually contain conditional exons and classified 8,813 conditional exons from the current RefSeq exon list. Among those, 31,673 introns containing conditional exons and 5,294 conditional exons classified from known exons cannot be inferred from RefSeq, UCSC or Ensembl annotations. Some of these de novo predictions were experimentally verified.}, } @article {pmid18652645, year = {2008}, author = {Jékely, G}, title = {Origin of the nucleus and Ran-dependent transport to safeguard ribosome biogenesis in a chimeric cell.}, journal = {Biology direct}, volume = {3}, number = {}, pages = {31}, pmid = {18652645}, issn = {1745-6150}, mesh = {Active Transport, Cell Nucleus/genetics ; Cell Nucleus/genetics/*metabolism ; Chimera/*metabolism ; Computer Simulation ; *Evolution, Molecular ; Models, Genetic ; Nuclear Envelope/genetics ; Ribosomal Proteins/genetics/metabolism ; Ribosomes/genetics/*metabolism ; Thermus thermophilus/*genetics/metabolism ; ran GTP-Binding Protein/*physiology ; }, abstract = {BACKGROUND: The origin of the nucleus is a central problem about the origin of eukaryotes. The common ancestry of nuclear pore complexes (NPC) and vesicle coating complexes indicates that the nucleus evolved via the modification of a pre-existing endomembrane system. Such an autogenous scenario is cell biologically feasible, but it is not clear what were the selective or neutral mechanisms that had led to the origin of the nuclear compartment.

RESULTS: A key selective force during the autogenous origin of the nucleus could have been the need to segregate ribosome factories from the cytoplasm where ribosomal proteins (RPs) of the protomitochondrium were synthesized. After its uptake by an anuclear cell the protomitochondrium transferred several of its RP genes to the host genome. Alphaproteobacterial RPs and archaebacterial-type host ribosomes were consequently synthesized in the same cytoplasm. This could have led to the formation of chimeric ribosomes. I propose that the nucleus evolved when the host cell compartmentalised its ribosome factories and the tightly linked genome to reduce ribosome chimerism. This was achieved in successive stages by first evolving karyopherin and RanGTP dependent chaperoning of RPs, followed by the evolution of a membrane network to serve as a diffusion barrier, and finally a hydrogel sieve to ensure selective permeability at nuclear pores. Computer simulations show that a gradual segregation of cytoplasm and nucleoplasm via these steps can progressively reduce ribosome chimerism.

CONCLUSION: Ribosome chimerism can provide a direct link between the selective forces for and the mechanisms of evolving nuclear transport and compartmentalisation. The detailed molecular scenario presented here provides a solution to the gradual evolution of nuclear compartmentalization from an anuclear stage.

REVIEWERS: This article was reviewed by Eugene V Koonin, Martijn Huynen, Anthony M. Poole and Patrick Forterre.}, } @article {pmid18628849, year = {2002}, author = {Paz-Ares, J and , }, title = {REGIA, an EU project on functional genomics of transcription factors from Arabidopsis Thaliana.}, journal = {Comparative and functional genomics}, volume = {3}, number = {2}, pages = {102-108}, pmid = {18628849}, issn = {1531-6912}, abstract = {Transcription factors (TFs) are regulatory proteins that have played a pivotal role in the evolution of eukaryotes and that also have great biotechnological potential. REGIA (REgulatory Gene Initiative in Arabidopsis) is an EU-funded project involving 29 European laboratories with the objective of determining the function of virtually all transcription factors from the model plant, Arabidopsis thaliana. REGIA involves: 1. the definition of TF gene expression patterns in Arabidopsis; 2. the identification of mutations at TF loci; 3. the ectopic expression of TFs (or derivatives) in Arabidopsis and in crop plants; 4. phenotypic analysis of the mutants and mis-expression lines, including both RNA and metabolic profiling; 5. the systematic analysis of interactions between TFs; and 6. the generation of a bioinformatics infrastructure to access and integrate all this information. We expect that this programme will establish the full biotechnological potential of plant TFs, and provide insights into hierarchies, redundancies, and interdependencies, and their evolution. The project involves the preparation of both a TF gene array for expression analysis and a normalised full length open reading frame (ORF) library of TFs in a yeast two hybrid vector; the applications of these resources should extend beyond the scope of this programme.}, } @article {pmid18600633, year = {2008}, author = {Vesteg, M and Krajcovic, J}, title = {On the origin of eukaryotic cytoskeleton.}, journal = {Rivista di biologia}, volume = {101}, number = {1}, pages = {109-118}, pmid = {18600633}, issn = {0035-6050}, mesh = {Animals ; Archaea/cytology/virology ; Archaeal Proteins/physiology ; Bacteria/cytology/virology ; Bacterial Proteins/physiology ; *Biological Evolution ; Cytoskeletal Proteins/genetics/physiology ; *Cytoskeleton/ultrastructure ; Escherichia coli Proteins/physiology ; Eukaryotic Cells/*ultrastructure/virology ; Evolution, Molecular ; Flagella/genetics/physiology ; Models, Biological ; Prokaryotic Cells/ultrastructure/virology ; Symbiosis ; Transduction, Genetic ; Tubulin/genetics/physiology ; Virus Replication ; }, abstract = {The origin of eukaryote-specific cytoskeletal proteins is an issue which is closely related to the origin of the domain Eukarya. As nearly all of these proteins are not found in prokaryotes, the prokaryotic origin of eukaryotic cytoskeletal network suggested by most models is questionable. Eukaryotic cytoskeletal proteins might descend from subpopulations of pre-cells co-existing with Bacteria and Archaea prior to the origin of eukaryotes. The pre-karyote (the host for a-proteobacterial ancestors of mitochondria) might have already possessed eukaryotic-like cytoskeleton. A possible role for viruses in the origin of eukaryotic cytoskeletal proteins is discussed. Viruses parasitizing on pre-cells and/or on the pre-karyote might have themselves used several eukaryotic-like cytoskeletal proteins for segregation and packing of their genomes.}, } @article {pmid18463089, year = {2008}, author = {Yutin, N and Makarova, KS and Mekhedov, SL and Wolf, YI and Koonin, EV}, title = {The deep archaeal roots of eukaryotes.}, journal = {Molecular biology and evolution}, volume = {25}, number = {8}, pages = {1619-1630}, pmid = {18463089}, issn = {1537-1719}, support = {//Intramural NIH HHS/United States ; }, mesh = {Archaea/*genetics ; Computational Biology ; *Eukaryotic Cells ; *Evolution, Molecular ; Likelihood Functions ; Models, Genetic ; Multigene Family/genetics ; *Phylogeny ; Sequence Alignment ; Species Specificity ; }, abstract = {The set of conserved eukaryotic protein-coding genes includes distinct subsets one of which appears to be most closely related to and, by inference, derived from archaea, whereas another one appears to be of bacterial, possibly, endosymbiotic origin. The "archaeal" genes of eukaryotes, primarily, encode components of information-processing systems, whereas the "bacterial" genes are predominantly operational. The precise nature of the archaeo-eukaryotic relationship remains uncertain, and it has been variously argued that eukaryotic informational genes evolved from the homologous genes of Euryarchaeota or Crenarchaeota (the major branches of extant archaea) or that the origin of eukaryotes lies outside the known diversity of archaea. We describe a comprehensive set of 355 eukaryotic genes of apparent archaeal origin identified through ortholog detection and phylogenetic analysis. Phylogenetic hypothesis testing using constrained trees, combined with a systematic search for shared derived characters in the form of homologous inserts in conserved proteins, indicate that, for the majority of these genes, the preferred tree topology is one with the eukaryotic branch placed outside the extant diversity of archaea although small subsets of genes show crenarchaeal and euryarchaeal affinities. Thus, the archaeal genes in eukaryotes appear to descend from a distinct, ancient, and otherwise uncharacterized archaeal lineage that acquired some euryarchaeal and crenarchaeal genes via early horizontal gene transfer.}, } @article {pmid18418736, year = {2008}, author = {Sundberg, BE and Wååg, E and Jacobsson, JA and Stephansson, O and Rumaks, J and Svirskis, S and Alsiö, J and Roman, E and Ebendal, T and Klusa, V and Fredriksson, R}, title = {The evolutionary history and tissue mapping of amino acid transporters belonging to solute carrier families SLC32, SLC36, and SLC38.}, journal = {Journal of molecular neuroscience : MN}, volume = {35}, number = {2}, pages = {179-193}, pmid = {18418736}, issn = {0895-8696}, mesh = {Amino Acid Transport System A/*genetics ; Amino Acid Transport Systems/*genetics ; Amino Acid Transport Systems, Neutral/*genetics ; Animals ; Anticonvulsants/pharmacology ; Cerebral Cortex/drug effects/physiology ; Diazepam/pharmacology ; Dopamine Agents/pharmacology ; Endocrine System/physiology ; *Evolution, Molecular ; Gene Expression/drug effects/physiology ; Humans ; In Situ Hybridization ; Levodopa/pharmacology ; Liver/physiology ; Male ; Mice ; Mice, Inbred Strains ; Muscle, Skeletal/physiology ; Nerve Tissue Proteins/*genetics ; *Phylogeny ; Rats ; Rats, Wistar ; Vesicular Inhibitory Amino Acid Transport Proteins/*genetics ; }, abstract = {Members of the solute carrier families (SLC) 32, 36, and 38, together also designated the beta-group of SLCs, are known to transport neutral amino acids. In this paper, we show that these three families were present before the split of the animal lineage and that they are likely to share a common decent. We also show that the APF transporters found in plants are most likely homologous to the mammalian beta-group, suggesting that this type of transporters arouse early in the evolution of eukaryotes. We performed detailed tissue expression analysis of all the members of the beta-group in rat and found several examples of highly specific expression patterns, with SLC38A7 being exclusively found in liver, SLC38A5 in blood, and SLC38A4 in muscle and liver. Moreover, we found that SLC38A10 is expressed in several endocrine organs. We also found that SLC38A1 is highly up regulated in the cortex from rats treated with diazepam and that SLC38A2 is significantly down regulated in the same tissue. In addition, we performed a detailed expression analysis of SLC38A1 and SLC38A6 in mouse brain using in situ hybridization, which showed that both these transporters are widely expressed in the brain.}, } @article {pmid18233696, year = {2007}, author = {Carlon, E and Dkhissi, A and Malki, ML and Blossey, R}, title = {Stability domains of actin genes and genomic evolution.}, journal = {Physical review. E, Statistical, nonlinear, and soft matter physics}, volume = {76}, number = {5 Pt 1}, pages = {051916}, doi = {10.1103/PhysRevE.76.051916}, pmid = {18233696}, issn = {1539-3755}, mesh = {Actins/*genetics ; Animals ; Computer Simulation ; *Evolution, Molecular ; Genome, Fungal/*genetics ; Genome, Plant/*genetics ; Genomic Instability/*genetics ; Introns/genetics ; *Models, Genetic ; Sequence Analysis, DNA/*methods ; Species Specificity ; }, abstract = {In eukaryotic genes, the protein coding sequence is split into several fragments, the exons, separated by noncoding DNA stretches, the introns. Prokaryotes do not have introns in their genomes. We report calculations of the stability domains of actin genes for various organisms in the animal, plant, and fungi kingdoms. Actin genes have been chosen because they have been highly conserved during evolution. In these genes, all introns were removed so as to mimic ancient genes at the time of the early eukaryotic development, i.e., before intron insertion. Common stability boundaries are found in evolutionarily distant organisms, which implies that these boundaries date from the early origin of eukaryotes. In general, the boundaries correspond with intron positions in the actins of vertebrates and other animals, but not much for plants and fungi. The sharpest boundary is found in a locus where fungi, algae, and animals have introns in positions separated by one nucleotide only, which identifies a hot spot for insertion. These results suggest that some introns may have been incorporated into the genomes through a thermodynamically driven mechanism, in agreement with previous observations on human genes. They also suggest a different mechanism for intron insertion in plants and animals.}, } @article {pmid18230802, year = {2008}, author = {Basu, MK and Carmel, L and Rogozin, IB and Koonin, EV}, title = {Evolution of protein domain promiscuity in eukaryotes.}, journal = {Genome research}, volume = {18}, number = {3}, pages = {449-461}, pmid = {18230802}, issn = {1088-9051}, support = {//Intramural NIH HHS/United States ; }, mesh = {Animals ; *Evolution, Molecular ; Fungal Proteins/chemistry ; Genomics ; Phylogeny ; Plant Proteins/chemistry ; Protein Interaction Domains and Motifs ; *Protein Structure, Tertiary ; }, abstract = {Numerous eukaryotic proteins contain multiple domains. Certain domains show a tendency to occur in diverse domain architectures and can be considered "promiscuous." These promiscuous domains are, typically, involved in protein-protein interactions and play crucial roles in interaction networks, particularly those that contribute to signal transduction. A systematic comparative-genomic analysis of promiscuous domains in eukaryotes is described. Two quantitative measures of domain promiscuity are introduced and applied to the analysis of 28 genomes of diverse eukaryotes. Altogether, 215 domains are identified as strongly promiscuous. The fraction of promiscuous domains in animals is shown to be significantly greater than that in fungi or plants. Evolutionary reconstructions indicate that domain promiscuity is a volatile, relatively fast-changing feature of eukaryotic proteins, with few domains remaining promiscuous throughout the evolution of eukaryotes. Some domains appear to have attained promiscuity independently in different lineages, for example, animals and plants. It is proposed that promiscuous domains persist within a relatively small pool of evolutionarily stable domain combinations from which numerous rare architectures emerge during evolution. Domain promiscuity positively correlates with the number of experimentally detected domain interactions and with the strength of purifying selection affecting a domain. Thus, evolution of promiscuous domains seems to be constrained by the diversity of their interaction partners. The set of promiscuous domains is enriched for domains mediating protein-protein interactions that are involved in various forms of signal transduction, especially in the ubiquitin system and in chromatin. Thus, a limited repertoire of promiscuous domains makes a major contribution to the diversity and evolvability of eukaryotic proteomes and signaling networks.}, } @article {pmid18058146, year = {2007}, author = {Zhu, S}, title = {Evidence for myxobacterial origin of eukaryotic defensins.}, journal = {Immunogenetics}, volume = {59}, number = {12}, pages = {949-954}, pmid = {18058146}, issn = {0093-7711}, mesh = {Amino Acid Sequence ; Animals ; Computational Biology ; Cysteine/chemistry ; Defensins/*chemistry/*genetics ; Eukaryotic Cells/*physiology ; Evolution, Molecular ; Models, Molecular ; Molecular Sequence Data ; Myxococcales/*chemistry/metabolism ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; }, abstract = {Antimicrobial defensins with the cysteine-stabilized alpha-helical and beta-sheet (CS alpha beta) motif are a large family of ancient, evolutionarily related innate immunity effectors of multicellular organisms. Although the widespread distribution in plants, fungi, and invertebrates suggests their uniqueness to Eukarya, it is unknown whether these eukaryotic defensins originated before or posterior to the emergence of eukaryotes. In this study, we provide evidence in support of the existence of defensin-like peptides (DLPs) in myxobacteria based on structural bioinformatics analysis, which recognized two bacterial peptides with a conserved cysteine-stabilized alpha-helical motif, a nested structural unit of the CS alpha beta motif. Similarity in sequence and structure to fungal DLPs together with restricted distribution to the myxobacteria as well as central role of the myxobacteria in the origin of eukaryotes suggest that the bacterial DLPs represent the ancestor of the eukaryotic defensins and could mediate immune defense of early eukaryotes after gene transfer to the proto-eukaryotic genome. Our work thus offers a basis for further investigation of prokaryotic origin of eukaryotic immune effector molecules.}, } @article {pmid17986453, year = {2008}, author = {Levy, A and Sela, N and Ast, G}, title = {TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates.}, journal = {Nucleic acids research}, volume = {36}, number = {Database issue}, pages = {D47-52}, pmid = {17986453}, issn = {1362-4962}, mesh = {Animals ; *DNA Transposable Elements ; *Databases, Genetic ; Exons ; Genomics ; Humans ; Internet ; Introns ; Invertebrates/genetics ; Mice ; MicroRNAs/chemistry/genetics ; Proteins/genetics ; *Retroelements ; *Transcription, Genetic ; Vertebrates/genetics ; }, abstract = {Transposed elements (TEs) are mobile genetic sequences. During the evolution of eukaryotes TEs were inserted into active protein-coding genes, affecting gene structure, expression and splicing patterns, and protein sequences. Genomic insertions of TEs also led to creation and expression of new functional non-coding RNAs such as microRNAs. We have constructed the TranspoGene database, which covers TEs located inside protein-coding genes of seven species: human, mouse, chicken, zebrafish, fruit fly, nematode and sea squirt. TEs were classified according to location within the gene: proximal promoter TEs, exonized TEs (insertion within an intron that led to exon creation), exonic TEs (insertion into an existing exon) or intronic TEs. TranspoGene contains information regarding specific type and family of the TEs, genomic and mRNA location, sequence, supporting transcript accession and alignment to the TE consensus sequence. The database also contains host gene specific data: gene name, genomic location, Swiss-Prot and RefSeq accessions, diseases associated with the gene and splicing pattern. In addition, we created microTranspoGene: a database of human, mouse, zebrafish and nematode TE-derived microRNAs. The TranspoGene and microTranspoGene databases can be used by researchers interested in the effect of TE insertion on the eukaryotic transcriptome. Publicly available query interfaces to TranspoGene and microTranspoGene are available at http://transpogene.tau.ac.il/ and http://microtranspogene.tau.ac.il, respectively. The entire database can be downloaded as flat files.}, } @article {pmid17977456, year = {2007}, author = {Brinkmann, H and Philippe, H}, title = {The diversity of eukaryotes and the root of the eukaryotic tree.}, journal = {Advances in experimental medicine and biology}, volume = {607}, number = {}, pages = {20-37}, doi = {10.1007/978-0-387-74021-8_2}, pmid = {17977456}, issn = {0065-2598}, mesh = {*Eukaryotic Cells ; *Evolution, Molecular ; *Genetic Variation ; Models, Biological ; Phylogeny ; Time Factors ; }, abstract = {More than 15 years ago, on the basis of phylogenetic analyses of a handful of anciently duplicated genes and of rRNA, Carl Woese proposed both a eubacterial rooting of the Tree of Life and a stepwise evolution of the eukaryotic cell. An important part of Woese's paradigm was the assumption that the so-called Archezoa were considered to be genuinely primitive because they were lacking mitochondria and several other organelles characteristic for most eukaryotes. Since then, enormous progress have been accomplished in sequencing technology and in phylogenetic reconstruction. In particular, it is now clear that a tree reconstruction artefact, known as Long Branch Attraction, is responsible for the early emergence of the fast evolving Archezoa in the eukaryotic tree. The corollary hypothesis that all extant eukaryotes are ancestrally mitochondrial is strongly supported by the discovery of rudimentary mitochondrial organelles in all analysed Archezoa. Today a consensus that divides the extant eukaryotes into six major groups is replacing Woese's paradigm, which needs, however, further confirmation. Recently, a molecular dating study based on a large phylogenomic dataset with a relaxed molecular clock and multiple time intervals yielded in a surprisingly recent time estimate of 1085 Mya for the origin of the extant eukaryotic diversity. Therefore, extant eukaryotes seem to be the product of a massive radiation that happened rather late, at least in terms of prokaryotic diversity. In multiple cases evolution has proceeded via secondary simplification of a complex ancestor, instead of the constant march towards rising complexity generally assumed. Therefore it is time to reevaluate the origin and evolution of eukaryotes, in light of the newly established phylogeny, by further integrating secondary simplification as an equal partner to complexification.}, } @article {pmid17974547, year = {2008}, author = {Basu, MK and Rogozin, IB and Deusch, O and Dagan, T and Martin, W and Koonin, EV}, title = {Evolutionary dynamics of introns in plastid-derived genes in plants: saturation nearly reached but slow intron gain continues.}, journal = {Molecular biology and evolution}, volume = {25}, number = {1}, pages = {111-119}, doi = {10.1093/molbev/msm234}, pmid = {17974547}, issn = {1537-1719}, support = {//Intramural NIH HHS/United States ; }, mesh = {DNA, Chloroplast/*genetics ; *Evolution, Molecular ; Genes, Plant/*genetics ; Introns/*genetics ; Plants/*genetics ; Plastids/*genetics ; Species Specificity ; }, abstract = {Some of the principal transitions in the evolution of eukaryotes are characterized by engulfment of prokaryotes by primitive eukaryotic cells. In particular, approximately 1.6 billion years ago, engulfment of a cyanobacterium that became the ancestor of chloroplasts and other plastids gave rise to Plantae, the major branch of eukaryotes comprised of glaucophytes, red algae, green algae, and green plants. After endosymbiosis, there was large-scale migration of genes from the endosymbiont to the nuclear genome of the host such that approximately 18% of the nuclear genes in Arabidopsis appear to be of chloroplast origin. To gain insights into the process of evolution of gene structure in these, originally, intronless genes, we compared the properties and the evolutionary dynamics of introns in genes of plastid origin and ancestral eukaryotic genes in Arabidopsis, poplar, and rice genomes. We found that intron densities in plastid-derived genes were slightly but significantly lower than those in ancestral eukaryotic genes. Although most of the introns in both categories of genes were conserved between monocots (rice) and dicots (Arabidopsis and poplar), lineage-specific intron gain was more pronounced in plastid-derived genes than in ancestral genes, whereas there was no significant difference in the intron loss rates between the 2 classes of genes. Thus, after the transfer to the nuclear genome, the plastid-derived genes have undergone a massive intron invasion that, by the time of the divergence of dicots and monocots (150-200 MYA), yielded intron densities only slightly lower than those in ancestral genes. Nevertheless, the accumulation of introns in plastid-derived genes appears not to have reached saturation and continues to this time, albeit at a low rate. The overall pattern of intron gain and loss in the plastid-derived genes is shaped by this continuing gain and the more general tendency for loss that is characteristic of the recent evolution of plant genes.}, } @article {pmid17901334, year = {2007}, author = {Morrison, HG and McArthur, AG and Gillin, FD and Aley, SB and Adam, RD and Olsen, GJ and Best, AA and Cande, WZ and Chen, F and Cipriano, MJ and Davids, BJ and Dawson, SC and Elmendorf, HG and Hehl, AB and Holder, ME and Huse, SM and Kim, UU and Lasek-Nesselquist, E and Manning, G and Nigam, A and Nixon, JE and Palm, D and Passamaneck, NE and Prabhu, A and Reich, CI and Reiner, DS and Samuelson, J and Svard, SG and Sogin, ML}, title = {Genomic minimalism in the early diverging intestinal parasite Giardia lamblia.}, journal = {Science (New York, N.Y.)}, volume = {317}, number = {5846}, pages = {1921-1926}, doi = {10.1126/science.1143837}, pmid = {17901334}, issn = {1095-9203}, support = {AI43273/AI/NIAID NIH HHS/United States ; R01 HG004164/HG/NHGRI NIH HHS/United States ; AI42488/AI/NIAID NIH HHS/United States ; R01 AI054693/AI/NIAID NIH HHS/United States ; AI51687/AI/NIAID NIH HHS/United States ; R01 AI048082/AI/NIAID NIH HHS/United States ; R01 HG004164-01/HG/NHGRI NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; *Biological Evolution ; DNA Replication/genetics ; *Eukaryotic Cells ; Gene Transfer, Horizontal ; Genes, Protozoan ; *Genome, Protozoan ; Genomics ; Giardia lamblia/classification/*genetics/physiology ; Metabolic Networks and Pathways/genetics ; Molecular Sequence Data ; Phylogeny ; Protein Kinases/genetics/metabolism ; Protozoan Proteins/chemistry/genetics/metabolism ; RNA Processing, Post-Transcriptional ; Signal Transduction ; Transcription, Genetic ; }, abstract = {The genome of the eukaryotic protist Giardia lamblia, an important human intestinal parasite, is compact in structure and content, contains few introns or mitochondrial relics, and has simplified machinery for DNA replication, transcription, RNA processing, and most metabolic pathways. Protein kinases comprise the single largest protein class and reflect Giardia's requirement for a complex signal transduction network for coordinating differentiation. Lateral gene transfer from bacterial and archaeal donors has shaped Giardia's genome, and previously unknown gene families, for example, cysteine-rich structural proteins, have been discovered. Unexpectedly, the genome shows little evidence of heterozygosity, supporting recent speculations that this organism is sexual. This genome sequence will not only be valuable for investigating the evolution of eukaryotes, but will also be applied to the search for new therapeutics for this parasite.}, } @article {pmid17826006, year = {2007}, author = {Sales-Pardo, M and Chan, AO and Amaral, LA and Guimerà, R}, title = {Evolution of protein families: is it possible to distinguish between domains of life?.}, journal = {Gene}, volume = {402}, number = {1-2}, pages = {81-93}, pmid = {17826006}, issn = {0378-1119}, support = {K25 GM069546-04/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Archaeal Proteins/classification/*genetics/metabolism ; Bacterial Proteins/classification/*genetics/metabolism ; Computer Simulation ; Databases, Protein ; *Evolution, Molecular ; Genome, Archaeal ; Genome, Bacterial ; Humans ; }, abstract = {Understanding evolutionary relationships between species can shed new light into the rooting of the tree of life and the origin of eukaryotes, thus, resulting in a long standing interest in accurately assessing evolutionary parameters at time scales on the order of a billion of years. Prior work suggests large variability in molecular substitution rates, however, we still do not know whether such variability is due to species-specific trends at a genomic scale, or whether it can be attributed to the fluctuations inherent in any stochastic process. Here, we study the statistical properties of gene and protein-family sizes in order to quantify the long time scale evolutionary differences and similarities across species. We first determine the protein families of 209 species of bacteria and 20 species of archaea. We find that we are unable to reject the null hypothesis that the protein-family sizes of these species are drawn from the same distribution. In addition, we find that for species classified in the same phylogenetic branch or in the same lifestyle group, family size distributions are not significantly more similar than for species in different branches. These two findings can be accounted for in terms of a dynamical birth, death, and innovation model that assumes identical protein-family evolutionary rates for all species. Our theoretical and empirical results thus strongly suggest that the variability empirically observed in protein-family size distributions is compatible with the expected stochastic fluctuations for an evolutionary process with identical genomic evolutionary rates. Our findings hold special importance for the plausibility of some theories of the origin of eukaryotes which require drastic changes in evolutionary rates for some period during the last 2 billion years.}, } @article {pmid17508407, year = {2007}, author = {Davidov, Y and Jurkevitch, E}, title = {Comments of Poole and Penny's essay "Evaluating hypotheses for the origin of eukaryotes", BioEssays 29:74-84.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {29}, number = {6}, pages = {615-616}, doi = {10.1002/bies.20587}, pmid = {17508407}, issn = {0265-9247}, mesh = {Archaea/*physiology ; *Biological Evolution ; Eukaryotic Cells/*physiology ; *Mitochondria ; Phagocytosis ; Phylogeny ; }, } @article {pmid17504772, year = {2007}, author = {Pisani, D and Cotton, JA and McInerney, JO}, title = {Supertrees disentangle the chimerical origin of eukaryotic genomes.}, journal = {Molecular biology and evolution}, volume = {24}, number = {8}, pages = {1752-1760}, doi = {10.1093/molbev/msm095}, pmid = {17504772}, issn = {0737-4038}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; DNA, Mitochondrial/genetics ; Eukaryotic Cells/classification/*physiology ; *Evolution, Molecular ; Genes, Archaeal ; *Genome, Archaeal ; *Genome, Bacterial ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; }, abstract = {Eukaryotes are traditionally considered to be one of the three natural divisions of the tree of life and the sister group of the Archaebacteria. However, eukaryotic genomes are replete with genes of eubacterial ancestry, and more than 20 mutually incompatible hypotheses have been proposed to account for eukaryote origins. Here we test the predictions of these hypotheses using a novel supertree-based phylogenetic signal-stripping method, and recover supertrees of life based on phylogenies for up to 5,741 single gene families distributed across 185 genomes. Using our signal-stripping method, we show that there are three distinct phylogenetic signals in eukaryotic genomes. In order of strength, these link eukaryotes with the Cyanobacteria, the Proteobacteria, and the Thermoplasmatales, an archaebacterial (euryarchaeotes) group. These signals correspond to distinct symbiotic partners involved in eukaryote evolution: plastids, mitochondria, and the elusive host lineage. According to our whole-genome data, eukaryotes are hardly the sister group of the Archaebacteria, because up to 83% of eukaryotic genes with a prokaryotic homolog have eubacterial, not archaebacterial, origins. The results reject all but two of the current hypotheses for the origin of eukaryotes: those assuming a sulfur-dependent or hydrogen-dependent syntrophy for the origin of mitochondria.}, } @article {pmid17501745, year = {2007}, author = {Derelle, R and Lopez, P and Le Guyader, H and Manuel, M}, title = {Homeodomain proteins belong to the ancestral molecular toolkit of eukaryotes.}, journal = {Evolution & development}, volume = {9}, number = {3}, pages = {212-219}, doi = {10.1111/j.1525-142X.2007.00153.x}, pmid = {17501745}, issn = {1520-541X}, mesh = {Animals ; Eukaryota/physiology ; *Evolution, Molecular ; Fungi/physiology ; Homeodomain Proteins/*metabolism ; Plants/metabolism ; }, abstract = {Multicellular organization arose several times by convergence during the evolution of eukaryotes (e.g., in terrestrial plants, several lineages of "algae," fungi, and metazoans). To reconstruct the evolutionary transitions between unicellularity and multicellularity, we need a proper understanding of the origin and diversification of regulatory molecules governing the construction of a multicellular organism in these various lineages. Homeodomain (HD) proteins offer a paradigm for studying such issues, because in multicellular eukaryotes, like animals, fungi and plants, these transcription factors are extensively used in fundamental developmental processes and are highly diversified. A number of large eukaryote lineages are exclusively unicellular, however, and it remains unclear to what extent this condition reflects their primitive lack of "good building blocks" such as the HD proteins. Taking advantage from the recent burst of sequence data from a wide variety of eukaryote taxa, we show here that HD-containing transcription factors were already existing and diversified (in at least two main classes) in the last common eukaryote ancestor. Although the family was retained and independently expanded in the multicellular taxa, it was lost in several lineages of unicellular parasites or intracellular symbionts. Our findings are consistent with the idea that the common ancestor of eukaryotes was complex in molecular terms, and already possessed many of the regulatory molecules, which later favored the multiple convergent acquisition of multicellularity.}, } @article {pmid17495008, year = {2007}, author = {Carmel, L and Wolf, YI and Rogozin, IB and Koonin, EV}, title = {Three distinct modes of intron dynamics in the evolution of eukaryotes.}, journal = {Genome research}, volume = {17}, number = {7}, pages = {1034-1044}, pmid = {17495008}, issn = {1088-9051}, mesh = {Algorithms ; Animals ; Decision Trees ; *Evolution, Molecular ; Introns/*genetics ; *Models, Genetic ; Multigene Family ; Probability ; Time ; }, abstract = {Several contrasting scenarios have been proposed for the origin and evolution of spliceosomal introns, a hallmark of eukaryotic genes. A comprehensive probabilistic model to obtain a definitive reconstruction of intron evolution was developed and applied to 391 sets of conserved genes from 19 eukaryotic species. It is inferred that a relatively high intron density was reached early, i.e., the last common ancestor of eukaryotes contained >2.15 introns/kilobase, and the last common ancestor of multicellular life forms harbored approximately 3.4 introns/kilobase, a greater intron density than in most of the extant fungi and in some animals. The rates of intron gain and intron loss appear to have been dropping during the last approximately 1.3 billion years, with the decline in the gain rate being much steeper. Eukaryotic lineages exhibit three distinct modes of evolution of the intron-exon structure. The primary, balanced mode, apparently, operates in all lineages. In this mode, intron gain and loss are strongly and positively correlated, in contrast to previous reports on inverse correlation between these processes. The second mode involves an elevated rate of intron loss and is prevalent in several lineages, such as fungi and insects. The third mode, characterized by elevated rate of intron gain, is seen only in deep branches of the tree, indicating that bursts of intron invasion occurred at key points in eukaryotic evolution, such as the origin of animals. Intron dynamics could depend on multiple mechanisms, and in the balanced mode, gain and loss of introns might share common mechanistic features.}, } @article {pmid17463271, year = {2007}, author = {Martin, W and Dagan, T and Koonin, EV and Dipippo, JL and Gogarten, JP and Lake, JA}, title = {The evolution of eukaryotes.}, journal = {Science (New York, N.Y.)}, volume = {316}, number = {5824}, pages = {542-3; author reply 542-3}, doi = {10.1126/science.316.5824.542c}, pmid = {17463271}, issn = {1095-9203}, mesh = {Archaeal Proteins/chemistry ; Bacterial Proteins/chemistry ; *Biological Evolution ; *Eukaryotic Cells ; Evolution, Molecular ; Fungal Proteins/chemistry ; Genomics ; Humans ; Mitochondria ; Phagocytosis ; Prokaryotic Cells ; Proteins/*chemistry ; }, } @article {pmid17429433, year = {2007}, author = {de Duve, C}, title = {The origin of eukaryotes: a reappraisal.}, journal = {Nature reviews. Genetics}, volume = {8}, number = {5}, pages = {395-403}, doi = {10.1038/nrg2071}, pmid = {17429433}, issn = {1471-0056}, mesh = {Animals ; *Biological Evolution ; Cell Membrane/physiology ; Cell Nucleus/physiology ; Chimerism ; Cytoskeleton/physiology ; Eukaryotic Cells/*physiology ; Humans ; Hydrogen/metabolism ; Mitochondria/metabolism/physiology ; Models, Biological ; Time Factors ; }, abstract = {Ever since the elucidation of the main structural and functional features of eukaryotic cells and subsequent discovery of the endosymbiotic origin of mitochondria and plastids, two opposing hypotheses have been proposed to account for the origin of eukaryotic cells. One hypothesis postulates that the main features of these cells, including their ability to capture food by endocytosis and to digest it intracellularly, were developed first, and later had a key role in the adoption of endosymbionts; the other proposes that the transformation was triggered by an interaction between two typical prokaryotic cells, one of which became the host and the other the endosymbiont. Re-examination of this question in the light of cell-biological and phylogenetic data leads to the conclusion that the first model is more likely to be the correct one.}, } @article {pmid17187354, year = {2007}, author = {Poole, AM and Penny, D}, title = {Evaluating hypotheses for the origin of eukaryotes.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {29}, number = {1}, pages = {74-84}, doi = {10.1002/bies.20516}, pmid = {17187354}, issn = {0265-9247}, mesh = {Archaea ; Bacteria ; *Biological Evolution ; *Eukaryotic Cells ; Mitochondria ; *Models, Biological ; Phylogeny ; Symbiosis ; }, abstract = {Numerous scenarios explain the origin of the eukaryote cell by fusion or endosymbiosis between an archaeon and a bacterium (and sometimes a third partner). We evaluate these hypotheses using the following three criteria. Can the data be explained by the null hypothesis that new features arise sequentially along a stem lineage? Second, hypotheses involving an archaeon and a bacterium should undergo standard phylogenetic tests of gene distribution. Third, accounting for past events by processes observed in modern cells is preferable to postulating unknown processes that have never been observed. For example, there are many eukaryote examples of bacteria as endosymbionts or endoparasites, but none known in archaea. Strictly post-hoc hypotheses that ignore this third criterion should be avoided. Applying these three criteria significantly narrows the number of plausible hypotheses. Given current knowledge, our conclusion is that the eukaryote lineage must have diverged from an ancestor of archaea well prior to the origin of the mitochondrion. Significantly, the absence of ancestrally amitochondriate eukaryotes (archezoa) among extant eukaryotes is neither evidence for an archaeal host for the ancestor of mitochondria, nor evidence against a eukaryotic host.}, } @article {pmid17156426, year = {2006}, author = {Poole, AM}, title = {Did group II intron proliferation in an endosymbiont-bearing archaeon create eukaryotes?.}, journal = {Biology direct}, volume = {1}, number = {}, pages = {36}, pmid = {17156426}, issn = {1745-6150}, abstract = {Martin & Koonin recently proposed that the eukaryote nucleus evolved as a quality control mechanism to prevent ribosome readthrough into introns. In their scenario, the bacterial ancestor of mitochondria was resident in an archaeal cell, and group II introns (carried by the fledgling mitochondrion) inserted into coding regions in the archaeal host genome. They suggest that if transcription and translation were coupled, and because splicing is expected to have been slower than translation, the effect of insertion would have been ribosome readthrough into introns, resulting in production of aberrant proteins. The emergence of the nuclear compartment would thus have served to separate transcription and splicing from translation, thereby alleviating this problem. In this article, I argue that Martin & Koonin's model is not compatible with current knowledge. The model requires that group II introns would spread aggressively through an archaeal genome. It is well known that selfish elements can spread through an outbreeding sexual population despite a substantial fitness cost to the host. The same is not true for asexual lineages however, where both theory and observation argue that such elements will be under pressure to reduce proliferation, and may be lost completely. The recent introduction of group II introns into archaea by horizontal transfer provides a natural test case with which to evaluate Martin & Koonin's model. The distribution and behaviour of these introns fits prior theoretical expectations, not the scenario of aggressive proliferation advocated by Martin & Koonin. I therefore conclude that the mitochondrial seed hypothesis for the origin of eukaryote introns, on which their model is based, better explains the early expansion of introns in eukaryotes. The mitochondrial seed hypothesis has the capacity to separate the origin of eukaryotes from the origin of introns, leaving open the possibility that the cell that engulfed the ancestor of mitochondria was a sexually outcrossing eukaryote cell.}, } @article {pmid17138626, year = {2007}, author = {Lucas, JI and Marín, I}, title = {A new evolutionary paradigm for the Parkinson disease gene DJ-1.}, journal = {Molecular biology and evolution}, volume = {24}, number = {2}, pages = {551-561}, doi = {10.1093/molbev/msl186}, pmid = {17138626}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Eukaryotic Cells/chemistry ; *Evolution, Molecular ; Genes, Bacterial ; Genes, Fungal ; Genes, Plant ; Intracellular Signaling Peptides and Proteins/*genetics ; Models, Molecular ; Molecular Sequence Data ; Oncogene Proteins/*genetics ; Parkinson Disease/*genetics ; Phylogeny ; Prokaryotic Cells/chemistry ; Protein Deglycase DJ-1 ; Sequence Alignment ; }, abstract = {The DJ-1 gene is extensively studied because of its involvement in familial Parkinson disease. DJ-1 belongs to a complex superfamily of genes that includes both prokaryotic and eukaryotic representatives. We determine that many prokaryotic groups, such as proteobacteria, cyanobacteria, spirochaetes, firmicutes, or fusobacteria, have genes, often incorrectly called "Thij," that are very close relatives of DJ-1, to the point that they cannot be clearly separated from the eukaryotic DJ-1 genes by phylogenetic analyses of their sequences. In addition, and contrary to a previous study that suggested that DJ-1 genes were animal specific, we show that DJ-1 genes are found in at least 5 of the 6 main eukaryotic groups: opisthokonta (both animals and fungi), plantae, chromalveolata, excavata, and amoebozoa. Our results thus provide strong evidence for DJ-1 genes originating before the origin of eukaryotes. Interestingly, we found that some fungal species, among them the model yeast Schizosaccharomyces pombe, have DJ-1-like genes, most likely orthologous to the animal genes. This finding opens new ways for the analysis of the functions of this group of genes.}, } @article {pmid17123864, year = {2007}, author = {Stelter, K and El-Sayed, NM and Seeber, F}, title = {The expression of a plant-type ferredoxin redox system provides molecular evidence for a plastid in the early dinoflagellate Perkinsus marinus.}, journal = {Protist}, volume = {158}, number = {1}, pages = {119-130}, doi = {10.1016/j.protis.2006.09.003}, pmid = {17123864}, issn = {1434-4610}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Dinoflagellida/enzymology/genetics/growth & development/*ultrastructure ; Fatty Acids/biosynthesis ; Ferredoxins/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Plant Proteins/chemistry/genetics/*metabolism ; Plastids/metabolism/*ultrastructure ; Terpenes/metabolism ; }, abstract = {Perkinsus marinus is a parasitic protozoan with a phylogenetic positioning between Apicomplexa and dinoflagellates. It is thus of interest for reconstructing the early evolution of eukaryotes, especially with regard to the acquisition of secondary plastids in these organisms. It is also an important pathogen of oysters, and the definition of parasite-specific metabolic pathways would be beneficial for the identification of efficient treatments for infected mollusks. Although these different scientific interests have resulted in the start of a genome project for this organism, it is still unknown whether P. marinus contains a plastid or plastid-like organelle like the related dinoflagellates and Apicomplexa. Here, we show that in vitro-cultivated parasites contain transcripts of the plant-type ferredoxin and its associated reductase. Both proteins are nuclear-encoded and possess N-terminal targeting sequences similar to those characterized in dinoflagellates. Since this redox pair is exclusively found in cyanobacteria and plastid-harboring organisms its presence also in P. marinus is highly indicative of a plastid. We also provide additional evidence for such an organelle by demonstrating pharmacological sensitivity to inhibitors of plastid-localized enzymes involved in fatty acid biosynthesis (e.g. acetyl-CoA carboxylase) and by detection of genes for three enzymes of plastid-localized isoprenoid biosynthesis (1-deoxy-D-xylulose 5-phosphate reductoisomerase, (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate reductase, and (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate synthase).}, } @article {pmid16984643, year = {2006}, author = {Koonin, EV and Senkevich, TG and Dolja, VV}, title = {The ancient Virus World and evolution of cells.}, journal = {Biology direct}, volume = {1}, number = {}, pages = {29}, pmid = {16984643}, issn = {1745-6150}, support = {R01 GM053190/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND: Recent advances in genomics of viruses and cellular life forms have greatly stimulated interest in the origins and evolution of viruses and, for the first time, offer an opportunity for a data-driven exploration of the deepest roots of viruses. Here we briefly review the current views of virus evolution and propose a new, coherent scenario that appears to be best compatible with comparative-genomic data and is naturally linked to models of cellular evolution that, from independent considerations, seem to be the most parsimonious among the existing ones.

RESULTS: Several genes coding for key proteins involved in viral replication and morphogenesis as well as the major capsid protein of icosahedral virions are shared by many groups of RNA and DNA viruses but are missing in cellular life forms. On the basis of this key observation and the data on extensive genetic exchange between diverse viruses, we propose the concept of the ancient virus world. The virus world is construed as a distinct contingent of viral genes that continuously retained its identity throughout the entire history of life. Under this concept, the principal lineages of viruses and related selfish agents emerged from the primordial pool of primitive genetic elements, the ancestors of both cellular and viral genes. Thus, notwithstanding the numerous gene exchanges and acquisitions attributed to later stages of evolution, most, if not all, modern viruses and other selfish agents are inferred to descend from elements that belonged to the primordial genetic pool. In this pool, RNA viruses would evolve first, followed by retroid elements, and DNA viruses. The Virus World concept is predicated on a model of early evolution whereby emergence of substantial genetic diversity antedates the advent of full-fledged cells, allowing for extensive gene mixing at this early stage of evolution. We outline a scenario of the origin of the main classes of viruses in conjunction with a specific model of precellular evolution under which the primordial gene pool dwelled in a network of inorganic compartments. Somewhat paradoxically, under this scenario, we surmise that selfish genetic elements ancestral to viruses evolved prior to typical cells, to become intracellular parasites once bacteria and archaea arrived at the scene. Selection against excessively aggressive parasites that would kill off the host ensembles of genetic elements would lead to early evolution of temperate virus-like agents and primitive defense mechanisms, possibly, based on the RNA interference principle. The emergence of the eukaryotic cell is construed as the second melting pot of virus evolution from which the major groups of eukaryotic viruses originated as a result of extensive recombination of genes from various bacteriophages, archaeal viruses, plasmids, and the evolving eukaryotic genomes. Again, this vision is predicated on a specific model of the emergence of eukaryotic cell under which archaeo-bacterial symbiosis was the starting point of eukaryogenesis, a scenario that appears to be best compatible with the data.

CONCLUSION: The existence of several genes that are central to virus replication and structure, are shared by a broad variety of viruses but are missing from cellular genomes (virus hallmark genes) suggests the model of an ancient virus world, a flow of virus-specific genes that went uninterrupted from the precellular stage of life's evolution to this day. This concept is tightly linked to two key conjectures on evolution of cells: existence of a complex, precellular, compartmentalized but extensively mixing and recombining pool of genes, and origin of the eukaryotic cell by archaeo-bacterial fusion. The virus world concept and these models of major transitions in the evolution of cells provide complementary pieces of an emerging coherent picture of life's history.

REVIEWERS: W. Ford Doolittle, J. Peter Gogarten, and Arcady Mushegian.}, } @article {pmid16907971, year = {2006}, author = {Koonin, EV}, title = {The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate?.}, journal = {Biology direct}, volume = {1}, number = {}, pages = {22}, pmid = {16907971}, issn = {1745-6150}, abstract = {BACKGROUND: Ever since the discovery of 'genes in pieces' and mRNA splicing in eukaryotes, origin and evolution of spliceosomal introns have been considered within the conceptual framework of the 'introns early' versus 'introns late' debate. The 'introns early' hypothesis, which is closely linked to the so-called exon theory of gene evolution, posits that protein-coding genes were interrupted by numerous introns even at the earliest stages of life's evolution and that introns played a major role in the origin of proteins by facilitating recombination of sequences coding for small protein/peptide modules. Under this scenario, the absence of spliceosomal introns in prokaryotes is considered to be a result of "genome streamlining". The 'introns late' hypothesis counters that spliceosomal introns emerged only in eukaryotes, and moreover, have been inserted into protein-coding genes continuously throughout the evolution of eukaryotes. Beyond the formal dilemma, the more substantial side of this debate has to do with possible roles of introns in the evolution of eukaryotes.

RESULTS: I argue that several lines of evidence now suggest a coherent solution to the introns-early versus introns-late debate, and the emerging picture of intron evolution integrates aspects of both views although, formally, there seems to be no support for the original version of introns-early. Firstly, there is growing evidence that spliceosomal introns evolved from group II self-splicing introns which are present, usually, in small numbers, in many bacteria, and probably, moved into the evolving eukaryotic genome from the alpha-proteobacterial progenitor of the mitochondria. Secondly, the concept of a primordial pool of 'virus-like' genetic elements implies that self-splicing introns are among the most ancient genetic entities. Thirdly, reconstructions of the ancestral state of eukaryotic genes suggest that the last common ancestor of extant eukaryotes had an intron-rich genome. Thus, it appears that ancestors of spliceosomal introns, indeed, have existed since the earliest stages of life's evolution, in a formal agreement with the introns-early scenario. However, there is no evidence that these ancient introns ever became widespread before the emergence of eukaryotes, hence, the central tenet of introns-early, the role of introns in early evolution of proteins, has no support. However, the demonstration that numerous introns invaded eukaryotic genes at the outset of eukaryotic evolution and that subsequent intron gain has been limited in many eukaryotic lineages implicates introns as an ancestral feature of eukaryotic genomes and refutes radical versions of introns-late. Perhaps, most importantly, I argue that the intron invasion triggered other pivotal events of eukaryogenesis, including the emergence of the spliceosome, the nucleus, the linear chromosomes, the telomerase, and the ubiquitin signaling system. This concept of eukaryogenesis, in a sense, revives some tenets of the exon hypothesis, by assigning to introns crucial roles in eukaryotic evolutionary innovation.

CONCLUSION: The scenario of the origin and evolution of introns that is best compatible with the results of comparative genomics and theoretical considerations goes as follows: self-splicing introns since the earliest stages of life's evolution--numerous spliceosomal introns invading genes of the emerging eukaryote during eukaryogenesis--subsequent lineage-specific loss and gain of introns. The intron invasion, probably, spawned by the mitochondrial endosymbiont, might have critically contributed to the emergence of the principal features of the eukaryotic cell. This scenario combines aspects of the introns-early and introns-late views.

REVIEWERS: this article was reviewed by W. Ford Doolittle, James Darnell (nominated by W. Ford Doolittle), William Martin, and Anthony Poole.}, } @article {pmid16846615, year = {2006}, author = {Bell, PJ}, title = {Sex and the eukaryotic cell cycle is consistent with a viral ancestry for the eukaryotic nucleus.}, journal = {Journal of theoretical biology}, volume = {243}, number = {1}, pages = {54-63}, doi = {10.1016/j.jtbi.2006.05.015}, pmid = {16846615}, issn = {0022-5193}, mesh = {Animals ; Cell Cycle/*physiology ; Cell Nucleus/physiology ; DNA Viruses/*physiology ; Eukaryotic Cells/*cytology ; Evolution, Molecular ; Lysogeny/physiology ; Meiosis/physiology ; Mitosis/physiology ; *Sex ; }, abstract = {The origin of the eukaryotic cell cycle, including mitosis, meiosis, and sex are as yet unresolved aspects of the evolution of the eukaryotes. The wide phylogenetic distribution of both mitosis and meiosis suggest that these processes are integrally related to the origin of the earliest eukaryotic cells. According to the viral eukaryogenesis (VE) hypothesis, the eukaryotes are a composite of three phylogenetically unrelated organisms: a viral lysogen that evolved into the nucleus, an archaeal cell that evolved into the eukaryotic cytoplasm, and an alpha-proteobacterium that evolved into the mitochondria. In the extended VE hypothesis presented here, the eukaryotic cell cycle arises as a consequence of the derivation of the nucleus from a lysogenic DNA virus.}, } @article {pmid16829542, year = {2006}, author = {Burki, F and Pawlowski, J}, title = {Monophyly of Rhizaria and multigene phylogeny of unicellular bikonts.}, journal = {Molecular biology and evolution}, volume = {23}, number = {10}, pages = {1922-1930}, doi = {10.1093/molbev/msl055}, pmid = {16829542}, issn = {0737-4038}, mesh = {Animals ; Eukaryotic Cells ; *Evolution, Molecular ; Models, Genetic ; Phylogeny ; Sequence Alignment ; Zooplankton/genetics ; }, abstract = {Reconstructing a global phylogeny of eukaryotes is an ongoing challenge of molecular phylogenetics. The availability of genomic data from a broad range of eukaryotic phyla helped in resolving the eukaryotic tree into a topology with a rather small number of large assemblages, but the relationships between these "supergroups" are yet to be confirmed. Rhizaria is the most recently recognized "supergroup," but, in spite of this important position within the tree of life, their representatives are still missing in global phylogenies of eukaryotes. Here, we report the first large-scale analysis of eukaryote phylogeny including data for 2 rhizarian species, the foraminiferan Reticulomyxa filosa and the chlorarachniophyte Bigelowiella natans. Our results confirm the monophyly of Rhizaria (Foraminifera + Cercozoa), with very high bootstrap supports in all analyses. The overall topology of our trees is in agreement with the current view of eukaryote phylogeny with basal division into "unikonts" (Opisthokonts and Ameobozoa) and "bikonts" (Plantae, alveolates, stramenopiles, and excavates). As expected, Rhizaria branch among bikonts; however, their phylogenetic position is uncertain. Depending on the data set and the type of analysis, Rhizaria branch as sister group to either stramenopiles or excavates. Overall, the relationships between the major groups of unicellular bikonts are poorly resolved, despite the use of 85 proteins and the largest taxonomic sampling for this part of the tree available to date. This may be due to an acceleration of evolutionary rates in some bikont phyla or be related to their rapid diversification in the early evolution of eukaryotes.}, } @article {pmid16701350, year = {2005}, author = {McInerney, JO and Wilkinson, M}, title = {New methods ring changes for the tree of life.}, journal = {Trends in ecology & evolution}, volume = {20}, number = {3}, pages = {105-107}, doi = {10.1016/j.tree.2005.01.007}, pmid = {16701350}, issn = {0169-5347}, abstract = {Relationships among prokaryotes and the origin of eukaryotes have both proven controversial, with results depending upon the gene sequences and methods used. Extensive horizontal gene transfer is one possible reason why inferring such deep phylogenetic relationships is difficult. In two recent papers, Lake and Rivera introduce new methods that can be used to reconstruct the genomic tree in the presence of horizontal gene transfers, but which suggest that a ring rather than a tree is a better representation of some parts of the history of life on Earth.}, } @article {pmid16539012, year = {2005}, author = {Xu, G and Fang, QQ and Sun, Y and Keirans, JE and Durden, LA}, title = {Hard tick calreticulin (CRT) gene coding regions have only one intron with conserved positions and variable sizes.}, journal = {The Journal of parasitology}, volume = {91}, number = {6}, pages = {1326-1331}, doi = {10.1645/GE-344R1.1}, pmid = {16539012}, issn = {0022-3395}, support = {AI 40729/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Calreticulin/chemistry/*genetics ; DNA Primers ; DNA, Complementary/chemistry ; Exons/*genetics ; Introns/*genetics ; Ixodidae/chemistry/*genetics ; Molecular Sequence Data ; Sequence Alignment ; }, abstract = {Calreticulin (CRT) is a unique eukaryotic gene. The CRT gene product, calreticulin, was first identified as a calcium binding protein in 1974, but further investigations have indicated that CRT protein performs many functions in cells, including involvement in evading the host's immune system by parasites. Many studies of CRT have been published since the molecule was first discovered; however, the CRT gene exon-intron structure is only known for a limited number of ectoparasite species. In this study, we compared tick CRT genomic sequences to the corresponding cDNA from 28 species and found that 2 exons and 1 intron are present in the tick CRT gene. The intron position is conserved in 28 hard ticks, but intron size and nucleotide sequences vary. Three tick introns possess duplicated fragments and are twice as long as other introns. All tick CRT introns obey the GT-AG rule in the splice-site junctions and are phase 1 introns. By comparing tick CRT introns to those of fruit fly, mouse, and human, we conclude that tick CRT introns belong to the intron-late type. The number and size of CRT introns have increased through the evolution of eukaryotes.}, } @article {pmid16492767, year = {2006}, author = {Graciet, E and Hu, RG and Piatkov, K and Rhee, JH and Schwarz, EM and Varshavsky, A}, title = {Aminoacyl-transferases and the N-end rule pathway of prokaryotic/eukaryotic specificity in a human pathogen.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {9}, pages = {3078-3083}, pmid = {16492767}, issn = {0027-8424}, support = {R56 DK039520/DK/NIDDK NIH HHS/United States ; R01 GM031530/GM/NIGMS NIH HHS/United States ; R01 DK039520/DK/NIDDK NIH HHS/United States ; DK39520/DK/NIDDK NIH HHS/United States ; R37 DK039520/DK/NIDDK NIH HHS/United States ; GM31530/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Aminoacyltransferases/chemistry/genetics/*metabolism ; Conserved Sequence ; Cysteine/genetics/metabolism ; Eukaryotic Cells/*enzymology ; Evolution, Molecular ; Half-Life ; Humans ; Malaria/enzymology ; Models, Biological ; Phylogeny ; Prokaryotic Cells/*enzymology ; Tyrosine/genetics/metabolism ; Vibrio vulnificus/enzymology/genetics ; }, abstract = {The N-end rule relates the in vivo half-life of a protein to the identity of its N-terminal residue. Primary destabilizing N-terminal residues (Nd(p)) are recognized directly by the targeting machinery. The recognition of secondary destabilizing N-terminal residues (Nd(s)) is preceded by conjugation of an Nd(p) residue to Nd(s) of a polypeptide substrate. In eukaryotes, ATE1-encoded arginyl-transferases (R(D,E,C*)-transferases) conjugate Arg (R), an Nd(p) residue, to Nd(s) residues Asp (D), Glu (E), or oxidized Cys residue (C*). Ubiquitin ligases recognize the N-terminal Arg of a substrate and target the (ubiquitylated) substrate to the proteasome. In prokaryotes such as Escherichia coli, Nd(p) residues Leu (L) or Phe (F) are conjugated, by the aat-encoded Leu/Phe-transferase (L/F(K,R)-transferase), to N-terminal Arg or Lys, which are Nd(s) in prokaryotes but Nd(p) in eukaryotes. In prokaryotes, substrates bearing the Nd(p) residues Leu, Phe, Trp, or Tyr are degraded by the proteasome-like ClpAP protease. Despite enzymological similarities between eukaryotic R(D,E,C*)-transferases and prokaryotic L/F(K,R)-transferases, there is no significant sequelogy (sequence similarity) between them. We identified an aminoacyl-transferase, termed Bpt, in the human pathogen Vibrio vulnificus. Although it is a sequelog of eukaryotic R(D,E,C*)-transferases, this prokaryotic transferase exhibits a "hybrid" specificity, conjugating Nd(p) Leu to Nd(s) Asp or Glu. Another aminoacyl-transferase, termed ATEL1, of the eukaryotic pathogen Plasmodium falciparum, is a sequelog of prokaryotic L/F(K,R)-transferases (Aat), but has the specificity of eukaryotic R(D,E,C*)-transferases (ATE1). Phylogenetic analysis suggests that the substrate specificity of R-transferases arose by two distinct routes during the evolution of eukaryotes.}, } @article {pmid16245570, year = {2005}, author = {Shatalkin, AI}, title = {[Animals (Animalia) in system of organisms. 2. Phylogenetic understanding of animals].}, journal = {Zhurnal obshchei biologii}, volume = {66}, number = {5}, pages = {389-415}, pmid = {16245570}, issn = {0044-4596}, mesh = {Animal Population Groups/*classification/genetics ; Animals ; Biological Evolution ; Biomarkers ; Eukaryotic Cells/classification ; *Phylogeny ; Species Specificity ; }, abstract = {The development of systematics in last decade has shown that typological classifications of five-six Kingdoms is not adequate for describing the diversity of organisms. Information from the sequences of small subunit rRNA is not sufficient to reconstruct the position of eukaryotes on the phylogenetic tree due to the effect of long branches. Totally new reconstruction of eukaryotic phylogeny was built upon the analysis of many new molecular markers. Evolution of eukaryotes had two mainstreams. One has been connected with diversification of ancestral biciliate forms (Bikonta). Sister-group of Bikonta (Unikonta) includes some originally uniciliate amoebae and moulds (Amoebozoa), and uniciliate eukaryotes with posterior cilium (Opisthokonta). The taxon Opisthokonta unites Fungi, Nuclearimorpha, Mesomycetozoa, Choanozoa and Metazoa. The latter three groups or only Metazoa are attributes to animals. The following differentiation of the groups used in systematic for the description of diversity of organisms is proposed. (1) Taxon is a group which is defined on the basis of ancestry: taxon includes all species descended from one ancestor. Taxon differs from logic classes of typology at an ontologic level. Taxon arises and exists, and its composition and occupied niches can constantly change; taxon can flourish or, on the contrary, fade up to full disappearance. Thus, the predicative characteristic of taxon, including characters which are considered significant, are not absolute. It is significant only at the moment of consideration. But characters (synapomorphies) are important as the practical tool for discerning taxa at given time period. Taxa unite species into unique classification. This understanding of taxon corresponds to monophyletic group sensu Willi Hennig. (2) Class of organisms is a group which is defined on the basis of characters: class includes all species having the given character. The class is only a logic object. Unlike taxa grouping species into classes may be through different and crossed classifications. Inside the given category of groups it is possible to distinguish: (2.1) Level of the organization (grade) described by the differences on the levels of organization: for example prokaryotic and eukaryotic levels of the organization. Eukaryotes can be divided into unicellular (Protoctista, Protista) and multicelluar (tissue-specific-Histonia) forms. (2.2) Types of the organization distinguishing groups of one level: for example, amoedoid type (Sarcodina), naked (Gymnamoebia), and testate (Testacea) amoebas. (2.3) Taxonomic groups as set-theoretical approximations of taxa. (2.4) Groups of the mixed nature. For example, Haeckel has recognized Protophyta and Protozoa describing the unicellular level of the organization inside plants and animals accordingly. Protozoa in Cavalier-Smith's system (2002, 2004) is also an example of groups of the mixed nature.}, } @article {pmid16240763, year = {2005}, author = {Lebkova, NP and Kuznetsova, AP}, title = {[Intracellular symbiosis and energetic role of bacteria in gill epithelium of freshwater mollusks and fishes].}, journal = {Izvestiia Akademii nauk. Seriia biologicheskaia}, volume = {}, number = {5}, pages = {628-635}, pmid = {16240763}, issn = {1026-3470}, mesh = {Animals ; Bacteria/isolation & purification ; Cyprinidae/microbiology/*physiology ; Endocytosis/*physiology ; Epithelial Cells/microbiology ; Gills/cytology/*microbiology ; Mollusca/cytology/microbiology/*physiology ; Perches/microbiology/*physiology ; *Symbiosis ; }, abstract = {Penetration of bacteria by endocytosis into gill epithelial cells has been revealed in animals of different evolutionary levels (freshwater mollusks and fishes). These data confirm the leading role of endosymbiosis in the origin of eukaryotes from prokaryotes and in the evolution of animal life.}, } @article {pmid16212260, year = {2005}, author = {Markov, AV and Kulikov, AM}, title = {[Homologous protein domains in superkingdoms Archaea, Bacteria, and Eukaryota and the problem of the origin of eukaryotes].}, journal = {Izvestiia Akademii nauk. Seriia biologicheskaia}, volume = {}, number = {4}, pages = {389-400}, pmid = {16212260}, issn = {1026-3470}, mesh = {Animals ; Archaea/*genetics/metabolism ; Archaeal Proteins/*genetics/metabolism ; Bacteria/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; Eukaryotic Cells/*physiology ; *Evolution, Molecular ; Mitochondria/genetics/metabolism ; Plastids/genetics/metabolism ; Protein Structure, Tertiary/physiology ; }, abstract = {The distribution of protein domains was analyzed in superkingdoms Archaea, Bacteria, and Eukaryota. About a half of eukaryotic domains have prokaryotic origin. Many domains related to information processing in the nucleocytoplasm were inherited from archaea. Sets of domains associated with metabolism and regulatory and signaling systems were inherited from bacteria. Many signaling and regulatory domains common for bacteria and eukaryotes were responsible for the cellular interaction of bacteria with other components of the microbial community but were involved in coordination of the activity of eukaryotic organelles and cells in multicellular organisms. Many eukaryotic domains of bacterial origin could not originate from ancestral mitochondria and plastids but rather were adopted from other bacteria. An archaeon with the induced incorporation of alien genetic material could be the ancestor of the eukaryotic nucleocytoplasm.}, } @article {pmid16118111, year = {2005}, author = {Archibald, JM}, title = {Jumping genes and shrinking genomes--probing the evolution of eukaryotic photosynthesis with genomics.}, journal = {IUBMB life}, volume = {57}, number = {8}, pages = {539-547}, doi = {10.1080/15216540500167732}, pmid = {16118111}, issn = {1521-6543}, mesh = {Eukaryota/*genetics ; *Evolution, Molecular ; Genomics/*methods ; Interspersed Repetitive Sequences/*genetics ; Photosynthesis/*genetics ; *Phylogeny ; Symbiosis/*genetics ; }, abstract = {The advent of comparative genomics has revolutionized the study of the origin and evolution of eukaryotes and their organelles. Genomic analysis has revealed that the endosymbiosis that gave rise to plastids--the light-harvesting apparatus of photosynthetic eukaryotes--had a profound impact on the genetic composition of the host, far beyond the contribution of cyanobacterial genes for plastid-specific functions. Here I discuss recent advances in our appreciation of the mosaic nature of the eukaryotic nuclear genome, and the ongoing role endosymbiosis plays in shaping its content.}, } @article {pmid16106042, year = {2005}, author = {Makarova, KS and Wolf, YI and Mekhedov, SL and Mirkin, BG and Koonin, EV}, title = {Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell.}, journal = {Nucleic acids research}, volume = {33}, number = {14}, pages = {4626-4638}, pmid = {16106042}, issn = {1362-4962}, support = {//Intramural NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Eukaryotic Cells/*physiology ; *Evolution, Molecular ; *Gene Duplication ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Genomics ; Molecular Sequence Data ; Phylogeny ; Proteins/*genetics ; Sequence Alignment ; }, abstract = {Gene duplication is a crucial mechanism of evolutionary innovation. A substantial fraction of eukaryotic genomes consists of paralogous gene families. We assess the extent of ancestral paralogy, which dates back to the last common ancestor of all eukaryotes, and examine the origins of the ancestral paralogs and their potential roles in the emergence of the eukaryotic cell complexity. A parsimonious reconstruction of ancestral gene repertoires shows that 4137 orthologous gene sets in the last eukaryotic common ancestor (LECA) map back to 2150 orthologous sets in the hypothetical first eukaryotic common ancestor (FECA) [paralogy quotient (PQ) of 1.92]. Analogous reconstructions show significantly lower levels of paralogy in prokaryotes, 1.19 for archaea and 1.25 for bacteria. The only functional class of eukaryotic proteins with a significant excess of paralogous clusters over the mean includes molecular chaperones and proteins with related functions. Almost all genes in this category underwent multiple duplications during early eukaryotic evolution. In structural terms, the most prominent sets of paralogs are superstructure-forming proteins with repetitive domains, such as WD-40 and TPR. In addition to the true ancestral paralogs which evolved via duplication at the onset of eukaryotic evolution, numerous pseudoparalogs were detected, i.e. homologous genes that apparently were acquired by early eukaryotes via different routes, including horizontal gene transfer (HGT) from diverse bacteria. The results of this study demonstrate a major increase in the level of gene paralogy as a hallmark of the early evolution of eukaryotes.}, } @article {pmid15975222, year = {2005}, author = {Rogozin, IB and Sverdlov, AV and Babenko, VN and Koonin, EV}, title = {Analysis of evolution of exon-intron structure of eukaryotic genes.}, journal = {Briefings in bioinformatics}, volume = {6}, number = {2}, pages = {118-134}, doi = {10.1093/bib/6.2.118}, pmid = {15975222}, issn = {1467-5463}, mesh = {Animals ; Biological Evolution ; Chromosome Mapping/*methods ; Conserved Sequence/genetics ; DNA Mutational Analysis/*methods ; *Eukaryotic Cells ; *Evolution, Molecular ; Exons/*genetics ; Humans ; Introns/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; Sequence Homology, Nucleic Acid ; }, abstract = {The availability of multiple, complete eukaryotic genome sequences allows one to address many fundamental evolutionary questions on genome scale. One such important, long-standing problem is evolution of exon-intron structure of eukaryotic genes. Analysis of orthologous genes from completely sequenced genomes revealed numerous shared intron positions in orthologous genes from animals and plants and even between animals, plants and protists. The data on shared and lineage-specific intron positions were used as the starting point for evolutionary reconstruction with parsimony and maximum-likelihood approaches. Parsimony methods produce reconstructions with intron-rich ancestors but also infer lineage-specific, in many cases, high levels of intron loss and gain. Different probabilistic models gave opposite results, apparently depending on model parameters and assumptions, from domination of intron loss, with extremely intron-rich ancestors, to dramatic excess of gains, to the point of denying any true conservation of intron positions among deep eukaryotic lineages. Development of models with adequate, realistic parameters and assumptions seems to be crucial for obtaining more definitive estimates of intron gain and loss in different eukaryotic lineages. Many shared intron positions were detected in ancestral eukaryotic paralogues which evolved by duplication prior to the divergence of extant eukaryotic lineages. These findings indicate that numerous introns were present in eukaryotic genes already at the earliest stages of evolution of eukaryotes and are compatible with the hypothesis that the original, catastrophic intron invasion accompanied the emergence of the eukaryotic cells. Comparison of various features of old and younger introns starts shedding light on probable mechanisms of intron insertion, indicating that propagation of old introns is unlikely to be a major mechanism for origin of new ones. The existence and structure of ancestral protosplice sites were addressed by examining the context of introns inserted within codons that encode amino acids conserved in all eukaryotes and, accordingly, are not subject to selection for splicing efficiency. It was shown that introns indeed predominantly insert into or are fixed in specific protosplice sites which have the consensus sequence (A/C)AG|Gt.}, } @article {pmid15851667, year = {2005}, author = {Simonson, AB and Servin, JA and Skophammer, RG and Herbold, CW and Rivera, MC and Lake, JA}, title = {Decoding the genomic tree of life.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102 Suppl 1}, number = {Suppl 1}, pages = {6608-6613}, pmid = {15851667}, issn = {0027-8424}, support = {T32 HG002536/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; *Genome ; Genomics ; Phylogeny ; }, abstract = {Genomes hold within them the record of the evolution of life on Earth. But genome fusions and horizontal gene transfer (HGT) seem to have obscured sufficiently the gene sequence record such that it is difficult to reconstruct the phylogenetic tree of life. HGT among prokaryotes is not random, however. Some genes (informational genes) are more difficult to transfer than others (operational genes). Furthermore, environmental, metabolic, and genetic differences among organisms restrict HGT, so that prokaryotes preferentially share genes with other prokaryotes having properties in common, including genome size, genome G+C composition, carbon utilization, oxygen utilization/sensitivity, and temperature optima, further complicating attempts to reconstruct the tree of life. A new method of phylogenetic reconstruction based on gene presence and absence, called conditioned reconstruction, has improved our prospects for reconstructing prokaryotic evolution. It is also able to detect past genome fusions, such as the fusion that appears to have created the first eukaryote. This genome fusion between a deep branching eubacterium, possibly an ancestor of the cyanobacterium and a proteobacterium, with an archaeal eocyte (crenarchaea), appears to be the result of an early symbiosis. Given new tools and new genes from relevant organisms, it should soon be possible to test current and future fusion theories for the origin of eukaryotes and to discover the general outlines of the prokaryotic tree of life.}, } @article {pmid15762985, year = {2005}, author = {Blair, JE and Shah, P and Hedges, SB}, title = {Evolutionary sequence analysis of complete eukaryote genomes.}, journal = {BMC bioinformatics}, volume = {6}, number = {}, pages = {53}, pmid = {15762985}, issn = {1471-2105}, mesh = {Animals ; Biodiversity ; Biological Evolution ; Computational Biology/*methods ; Databases, Genetic ; Databases, Protein ; Eukaryotic Cells/cytology ; *Evolution, Molecular ; Fossils ; Gene Duplication ; *Genome ; Genome, Archaeal ; Humans ; Models, Genetic ; Phylogeny ; Programming Languages ; Proteins ; Sequence Analysis ; Sequence Analysis, DNA ; Sequence Analysis, Protein ; Software ; Time Factors ; }, abstract = {BACKGROUND: Gene duplication and gene loss during the evolution of eukaryotes have hindered attempts to estimate phylogenies and divergence times of species. Although current methods that identify clusters of orthologous genes in complete genomes have helped to investigate gene function and gene content, they have not been optimized for evolutionary sequence analyses requiring strict orthology and complete gene matrices. Here we adopt a relatively simple and fast genome comparison approach designed to assemble orthologs for evolutionary analysis. Our approach identifies single-copy genes representing only species divergences (panorthologs) in order to minimize potential errors caused by gene duplication. We apply this approach to complete sets of proteins from published eukaryote genomes specifically for phylogeny and time estimation.

RESULTS: Despite the conservative criterion used, 753 panorthologs (proteins) were identified for evolutionary analysis with four genomes, resulting in a single alignment of 287,000 amino acids. With this data set, we estimate that the divergence between deuterostomes and arthropods took place in the Precambrian, approximately 400 million years before the first appearance of animals in the fossil record. Additional analyses were performed with seven, 12, and 15 eukaryote genomes resulting in similar divergence time estimates and phylogenies.

CONCLUSION: Our results with available eukaryote genomes agree with previous results using conventional methods of sequence data assembly from genomes. They show that large sequence data sets can be generated relatively quickly and efficiently for evolutionary analyses of complete genomes.}, } @article {pmid15693617, year = {2004}, author = {Horiike, T and Hamada, K and Miyata, D and Shinozawa, T}, title = {The origin of eukaryotes is suggested as the symbiosis of pyrococcus into gamma-proteobacteria by phylogenetic tree based on gene content.}, journal = {Journal of molecular evolution}, volume = {59}, number = {5}, pages = {606-619}, pmid = {15693617}, issn = {0022-2844}, mesh = {Eukaryotic Cells/*cytology/physiology ; Gammaproteobacteria/*cytology/*genetics/physiology ; Genome ; Mosaicism ; Open Reading Frames/genetics ; *Phylogeny ; Pyrococcus/*genetics/*physiology ; Symbiosis/*physiology ; }, abstract = {Attempts were made to define the relationship among the three domains (eukaryotes, archaea, and eubacteria) using phylogenetic tree analyses of 16S rRNA sequences as well as of other protein sequences. Since the results are inconsistent, it is implied that the eukaryotic genome has a chimeric structure. In our previous studies, the origin of eukaryotes to be the symbiosis of archaea into eubacteria using the whole open reading frames (ORF) of many genomes was suggested. In these studies, the species participating in the symbiosis were not clarified, and the effect of gene duplication after speciation (in-paralog) was not addressed. To avoid the influence of the in-paralog, we developed a new method to calculate orthologous ORFs. Furthermore, we separated eukaryotic in-paralogs into three groups by sequence similarity to archaea, eubacteria (other than alpha-proteobacteria), and alpha-proteobacteria and treated them as individual organisms. The relationship between the three ORF groups and the functional classification was clarified by this analysis. The introduction of this new method into the phylogenetic tree analysis of 66 organisms (4 eukaryotes, 13 archaea, and 49 eubacteria) based on gene content suggests the symbiosis of pyrococcus into gamma-proteobacteria as the origin of eukaryotes.}, } @article {pmid15655358, year = {2005}, author = {Jékely, G}, title = {Glimpsing over the event horizon: evolution of nuclear pores and envelope.}, journal = {Cell cycle (Georgetown, Tex.)}, volume = {4}, number = {2}, pages = {297-299}, pmid = {15655358}, issn = {1551-4005}, mesh = {Active Transport, Cell Nucleus ; Animals ; Biological Evolution ; Cell Lineage ; Coated Vesicles/physiology/ultrastructure ; Eukaryotic Cells/physiology/*ultrastructure ; *Evolution, Molecular ; Humans ; Intracellular Membranes/physiology/ultrastructure ; Nuclear Envelope/physiology/*ultrastructure ; Nuclear Pore/physiology/*ultrastructure ; Phylogeny ; }, abstract = {The origin of eukaryotes from prokaryotic ancestors is one of the major evolutionary transitions in the history of life. The nucleus, a membrane bound compartment for confining the genome, is a central feature of eukaryotic cells and its origin also has to be a central feature of any workable theory that ventures to explain eukaryotic origins. Recent bioinformatic analyses of components of the nuclear pore complex (NPC), the nuclear envelope (NE), and the nuclear transport systems revealed exciting evolutionary connections (e.g., between NPC and coated vesicles) and provided a useful record of the phyletic distribution and history of NPC and NE components. These analyses allow us to refine theories on the origin and evolution of the nucleus, and consequently, of the eukaryotic cell.}, } @article {pmid15591201, year = {2004}, author = {Papke, RT and Koenig, JE and Rodríguez-Valera, F and Doolittle, WF}, title = {Frequent recombination in a saltern population of Halorubrum.}, journal = {Science (New York, N.Y.)}, volume = {306}, number = {5703}, pages = {1928-1929}, doi = {10.1126/science.1103289}, pmid = {15591201}, issn = {1095-9203}, mesh = {Alleles ; DNA, Archaeal ; Genes, Archaeal ; Genes, rRNA ; Genetic Linkage ; Genetic Variation ; Halobacteriaceae/classification/*genetics/isolation & purification ; Linkage Disequilibrium ; Molecular Sequence Data ; Mutation ; Phylogeny ; Polymerase Chain Reaction ; *Recombination, Genetic ; Ribotyping ; Sequence Analysis, DNA ; Sodium Chloride ; Spain ; *Water Microbiology ; }, abstract = {Sex and recombination are driving forces in the evolution of eukaryotes. Homologous recombination is known to be the dominant process in the divergence of many bacterial species. For Archaea, the only direct evidence bearing on the importance or natural occurrence of homologous recombination is anecdotal reports of mosaicism from comparative genomic studies. Genetic studies, however, reveal that recombination may play a significant role in generating diversity among members of at least one archaeal group, the haloarchaea. We used multi-locus sequence typing to demonstrate that haloarchaea exchange genetic information promiscuously, exhibiting a degree of linkage equilibrium approaching that of a sexual population.}, } @article {pmid15576487, year = {2004}, author = {Li, Y and Kelly, WG and Logsdon, JM and Schurko, AM and Harfe, BD and Hill-Harfe, KL and Kahn, RA}, title = {Functional genomic analysis of the ADP-ribosylation factor family of GTPases: phylogeny among diverse eukaryotes and function in C. elegans.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {18}, number = {15}, pages = {1834-1850}, doi = {10.1096/fj.04-2273com}, pmid = {15576487}, issn = {1530-6860}, support = {R01 GM067226/GM/NIGMS NIH HHS/United States ; R01 GM068029/GM/NIGMS NIH HHS/United States ; }, mesh = {ADP-Ribosylation Factors/*classification/genetics/*physiology ; Animals ; Caenorhabditis elegans/*embryology/*enzymology/genetics ; Eukaryotic Cells/enzymology ; Genomics ; Green Fluorescent Proteins/metabolism ; Membrane Proteins/classification ; *Phylogeny ; RNA Interference ; }, abstract = {ADP-ribosylation factor (Arf) and Arf-like (Arl) proteins are a family of highly conserved 21 kDa GTPases that emerged early in the evolution of eukaryotes. These proteins serve regulatory roles in vesicular traffic, lipid metabolism, microtubule dynamics, development, and likely other cellular processes. We found evidence for the presence of 6 Arf family members in the protist Giardia lamblia and 22 members in mammals. A phylogenetic analysis was performed to delineate the evolutionary relationships among Arf family members and to attempt to organize them by both their evolutionary origins and functions in cells and/or organisms. The approximately 100 protein sequences analyzed from animals, fungi, plants, and protists clustered into 11 groups, including Arfs, nine Arls, and Sar proteins. To begin functional analyses of the family in a metazoan model organism, we examined roles for all three C. elegans Arfs (Arf-1, Arf-3, and Arf-6) and three Arls (Arl-1, Arl-2, and Arl-3) by use of RNA-mediated interference (RNAi). Injection of double-stranded RNA (dsRNA) encoding Arf-1 or Arf-3 into N2 hermaphrodites produced embryonic lethality in their offspring and, later, sterility in the injected animals themselves. Injection of Arl-2 dsRNA resulted in a disorganized germline and sterility in early offspring, with later offspring exhibiting an early embryonic arrest. Thus, of the six Arf family members examined in C. elegans, at least three are required for embryogenesis. These data represent the first analysis of the role(s) of multiple members of this family in the development of a multicellular organism.}, } @article {pmid15522791, year = {2004}, author = {Vishwanath, P and Favaretto, P and Hartman, H and Mohr, SC and Smith, TF}, title = {Ribosomal protein-sequence block structure suggests complex prokaryotic evolution with implications for the origin of eukaryotes.}, journal = {Molecular phylogenetics and evolution}, volume = {33}, number = {3}, pages = {615-625}, doi = {10.1016/j.ympev.2004.07.003}, pmid = {15522791}, issn = {1055-7903}, mesh = {Amino Acid Sequence ; Animals ; Biological Evolution ; Escherichia coli/genetics ; Eukaryotic Cells ; *Evolution, Molecular ; Genes, Bacterial ; Humans ; Likelihood Functions ; Molecular Sequence Data ; Phylogeny ; Proteins/chemistry ; RNA/metabolism ; Ribosomal Proteins/*chemistry/genetics ; }, abstract = {Amino acid sequence alignments of orthologous ribosomal proteins found in Bacteria, Archaea, and Eukaryota display, relative to one another, an unusual segment or block structure, with major evolutionary implications. Within each of the prokaryotic phylodomains the sequences exhibit substantial similarity, but cross-domain alignments break up into (a) universal blocks (conserved in both phylodomains), (b) bacterial blocks (unalignable with any archaeal counterparts), and (c) archaeal blocks (unalignable with any bacterial counterparts). Sequences of those eukaryotic cytoplasmic riboproteins that have orthologs in both Bacteria and Archaea, exclusively match the archaeal block structure. The distinct blocks do not correlate consistently with any identifiable functional or structural feature including RNA and protein contacts. This phylodomain-specific block pattern also exists in a number of other proteins associated with protein synthesis, but not among enzymes of intermediary metabolism. While the universal blocks imply that modern Bacteria and Archaea (as defined by their translational machinery) clearly have had a common ancestor, the phylodomain-specific blocks imply that these two groups derive from single, phylodomain-specific types that came into existence at some point long after that common ancestor. The simplest explanation for this pattern would be a major evolutionary bottleneck, or other scenario that drastically limited the progenitors of modern prokaryotic diversity at a time considerably after the evolution of a fully functional translation apparatus. The vast range of habitats and metabolisms that prokaryotes occupy today would thus reflect divergent evolution after such a restricting event. Interestingly, phylogenetic analysis places the origin of eukaryotes at about the same time and shows a closer relationship of the eukaryotic ribosome-associated proteins to crenarchaeal rather than euryarchaeal counterparts.}, } @article {pmid15486256, year = {2004}, author = {Raoult, D and Audic, S and Robert, C and Abergel, C and Renesto, P and Ogata, H and La Scola, B and Suzan, M and Claverie, JM}, title = {The 1.2-megabase genome sequence of Mimivirus.}, journal = {Science (New York, N.Y.)}, volume = {306}, number = {5700}, pages = {1344-1350}, doi = {10.1126/science.1101485}, pmid = {15486256}, issn = {1095-9203}, mesh = {Acanthamoeba/virology ; Animals ; Base Composition ; Computational Biology ; DNA Repair/genetics ; DNA Topoisomerases/genetics ; DNA Viruses/classification/*genetics/metabolism ; DNA, Viral/chemistry/genetics ; Enzymes/genetics/metabolism ; Genes, Viral ; *Genome, Viral ; Inteins ; Introns ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Protein Biosynthesis ; Protein Folding ; Proteome ; RNA, Transfer/analysis ; RNA, Viral/analysis ; Sequence Analysis, DNA ; Viral Proteins/chemistry/genetics/metabolism ; }, abstract = {We recently reported the discovery and preliminary characterization of Mimivirus, the largest known virus, with a 400-nanometer particle size comparable to mycoplasma. Mimivirus is a double-stranded DNA virus growing in amoebae. We now present its 1,181,404-base pair genome sequence, consisting of 1262 putative open reading frames, 10% of which exhibit a similarity to proteins of known functions. In addition to exceptional genome size, Mimivirus exhibits many features that distinguish it from other nucleocytoplasmic large DNA viruses. The most unexpected is the presence of numerous genes encoding central protein-translation components, including four amino-acyl transfer RNA synthetases, peptide release factor 1, translation elongation factor EF-TU, and translation initiation factor 1. The genome also exhibits six tRNAs. Other notable features include the presence of both type I and type II topoisomerases, components of all DNA repair pathways, many polysaccharide synthesis enzymes, and one intein-containing gene. The size and complexity of the Mimivirus genome challenge the established frontier between viruses and parasitic cellular organisms. This new sequence data might help shed a new light on the origin of DNA viruses and their role in the early evolution of eukaryotes.}, } @article {pmid15357876, year = {2004}, author = {Karev, GP and Wolf, YI and Berezovskaya, FS and Koonin, EV}, title = {Gene family evolution: an in-depth theoretical and simulation analysis of non-linear birth-death-innovation models.}, journal = {BMC evolutionary biology}, volume = {4}, number = {}, pages = {32}, pmid = {15357876}, issn = {1471-2148}, mesh = {*Birth Rate ; Computer Simulation/*statistics & numerical data ; Empirical Research ; *Evolution, Molecular ; Genetics, Population/*methods ; Genome, Human ; Humans ; *Models, Genetic ; Monte Carlo Method ; *Mortality ; *Nonlinear Dynamics ; Proteome/genetics ; }, abstract = {BACKGROUND: The size distribution of gene families in a broad range of genomes is well approximated by a generalized Pareto function. Evolution of ensembles of gene families can be described with Birth, Death, and Innovation Models (BDIMs). Analysis of the properties of different versions of BDIMs has the potential of revealing important features of genome evolution.

RESULTS: In this work, we extend our previous analysis of stochastic BDIMs. In addition to the previously examined rational BDIMs, we introduce potentially more realistic logistic BDIMs, in which birth/death rates are limited for the largest families, and show that their properties are similar to those of models that include no such limitation. We show that the mean time required for the formation of the largest gene families detected in eukaryotic genomes is limited by the mean number of duplications per gene and does not increase indefinitely with the model degree. Instead, this time reaches a minimum value, which corresponds to a non-linear rational BDIM with the degree of approximately 2.7. Even for this BDIM, the mean time of the largest family formation is orders of magnitude greater than any realistic estimates based on the timescale of life's evolution. We employed the embedding chains technique to estimate the expected number of elementary evolutionary events (gene duplications and deletions) preceding the formation of gene families of the observed size and found that the mean number of events exceeds the family size by orders of magnitude, suggesting a highly dynamic process of genome evolution. The variance of the time required for the formation of the largest families was found to be extremely large, with the coefficient of variation >> 1. This indicates that some gene families might grow much faster than the mean rate such that the minimal time required for family formation is more relevant for a realistic representation of genome evolution than the mean time. We determined this minimal time using Monte Carlo simulations of family growth from an ensemble of simultaneously evolving singletons. In these simulations, the time elapsed before the formation of the largest family was much shorter than the estimated mean time and was compatible with the timescale of evolution of eukaryotes.

CONCLUSIONS: The analysis of stochastic BDIMs presented here shows that non-linear versions of such models can well approximate not only the size distribution of gene families but also the dynamics of their formation during genome evolution. The fact that only higher degree BDIMs are compatible with the observed characteristics of genome evolution suggests that the growth of gene families is self-accelerating, which might reflect differential selective pressure acting on different genes.}, } @article {pmid15356622, year = {2004}, author = {Rivera, MC and Lake, JA}, title = {The ring of life provides evidence for a genome fusion origin of eukaryotes.}, journal = {Nature}, volume = {431}, number = {7005}, pages = {152-155}, doi = {10.1038/nature02848}, pmid = {15356622}, issn = {1476-4687}, mesh = {Bacteria/genetics ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; DNA, Mitochondrial/genetics ; Eukaryotic Cells/*metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome ; *Genomics/methods ; *Models, Genetic ; Organelles/genetics ; Photosynthesis ; *Phylogeny ; Prokaryotic Cells/metabolism ; Recombination, Genetic/*genetics ; Saccharomyces cerevisiae/genetics ; Schizosaccharomyces/genetics ; }, abstract = {Genomes hold within them the record of the evolution of life on Earth. But genome fusions and horizontal gene transfer seem to have obscured sufficiently the gene sequence record such that it is difficult to reconstruct the phylogenetic tree of life. Here we determine the general outline of the tree using complete genome data from representative prokaryotes and eukaryotes and a new genome analysis method that makes it possible to reconstruct ancient genome fusions and phylogenetic trees. Our analyses indicate that the eukaryotic genome resulted from a fusion of two diverse prokaryotic genomes, and therefore at the deepest levels linking prokaryotes and eukaryotes, the tree of life is actually a ring of life. One fusion partner branches from deep within an ancient photosynthetic clade, and the other is related to the archaeal prokaryotes. The eubacterial organism is either a proteobacterium, or a member of a larger photosynthetic clade that includes the Cyanobacteria and the Proteobacteria.}, } @article {pmid15353560, year = {2004}, author = {Snel, B and van Noort, V and Huynen, MA}, title = {Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes.}, journal = {Nucleic acids research}, volume = {32}, number = {16}, pages = {4725-4731}, pmid = {15353560}, issn = {1362-4962}, mesh = {Animals ; Bacillus subtilis/genetics/metabolism ; Caenorhabditis elegans/genetics/metabolism ; Escherichia coli/genetics/metabolism ; Eukaryotic Cells/*metabolism ; *Evolution, Molecular ; Gene Duplication ; *Gene Expression Regulation ; Prokaryotic Cells/*metabolism ; Regulon ; Saccharomyces cerevisiae/genetics/metabolism ; }, abstract = {Differences between species have been suggested to largely reside in the network of connections among the genes. Nevertheless, the rate at which these connections evolve has not been properly quantified. Here, we measure the extent to which co-regulation between pairs of genes is conserved over large phylogenetic distances; between two eukaryotes Caenorhabditis elegans and Saccharomyces cerevisiae, and between two prokaryotes Escherichia coli and Bacillus subtilis. We first construct a reliable set of co-regulated genes by combining various functional genomics data from yeast, and subsequently determine conservation of co-regulation in worm from the distribution of co-expression values. For B.subtilis and E.coli, we use known operons and regulons. We find that between 76 and 80% of the co-regulatory connections are conserved between orthologous pairs of genes, which is very high compared with previous estimates and expectations regarding network evolution. We show that in the case of gene duplication after speciation, one of the two inparalogous genes tends to retain its original co-regulatory relationship, while the other loses this link and is presumably free for differentiation or sub-functionalization. The high level of co-regulation conservation implies that reliably predicted functional relationships from functional genomics data in one species can be transferred with high accuracy to another species when that species also harbours the associated genes.}, } @article {pmid15288023, year = {2004}, author = {Money, NP and Davis, CM and Ravishankar, JP}, title = {Biomechanical evidence for convergent evolution of the invasive growth process among fungi and oomycete water molds.}, journal = {Fungal genetics and biology : FG & B}, volume = {41}, number = {9}, pages = {872-876}, doi = {10.1016/j.fgb.2004.06.001}, pmid = {15288023}, issn = {1087-1845}, mesh = {Biological Evolution ; Fungi/*growth & development/metabolism ; Hydrostatic Pressure ; Hyphae/genetics/*growth & development ; Morphogenesis ; Oomycetes/*growth & development/metabolism ; Osmotic Pressure ; }, abstract = {Diverse microorganisms traditionally called fungi are recognized as members of two kingdoms: mushroom-forming species and their relatives in the Fungi, and oomycete water molds in the Stramenopila. Phylogenetic analysis suggests that these kingdoms diverged early in the evolution of eukaryotes. The phylogenetic detachment of the fungi and oomycetes is reflected in radical differences in their biochemistry, cell structure, and development. In terms of their biological activities, however, they show great similarity, because both groups form colonies of filamentous hyphae that invade and decompose solid food sources. Here we present biomechanical evidence of the convergent evolution of the invasive growth process in these microorganisms. Using miniature strain gauges to measure the forces exerted by single hyphae, we show that the hyphae of species in both kingdoms exert up to 2 atmospheres of hydrostatic pressure as they extend at their tips. No other eukaryotes have adopted this process for meeting their nutritional needs.}, } @article {pmid15247395, year = {2004}, author = {Bouarab, K and Adas, F and Gaquerel, E and Kloareg, B and Salaün, JP and Potin, P}, title = {The innate immunity of a marine red alga involves oxylipins from both the eicosanoid and octadecanoid pathways.}, journal = {Plant physiology}, volume = {135}, number = {3}, pages = {1838-1848}, pmid = {15247395}, issn = {0032-0889}, mesh = {Acetates/pharmacology ; Alcohol Oxidoreductases/metabolism ; Cyclopentanes/pharmacology ; Eicosanoids/*metabolism ; Immunity, Innate/*immunology ; *Lipid Metabolism ; Oxidation-Reduction ; Oxylipins ; Plant Growth Regulators/pharmacology ; Rhodophyta/drug effects/*immunology ; Seawater ; Stearic Acids/*metabolism ; }, abstract = {The oxygenated derivatives of fatty acids, known as oxylipins, are pivotal signaling molecules in animals and terrestrial plants. In animal systems, eicosanoids regulate cell differentiation, immune responses, and homeostasis. In contrast, terrestrial plants use derivatives of C18 and C16 fatty acids as developmental or defense hormones. Marine algae have emerged early in the evolution of eukaryotes as several distinct phyla, independent from the animal and green-plant lineages. The occurrence of oxylipins of the eicosanoid family is well documented in marine red algae, but their biological roles remain an enigma. Here we address the hypothesis that they are involved with the defense mechanisms of the red alga Chondrus crispus. By investigating its association with a green algal endophyte Acrochaete operculata, which becomes invasive in the diploid generation of this red alga, we showed that (1) when challenged by pathogen extracts, the resistant haploid phase of C. crispus produced both C20 and C18 oxylipins, (2) elicitation with pathogen extracts or methyl jasmonate activated the metabolism of C20 and C18 polyunsaturated fatty acids to generate hydroperoxides and cyclopentenones such as prostaglandins and jasmonates, and (3) C20 and C18 hydroperoxides as well as methyl jasmonate did induce shikimate dehydrogenase and Phe ammonialyase activities in C. crispus and conferred an induced resistance to the diploid phase, while inhibitors of fatty acid oxidation reduced the natural resistance of the haploid generation. The dual nature of oxylipin metabolism in this alga suggests that early eukaryotes featured both animal- (eicosanoids) and plant-like (octadecanoids) oxylipins as essential components of innate immunity mechanisms.}, } @article {pmid15238514, year = {2004}, author = {Young, JA and Hyppa, RW and Smith, GR}, title = {Conserved and nonconserved proteins for meiotic DNA breakage and repair in yeasts.}, journal = {Genetics}, volume = {167}, number = {2}, pages = {593-605}, pmid = {15238514}, issn = {0016-6731}, support = {GM-32194/GM/NIGMS NIH HHS/United States ; }, mesh = {*Conserved Sequence ; DNA Damage ; DNA Repair/*genetics ; DNA, Fungal/*genetics ; Fungal Proteins/*genetics ; Meiosis/genetics ; Saccharomyces cerevisiae/cytology/genetics ; Schizosaccharomyces/cytology/genetics ; Yeasts/*genetics ; }, abstract = {During meiosis DNA double-strand breaks initiate recombination in the distantly related budding and fission yeasts and perhaps in most eukaryotes. Repair of broken meiotic DNA is essential for formation of viable gametes. We report here distinct but overlapping sets of proteins in these yeasts required for formation and repair of double-strand breaks. Meiotic DNA breakage in Schizosaccharomyces pombe did not require Rad50 or Rad32, although the homologs Rad50 and Mre11 are required in Saccharomyces cerevisiae; these proteins are required for meiotic DNA break repair in both yeasts. DNA breakage required the S. pombe midmeiosis transcription factor Mei4, but the structurally unrelated midmeiosis transcription factor Ndt80 is not required for breakage in S. cerevisiae. Rhp51, Swi5, and Rad22 + Rti1 were required for full levels of DNA repair in S. pombe, as are the related S. cerevisiae proteins Rad51, Sae3, and Rad52. Dmc1 was not required for repair in S. pombe, but its homolog Dmc1 is required in the well-studied strain SK1 of S. cerevisiae. Additional proteins required in one yeast have no obvious homologs in the other yeast. The occurrence of conserved and nonconserved proteins indicates potential diversity in the mechanism of meiotic recombination and divergence of the machinery during the evolution of eukaryotes.}, } @article {pmid15155803, year = {2004}, author = {Maćasev, D and Whelan, J and Newbigin, E and Silva-Filho, MC and Mulhern, TD and Lithgow, T}, title = {Tom22', an 8-kDa trans-site receptor in plants and protozoans, is a conserved feature of the TOM complex that appeared early in the evolution of eukaryotes.}, journal = {Molecular biology and evolution}, volume = {21}, number = {8}, pages = {1557-1564}, doi = {10.1093/molbev/msh166}, pmid = {15155803}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; Carrier Proteins/*genetics ; Diatoms/*genetics ; Dictyostelium/*genetics ; Membrane Transport Proteins/*genetics ; Mitochondria/*genetics/metabolism ; Mitochondrial Membrane Transport Proteins ; Mitochondrial Precursor Protein Import Complex Proteins ; Molecular Sequence Data ; Plasmodium falciparum/genetics ; Receptors, Cell Surface/*genetics ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/genetics ; }, abstract = {One of the earliest events in the evolution of mitochondria was the development a means to translocate proteins made in the cytosol into the "protomitochondrion." How this was achieved remains uncertain, and the nature of the earliest version of the protein translocation machinery is not known. Comparative sequence analysis suggests three subunits, Tom40, Tom7, and Tom22 as common elements of the protein translocase in the mitochondrial outer membrane in diverse extant eukaryotes. Tom22, the 22-kDa subunit, plays a critical role in the function of this complex in fungi and animals, and we show that an 8-kDa subunit of the plant translocase is a truncated form of Tom22. It has a single transmembrane segment conforming in sequence to the same region of Tom22 from other eukaryotic lineages and a short carboxy-terminal trans domain located in the mitochondrial intermembrane space. The trans domain from the Arabidopsis thaliana protein functions in yeast lacking their own Tom22 by complementing protein import defects and restoring cell growth. Moreover, we have identified orthologs of Tom22, Tom7, and Tom40 in diverse eukaryotes such as the diatom Phaeodactylum tricornutum, the amoebic slime Dictyostelium discoideum, and the protozoan parasite Plasmodium falciparum. This finding strongly suggests these subunits as the core of the protein translocase in the earliest mitochondria.}, } @article {pmid15144062, year = {2004}, author = {Kiefel, BR and Gilson, PR and Beech, PL}, title = {Diverse eukaryotes have retained mitochondrial homologues of the bacterial division protein FtsZ.}, journal = {Protist}, volume = {155}, number = {1}, pages = {105-115}, doi = {10.1078/1434461000168}, pmid = {15144062}, issn = {1434-4610}, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/*genetics/physiology ; Biological Evolution ; Chloroplasts/genetics ; Chrysophyta/genetics ; Conserved Sequence ; Cyanophora/genetics ; Cytoskeletal Proteins/*genetics/physiology ; Diatoms/genetics ; Dictyostelium/genetics ; Eukaryota/genetics ; *Eukaryotic Cells ; Fungi/genetics ; Genes, Essential ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Phytophthora/genetics ; Plants/genetics ; Sequence Alignment ; Sequence Homology ; }, abstract = {Mitochondrial fission requires the division of both the inner and outer mitochondrial membranes. Dynamin-related proteins operate in division of the outer membrane of probably all mitochondria, and also that of chloroplasts--organelles that have a bacterial origin like mitochondria. How the inner mitochondrial membrane divides is less well established. Homologues of the major bacterial division protein, FtsZ, are known to reside inside mitochondria of the chromophyte alga Mallomonas, a red alga, and the slime mould Dictyostelium discoideum, where these proteins are likely to act in division of the organelle. Mitochondrial FtsZ is, however, absent from the genomes of higher eukaryotes (animals, fungi, and plants), even though FtsZs are known to be essential for the division of probably all chloroplasts. To begin to understand why higher eukaryotes have lost mitochondrial FtsZ, we have sampled various diverse protists to determine which groups have retained the gene. Database searches and degenerate PCR uncovered genes for likely mitochondrial FtsZs from the glaucocystophyte Cyanophora paradoxa, the oomycete Phytophthora infestans, two haptophyte algae, and two diatoms--one being Thalassiosira pseudonana, the draft genome of which is now available. From Thalassiosira we also identified two chloroplast FtsZs, one of which appears to be undergoing a C-terminal shortening that may be common to many organellar FtsZs. Our data indicate that many protists still employ the FtsZ-based ancestral mitochondrial division mechanism, and that mitochondrial FtsZ has been lost numerous times in the evolution of eukaryotes.}, } @article {pmid14963098, year = {2004}, author = {Friedman, R and Hughes, AL}, title = {Two patterns of genome organization in mammals: the chromosomal distribution of duplicate genes in human and mouse.}, journal = {Molecular biology and evolution}, volume = {21}, number = {6}, pages = {1008-1013}, doi = {10.1093/molbev/msh076}, pmid = {14963098}, issn = {0737-4038}, support = {GM066710/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Chromosomes/*genetics ; Databases, Genetic ; *Evolution, Molecular ; Gene Rearrangement/genetics ; Genes, Duplicate/*genetics ; *Genome, Human ; Humans ; Mice/*genetics ; Multigene Family/genetics ; Sequence Homology ; }, abstract = {Gene duplication occurs repeatedly in the evolution of genomes, and the rearrangement of genomic segments has also occurred repeatedly over the evolution of eukaryotes. We studied the interaction of these two factors in mammalian evolution by comparing the chromosomal distribution of multigene families in human and mouse. In both species, gene families tended to be confined to a single chromosome to a greater extent than expected by chance. The average number of families shared between chromosomes was nearly 60% higher in mouse than in human, and human chromosomes rarely shared large numbers of gene families with more than one or two other chromosomes, whereas mouse chromosomes frequently did so. A higher proportion of duplicate gene pairs on the same chromosome originated from recent duplications in human than in mouse, whereas a higher proportion of duplicate gene pairs on separate chromosomes arose from ancient duplications in human than in mouse. These observations are most easily explained by the hypotheses that (1) most gene duplications arise in tandem and are subsequently separated by segmental rearrangement events, and (2) that the process of segmental rearrangement has occurred at a higher rate in the lineage of mouse than in that of human.}, } @article {pmid14657101, year = {2003}, author = {Longet, D and Archibald, JM and Keeling, PJ and Pawlowski, J}, title = {Foraminifera and Cercozoa share a common origin according to RNA polymerase II phylogenies.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {53}, number = {Pt 6}, pages = {1735-1739}, doi = {10.1099/ijs.0.02597-0}, pmid = {14657101}, issn = {1466-5026}, mesh = {Animals ; Classification ; DNA, Ribosomal/*genetics ; Eukaryotic Cells/enzymology ; *Phylogeny ; RNA Polymerase II/classification/*genetics ; }, abstract = {Phylogenetic analysis of small and large subunits of rDNA genes suggested that Foraminifera originated early in the evolution of eukaryotes, preceding the origin of other rhizopodial protists. This view was recently challenged by the analysis of actin and ubiquitin protein sequences, which revealed a close relationship between Foraminifera and Cercozoa, an assemblage of various filose amoebae and amoeboflagellates that branch in the so-called crown of the SSU rDNA tree of eukaryotes. To further test this hypothesis, we sequenced a fragment of the largest subunit of the RNA polymerase II (RPB1) from five foraminiferans, two cercozoans and the testate filosean Gromia oviformis. Analysis of our data confirms a close relationship between Foraminifera and Cercozoa and points to Gromia as the closest relative of Foraminifera.}, } @article {pmid14579253, year = {2003}, author = {Jékely, G}, title = {Small GTPases and the evolution of the eukaryotic cell.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {25}, number = {11}, pages = {1129-1138}, doi = {10.1002/bies.10353}, pmid = {14579253}, issn = {0265-9247}, mesh = {Animals ; *Biological Evolution ; Cell Nucleus ; Eukaryotic Cells/cytology/*physiology ; GTP Phosphohydrolases/classification/*genetics/*metabolism ; Intracellular Membranes/metabolism ; Mitosis ; Molecular Sequence Data ; Phagocytosis ; Phylogeny ; ras Proteins/classification/genetics/metabolism ; }, abstract = {The origin of eukaryotes is one of the major challenges of evolutionary cell biology. Other than the endosymbiotic origin of mitochondria and chloroplasts, the steps leading to eukaryotic endomembranes and endoskeleton are poorly understood. Ras-family small GTPases are key regulators of cytoskeleton dynamics, vesicular trafficking and nuclear function. They are specific for eukaryotes and their expansion probably traces the evolution of core eukaryote features. The phylogeny of small GTPases suggests that the first endomembranes to evolve during eukaryote evolution had secretory, and not phagocytic, function. Based on the reconstruction of putative roles for ancestral small GTPases, a hypothetical scenario on the origins of the first endomembranes, the nucleus, and phagocytosis is presented.}, } @article {pmid12949145, year = {2003}, author = {Cardazzo, B and Bargelloni, L and Toffolatti, L and Patarnello, T}, title = {Intervening sequences in paralogous genes: a comparative genomic approach to study the evolution of X chromosome introns.}, journal = {Molecular biology and evolution}, volume = {20}, number = {12}, pages = {2034-2041}, doi = {10.1093/molbev/msg213}, pmid = {12949145}, issn = {0737-4038}, mesh = {Animals ; DNA Transposable Elements/genetics ; Databases, Protein ; *Evolution, Molecular ; Gene Duplication ; *Genes ; Humans ; *Introns ; Mice ; Phylogeny ; Sequence Homology ; *X Chromosome ; }, abstract = {The enlargement of the genome size and the decrease in genome compactness with increase in the number and size of introns is a general pattern during the evolution of eukaryotes. Among the possible mechanisms for modifying intron size, it has been suggested that the insertion of transposable elements might have an important role in driving intron evolution. The analysis of large portions of the human genome demonstrated that a relatively recent (50 to 100 MYA) accumulation of transposable elements appears to be biased, favoring a preferential insertion of LINE1 transposons into sex chromosomes rather than into autosomes. In the present work, the effect of chromosomal location on the increase in size of introns was evaluated with a comparative analysis performed on pairs of human paralogous genes, one located on the X chromosome and the second on an autosome. A phylogenetic analysis was also performed on the X-encoded proteins and their paralogs to confirm orthology-paralogy and to approximately estimate the time of gene duplication. Statistical analysis of total intron length for each pair of paralogous genes provided no evidence for a larger size of introns in the gene copies located on the X chromosome. On the opposite, introns of autosomal genes were found to be significantly longer than introns of their X-linked paralogs. Likewise, LINE1 elements were not significantly more frequent in X-chromosome introns, whereas the frequency of SINE elements showed a marginally significant bias toward autosomal introns.}, } @article {pmid12868611, year = {2003}, author = {Patthy, L}, title = {Modular assembly of genes and the evolution of new functions.}, journal = {Genetica}, volume = {118}, number = {2-3}, pages = {217-231}, pmid = {12868611}, issn = {0016-6707}, mesh = {*Evolution, Molecular ; Exons ; *Genes ; Genome ; Introns ; Proteins/genetics ; }, abstract = {Modular assembly of novel genes from existing genes has long been thought to be an important source of evolutionary novelty. Thanks to major advances in genomic studies it has now become clear that this mechanism contributed significantly to the evolution of novel biological functions in different evolutionary lineages. Analyses of completely sequenced bacterial, archaeal and eukaryotic genomes has revealed that modular assembly of novel constituents of various eukaryotic intracellular signalling pathways played a major role in the evolution of eukaryotes. Comparison of the genomes of single-celled eukaryotes, multicellular plants and animals has also shown that the evolution of multicellularity was accompanied by the assembly of numerous novel extracellular matrix proteins and extracellular signalling proteins that are absolutely essential for multicellularity. There is now strong evidence that exon-shuffling played a general role in the assembly of the modular proteins involved in extracellular communications of metazoa. Although some of these proteins seem to be shared by all major groups of metazoa, others are restricted to certain evolutionary lineages. The genomic features of the chordates appear to have favoured intronic recombination as evidenced by the fact that exon-shuffling continued to be a major source of evolutionary novelty during vertebrate evolution.}, } @article {pmid12836681, year = {2003}, author = {Spring, J}, title = {Major transitions in evolution by genome fusions: from prokaryotes to eukaryotes, metazoans, bilaterians and vertebrates.}, journal = {Journal of structural and functional genomics}, volume = {3}, number = {1-4}, pages = {19-25}, pmid = {12836681}, issn = {1345-711X}, mesh = {Animals ; *Biological Evolution ; Eukaryotic Cells/*metabolism ; Gene Duplication ; *Genome ; Humans ; Prokaryotic Cells/*metabolism ; Vertebrates/*metabolism ; }, abstract = {The major transitions in human evolution from prokaryotes to eukaryotes, from protozoans to metazoans, from the first animals to bilaterians and finally from a primitive chordate to vertebrates were all accompanied by increases in genome complexity. Rare fusion of divergent genomes rather than continuous single gene duplications could explain these jumps in evolution. The origin of eukaryotes was proposed to be due to a symbiosis of Archaea and Bacteria. Symbiosis is clearly seen as the source for mitochondria. A fundamental difference of higher eukaryotes is the cycle from haploidy to diploidy, a well-regulated genome duplication. Of course, self-fertilization exists, but the potential of sex increases with the difference of the haploid stages, such as the sperm and the egg. What should be the advantage of having two identical copies of a gene? Still, genes duplicate all the time and even genomes duplicate rather often. In plants, polyploidy is well recognized, but seems to be abundant in fungi and even in animals, too. However, hybridization, rather than autopolyploidy, seems to be the potential mechanism for creating something new. The problem with chimaeric, symbiotic or reticulate evolution events is that they blur phylogenetic lineages. Unrecognized paralogous genes or random loss of one of the paralogs in different lineages can lead to false conclusions. Horizontal genome transfer, genome fusion or hybridization might be only truly innovative combined with rare geological transitions such as change to an oxygen atmosphere, snowball Earth events or the Cambrian explosion, but correlates well with the major transitions in evolution.}, } @article {pmid12832624, year = {2003}, author = {Theissen, U and Hoffmeister, M and Grieshaber, M and Martin, W}, title = {Single eubacterial origin of eukaryotic sulfide:quinone oxidoreductase, a mitochondrial enzyme conserved from the early evolution of eukaryotes during anoxic and sulfidic times.}, journal = {Molecular biology and evolution}, volume = {20}, number = {9}, pages = {1564-1574}, doi = {10.1093/molbev/msg174}, pmid = {12832624}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Anaerobiosis ; Animals ; Bacteria/enzymology/genetics ; Conserved Sequence ; DNA, Mitochondrial/genetics ; Eukaryotic Cells ; *Evolution, Molecular ; Gene Duplication ; Humans ; Mitochondria/*enzymology/genetics ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Quinone Reductases/*genetics ; Sequence Homology, Amino Acid ; Sulfides/metabolism ; }, abstract = {Mitochondria occur as aerobic, facultatively anaerobic, and, in the case of hydrogenosomes, strictly anaerobic forms. This physiological diversity of mitochondrial oxygen requirement is paralleled by that of free-living alpha-proteobacteria, the group of eubacteria from which mitochondria arose, many of which are facultative anaerobes. Although ATP synthesis in mitochondria usually involves the oxidation of reduced carbon compounds, many alpha-proteobacteria and some mitochondria are known to use sulfide (H2S) as an electron donor for the respiratory chain and its associated ATP synthesis. In many eubacteria, the oxidation of sulfide involves the enzyme sulfide:quinone oxidoreductase (SQR). Nuclear-encoded homologs of SQR are found in several eukaryotic genomes. Here we show that eukaryotic SQR genes characterized to date can be traced to a single acquisition from a eubacterial donor in the common ancestor of animals and fungi. Yet, SQR is not a well-conserved protein, and our analyses suggest that the SQR gene has furthermore undergone some lateral transfer among prokaryotes during evolution, leaving the precise eubacterial lineage from which eukaryotes obtained their SQR difficult to discern with phylogenetic methods. Newer geochemical data and microfossil evidence indicate that major phases of early eukaryotic diversification occurred during a period of the Earth's history from 1 to 2 billion years before present in which the subsurface ocean waters contained almost no oxygen but contained high concentrations of sulfide, suggesting that the ability to deal with sulfide was essential for prokaryotes and eukaryotes during that time. Notwithstanding poor resolution in deep SQR phylogeny and lack of a specifically alpha-protebacterial branch for the eukaryotic enzyme on the basis of current lineage sampling, a single eubacterial origin of eukaryotic SQR and the evident need of ancient eukaryotes to deal with sulfide, a process today germane to mitochondrial quinone reduction, are compatible with the view that eukaryotic SQR was an acquisition from the mitochondrial endosymbiont.}, } @article {pmid12732534, year = {2003}, author = {Stoeck, T and Epstein, S}, title = {Novel eukaryotic lineages inferred from small-subunit rRNA analyses of oxygen-depleted marine environments.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {5}, pages = {2657-2663}, pmid = {12732534}, issn = {0099-2240}, mesh = {Anaerobiosis ; Animals ; Chlorophyta/genetics/isolation & purification ; Ciliophora/genetics/isolation & purification ; Eukaryota/genetics/isolation & purification ; *Eukaryotic Cells ; Evolution, Molecular ; Fungi/genetics/isolation & purification ; Geologic Sediments/microbiology ; *Marine Biology ; Massachusetts ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal/*analysis/*genetics ; Water Microbiology ; }, abstract = {Microeukaryotes in oxygen-depleted environments are among the most diverse, as well as the least studied, organisms. We conducted a cultivation-independent, small-subunit (SSU) rRNA-based survey of microeukaryotes in suboxic waters and anoxic sediments in the great Sippewisset salt marsh, Cape Cod, Mass. We generated two clone libraries and analyzed approximately 300 clones, which contained a large diversity of microeukaryotic SSU rRNA signatures. Only a few of these signatures were closely related (sequence similarity of >97%) to the sequences reported earlier. The bulk of our sequences represented deep novel branches within green algae, fungi, cercozoa, stramenopiles, alveolates, euglenozoa and unclassified flagellates. In addition, a significant number of detected rRNA sequences exhibited no affiliation to known organisms and sequences and thus represent novel lineages of the highest taxonomical order, most of them branching off the base of the global phylogenetic tree. This suggests that oxygen-depleted environments harbor diverse communities of novel organisms, which may provide an interesting window into the early evolution of eukaryotes.}, } @article {pmid12689729, year = {2003}, author = {Watson, RA and Pollack, JB}, title = {A computational model of symbiotic composition in evolutionary transitions.}, journal = {Bio Systems}, volume = {69}, number = {2-3}, pages = {187-209}, doi = {10.1016/s0303-2647(02)00135-1}, pmid = {12689729}, issn = {0303-2647}, mesh = {Adaptation, Physiological/*genetics ; *Algorithms ; Animals ; Computer Simulation ; *Ecosystem ; *Epistasis, Genetic ; Genetic Variation ; Humans ; *Models, Genetic ; Population Dynamics ; Selection, Genetic ; Symbiosis/*genetics ; }, abstract = {Several of the major transitions in evolutionary history, such as the symbiogenic origin of eukaryotes from prokaryotes, share the feature that existing entities became the components of composite entities at a higher-level of organization. This composition of pre-adapted extant entities into a new whole is a fundamentally different source of variation from the gradual accumulation of small random variations, and it has some interesting consequences for issues of evolvability. Intuitively, the pre-adaptation of sets of features in reproductively independent specialists suggests a form of 'divide and conquer' decomposition of the adaptive domain. Moreover, the compositions resulting from one level may become the components for compositions at the next level, thus scaling-up the variation mechanism. In this paper, we explore and develop these concepts using a simple abstract model of symbiotic composition to examine its impact on evolvability. To exemplify the adaptive capacity of the composition model, we employ a scale-invariant fitness landscape exhibiting significant ruggedness at all scales. Whilst innovation by mutation and by conventional evolutionary algorithms becomes increasingly more difficult as evolution continues in this landscape, innovation by composition is not impeded as it discovers and assembles component entities through successive hierarchical levels.}, } @article {pmid12615008, year = {2003}, author = {Osborn, TC and Pires, JC and Birchler, JA and Auger, DL and Chen, ZJ and Lee, HS and Comai, L and Madlung, A and Doerge, RW and Colot, V and Martienssen, RA}, title = {Understanding mechanisms of novel gene expression in polyploids.}, journal = {Trends in genetics : TIG}, volume = {19}, number = {3}, pages = {141-147}, doi = {10.1016/s0168-9525(03)00015-5}, pmid = {12615008}, issn = {0168-9525}, support = {R01 GM067015-01A1/GM/NIGMS NIH HHS/United States ; }, mesh = {Biological Evolution ; Gene Dosage ; *Gene Expression Regulation ; Genes, Plant ; Genetic Variation ; Genome, Plant ; Models, Genetic ; Plants/*genetics ; *Polyploidy ; Selection, Genetic ; }, abstract = {Polyploidy has long been recognized as a prominent force shaping the evolution of eukaryotes, especially flowering plants. New phenotypes often arise with polyploid formation and can contribute to the success of polyploids in nature or their selection for use in agriculture. Although the causes of novel variation in polyploids are not well understood, they could involve changes in gene expression through increased variation in dosage-regulated gene expression, altered regulatory interactions, and rapid genetic and epigenetic changes. New research approaches are being used to study these mechanisms and the results should provide a more complete understanding of polyploidy.}, } @article {pmid12594927, year = {2003}, author = {Embley, TM and van der Giezen, M and Horner, DS and Dyal, PL and Foster, P}, title = {Mitochondria and hydrogenosomes are two forms of the same fundamental organelle.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {358}, number = {1429}, pages = {191-201; discussion 201-2}, pmid = {12594927}, issn = {0962-8436}, mesh = {Anaerobiosis ; *Biological Evolution ; Eukaryotic Cells/*cytology/enzymology/metabolism ; Hydrogen/*metabolism ; Hydrogenase/genetics/metabolism ; Mitochondria/*metabolism ; Organelles/*metabolism ; Phylogeny ; }, abstract = {Published data suggest that hydrogenosomes, organelles found in diverse anaerobic eukaryotes that make energy and hydrogen, were once mitochondria. As hydrogenosomes generally lack a genome, the conversion is probably one way. The sources of the key hydrogenosomal enzymes, pyruvate : ferredoxin oxidoreductase (PFO) and hydrogenase, are not resolved by current phylogenetic analyses, but it is likely that both were present at an early stage of eukaryotic evolution. Once thought to be restricted to a few unusual anaerobic eukaryotes, the proteins are intimately integrated into the fabric of diverse eukaryotic cells, where they are targeted to different cell compartments, and not just hydrogenosomes. There is no evidence supporting the view that PFO and hydrogenase originated from the mitochondrial endosymbiont, as posited by the hydrogen hypothesis for eukaryogenesis. Other organelles derived from mitochondria have now been described in anaerobic and parasitic microbial eukaryotes, including species that were once thought to have diverged before the mitochondrial symbiosis. It thus seems possible that all eukaryotes may eventually be shown to contain an organelle of mitochondrial ancestry, to which different types of biochemistry can be targeted. It remains to be seen if, despite their obvious differences, this family of organelles shares a common function of importance for the eukaryotic cell, other than energy production, that might provide the underlying selection pressure for organelle retention.}, } @article {pmid12553882, year = {2003}, author = {Iyer, LM and Koonin, EV and Aravind, L}, title = {Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases.}, journal = {BMC structural biology}, volume = {3}, number = {}, pages = {1}, pmid = {12553882}, issn = {1472-6807}, mesh = {Amino Acid Sequence ; Bacteria/enzymology/genetics ; Bacteriophages/enzymology ; Binding Sites ; Catalytic Domain ; Conserved Sequence ; DNA-Directed RNA Polymerases/*chemistry/*genetics/metabolism ; Eukaryotic Cells/*enzymology ; *Evolution, Molecular ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Tertiary ; Protein Subunits ; RNA-Dependent RNA Polymerase/*chemistry/*genetics/metabolism ; Sequence Alignment ; }, abstract = {BACKGROUND: The eukaryotic RNA-dependent RNA polymerase (RDRP) is involved in the amplification of regulatory microRNAs during post-transcriptional gene silencing. This enzyme is highly conserved in most eukaryotes but is missing in archaea and bacteria. No evolutionary relationship between RDRP and other polymerases has been reported so far, hence the origin of this eukaryote-specific polymerase remains a mystery.

RESULTS: Using extensive sequence profile searches, we identified bacteriophage homologs of the eukaryotic RDRP. The comparison of the eukaryotic RDRP and their homologs from bacteriophages led to the delineation of the conserved portion of these enzymes, which is predicted to harbor the catalytic site. Further, detailed sequence comparison, aided by examination of the crystal structure of the DNA-dependent RNA polymerase (DDRP), showed that the RDRP and the beta' subunit of DDRP (and its orthologs in archaea and eukaryotes) contain a conserved double-psi beta-barrel (DPBB) domain. This DPBB domain contains the signature motif DbDGD (b is a bulky residue), which is conserved in all RDRPs and DDRPs and contributes to catalysis via a coordinated divalent cation. Apart from the DPBB domain, no similarity was detected between RDRP and DDRP, which leaves open two scenarios for the origin of RDRP: i) RDRP evolved at the onset of the evolution of eukaryotes via a duplication of the DDRP beta' subunit followed by dramatic divergence that obliterated the sequence similarity outside the core catalytic domain and ii) the primordial RDRP, which consisted primarily of the DPBB domain, evolved from a common ancestor with the DDRP at a very early stage of evolution, during the RNA world era. The latter hypothesis implies that RDRP had been subsequently eliminated from cellular life forms and might have been reintroduced into the eukaryotic genomes through a bacteriophage. Sequence and structure analysis of the DDRP led to further insights into the evolution of RNA polymerases. In addition to the beta' subunit, beta subunit of DDRP also contains a DPBB domain, which is, however, distorted by large inserts and does not harbor a counterpart of the DbDGD motif. The DPBB domains of the two DDRP subunits together form the catalytic cleft, with the domain from the beta' subunit supplying the metal-coordinating DbDGD motif and the one from the beta subunit providing two lysine residues involved in catalysis. Given that the two DPBB domains of DDRP contribute completely different sets of active residues to the catalytic center, it is hypothesized that the ultimate ancestor of RNA polymerases functioned as a homodimer of a generic, RNA-binding DPBB domain. This ancestral protein probably did not have catalytic activity and served as a cofactor for a ribozyme RNA polymerase. Subsequent evolution of DDRP and RDRP involved accretion of distinct sets of additional domains. In the DDRPs, these included a RNA-binding Zn-ribbon, an AT-hook-like module and a sandwich-barrel hybrid motif (SBHM) domain. Further, lineage-specific accretion of SBHM domains and other, DDRP-specific domains is observed in bacterial DDRPs. In contrast, the orthologs of the beta' subunit in archaea and eukaryotes contains a four-stranded alpha + beta domain that is shared with the alpha-subunit of bacterial DDRP, eukaryotic DDRP subunit RBP11, translation factor eIF1 and type II topoisomerases. The additional domains of the RDRPs remain to be characterized.

CONCLUSIONS: Eukaryotic RNA-dependent RNA polymerases share the catalytic double-psi beta-barrel domain, containing a signature metal-coordinating motif, with the universally conserved beta' subunit of DNA-dependent RNA polymerases. Beyond this core catalytic domain, the two classes of RNA polymerases do not have common domains, suggesting early divergence from a common ancestor, with subsequent independent domain accretion. The beta-subunit of DDRP contains another, highly diverged DPBB domain. The presence of two distinct DPBB domains in two subunits of DDRP is compatible with the hypothesis that the ith the hypothesis that the ultimate ancestor of RNA polymerases was a RNA-binding DPBB domain that had no catalytic activity but rather functioned as a homodimeric cofactor for a ribozyme polymerase.}, } @article {pmid12546782, year = {2003}, author = {Andersson, JO and Sjögren, AM and Davis, LA and Embley, TM and Roger, AJ}, title = {Phylogenetic analyses of diplomonad genes reveal frequent lateral gene transfers affecting eukaryotes.}, journal = {Current biology : CB}, volume = {13}, number = {2}, pages = {94-104}, doi = {10.1016/s0960-9822(03)00003-4}, pmid = {12546782}, issn = {0960-9822}, mesh = {Adaptation, Physiological ; Aldehyde Oxidoreductases/genetics ; Aldehyde-Lyases/genetics ; Amino Acyl-tRNA Synthetases/genetics ; Anaerobiosis ; Animals ; DNA, Protozoan/genetics ; Diplomonadida/enzymology/*genetics/physiology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Protozoan ; Giardia lamblia/enzymology/*genetics/physiology ; Molecular Sequence Data ; Phylogeny ; Protozoan Proteins/genetics ; Threonine Dehydratase/genetics ; Transaminases/genetics ; }, abstract = {BACKGROUND: Lateral gene transfer (LGT) is an important evolutionary mechanism among prokaryotes. The situation in eukaryotes is less clear; the human genome sequence failed to give strong support for any recent transfers from prokaryotes to vertebrates, yet a number of LGTs from prokaryotes to protists (unicellular eukaryotes) have been documented. Here, we perform a systematic analysis to investigate the impact of LGT on the evolution of diplomonads, a group of anaerobic protists.

RESULTS: Phylogenetic analyses of 15 genes present in the genome of the Atlantic Salmon parasite Spironucleus barkhanus and/or the intestinal parasite Giardia lamblia show that most of these genes originated via LGT. Half of the genes are putatively involved in processes related to an anaerobic lifestyle, and this finding suggests that a common ancestor, which most probably was aerobic, of Spironucleus and Giardia adapted to an anaerobic environment in part by acquiring genes via LGT from prokaryotes. The sources of the transferred diplomonad genes are found among all three domains of life, including other eukaryotes. Many of the phylogenetic reconstructions show eukaryotes emerging in several distinct regions of the tree, strongly suggesting that LGT not only involved diplomonads, but also involved other eukaryotic groups.

CONCLUSIONS: Our study shows that LGT is a significant evolutionary mechanism among diplomonads in particular and protists in general. These findings provide insights into the evolution of biochemical pathways in early eukaryote evolution and have important implications for studies of eukaryotic genome evolution and organismal relationships. Furthermore, "fusion" hypotheses for the origin of eukaryotes need to be rigorously reexamined in the light of these results.}, } @article {pmid12526848, year = {2003}, author = {Lalucque, H and Silar, P}, title = {NADPH oxidase: an enzyme for multicellularity?.}, journal = {Trends in microbiology}, volume = {11}, number = {1}, pages = {9-12}, doi = {10.1016/s0966-842x(02)00007-0}, pmid = {12526848}, issn = {0966-842X}, mesh = {Amino Acid Sequence ; Ascomycota/genetics/isolation & purification/physiology ; Eukaryotic Cells/physiology ; Humans ; Molecular Sequence Data ; NADPH Oxidases/genetics/*physiology ; Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; Signal Transduction ; }, abstract = {Multicellularity has evolved several times during the evolution of eukaryotes. One evolutionary pressure that permits multicellularity relates to the division of work, where one group of cells functions as nutrient providers and the other in specialized roles such as defence or reproduction. This requires signalling systems to ensure harmonious development of multicellular structures. Here, we show that NADPH oxidases are specifically present in organisms that differentiate multicellular structures during their life cycle and are absent from unicellular life forms. The biochemical properties of these enzymes make them ideal candidates for a role in intercellular signalling.}, } @article {pmid12361302, year = {2002}, author = {Katz, LA}, title = {Lateral gene transfers and the evolution of eukaryotes: theories and data.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {52}, number = {Pt 5}, pages = {1893-1900}, doi = {10.1099/00207713-52-5-1893}, pmid = {12361302}, issn = {1466-5026}, mesh = {Animals ; *Biological Evolution ; Ecosystem ; Eukaryotic Cells ; *Gene Transfer, Horizontal ; Genetics, Microbial ; Genome, Human ; Humans ; Metabolism ; *Models, Genetic ; Organelles/genetics ; }, abstract = {Vertical transmission of heritable material, a cornerstone of the Darwinian theory of evolution, is inadequate to describe the evolution of eukaryotes, particularly microbial eukaryotes. This is because eukaryotic cells and eukaryotic genomes are chimeric, having evolved through a combination of vertical (parent to offspring) and lateral (trans-species) transmission. Observations on widespread chimerism in eukaryotes have led to new and revised hypothesis for the origin and diversification of eukaryotes that provide specific predictions on the tempo (early vs continuous transfers) and mode (nature of donor and recipient lineages) of lateral gene transfers (LGTs). Analyses of available data indicate that LGTs in eukaryotes largely fall into two categories: (1) LGTs from organelles to the nucleus, only a few of which appear to have occurred at the time of the origin of eukaryotes, and (2) anomalous LGTs involving diverse donor and recipient lineages. Further testing of hypotheses on the origin and diversification of eukaryotes will require complete genome sequences from a number of diverse eukaryotes and prokaryotes combined with sequences of targeted genes from a broad phylogenetic sample.}, } @article {pmid12183131, year = {2002}, author = {Imai, H and Satta, Y and Wada, M and Takahata, N}, title = {Estimation of the highest chromosome number of eukaryotes based on the minimum interaction theory.}, journal = {Journal of theoretical biology}, volume = {217}, number = {1}, pages = {61-74}, doi = {10.1006/jtbi.2002.3016}, pmid = {12183131}, issn = {0022-5193}, mesh = {Animals ; *Chromosomes ; Eukaryotic Cells/*physiology ; *Evolution, Molecular ; Karyotyping ; *Models, Genetic ; Species Specificity ; }, abstract = {According to the minimum interaction theory, the chromosome evolution of eukaryotes proceeds as a whole toward increasing the chromosome number. This raises the following two questions: what was the starting chromosome number of eukaryotes and does the chromosome number increase infinitely? We attempted to provide a theoretical framework to resolve these questions. We propose that the species with n=2 observed in Protozoa, Platyhelminthes, Annelid, Algae, Fungi and higher plants would be chromosomal relicts conserving the karyotypes of ancestral eukaryotes. We also propose that the ideal highest number of eukaryotes (n(max)) can be given by an inverse of the minimum terminal interference distance (It(min)) in crossing-over (n(max)=100/It(min)). AsIt(min) =0.6 in mammals, n(max) approximately 166. On the other hand, the value estimated by computer simulations is somewhat lower with n(max)=133-138. Our arguments can be applied to other eukaryotes, if they have a localized centromere and the ratio of total synaptonemal complex/nuclear volume is comparable to that of mammals. We revealed that the index of gene shuffling per karyotypes (G) by means of the total number of gamete types with different gene combinations can be formulated asG =2(n+Fxi), where Fxi means interstitial chiasma frequency per cell corresponding to crossing-over mediated by the recombination nodule. The Fxi value increases in proportion to the n value in areas where n<40, but decreases gradually when n>40 and becomes zero when n>83. Therefore, in the ultimate karyotype with n(max)=166, FXi=0 andG =2(n)=2(166), where gene shuffling is guaranteed by the random orientation of chromosomes at the equatorial plate of meiotic metaphase I.}, } @article {pmid12154373, year = {2002}, author = {Shuman, S}, title = {What messenger RNA capping tells us about eukaryotic evolution.}, journal = {Nature reviews. Molecular cell biology}, volume = {3}, number = {8}, pages = {619-625}, doi = {10.1038/nrm880}, pmid = {12154373}, issn = {1471-0072}, mesh = {Acid Anhydride Hydrolases/chemistry/metabolism ; Amino Acid Sequence ; Animals ; *Biological Evolution ; DNA Viruses/enzymology ; Eukaryotic Cells/*physiology ; Fungal Proteins/metabolism ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Plant Proteins/metabolism ; Protein Structure, Tertiary ; RNA Caps/*metabolism ; *RNA Processing, Post-Transcriptional ; Sequence Alignment ; }, abstract = {The 5' cap is a unique feature of eukaryotic cellular and viral messenger RNA that is absent from the bacterial and archaeal domains of life. The cap is formed by three enzymatic reactions at the 5' terminus of nascent mRNAs. Although the capping pathway is conserved in all eukaryotes, the structure and genetic organization of the component enzymes vary between species. These differences provide insights into the evolution of eukaryotes and eukaryotic viruses.}, } @article {pmid12097341, year = {2002}, author = {Lespinet, O and Wolf, YI and Koonin, EV and Aravind, L}, title = {The role of lineage-specific gene family expansion in the evolution of eukaryotes.}, journal = {Genome research}, volume = {12}, number = {7}, pages = {1048-1059}, pmid = {12097341}, issn = {1088-9051}, mesh = {Animals ; Arabidopsis/genetics ; Caenorhabditis elegans/genetics ; Cell Lineage/genetics/physiology ; Computational Biology ; Drosophila melanogaster/genetics ; Eukaryotic Cells/chemistry/metabolism/*physiology ; *Evolution, Molecular ; *Gene Duplication ; Genes, Helminth/genetics/physiology ; Genes, Insect/genetics/physiology ; Genome, Fungal ; Genome, Plant ; Multigene Family/*genetics/physiology ; Phylogeny ; Saccharomyces cerevisiae/genetics ; Schizosaccharomyces/genetics ; Species Specificity ; }, abstract = {A computational procedure was developed for systematic detection of lineage-specific expansions (LSEs) of protein families in sequenced genomes and applied to obtain a census of LSEs in five eukaryotic species, the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and the green plant Arabidopsis thaliana. A significant fraction of the proteins encoded in each of these genomes, up to 80% in A. thaliana, belong to LSEs. Many paralogous gene families in each of the analyzed species are almost entirely comprised of LSEs, indicating that their diversification occurred after the divergence of the major lineages of the eukaryotic crown group. The LSEs show readily discernible patterns of protein functions. The functional categories most prone to LSE are structural proteins, enzymes involved in an organism's response to pathogens and environmental stress, and various components of signaling pathways responsible for specificity, including ubiquitin ligase E3 subunits and transcription factors. The functions of several previously uncharacterized, vastly expanded protein families were predicted through in-depth protein sequence analysis, for example, small-molecule kinases and methylases that are expanded independently in the fly and in the nematode. The functions of several other major LSEs remain mysterious; these protein families are attractive targets for experimental discovery of novel, lineage-specific functions in eukaryotes. LSEs seem to be one of the principal means of adaptation and one of the most important sources of organizational and regulatory diversity in crown-group eukaryotes.}, } @article {pmid12034489, year = {2002}, author = {Zhang, X and Yang, H and Yu, J and Chen, C and Zhang, G and Bao, J and Du, Y and Kibukawa, M and Li, Z and Wang, J and Hu, S and Dong, W and Wang, J and Gregersen, N and Niebuhr, E and Bolund, L}, title = {Genomic organization, transcript variants and comparative analysis of the human nucleoporin 155 (NUP155) gene.}, journal = {Gene}, volume = {288}, number = {1-2}, pages = {9-18}, doi = {10.1016/s0378-1119(02)00470-5}, pmid = {12034489}, issn = {0378-1119}, mesh = {3T3 Cells ; *Alternative Splicing ; Amino Acid Sequence ; Animals ; DNA/chemistry/genetics ; DNA, Complementary/chemistry/genetics ; Gene Expression ; Gene Library ; Genes/genetics ; Humans ; Mice ; Molecular Sequence Data ; Nuclear Pore Complex Proteins/*genetics ; Rats ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Takifugu/genetics ; Transcription, Genetic ; Tumor Cells, Cultured ; }, abstract = {Nucleoporin 155 (Nup155) is a major component of the nuclear pore complex (NPC) involved in cellular nucleo-cytoplasmic transport. We have acquired the complete sequence and interpreted the genomic organization of the Nup155 orthologos from human (Homo sapiens) and pufferfish (Fugu rubripes), which are approximately 80 and 8 kb in length, respectively. The human gene is ubiquitously expressed in many tissues analyzed and has two major transcript variants, resulted from an alternative usage of the 5' cryptic or consensus splice donor in intron 1 and two polyadenylation signals. We have also cloned DNA complementary to RNAs of the Nup155 orthologs from Fugu and mouse. Comparative analysis of the Nup155 orthologs in many species, including H. sapiens, Mus musculus, Rattus norvegicus, F. rubripes, Arabidopsis thaliana, Drosophila melanogaster, and Saccharomyces cerevisiae, has revealed two paralogs in S. cerevisiae but only a single gene with increasing number of introns in more complex organisms. The amino acid sequences of the Nup155 orthologos are highly conserved in the evolution of eukaryotes. Different gene orders in the human and Fugu genomic regions harboring the Nup155 orthologs advocate cautious interpretation of synteny in comparative genomic analysis even within the vertebrate lineage.}, } @article {pmid11950614, year = {2002}, author = {Zerges, W}, title = {Does complexity constrain organelle evolution?.}, journal = {Trends in plant science}, volume = {7}, number = {4}, pages = {175-182}, doi = {10.1016/s1360-1385(02)02233-1}, pmid = {11950614}, issn = {1360-1385}, mesh = {*Biological Evolution ; Chloroplasts/genetics/physiology ; Light ; Mitochondria/genetics/physiology ; Organelles/genetics/*physiology ; Oxidation-Reduction ; Photosynthesis/genetics/*physiology ; Photosynthetic Reaction Center Complex Proteins/genetics/*metabolism ; *Selection, Genetic ; }, abstract = {The evolution of eukaryotes was punctuated by invasions of the bacteria that have evolved to mitochondria and plastids. These bacterial endosymbionts founded major eukaryotic lineages by enabling them to carry out aerobic respiration and oxygenic photosynthesis. Yet, having evolved as free-living organisms, they were at first poorly adapted organelles. Although mitochondria and plastids have integrated within the physiology of eukaryotic cells, this integration has probably been constrained by the high level of complexity of their bacterial ancestors and the inability of gradual evolutionary processes to drastically alter complex systems. Here, I review complex processes that directly involve translation of plastid mRNAs and how they could constrain transfer to the nucleus of the genes encoding them.}, } @article {pmid11931142, year = {2002}, author = {Cavalier-Smith, T}, title = {The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {52}, number = {Pt 2}, pages = {297-354}, doi = {10.1099/00207713-52-2-297}, pmid = {11931142}, issn = {1466-5026}, mesh = {Animals ; *Biological Evolution ; Eukaryota/*classification/physiology ; Eukaryotic Cells/classification/physiology ; Phagocytosis ; Phylogeny ; }, abstract = {Eukaryotes and archaebacteria form the clade neomura and are sisters, as shown decisively by genes fragmented only in archaebacteria and by many sequence trees. This sisterhood refutes all theories that eukaryotes originated by merging an archaebacterium and an alpha-proteobacterium, which also fail to account for numerous features shared specifically by eukaryotes and actinobacteria. I revise the phagotrophy theory of eukaryote origins by arguing that the essentially autogenous origins of most eukaryotic cell properties (phagotrophy, endomembrane system including peroxisomes, cytoskeleton, nucleus, mitosis and sex) partially overlapped and were synergistic with the symbiogenetic origin of mitochondria from an alpha-proteobacterium. These radical innovations occurred in a derivative of the neomuran common ancestor, which itself had evolved immediately prior to the divergence of eukaryotes and archaebacteria by drastic alterations to its eubacterial ancestor, an actinobacterial posibacterium able to make sterols, by replacing murein peptidoglycan by N-linked glycoproteins and a multitude of other shared neomuran novelties. The conversion of the rigid neomuran wall into a flexible surface coat and the associated origin of phagotrophy were instrumental in the evolution of the endomembrane system, cytoskeleton, nuclear organization and division and sexual life-cycles. Cilia evolved not by symbiogenesis but by autogenous specialization of the cytoskeleton. I argue that the ancestral eukaryote was uniciliate with a single centriole (unikont) and a simple centrosomal cone of microtubules, as in the aerobic amoebozoan zooflagellate Phalansterium. I infer the root of the eukaryote tree at the divergence between opisthokonts (animals, Choanozoa, fungi) with a single posterior cilium and all other eukaryotes, designated 'anterokonts' because of the ancestral presence of an anterior cilium. Anterokonts comprise the Amoebozoa, which may be ancestrally unikont, and a vast ancestrally biciliate clade, named 'bikonts'. The apparently conflicting rRNA and protein trees can be reconciled with each other and this ultrastructural interpretation if long-branch distortions, some mechanistically explicable, are allowed for. Bikonts comprise two groups: corticoflagellates, with a younger anterior cilium, no centrosomal cone and ancestrally a semi-rigid cell cortex with a microtubular band on either side of the posterior mature centriole; and Rhizaria [a new infrakingdom comprising Cercozoa (now including Ascetosporea classis nov.), Retaria phylum nov., Heliozoa and Apusozoa phylum nov.], having a centrosomal cone or radiating microtubules and two microtubular roots and a soft surface, frequently with reticulopodia. Corticoflagellates comprise photokaryotes (Plantae and chromalveolates, both ancestrally with cortical alveoli) and Excavata (a new protozoan infrakingdom comprising Loukozoa, Discicristata and Archezoa, ancestrally with three microtubular roots). All basal eukaryotic radiations were of mitochondrial aerobes; hydrogenosomes evolved polyphyletically from mitochondria long afterwards, the persistence of their double envelope long after their genomes disappeared being a striking instance of membrane heredity. I discuss the relationship between the 13 protozoan phyla recognized here and revise higher protozoan classification by updating as subkingdoms Lankester's 1878 division of Protozoa into Corticata (Excavata, Alveolata; with prominent cortical microtubules and ancestrally localized cytostome--the Parabasalia probably secondarily internalized the cytoskeleton) and Gymnomyxa [infrakingdoms Sarcomastigota (Choanozoa, Amoebozoa) and Rhizaria; both ancestrally with a non-cortical cytoskeleton of radiating singlet microtubules and a relatively soft cell surface with diffused feeding]. As the eukaryote root almost certainly lies within Gymnomyxa, probably among the Sarcomastigota, Corticata are derived. Following the single symbiogenetic origin of chloroplasts in a corticoflagellate host with cortical alveoli, this ancestral plant radiated rapidly into glaucophytes, green plants and red algae. Secondary symbiogeneses subsequently transferred plastids laterally into different hosts, making yet more complex cell chimaeras--probably only thrice: from a red alga to the corticoflagellate ancestor of chromalveolates (Chromista plus Alveolata), from green algae to a secondarily uniciliate cercozoan to form chlorarachneans and independently to a biciliate excavate to yield photosynthetic euglenoids. Tertiary symbiogenesis involving eukaryotic algal symbionts replaced peridinin-containing plastids in two or three dinoflagellate lineages, but yielded no major novel groups. The origin and well-resolved primary bifurcation of eukaryotes probably occurred in the Cryogenian Period, about 850 million years ago, much more recently than suggested by unwarranted backward extrapolations of molecular 'clocks' or dubious interpretations as 'eukaryotic' of earlier large microbial fossils or still more ancient steranes. The origin of chloroplasts and the symbiogenetic incorporation of a red alga into a corticoflagellate to create chromalveolates may both have occurred in a big bang after the Varangerian snowball Earth melted about 580 million years ago, thereby stimulating the ensuing Cambrian explosion of animals and protists in the form of simultaneous, poorly resolved opisthokont and anterokont radiations.}, } @article {pmid11580860, year = {2001}, author = {Hedges, SB and Chen, H and Kumar, S and Wang, DY and Thompson, AS and Watanabe, H}, title = {A genomic timescale for the origin of eukaryotes.}, journal = {BMC evolutionary biology}, volume = {1}, number = {}, pages = {4}, pmid = {11580860}, issn = {1471-2148}, mesh = {Animals ; Archaea/genetics ; Eubacterium/genetics ; *Eukaryotic Cells ; *Evolution, Molecular ; Genetic Variation/genetics ; *Genome ; Genome, Archaeal ; Genome, Bacterial ; Genome, Protozoan ; Giardia/genetics ; Models, Genetic ; Phylogeny ; }, abstract = {BACKGROUND: Genomic sequence analyses have shown that horizontal gene transfer occurred during the origin of eukaryotes as a consequence of symbiosis. However, details of the timing and number of symbiotic events are unclear. A timescale for the early evolution of eukaryotes would help to better understand the relationship between these biological events and changes in Earth's environment, such as the rise in oxygen. We used refined methods of sequence alignment, site selection, and time estimation to address these questions with protein sequences from complete genomes of prokaryotes and eukaryotes.

RESULTS: Eukaryotes were found to evolve faster than prokaryotes, with those eukaryotes derived from eubacteria evolving faster than those derived from archaebacteria. We found an early time of divergence (approximately 4 billion years ago, Ga) for archaebacteria and the archaebacterial genes in eukaryotes. Our analyses support at least two horizontal gene transfer events in the origin of eukaryotes, at 2.7 Ga and 1.8 Ga. Time estimates for the origin of cyanobacteria (2.6 Ga) and the divergence of an early-branching eukaryote that lacks mitochondria (Giardia) (2.2 Ga) fall between those two events.

CONCLUSIONS: We find support for two symbiotic events in the origin of eukaryotes: one premitochondrial and a later mitochondrial event. The appearance of cyanobacteria immediately prior to the earliest undisputed evidence for the presence of oxygen (2.4-2.2 Ga) suggests that the innovation of oxygenic photosynthesis had a relatively rapid impact on the environment as it set the stage for further evolution of the eukaryotic cell.}, } @article {pmid11568444, year = {2001}, author = {Gladyshev, VN and Kryukov, GV}, title = {Evolution of selenocysteine-containing proteins: significance of identification and functional characterization of selenoproteins.}, journal = {BioFactors (Oxford, England)}, volume = {14}, number = {1-4}, pages = {87-92}, doi = {10.1002/biof.5520140112}, pmid = {11568444}, issn = {0951-6433}, support = {GM61603/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Archaea/enzymology ; Bacteria/enzymology ; *Biological Evolution ; Mammals ; Protein Biosynthesis ; Proteins/chemistry/*genetics ; Selenium/metabolism ; Selenocysteine/*metabolism ; Selenoproteins ; Vertebrates ; }, abstract = {In the genetic code, UGA serves as either a signal for termination or a codon for selenocysteine (Sec). Sec rarely occurs in protein and is different from other amino acids in that much of the biosynthetic machinery governing its incorporation into protein is unique to this amino acid. Sec-containing proteins have diverse functions and lack a common amino acid motif or consensus sequence. Sec has previously been considered to be a relic of the primordial genetic code that was counter-selected by the presence of oxygen in the atmosphere. In the present report, it is proposed that Sec was added to the already existing genetic code and its use has accumulated during evolution of eukaryotes culminating in vertebrates. The more recently evolved selenoproteins appear to take advantage of unique redox properties of Sec that are superior to those of Cys for specific biological functions. Further understanding of the evolution of selenoproteins as well as biological properties and biomedical applications of the trace element selenium requires identification and functional characterization of all mammalian selenoproteins.}, } @article {pmid11528391, year = {2001}, author = {Podani, J and Oltvai, ZN and Jeong, H and Tombor, B and Barabási, AL and Szathmáry, E}, title = {Comparable system-level organization of Archaea and Eukaryotes.}, journal = {Nature genetics}, volume = {29}, number = {1}, pages = {54-56}, doi = {10.1038/ng708}, pmid = {11528391}, issn = {1061-4036}, mesh = {Archaea/*genetics/metabolism ; *Biological Evolution ; *Eukaryotic Cells/metabolism ; }, abstract = {A central and long-standing issue in evolutionary theory is the origin of the biological variation upon which natural selection acts. Some hypotheses suggest that evolutionary change represents an adaptation to the surrounding environment within the constraints of an organism's innate characteristics. Elucidation of the origin and evolutionary relationship of species has been complemented by nucleotide sequence and gene content analyses, with profound implications for recognizing life's major domains. Understanding of evolutionary relationships may be further expanded by comparing systemic higher-level organization among species. Here we employ multivariate analyses to evaluate the biochemical reaction pathways characterizing 43 species. Comparison of the information transfer pathways of Archaea and Eukaryotes indicates a close relationship between these domains. In addition, whereas eukaryotic metabolic enzymes are primarily of bacterial origin, the pathway-level organization of archaeal and eukaryotic metabolic networks is more closely related. Our analyses therefore suggest that during the symbiotic evolution of eukaryotes, incorporation of bacterial metabolic enzymes into the proto-archaeal proteome was constrained by the host's pre-existing metabolic architecture.}, } @article {pmid11523012, year = {2001}, author = {Bell, PJ}, title = {Viral eukaryogenesis: was the ancestor of the nucleus a complex DNA virus?.}, journal = {Journal of molecular evolution}, volume = {53}, number = {3}, pages = {251-256}, doi = {10.1007/s002390010215}, pmid = {11523012}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Cell Nucleus/enzymology/genetics/*physiology ; DNA Ligases/chemistry ; DNA Viruses/enzymology/genetics/*physiology ; Eukaryotic Cells/*cytology/enzymology ; Membrane Fusion ; *Models, Biological ; Molecular Sequence Data ; Nucleotidyltransferases/chemistry ; Phagocytosis ; *Phylogeny ; Prokaryotic Cells/cytology/*virology ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {In the theory of viral eukaryogenesis I propose here, the eukaryotic nucleus evolved from a complex DNA virus. It is proposed that the virus established a persistent presence in the cytoplasm of a methanogenic mycoplasma and evolved into the eukaryotic nucleus by acquiring a set of essential genes from the host genome and eventually usurping its role. It is proposed that several characteristic features of the eukaryotic nucleus derive from its viral ancestry. These include mRNA capping, linear chromosomes, and separation of transcription from translation. In the model, phagocytosis and other membrane fusion-based processes are derived from viral membrane fusion processes and evolved in concert with the nucleus. The coevolution of phagocytosis and the nucleus rendered much of the host archaeal genome redundant since the protoeukaryote could obtain raw materials and energy by engulfing bacterial syntrophs/prey. This redundancy allowed loss of the archaeal chromosome, generating an organism with eukaryotic features. The evolution of phagocytosis allowed the eukaryotes to be the first organisms to occupy the niche of predator.}, } @article {pmid11485800, year = {2001}, author = {Wolf, YI and Koonin, EV}, title = {Origin of an animal mitochondrial DNA polymerase subunit via lineage-specific acquisition of a glycyl-tRNA synthetase from bacteria of the Thermus-Deinococcus group.}, journal = {Trends in genetics : TIG}, volume = {17}, number = {8}, pages = {431-433}, doi = {10.1016/s0168-9525(01)02370-8}, pmid = {11485800}, issn = {0168-9525}, mesh = {Animals ; DNA-Directed DNA Polymerase/*chemistry/*genetics ; Drosophila melanogaster ; Evolution, Molecular ; Glycine-tRNA Ligase/*genetics ; Mitochondria/*enzymology ; Models, Genetic ; Phylogeny ; Protein Structure, Tertiary ; Xenopus laevis ; }, abstract = {Phylogenetic tree analysis shows that the accessory subunit animal mitochondrial DNA polymerase emerges as a result of horizontal transfer of the gene encoding glycyl-tRNA synthetase from a bacterium of the Thermus-Deinococcus group into the animal nuclear genome. This acquisition by a distinct eukaryotic lineage of a gene encoding a mitochondrial protein from a nonmitochondrial bacterial source underscores the contribution of different types of horizontal transfer event to the evolution of eukaryotes.}, } @article {pmid11357388, year = {2001}, author = {Kuznetsov, AP and Lebkova, NP}, title = {[Significance of the energy of symbiotic bacteria in metabolism of hydrothermal and other chemotrophic biota of the ocean].}, journal = {Izvestiia Akademii nauk. Seriia biologicheskaia}, volume = {}, number = {2}, pages = {220-226}, pmid = {11357388}, issn = {1026-3470}, mesh = {Aerobiosis ; Animals ; Bacteria/*metabolism ; Biological Evolution ; Ecosystem ; *Energy Metabolism ; Microscopy, Electron ; Mitochondria/*metabolism ; Mollusca/*metabolism/microbiology/ultrastructure ; Oceans and Seas ; Symbiosis ; }, abstract = {The bacterial origin of eukaryotic mitochondria, specifically in Metazoa, as a mechanism of their basic (aerobic) respiration and the role of symbiotic bacteria during the supply of energy to the metazoan host is proved for the first time from the viewpoint of the monophyletic development of the organic world and the origin of eukaryotes as descendants of prokaryotes Representatives of the hydrothermal bacteriochemosymbiotrophic bottom fauna of the open sea were used as examples.}, } @article {pmid11329010, year = {2001}, author = {Kolkman, JA and Stemmer, WP}, title = {Directed evolution of proteins by exon shuffling.}, journal = {Nature biotechnology}, volume = {19}, number = {5}, pages = {423-428}, doi = {10.1038/88084}, pmid = {11329010}, issn = {1087-0156}, mesh = {*Directed Molecular Evolution ; Eukaryotic Cells ; *Exons ; Gene Rearrangement ; Genome, Human ; Genomic Library ; Humans ; Introns ; Protein Structure, Tertiary/*genetics ; }, abstract = {Evolution of eukaryotes is mediated by sexual recombination of parental genomes. Crossovers occur in random, but homologous, positions at a frequency that depends on DNA length. As exons occupy only 1% of the human genome and introns about 24%, by far most of the crossovers occur between exons, rather than inside. The natural process of creating new combinations of exons by intronic recombination is called exon shuffling. Our group is developing in vitro formats for exon shuffling and applying these to the directed evolution of proteins. Based on the splice frame junctions, nine classes of exons and three classes of introns can be distinguished. Splice frame diagrams of natural genes show how the splice frame rules govern exon shuffling. Here, we review various approaches to constructing libraries of exon-shuffled genes. For example, exon shuffling of human pharmaceutical proteins can generate libraries in which all of the sequences are fully human, without the point mutations that raise concerns about immunogenicity.}, } @article {pmid11305786, year = {2001}, author = {Ma, J and Hwang, KK and Worman, HJ and Courvalin, JC and Eissenberg, JC}, title = {Expression and functional analysis of three isoforms of human heterochromatin-associated protein HP1 in Drosophila.}, journal = {Chromosoma}, volume = {109}, number = {8}, pages = {536-544}, doi = {10.1007/s004120000113}, pmid = {11305786}, issn = {0009-5915}, support = {CA66974/CA/NCI NIH HHS/United States ; GM57005/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Chromobox Protein Homolog 5 ; Chromosomal Proteins, Non-Histone/chemistry/genetics/*physiology ; Chromosome Mapping ; Drosophila/*genetics ; Gene Silencing/physiology ; Humans ; Molecular Sequence Data ; Protein Isoforms/chemistry/genetics/*physiology ; Sequence Homology, Amino Acid ; Transformation, Genetic ; }, abstract = {Heterochromatin-associated protein 1 (HP1) is a nonhistone chromosomal protein associated with pericentromeric heterochromatin in Drosophila. HP1-like proteins have also been found associated with heterochromatin in human cells. The goal of this study was to determine whether proteins of the structurally conserved human HP1 family exhibit conserved heterochromatin targeting and silencing properties in Drosophila. We established transgenic lines of Drosophila melanogaster expressing each of the three human HP1 proteins, HP1Hsalpha, HP1HSbeta, and HP1Hsgamma, under the Hsp70 heat shock promoter. We show that all three isoforms of human HP1 are stably expressed in Drosophila and are associated with heterochromatin in Drosophila chromosomes. Like Drosophila HP1, all three human HP1 proteins are delocalized by an HP1-POLYCOMB chimeric protein, implying that both human HP1 and Drosophila HP1 interact in a common protein complex, and that at least some aspects of heterochromatin structure are highly conserved throughout the evolution of eukaryotes. Ectopic expression of two of the three human HP1 family proteins significantly enhances heterochromatic silencing in Drosophila.}, } @article {pmid11249186, year = {2001}, author = {Cheney, SA and Lafranchi-Tristem, NJ and Bourges, D and Canning, EU}, title = {Relationships of microsporidian genera, with emphasis on the polysporous genera, revealed by sequences of the largest subunit of RNA polymerase II (RPB1).}, journal = {The Journal of eukaryotic microbiology}, volume = {48}, number = {1}, pages = {111-117}, doi = {10.1111/j.1550-7408.2001.tb00422.x}, pmid = {11249186}, issn = {1066-5234}, mesh = {Animals ; DNA, Protozoan/*analysis ; Fishes/parasitology ; Humans ; Insecta/parasitology ; Microsporidia/*classification/*enzymology/genetics ; Microsporidiosis/parasitology ; Molecular Sequence Data ; Phylogeny ; RNA Polymerase II/*genetics ; *Sequence Analysis, DNA ; }, abstract = {Molecular data have proved useful as an alternative to morphological data in showing the relationships of genera within the phylum Microsporidia, but until now have been available only for ribosomal genes. In previous studies protein-coding genes of microsporidia have been used only to assess their position in the evolution of eukaryotes. For the first time we report on the use of a protein-coding gene, the A-G region of the largest subunit of RNA polymerase II (RPB1) from 14 mainly polysporous species, to generate an alternative phylogeny for microsporidia. Using the amino acid sequences, the genera and species fell into the same main groupings as had been obtained with 16S rDNA sequences, but the RPB1 data provided better resolution within these groups. The results supported the pairings of Trachipleistophora hominis with Vavraia culicis and Pleistophora hippoglossoideos with Pleistophora typicalis. They also confirmed that the genus Pleistophora is not monophyletic and that it will be necessary to transfer Pleistophora ovariae and Pleistophora mirandellae into one or more other genera, as has already been effected for Pleistophora anguillarum.}, } @article {pmid11183772, year = {2000}, author = {Phillips, K and Luisi, B}, title = {The virtuoso of versatility: POU proteins that flex to fit.}, journal = {Journal of molecular biology}, volume = {302}, number = {5}, pages = {1023-1039}, doi = {10.1006/jmbi.2000.4107}, pmid = {11183772}, issn = {0022-2836}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Central Nervous System/embryology/growth & development ; Crystallography, X-Ray ; DNA/genetics/*metabolism ; DNA-Binding Proteins/*chemistry/*metabolism ; Dimerization ; Gene Expression Regulation ; Host Cell Factor C1 ; Humans ; Octamer Transcription Factor-1 ; Octamer Transcription Factor-2 ; Pituitary Gland/growth & development/physiology ; Pliability ; Promoter Regions, Genetic/genetics ; Protein Structure, Tertiary ; Substrate Specificity ; Trans-Activators/chemistry/metabolism ; Transcription Factor Pit-1 ; Transcription Factors/*chemistry/*metabolism ; }, abstract = {During the evolution of eukaryotes, a new structural motif arose by the fusion of genes encoding two different types of DNA-binding domain. The family of transcription factors which contain this domain, the POU proteins, have come to play essential roles not only in the development of highly specialised tissues, such as complex neuronal systems, but also in more general cellular housekeeping. Members of the POU family recognise defined DNA sequences, and a well-studied subset have specificity for a motif known as the octamer element which is found in the promoter region of a variety of genes. The structurally bipartite POU domain has intrinsic conformational flexibility and this feature appears to confer functional diversity to this class of transcription factors. The POU domain for which we have the most structural data is from Oct-1, which binds an eight base-pair target and variants of this octamer site. The two-part DNA-binding domain partially encircles the DNA, with the sub-domains able to assume a variety of conformations, dependent on the DNA element. Crystallographic and biochemical studies have shown that the binary complex provides distinct platforms for the recruitment of specific regulators to control transcription. The conformability of the POU domain in moulding to DNA elements and co-regulators provides a mechanism for combinatorial assembly as well as allosteric molecular recognition. We review here the structure and function of the diverse POU proteins and discuss the role of the proteins' plasticity in recognition and transcriptional regulation.}, } @article {pmid11070057, year = {2000}, author = {Horner, DS and Foster, PG and Embley, TM}, title = {Iron hydrogenases and the evolution of anaerobic eukaryotes.}, journal = {Molecular biology and evolution}, volume = {17}, number = {11}, pages = {1695-1709}, doi = {10.1093/oxfordjournals.molbev.a026268}, pmid = {11070057}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Anaerobiosis ; Animals ; Cytosol/enzymology ; DNA, Complementary/chemistry/genetics ; DNA, Protozoan/chemistry/genetics ; Diplomonadida/enzymology/genetics ; Entamoeba histolytica/enzymology/genetics ; Eukaryota/enzymology/*genetics ; Eukaryotic Cells/enzymology ; *Evolution, Molecular ; Hydrogenase/*genetics ; Iron-Sulfur Proteins/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Trichomonas vaginalis/enzymology/genetics ; }, abstract = {Hydrogenases, oxygen-sensitive enzymes that can make hydrogen gas, are key to the function of hydrogen-producing organelles (hydrogenosomes), which occur in anaerobic protozoa scattered throughout the eukaryotic tree. Hydrogenases also play a central role in the hydrogen and syntrophic hypotheses for eukaryogenesis. Here, we show that sequences related to iron-only hydrogenases ([Fe] hydrogenases) are more widely distributed among eukaryotes than reports of hydrogen production have suggested. Genes encoding small proteins which contain conserved structural features unique to [Fe] hydrogenases were identified on all well-surveyed aerobic eukaryote genomes. Longer sequences encoding [Fe] hydrogenases also occur in the anaerobic eukaryotes Entamoeba histolytica and Spironucleus barkhanus, both of which lack hydrogenosomes. We also identified a new [Fe] hydrogenase sequence from Trichomonas vaginalis, bringing the total of [Fe] hydrogenases reported for this organism to three, all of which may function within its hydrogenosomes. Phylogenetic analysis and hypothesis testing using likelihood ratio tests and parametric bootstrapping suggest that the [Fe] hydrogenases in anaerobic eukaryotes are not monophyletic. Iron-only hydrogenases from Entamoeba, Spironucleus, and Trichomonas are plausibly monophyletic, consistent with the hypothesis that a gene for [Fe] hydrogenase was already present on the genome of the common, perhaps also anaerobic, ancestor of these phylogenetically distinct eukaryotes. Trees where the [Fe] hydrogenase from the hydrogenosomal ciliate Nyctotherus was constrained to be monophyletic with the other eukaryote sequences were rejected using a likelihood ratio test of monophyly. In most analyses, the Nyctotherus sequence formed a sister group with a [Fe] hydrogenase on the genome of the eubacterium Desulfovibrio vulgaris. Thus, it is possible that Nyctotherus obtained its hydrogenosomal [Fe] hydrogenase from a different source from Trichomonas for its hydrogenosomes. We find no support for the hypothesis that components of the Nyctotherus [Fe] hydrogenase fusion protein derive from the mitochondrial respiratory chain.}, } @article {pmid10808550, year = {2000}, author = {Kostianovsky, M}, title = {Evolutionary origin of eukaryotic cells.}, journal = {Ultrastructural pathology}, volume = {24}, number = {2}, pages = {59-66}, doi = {10.1080/01913120050118521}, pmid = {10808550}, issn = {0191-3123}, mesh = {Archaea/cytology/metabolism ; *Biological Evolution ; Eukaryotic Cells/*cytology/*metabolism ; Evolution, Molecular ; Gene Transfer Techniques ; Humans ; *Phylogeny ; Prokaryotic Cells/cytology/metabolism ; }, abstract = {This article reviews literature on the transition from rudimentary prokaryotic life to eukaryotes. An overview of the differences between these organisms and theories of eukaryogenesis are reviewed. Various methods of investigating the transformation from prokaryotes to eukaryotes are elaborated, including the fossil, the molecular and living records, and examples are given. Lastly, the recent molecular studies and the impact on phylogenetic classification for the tree of life, based on molecular evolution, are discussed.}, } @article {pmid10791428, year = {2000}, author = {Kuroiwa, T}, title = {The discovery of the division apparatus of plastids and mitochondria.}, journal = {Journal of electron microscopy}, volume = {49}, number = {1}, pages = {123-134}, doi = {10.1093/oxfordjournals.jmicro.a023776}, pmid = {10791428}, issn = {0022-0744}, mesh = {Animals ; Bacterial Proteins/chemistry/genetics/physiology ; Cell Division ; Chloroplasts/physiology/*ultrastructure ; *Cytoskeletal Proteins ; Evolution, Molecular ; Microscopy, Electron ; Mitochondria/physiology/*ultrastructure ; Plastids/physiology/*ultrastructure ; Rhodophyta/physiology/*ultrastructure ; }, abstract = {Mitochondria and plastids contain distinct genomes and multiply by binary division of existing organelles. Mitochondrial and plastid division can be clearly separated into two main events: division of the organelle nuclei (nucleoids), and subsequent division of the rest of the organelles, the process of organellokinesis. Organellokinesis makes use of organelle dividing apparatuses such as plastid-dividing ring (PD ring) and mitochondrion-dividing ring (MD ring). The plastid-dividing apparatus (PD apparatus) is composed of three electron-dense rings (the outer, middle and inner), while the mitochondrion-dividing apparatus (MD apparatus) is a pair of electron-dense rings in cytoplasm and inner ring in the mitochondrial matrix. The behaviour of both the PD and MD apparatuses throughout organelle division in Cyanidioschyzon merolae has been studied in detail by electron microscopy. When cells enter mitosis, the inner PD ring forms first, followed by the outer and middle rings and finally the MD rings. The PD rings begin to contract before the MD rings. However, the MD rings start to contract at about 4 times the speed of the PD rings and catch up to the PD rings. The cross-sectional areas of both the outer PD and MD rings increase as contraction in the plane of division progress. This suggests that the outer rings of organelle dividing apparatuses (OD apparatus) provide the motive force for contraction. FtsZ protein is located on the bacterial contractile ring at the equator of dividing bacteria, and controls bacterial division. Since FtsZ contains a tubulin motif, and host eukaryotic organisms and chloroplasts evolved from bacteria, there is debate whether that tubulins found in the cytoskeleton and the inner or outer PD ring evolved from FtsZ protein during eukaryogenesis.}, } @article {pmid10690412, year = {1999}, author = {Lang, BF and Gray, MW and Burger, G}, title = {Mitochondrial genome evolution and the origin of eukaryotes.}, journal = {Annual review of genetics}, volume = {33}, number = {}, pages = {351-397}, doi = {10.1146/annurev.genet.33.1.351}, pmid = {10690412}, issn = {0066-4197}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Eukaryotic Cells ; *Evolution, Molecular ; Fungi/genetics ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {Recent results from ancestral (minimally derived) protists testify to the tremendous diversity of the mitochondrial genome in various eukaryotic lineages, but also reinforce the view that mitochondria, descendants of an endosymbiotic alpha-Proteobacterium, arose only once in evolution. The serial endosymbiosis theory, currently the most popular hypothesis to explain the origin of mitochondria, postulates the capture of an alpha-proteobacterial endosymbiont by a nucleus-containing eukaryotic host resembling extant amitochondriate protists. New sequence data have challenged this scenario, instead raising the possibility that the origin of the mitochondrion was coincident with, and contributed substantially to, the origin of the nuclear genome of the eukaryotic cell. Defining more precisely the alpha-proteobacterial ancestry of the mitochondrial genome, and the contribution of the endosymbiotic event to the nuclear genome, will be essential for a full understanding of the origin and evolution of the eukaryotic cell as a whole.}, } @article {pmid10638755, year = {2000}, author = {Bernhard, JM and Buck, KR and Farmer, MA and Bowser, SS}, title = {The Santa Barbara Basin is a symbiosis oasis.}, journal = {Nature}, volume = {403}, number = {6765}, pages = {77-80}, doi = {10.1038/47476}, pmid = {10638755}, issn = {0028-0836}, mesh = {Animals ; Bacteria/ultrastructure ; *Bacterial Physiological Phenomena ; California ; Eukaryota/*microbiology/ultrastructure ; Eukaryotic Cells/microbiology/ultrastructure ; Geologic Sediments ; Invertebrates/microbiology ; *Symbiosis ; Thiotrichaceae/physiology/ultrastructure ; }, abstract = {It is generally agreed that the origin and initial diversification of Eucarya occurred in the late Archaean or Proterozoic Eons when atmospheric oxygen levels were low and the risk of DNA damage due to ultraviolet radiation was high. Because deep water provides refuge against ultraviolet radiation and early eukaryotes may have been aerotolerant anaerobes, deep-water dysoxic environments are likely settings for primeval eukaryotic diversification. Fossil evidence shows that deep-sea microbial mats, possibly of sulphur bacteria similar to Beggiatoa, existed during that time. Here we report on the eukaryotic community of a modern analogue, the Santa Barbara Basin (California, USA). The Beggiatoa mats of these severely dysoxic and sulphidic sediments support a surprisingly abundant protistan and metazoan meiofaunal community, most members of which harbour prokaryotic symbionts. Many of these taxa are new to science, and both microaerophilic and anaerobic taxa appear to be represented. Compared with nearby aerated sites, the Santa Barbara Basin is a 'symbiosis oasis' offering a new source of organisms for testing symbiosis hypotheses of eukaryogenesis.}, } @article {pmid10577396, year = {1999}, author = {Tsurimoto, T}, title = {PCNA binding proteins.}, journal = {Frontiers in bioscience : a journal and virtual library}, volume = {4}, number = {}, pages = {D849-58}, doi = {10.2741/tsurimoto}, pmid = {10577396}, issn = {1093-9946}, mesh = {Animals ; Base Pair Mismatch ; Cell Cycle ; Chromatin/genetics/physiology ; Cyclin-Dependent Kinase Inhibitor p21 ; Cyclin-Dependent Kinases/metabolism ; Cyclins/metabolism ; DNA/chemistry/*metabolism ; DNA Repair/physiology ; DNA-Binding Proteins/metabolism/physiology ; DNA-Directed DNA Polymerase/metabolism ; *Homeodomain Proteins ; Humans ; Minor Histocompatibility Antigens ; Proliferating Cell Nuclear Antigen/chemistry/*metabolism/*physiology ; Protein Binding ; *Proto-Oncogene Proteins c-bcl-2 ; Replication Protein C ; *Repressor Proteins ; *Saccharomyces cerevisiae Proteins ; }, abstract = {PCNA (proliferating cell nuclear antigen), originally characterized as a DNA polymerase accessory protein, functions as a DNA sliding clamp for DNA polymerase delta and is an essential component for eukaryotic chromosomal DNA replication. Recent studies have revealed a striking feature of PCNA in its ability to interact with multiple partners, involved, for example, in Okazaki fragment joining, DNA repair, DNA methylation and chromatin assembly. Since these reactions take place mainly on replicating DNA, PCNA has applications as a marker for DNA synthesis. It is of interest that proteins involved in cell cycle regulation may also exhibit PCNA binding activity. For example, the CDK inhibitor, p21 (Cip1/Waf1) interacts with PCNA blocking its activity necessary for DNA replication and also affecting interactions with other PCNA binding proteins. The available data indicate that DNA sliding clamps have generated additional functions with evolution of eukaryotes from simple prokaryotes. In mammalian cells, they play key roles in controlling DNA synthesis reactions and the reorganization of replicated DNA at replication forks. Several cell cycle regulation proteins target these processes by affecting PCNA actions}, } @article {pmid10574716, year = {1999}, author = {Dilbeck, V and Berberof, M and Van Cauwenberge, A and Alexandre, H and Pays, E}, title = {Characterization of a coiled coil protein present in the basal body of Trypanosoma brucei.}, journal = {Journal of cell science}, volume = {112 (Pt 24)}, number = {}, pages = {4687-4694}, doi = {10.1242/jcs.112.24.4687}, pmid = {10574716}, issn = {0021-9533}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; DNA, Complementary ; Fluorescent Antibody Technique ; HeLa Cells ; Humans ; Mice ; Molecular Sequence Data ; Protozoan Proteins/*genetics/metabolism ; Subcellular Fractions/metabolism ; Trypanosoma brucei brucei/*genetics ; }, abstract = {TBBC (for Trypanosoma brucei basal body component) is a unique gene transcribed in a 4.8 kb mRNA encoding a 1,410 amino acid protein that consists almost entirely of a coiled coil structure. This protein appeared to localize in the basal body, with an accessory presence at the posterior end of the cell, the nucleus and over the flagellum. Since the two other known components of the trypanosome basal body are (gamma)-tubulin and an uncharacterized component termed BBA4 we performed double immunofluorescence experiments with anti-TBBC and either anti-BBA4 or anti-(gamma)-tubulin antibodies. These three components did not colocalize but were very closely associated, BBA4 being the most proximal to the kinetoplast DNA. Anti-TBBC antibodies detected a 170 kDa protein in western blots of total HeLa cell extracts. Moreover, these antibodies stained the centriole of HeLa and COS cells as well as the centriole of mouse spermatozoa, indicating that a TBBC-like centriolar component has been conserved during the evolution of eukaryotes.}, } @article {pmid10527923, year = {1999}, author = {Katz, LA}, title = {The Tangled Web: Gene Genealogies and the Origin of Eukaryotes.}, journal = {The American naturalist}, volume = {154}, number = {S4}, pages = {S137-S145}, doi = {10.1086/303289}, pmid = {10527923}, issn = {1537-5323}, abstract = {Accessing data from the genomes of organisms (individual genes) and analyzing these data using sophisticated alignment and phylogenetic methods led to the expectation that we would be able to paint a clear picture of the evolution of eukaryotes. Previous analyses based on morphology and ultrastructure failed to pinpoint both the sister taxon to eukaryotes and the branching order of eukaryotic lineages. However, the expectation that molecular data would provide resolution has not been met since a growing number of gene genealogies present conflicting hypotheses for the origin and diversification of eukaryotes. Instead of reconstructing a simple bifurcating tree of life, these gene genealogies have generated a complex picture of eukaryotic genomes whereby ancient lateral transfers (of individual genes or perhaps even entire genomes) has tangled the evolutionary history of eukaryotes. Resolution of these conflicting genealogies comes in recognizing that eukaryotes are chimeric, containing genetic information from multiple ancestral lineages.}, } @article {pmid10467746, year = {1999}, author = {Vellai, T and Vida, G}, title = {The origin of eukaryotes: the difference between prokaryotic and eukaryotic cells.}, journal = {Proceedings. Biological sciences}, volume = {266}, number = {1428}, pages = {1571-1577}, pmid = {10467746}, issn = {0962-8452}, mesh = {Animals ; *Biological Evolution ; DNA/genetics ; Eukaryotic Cells/*classification ; Genome ; Models, Genetic ; Phylogeny ; Prokaryotic Cells/*classification ; }, abstract = {Eukaryotes have long been thought to have arisen by evolving a nucleus, endomembrane, and cytoskeleton. In contrast, it was recently proposed that the first complex cells, which were actually proto-eukaryotes, arose simultaneously with the acquisition of mitochondria. This so-called symbiotic association hypothesis states that eukaryotes emerged when some ancient anaerobic archaebacteria (hosts) engulfed respiring alpha-proteobacteria (symbionts), which evolved into the first energy-producing organelles. Therefore, the intracellular compartmentalization of the energy-converting metabolism that was bound originally to the plasma membrane appears to be the key innovation towards eukaryotic genome and cellular organization. The novel energy metabolism made it possible for the nucleotide synthetic apparatus of cells to be no longer limited by subsaturation with substrates and catalytic components. As a consequence, a considerable increase has occurred in the size and complexity of eukaryotic genomes, providing the genetic basis for most of the further evolutionary changes in cellular complexity. On the other hand, the active uptake of exogenous DNA, which is general in bacteria, was no longer essential in the genome organization of eukaryotes. The mitochondrion-driven scenario for the first eukaryotes explains the chimera-like composition of eukaryotic genomes as well as the metabolic and cellular organization of eukaryotes.}, } @article {pmid10461380, year = {1999}, author = {Lang, BF and Seif, E and Gray, MW and O'Kelly, CJ and Burger, G}, title = {A comparative genomics approach to the evolution of eukaryotes and their mitochondria.}, journal = {The Journal of eukaryotic microbiology}, volume = {46}, number = {4}, pages = {320-326}, doi = {10.1111/j.1550-7408.1999.tb04611.x}, pmid = {10461380}, issn = {1066-5234}, mesh = {Animals ; Base Sequence ; Chromosome Mapping ; Conserved Sequence ; DNA, Mitochondrial/*genetics ; Databases, Factual ; Endoribonucleases/chemistry/genetics ; Eukaryotic Cells/*physiology ; *Evolution, Molecular ; *Genome ; Genome, Fungal ; Mitochondria/*genetics ; Molecular Sequence Data ; Organelles/genetics ; Phylogeny ; RNA, Catalytic/chemistry/genetics ; Ribonuclease P ; Ribosomal Proteins/genetics ; Sequence Analysis, DNA ; }, abstract = {The Organelle Genome Megasequencing Program (OGMP) investigates mitochondrial genome diversity and evolution by systematically determining the complete mitochondrial DNA (mtDNA) sequences of a phylogenetically broad selection of protists. The mtDNAs of lower fungi and choanoflagellates are being analyzed by the Fungal Mitochondrial Genome Project (FMGP), a sister project to the OGMP. Some of the most interesting protists include the jakobid flagellates Reclinomonas americana, Malawimonas jakobiformis, and Jakoba libera, which share ultrastructural similarities with amitochondriate retortamonads, and harbor mitochondrial genes not seen before in mtDNAs of other organisms. In R. americana and J. libera, gene clusters are found that resemble, to an unprecedented degree, the contiguous ribosomal protein operons str, S10, spc, and alpha of eubacteria. In addition, their mtDNAs code for an RNase P RNA that displays all the elements of a bacterial minimum consensus structure. This structure has been instrumental in detecting the rnpB gene in additional protists. Gene repertoire and gene order comparisons as well as multiple-gene phylogenies support the view of a single endosymbiotic origin of mitochondria, whose closest extant relatives are Rickettsia-type alpha-Proteobacteria.}, } @article {pmid10383869, year = {1999}, author = {Potin, P and Bouarab, K and Küpper, F and Kloareg, B}, title = {Oligosaccharide recognition signals and defence reactions in marine plant-microbe interactions.}, journal = {Current opinion in microbiology}, volume = {2}, number = {3}, pages = {276-283}, doi = {10.1016/S1369-5274(99)80048-4}, pmid = {10383869}, issn = {1369-5274}, mesh = {Bacteria/*growth & development ; Eukaryota/microbiology/*physiology ; Models, Biological ; Oceans and Seas ; Oligosaccharides/*metabolism ; *Signal Transduction ; Water Microbiology ; }, abstract = {Recent findings on the involvement of oligosaccharide signals in pathogen recognition and defence reactions in marine algae shine a new light on the ecology of their interactions with associated microorganisms. Since the marine environment encompasses lineages that have diverged a long time ago from the terrestrial phyla, these results suggest that cell-cell recognition pathways typical of terrestrial plants appeared very early in the evolution of eukaryotes. Production of oligosaccharides from marine algae using microbial recombinant polysaccharidases is also of industrial interest as plants can be protected from infections by preincubation in the presence of appropriate signals that mimic the attacks by pathogens.}, } @article {pmid10368959, year = {1999}, author = {Brinkmann, H and Philippe, H}, title = {Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies.}, journal = {Molecular biology and evolution}, volume = {16}, number = {6}, pages = {817-825}, doi = {10.1093/oxfordjournals.molbev.a026166}, pmid = {10368959}, issn = {0737-4038}, mesh = {Archaea/*genetics ; Archaeal Proteins/genetics ; Bacteria/*genetics ; Bacterial Proteins/genetics ; Evolution, Molecular ; GTP Phosphohydrolases/genetics ; Genes, Archaeal ; Genes, Bacterial ; *Phylogeny ; Receptors, Cytoplasmic and Nuclear/genetics ; Receptors, Peptide/genetics ; Signal Recognition Particle/genetics ; Time Factors ; }, abstract = {The 54-kDa signal recognition particle and the receptor SR alpha, two proteins involved in the cotranslational translocation of proteins, are paralogs. They originate from a gene duplication that occurred prior to the last universal common ancestor, allowing one to root the universal tree of life. Phylogenetic analysis using standard methods supports the generally accepted cluster of Archaea and Eucarya. However, a new method increasing the signal-to-noise ratio strongly suggests that this result is due to a long-branch attraction artifact, with the Bacteria evolving fastest. In fact, the Archaea/Eucarya sisterhood is recovered only by the fast-evolving positions. In contrast, the most slowly evolving positions, which are the most likely to retain the ancient phylogenetic signal, support the monophyly of prokaryotes. Such a eukaryotic rooting provides a simple explanation for the high similarity of Archaea and Bacteria observed in complete-genome analysis, and should prompt a reconsideration of current views on the origin of eukaryotes.}, } @article {pmid28296493, year = {1999}, author = {Hasegawa, M and Hashimoto, T}, title = {Phylogenetic Position of Amitochondriate Protists in the Evolution of Eukaryotes.}, journal = {The Biological bulletin}, volume = {196}, number = {3}, pages = {389-392}, doi = {10.2307/1542977}, pmid = {28296493}, issn = {1939-8697}, } @article {pmid28296492, year = {1999}, author = {Doolittle, WF}, title = {Rethinking the Origin of Eukaryotes.}, journal = {The Biological bulletin}, volume = {196}, number = {3}, pages = {378-380}, doi = {10.2307/1542974}, pmid = {28296492}, issn = {1939-8697}, } @article {pmid10203753, year = {1999}, author = {López-Garćia, P and Moreira, D}, title = {Metabolic symbiosis at the origin of eukaryotes.}, journal = {Trends in biochemical sciences}, volume = {24}, number = {3}, pages = {88-93}, doi = {10.1016/s0968-0004(98)01342-5}, pmid = {10203753}, issn = {0968-0004}, mesh = {Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; Biological Evolution ; Eukaryotic Cells ; Hydrogen/metabolism ; Mitochondria/metabolism ; *Models, Biological ; Symbiosis/*physiology ; }, abstract = {Thirty years after Margulis revived the endosymbiosis theory for the origin of mitochondria and chloroplasts, two novel symbiosis hypotheses for the origin of eukaryotes have been put forward. Both propose that eukaryotes arose through metabolic symbiosis (syntrophy) between eubacteria and methanogenic Archaea. They also propose that this was mediated by interspecies hydrogen transfer and that, initially, mitochondria were anaerobic. These hypotheses explain the mosaic character of eukaryotes (i.e. an archaeal-like genetic machinery and a eubacterial-like metabolism), as well as distinct eukaryotic characteristics (which are proposed to be products of symbiosis). Combined data from comparative genomics, microbial ecology and the fossil record should help to test their validity.}, } @article {pmid10080177, year = {1999}, author = {Herbert, A and Rich, A}, title = {RNA processing and the evolution of eukaryotes.}, journal = {Nature genetics}, volume = {21}, number = {3}, pages = {265-269}, doi = {10.1038/6780}, pmid = {10080177}, issn = {1061-4036}, mesh = {Animals ; *Biological Evolution ; DNA/genetics ; Embryo, Mammalian/physiology ; Embryo, Nonmammalian ; Eukaryotic Cells/*physiology ; Female ; Genome ; Male ; RNA Editing ; *RNA Processing, Post-Transcriptional ; Short Interspersed Nucleotide Elements ; }, abstract = {In eukaryotes, RNA processing events, including alternative splicing and RNA editing, can generate many different messages from a single gene. As a consequence, the RNA pool, which we refer to here as the 'ribotype', has a different information content from the genotype and can vary as circumstances change. The outcome of a single RNA processing event often regulates the outcome of another, giving rise to networks that affect the composition and expression of a particular ribotype. Successful ribotypes are determined by natural selection, and can be incorporated into the genome over time by reverse transcription. Eukaryotic evolution is therefore influenced by the alternate ways in which RNAs are processed and the continual interplay between RNA and DNA.}, } @article {pmid21238406, year = {1998}, author = {Katz, LA}, title = {Changing perspectives on the origin of eukaryotes.}, journal = {Trends in ecology & evolution}, volume = {13}, number = {12}, pages = {493-497}, doi = {10.1016/s0169-5347(98)01490-6}, pmid = {21238406}, issn = {0169-5347}, abstract = {From the initial application of molecular techniques to the study of microbial organisms, three domains of life emerged, with eukaryotes and archaea as sister taxa. However, recent analyses of an expanding molecular data set reveal that the eukaryotic genome is chimeric with respect to archaea and bacteria. Moreover, there is now evidence that the primitive eukaryotic group `Archezoa' once harbored mitochondia. These discoveries have challenged the traditional stepwise model of the evolution of eukaryotes, in which the nucleus and microtubules evolve before the acquisition of mitochondria, and consequently compel a revision of existing models of the origin of eukaryotic cells.}, } @article {pmid9803418, year = {1998}, author = {Smith, MW and Aley, SB and Sogin, M and Gillin, FD and Evans, GA}, title = {Sequence survey of the Giardia lamblia genome.}, journal = {Molecular and biochemical parasitology}, volume = {95}, number = {2}, pages = {267-280}, doi = {10.1016/s0166-6851(98)00113-3}, pmid = {9803418}, issn = {0166-6851}, support = {AI24285/AI/NIAID NIH HHS/United States ; GM53835/GM/NIGMS NIH HHS/United States ; HG00202/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Cosmids/genetics ; Evolution, Molecular ; Gene Library ; Genes, Protozoan ; *Genome, Protozoan ; Giardia lamblia/*genetics ; Molecular Sequence Data ; Phosphoric Monoester Hydrolases/genetics ; Phosphotransferases/genetics ; Protein Processing, Post-Translational ; Protozoan Proteins/genetics/metabolism ; *Sequence Analysis, DNA ; }, abstract = {The parasitic protozoan Giardia lamblia represents one of the earliest diverging lineages in the evolutionary history of eukaryotic organisms as well as an important human pathogen. A representative sampling of gene sequences from this early diverging protozoan could provide insights into genotypic and phenotypic innovations associated with the origin of eukaryotes. Currently, known giardial gene sequences are heavily biased toward a few gene families, including variant surface proteins (VSPs), structural proteins, and ribosomal RNA genes. One-pass sequences of Giardia genomic DNA were obtained using vector flanking priming sequences on the ends of cosmids in two independent libraries. Comparisons of 2304 of these sequences against the GenBank database identified 205 potential giardial genes with BLAST scores P(n) < 10(9). These coding regions encompass a wide range of metabolic, repair, and signaling enzymes, and include some genes not predicted by our current understanding of Giardia biochemistry. The efficiency of identification of putative genes is consistent with earlier findings that coding regions in the Giardia genome are densely packed and do not appear to contain introns. Our current results suggest that direct genome sequencing is an efficient method for identifying giardial genes for evolutionary and biochemical studies.}, } @article {pmid9797402, year = {1998}, author = {Moreira, D and Lopez-Garcia, P}, title = {Symbiosis between methanogenic archaea and delta-proteobacteria as the origin of eukaryotes: the syntrophic hypothesis.}, journal = {Journal of molecular evolution}, volume = {47}, number = {5}, pages = {517-530}, doi = {10.1007/pl00006408}, pmid = {9797402}, issn = {1432-1432}, abstract = {We present a novel hypothesis for the origin of the eukaryotic cell, or eukaryogenesis, based on a metabolic symbiosis (syntrophy) between a methanogenic archaeon (methanobacterial-like) and a delta-proteobacterium (an ancestral sulfate-reducing myxobacterium). This syntrophic symbiosis was originally mediated by interspecies H2 transfer in anaerobic, possibly moderately thermophilic, environments. During eukaryogenesis, progressive cellular and genomic cointegration of both types of prokaryotic partners occurred. Initially, the establishment of permanent consortia, accompanied by extensive membrane development and close cell-cell interactions, led to a highly evolved symbiotic structure already endowed with some primitive eukaryotic features, such as a complex membrane system defining a protonuclear space (corresponding to the archaeal cytoplasm), and a protoplasmic region (derived from fusion of the surrounding bacterial cells). Simultaneously, bacterial-to-archaeal preferential gene transfer and eventual replacement took place. Bacterial genome extinction was thus accomplished by gradual transfer to the archaeal host, where genes adapted to a new genetic environment. Emerging eukaryotes would have inherited archaeal genome organization and dynamics and, consequently, most DNA-processing information systems. Conversely, primordial genes for social and developmental behavior would have been provided by the ancient myxobacterial symbiont. Metabolism would have been issued mainly from the versatile bacterial organotrophy, and progressively, methanogenesis was lost.}, } @article {pmid9742730, year = {1998}, author = {Chela-Flores, J}, title = {A search for extraterrestrial eukaryotes: physical and paleontological aspects.}, journal = {Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life}, volume = {28}, number = {4-6}, pages = {583-596}, pmid = {9742730}, issn = {0169-6149}, mesh = {Biological Evolution ; Earth, Planet ; *Eukaryotic Cells ; *Exobiology ; *Extraterrestrial Environment ; Heterochromatin/genetics ; Jupiter ; Origin of Life ; Paleontology ; Planets ; Prokaryotic Cells ; Research Design ; Solar System ; }, abstract = {Physical and biochemical aspects of a proposed search for extraterrestrial eukaryotes (SETE) are considered. Such a program should approach the distinction between a primitive eukaryote and an archaebacteria. The emphasis on gene silencing suggests a possible assay suitable for a robotic investigation of eukaryoticity, so as to be able to decide whether the first steps towards eukaryogenesis have been taken in an extraterrestrial planet, or satellite. The experiment would consist of searching for cellular division and the systematic related delay in replication of heterochromatic chromosome segments. It should be noticed that the direct search for a membrane-bounded set of chromosomes does not necessarily determine eukaryotic identity, as there are prokaryotes that have membrane-bounded nucleoids. A closer look at the protein fraction of chromatin (mainly histones) does not help either, as there are some eukaryotes that may lack histones; there are also some bacteria as well as archaebacteria with histone-like proteins in their nucleoids. Comments on the recent suggestion of possible environments for a SETE program are discussed: the deep crust of Mars, and the Jovian satellite Europa, provided the existence of an ocean under its ice-covered surface is confirmed by the current Galileo mission.}, } @article {pmid9656480, year = {1998}, author = {Ribeiro, S and Golding, GB}, title = {The mosaic nature of the eukaryotic nucleus.}, journal = {Molecular biology and evolution}, volume = {15}, number = {7}, pages = {779-788}, doi = {10.1093/oxfordjournals.molbev.a025983}, pmid = {9656480}, issn = {0737-4038}, mesh = {Alcohol Oxidoreductases/genetics ; Algorithms ; Arginine-tRNA Ligase/genetics ; *Eukaryotic Cells ; *Genes ; Genes, Archaeal ; Genes, Bacterial ; Gram-Negative Bacteria/genetics ; Gram-Positive Bacteria/genetics ; Likelihood Functions ; Methanococcus/*genetics ; *Phylogeny ; Sequence Homology, Amino Acid ; Transaldolase/genetics ; }, abstract = {The phylogenies for each of the protein-coding genes from the Methanococcus jannaschii genome were surveyed to determine the history of the major groups of life. For each gene, homologous sequences from other archaea, eucarya, and Gram-positive and Gram-negative bacteria were collected and aligned, and a phylogeny was reconstructed with a maximum-likelihood algorithm. The majority of significant phylogenies favor the eucarya and the archaca as sister groups. A smaller, but still substantial, portion of these significant phylogenies favor an eucarya/Gram-negative clade. These results indicate that support for the early history of life is not unequivocal. A chimeric origin of eukaryotes or an ancient, massive horizontal transfer of genes from Gram-negative bacteria to eucarya can explain many of the observed phylogenies.}, } @article {pmid9545461, year = {1998}, author = {Vellai, T and Takács, K and Vida, G}, title = {A new aspect to the origin and evolution of eukaryotes.}, journal = {Journal of molecular evolution}, volume = {46}, number = {5}, pages = {499-507}, doi = {10.1007/pl00006331}, pmid = {9545461}, issn = {0022-2844}, mesh = {*Biological Evolution ; DNA Replication ; Energy Metabolism ; Escherichia coli/genetics/growth & development ; Eukaryotic Cells/*physiology ; Genetic Vectors ; *Genome, Bacterial ; *Models, Biological ; Organelles/metabolism ; Prokaryotic Cells/*physiology ; }, abstract = {One of the most important omissions in recent evolutionary theory concerns how eukaryotes could emerge and evolve. According to the currently accepted views, the first eukaryotic cell possessed a nucleus, an endomembrane system, and a cytoskeleton but had an inefficient prokaryotic-like metabolism. In contrast, one of the most ancient eukaryotes, the metamonada Giardia lamblia, was found to have formerly possessed mitochondria. In sharp contrast with the traditional views, this paper suggests, based on the energetic aspect of genome organization, that the emergence of eukaryotes was promoted by the establishment of an efficient energy-converting organelle, such as the mitochondrion. Mitochondria were acquired by the endosymbiosis of ancient alpha-purple photosynthetic Gram-negative eubacteria that reorganized the prokaryotic metabolism of the archaebacterial-like ancestral host cells. The presence of an ATP pool in the cytoplasm provided by this cell organelle allowed a major increase in genome size. This evolutionary change, the remarkable increase both in genome size and complexity, explains the origin of the eukaryotic cell itself. The loss of cell wall and the appearance of multicellularity can also be explained by the acquisition of mitochondria. All bacteria use chemiosmotic mechanisms to harness energy; therefore the periplasm bounded by the cell wall is an essential part of prokaryotic cells. Following the establishment of mitochondria, the original plasma membrane-bound metabolism of prokaryotes, as well as the funcion of the periplasm providing a compartment for the formation of different ion gradients, has been transferred into the inner mitochondrial membrane and intermembrane space. After the loss of the essential function of periplasm, the bacterial cell wall could also be lost, which enabled the naked cells to establish direct connections among themselves. The relatively late emergence of mitochondria may be the reason why multicellularity evolved so slowly.}, } @article {pmid9525043, year = {1998}, author = {Chela-Flores, J}, title = {First steps in eukaryogenesis: physical phenomena in the origin and evolution of chromosome structure.}, journal = {Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life}, volume = {28}, number = {2}, pages = {215-225}, doi = {10.1023/a:1006573617971}, pmid = {9525043}, issn = {0169-6149}, mesh = {Animals ; *Biological Evolution ; Chromosomes/*genetics/ultrastructure ; DNA/chemistry/genetics ; DNA Replication ; Gene Expression Regulation ; Heterochromatin/genetics/ultrastructure ; Mammals ; *Origin of Life ; Platypus ; Tachyglossidae ; X Chromosome ; }, abstract = {Our present understanding of the origin and evolution of chromosomes differs considerably from current understanding of the origin and evolution of the cell itself. Chromosome origins have been less prominent in research, as the emphasis has not shifted so far appreciably from the phenomenon of primeval nucleic acid encapsulation to that of the origin of gene organization, expression, and regulation. In this work we discuss some reasons why preliminary steps in this direction are being taken. We have been led to examine properties that have contributed to raise the ancestral prokaryotic programmes to a level where we can appreciate in eukaryotes a clear departure from earlier themes in the evolution of the cell from the last common ancestor. We shift our point of view from evolution of cell morphology to the point of view of the genes. In particular, we focus attention on possible physical bases for the way transmission of information has evolved in eukaryotes, namely, the inactivation of whole chromosomes. The special case of the inactivation of the X chromosome in mammals is discussed, paying particular attention to the physical process of the spread of X inactivation in monotremes (platypus and echidna). When experimental data is unavailable some theoretical analysis is possible based on the idea that in certain cases collective phenomena in genetics, rather than chemical detail, are better correlates of complex chemical processes.}, } @article {pmid9391098, year = {1997}, author = {Bharathan, G and Janssen, BJ and Kellogg, EA and Sinha, N}, title = {Did homeodomain proteins duplicate before the origin of angiosperms, fungi, and metazoa?.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {94}, number = {25}, pages = {13749-13753}, pmid = {9391098}, issn = {0027-8424}, mesh = {Amino Acid Sequence ; Animals ; *Evolution, Molecular ; Fungi/genetics ; *Genes, Homeobox ; Homeodomain Proteins/chemistry/*genetics ; Humans ; Magnoliopsida/genetics ; Models, Genetic ; Molecular Sequence Data ; *Multigene Family ; Phylogeny ; Protein Structure, Secondary ; Sequence Homology, Amino Acid ; }, abstract = {Homeodomain proteins are transcription factors that play a critical role in early development in eukaryotes. These proteins previously have been classified into numerous subgroups whose phylogenetic relationships are unclear. Our phylogenetic analysis of representative eukaryotic sequences suggests that there are two major groups of homeodomain proteins, each containing sequences from angiosperms, metazoa, and fungi. This result, based on parsimony and neighbor-joining analyses of primary amino acid sequences, was supported by two additional features of the proteins. The two protein groups are distinguished by an insertion/deletion in the homeodomain, between helices I and II. In addition, an amphipathic alpha-helical secondary structure in the region N terminal of the homeodomain is shared by angiosperm and metazoan sequences in one group. These results support the hypothesis that there was at least one duplication of homeobox genes before the origin of angiosperms, fungi, and metazoa. This duplication, in turn, suggests that these proteins had diverse functions early in the evolution of eukaryotes. The shared secondary structure in angiosperm and metazoan sequences points to an ancient conserved functional domain.}, } @article {pmid9190805, year = {1997}, author = {Karlin, S and Mrázek, J and Campbell, AM}, title = {Compositional biases of bacterial genomes and evolutionary implications.}, journal = {Journal of bacteriology}, volume = {179}, number = {12}, pages = {3899-3913}, pmid = {9190805}, issn = {0021-9193}, support = {5R01GM10452-32/GM/NIGMS NIH HHS/United States ; 5R01HG00335-08/HG/NHGRI NIH HHS/United States ; 9R01GM51117-28/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics ; *Genome, Bacterial ; Oligonucleotides/*analysis ; Phylogeny ; }, abstract = {We compare and contrast genome-wide compositional biases and distributions of short oligonucleotides across 15 diverse prokaryotes that have substantial genomic sequence collections. These include seven complete genomes (Escherichia coli, Haemophilus influenzae, Mycoplasma genitalium, Mycoplasma pneumoniae, Synechocystis sp. strain PCC6803, Methanococcus jannaschii, and Pyrobaculum aerophilum). A key observation concerns the constancy of the dinucleotide relative abundance profiles over multiple 50-kb disjoint contigs within the same genome. (The profile is rhoXY* = fXY*/fX*fY* for all XY, where fX* denotes the frequency of the nucleotide X and fY* denotes the frequency of the dinucleotide XY, both computed from the sequence concatenated with its inverted complementary sequence.) On the basis of this constancy, we refer to the collection [rhoXY*] as the genome signature. We establish that the differences between [rhoXY*] vectors of 50-kb sample contigs of different genomes virtually always exceed the differences between those of the same genomes. Various di- and tetranucleotide biases are identified. In particular, we find that the dinucleotide CpG=CG is underrepresented in many thermophiles (e.g., M. jannaschii, Sulfolobus sp., and M. thermoautotrophicum) but overrepresented in halobacteria. TA is broadly underrepresented in prokaryotes and eukaryotes, but normal counts appear in Sulfolobus and P. aerophilum sequences. More than for any other bacterial genome, palindromic tetranucleotides are underrepresented in H. influenzae. The M. jannaschii sequence is unprecedented in its extreme underrepresentation of CTAG tetranucleotides and in the anomalous distribution of CTAG sites around the genome. Comparative analysis of numbers of long tetranucleotide microsatellites distinguishes H. influenzae. Dinucleotide relative abundance differences between bacterial sequences are compared. For example, in these assessments of differences, the cyanobacteria Synechocystis, Synechococcus, and Anabaena do not form a coherent group and are as far from each other as general gram-negative sequences are from general gram-positive sequences. The difference of M. jannaschii from low-G+C gram-positive proteobacteria is one-half of the difference from gram-negative proteobacteria. Interpretations and hypotheses center on the role of the genome signature in highlighting similarities and dissimilarities across different classes of prokaryotic species, possible mechanisms underlying the genome signature, the form and level of genome compositional flux, the use of the genome signature as a chronometer of molecular phylogeny, and implications with respect to the three putative eubacterial, archaeal, and eukaryote domains of life and to the origin and early evolution of eukaryotes.}, } @article {pmid9112752, year = {1997}, author = {Ruvinsky, A}, title = {Sex, meiosis and multicellularity.}, journal = {Acta biotheoretica}, volume = {45}, number = {2}, pages = {127-141}, doi = {10.1023/a:1000334022255}, pmid = {9112752}, issn = {0001-5342}, mesh = {Animals ; *Biological Evolution ; Cell Aggregation/physiology ; Female ; Male ; Meiosis/*physiology ; *Phylogeny ; Reproduction/physiology ; *Sex ; }, abstract = {The origin and progress of multicellularity, which is one of the crucial steps in the evolution of life, remains unclear and stringent phylogenetic reconstruction of the process is difficult. However, further theoretical considerations of the problem could be useful for the creation of a verifiable hypothesis. Sex as a ubiquitous biological phenomenon is usually considered as something entirely linked with reproduction. This is mostly true for modem multicellular organisms, but at the earliest stage of evolution of eukaryotes it was not so. At that time the sexual process had nothing to do with reproduction, and only later, sex and reproduction merged together. One of the aims of this paper is to consider the sexual process as a likely basis for the establishment of multicellularity and to discuss the early stages of evolution of the multicellularity from this perspective. It is suggested that mitotic reproduction of cells at different stages of the sexual cycle of unicellular ancestors might be the starting points for independent transition to multicellularity in different taxa. Numerous consequences of these transitions, including evolution of bisexuality and development of novel meiotic functions in animals, are discussed.}, } @article {pmid9066796, year = {1997}, author = {Tourasse, NJ and Gouy, M}, title = {Evolutionary distances between nucleotide sequences based on the distribution of substitution rates among sites as estimated by parsimony.}, journal = {Molecular biology and evolution}, volume = {14}, number = {3}, pages = {287-298}, doi = {10.1093/oxfordjournals.molbev.a025764}, pmid = {9066796}, issn = {0737-4038}, mesh = {Algorithms ; *Biological Evolution ; Computer Simulation ; *Eukaryotic Cells ; *Models, Genetic ; *Mutagenesis ; Proteins/genetics ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; Reproducibility of Results ; Software ; }, abstract = {The rate of evolution of macromolecules such as ribosomal RNAs and proteins varies along the molecule because structural and functional constraints differ between sites. Many studies have shown that ignoring this variation in computing evolutionary distances leads to severe underestimation of sequence divergences, and thus can lead to misleading evolutionary tree inferences. We propose here a new parsimony-based method for computing evolutionary distances between pairs of sequences that takes into account this variation and estimates it from the data. This method applies to the number of substitutions per site in ribosomal RNA genes as well as to the number of nonsynonymous substitutions per codon for protein-coding genes and is especially suitable when large data sets (> or = 100 sequences) are analyzed. First, starting from a phylogeny constructed with usual distances, the maximum-parsimony method is used to infer the distribution of the number of substitutions that have occurred at each site (or codon) along this tree. This distribution is then fitted to an "invariant + truncated negative binomial" distribution that allows for invariant sites. Maximum-likelihood fitting of this distribution to different data sets showed that it agreed very well with real data. Noticeably, allowing for invariant sites seemed to be very important. Finally, two distance estimates were developed by introducing the distribution of site variability into the substitution models of Jukes and Cantor and of Kimura. The use of different numbers of aligned sequences (up to 1,000 rRNA sequences) showed that the parameters of the model are very sensitive to the number of sequences used to estimate them. However, if at least 100 sequences are considered, the two new distance estimates are quite stable with respect to the number of sequences used to fit the distribution. This stability is true for low as well as for high evolutionary distances. These new distances appeared to be much better estimates of the number of substitutions per site than the classical distances of Jukes and Cantor and of Kimura, which both greatly underestimate this number, so that they can serve as indexes to detect saturation. We conclude that the new distances are particularly suitable for phylogenetic analysis when very distantly related species and relatively large data sets are considered. Trees reconstructed using these distances are generally different from those constructed by means of the classical estimates. Using this new method, we showed that the mean evolutionary distance between Prokaryotes and Eukaryotes is substantially higher for the small-subunit than for the large-subunit rRNAs. This suggests than the former might have experienced a drastic change during the early evolution of Eukaryotes.}, } @article {pmid9331221, year = {1997}, author = {Klotz, C and Garreau de Loubresse, N and Ruiz, F and Beisson, J}, title = {Genetic evidence for a role of centrin-associated proteins in the organization and dynamics of the infraciliary lattice in Paramecium.}, journal = {Cell motility and the cytoskeleton}, volume = {38}, number = {2}, pages = {172-186}, doi = {10.1002/(SICI)1097-0169(1997)38:2<172::AID-CM6>3.0.CO;2-9}, pmid = {9331221}, issn = {0886-1544}, mesh = {Animals ; Calcium-Binding Proteins/genetics/*metabolism ; Centrosome/metabolism ; *Chromosomal Proteins, Non-Histone ; Cilia/*chemistry/genetics/*ultrastructure ; Contractile Proteins/genetics/metabolism ; Fluorescent Antibody Technique, Indirect ; Microscopy, Immunoelectron ; Mutation ; Paramecium ; }, abstract = {Within the superfamily of "EF-hand Ca2+-modulated proteins," centrins constitute a family of cytoskeletal proteins that are highly conserved from lower eukaryotes to man. Their cytoskeletal specialization is manifest in their capacity to form filamentous contractile arrays of various shapes and functions and by their association with microtubule organizing centres (MTOCs). While the latter property has been conserved throughout the evolution of eukaryotes, centrin-based contractile structures are only found in protists where they form arrays of widely diverse organization and function. In the ciliate Paramecium tetraurelia, three centrin genes have been characterized, which may be part of a larger centrin gene family [Madeddu et al., 1996: Eur J. Biochem. 238:121-128]. The products of these genes were originally identified as components of the infraciliary lattice, a contractile cytoskeletal network [Garreau de Loubresse et al., 1991: Biol. Cell 71:217-225]. We show here that centrins are localized not only in this lattice but also in basal bodies and in the cord, a filamentous structure associated with the oral apparatus. We demonstrate that in the infraciliary lattice, but not in basal bodies, centrins are associated with high-molecular-weight proteins (ca. 350 kD). Their role in the biogenesis of the infraciliary lattice is documented by cytological and biochemical properties of the mutant "démaillé" (dem1) characterized by altered centrin-associated proteins and abnormal organization and dynamics of the infraciliary lattice.}, } @article {pmid8993569, year = {1996}, author = {Dodt, G and Braverman, N and Valle, D and Gould, SJ}, title = {From expressed sequence tags to peroxisome biogenesis disorder genes.}, journal = {Annals of the New York Academy of Sciences}, volume = {804}, number = {}, pages = {516-523}, doi = {10.1111/j.1749-6632.1996.tb18641.x}, pmid = {8993569}, issn = {0077-8923}, mesh = {Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Biological Transport ; Cloning, Molecular/*methods ; DNA, Complementary/genetics ; Fungal Proteins/genetics ; Genetic Complementation Test ; Humans ; Microbodies/*metabolism ; Molecular Sequence Data ; Peroxisomal Disorders/*genetics ; Sequence Tagged Sites ; }, abstract = {Isolation of human disease genes is a challenging process and can often only be achieved by labor-intensive positional cloning techniques. Fortunately, there are alternative strategies for isolation of peroxisome biogenesis disorder genes. The first, functional complementation, was established as a viable approach by Fujiki and colleagues, who identified PAF-1, the first known peroxisome biogenesis disorder gene. The second strategy, computer-based homology probing, relies on (1) the fact that peroxisome assembly has been conserved throughout the evolution of eukaryotes, (2) knowledge of the amino acid sequences of an increasing number of yeast peroxisome assembly (PAS) genes, and (3) the existence of sequence data from large numbers of human genes. The recent development of the expressed sequence tag (EST) database (dbEST) is fulfilling the last of these requirements. We have applied the homology probing strategy in the search for candidate genes for the peroxisome biogenesis disorders by routinely screening the database of ESTs for genes with significant sequence similarity to yeast PAS genes. The validity of this approach is demonstrated by its use in identifying PXR1 as the human orthologue of the Pichia pastoris PAS8 gene and PXAAA1 as a human homologue of the Pichia pastoris PAS5 gene. Furthermore, detailed analysis of PXR1 has revealed that mutations in this gene are responsible for complementation group 2 of the peroxisome biogenesis disorders. The demonstration that human homologues of yeast PAS genes exist and that mutations in these genes cause peroxisome biogenesis disorders demonstrates that yeast pas mutants are accurate and useful models for the analysis of these diseases.}, } @article {pmid8875863, year = {1996}, author = {Theissen, G and Kim, JT and Saedler, H}, title = {Classification and phylogeny of the MADS-box multigene family suggest defined roles of MADS-box gene subfamilies in the morphological evolution of eukaryotes.}, journal = {Journal of molecular evolution}, volume = {43}, number = {5}, pages = {484-516}, pmid = {8875863}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animals ; Conserved Sequence/*genetics ; DNA-Binding Proteins/*genetics ; Genes, Homeobox/genetics ; Genes, Plant/genetics ; Molecular Sequence Data ; Multigene Family/*genetics ; *Phylogeny ; Plant Development ; Plants/genetics ; Sequence Alignment ; }, abstract = {The MADS-box encodes a novel type of DNA-binding domain found so far in a diverse group of transcription factors from yeast, animals, and seed plants. Here, our first aim was to evaluate the primary structure of the MADS-box. Compilation of the 107 currently available MADS-domain sequences resulted in a signature which can strictly discriminate between genes possessing or lacking a MADS-domain and allowed a classification of MADS-domain proteins into several distinct subfamilies. A comprehensive phylogenetic analysis of known eukaryotic MADS-box genes, which is the first comprising animal as well as fungal and plant homologs, showed that the vast majority of subfamily members appear on distinct subtrees of phylogenetic trees, suggesting that subfamilies represent monophyletic gene clades and providing the proposed classification scheme with a sound evolutionary basis. A reconstruction of the history of the MADS-box gene subfamilies based on the taxonomic distribution of contemporary subfamily members revealed that each subfamily comprises highly conserved putative orthologs and recent paralogs. Some subfamilies must be very old (1,000 MY or more), while others are more recent. In general, subfamily members tend to share highly similar sequences, expression patterns, and related functions. The defined species distribution, specific function, and strong evolutionary conservation of the members of most subfamilies suggest that the establishment of different subfamilies was followed by rapid fixation and was thus highly advantageous during eukaryotic evolution. These gene subfamilies may have been essential prerequisites for the establishment of several complex eukaryotic body structures, such as muscles in animals and certain reproductive structures in higher plants, and of some signal transduction pathways. Phylogenetic trees indicate that after establishment of different subfamilies, additional gene duplications led to a further increase in the number of MADS-box genes. However, several molecular mechanisms of MADS-box gene diversification were used to a quite different extent during animal and plant evolution. Known plant MADS-domain sequences diverged much faster than those of animals, and gene duplication and sequence diversification were extensively used for the creation of new genes during plant evolution, resulting in a relatively large number of interacting genes. In contrast, the available data on animal genes suggest that increase in gene number was only moderate in the lineage leading to mammals, but in the case of MEF2-like gene products, heterodimerization between different splice variants may have increased the combinatorial possibilities of interactions considerably. These observations demonstrate that in metazoan and plant evolution, increased combinatorial possibilities of MADS-box gene product interactions correlated with the evolution of increasingly complex body plans.}, } @article {pmid8755547, year = {1996}, author = {Baldauf, SL and Palmer, JD and Doolittle, WF}, title = {The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {93}, number = {15}, pages = {7749-7754}, pmid = {8755547}, issn = {0027-8424}, support = {GM35087/GM/NIGMS NIH HHS/United States ; }, mesh = {Adenosine Triphosphatases/genetics ; Amino Acid Sequence ; Animals ; Bacteria/genetics ; Consensus Sequence ; *Evolution, Molecular ; Genetic Variation ; Humans ; Molecular Sequence Data ; *Multigene Family ; Peptide Elongation Factor G ; Peptide Elongation Factor Tu/chemistry/*genetics ; Peptide Elongation Factors/chemistry/*genetics ; *Phylogeny ; Plants/genetics ; Sequence Homology, Amino Acid ; }, abstract = {The genes for the protein synthesis elongation factors Tu (EF-Tu) and G (EF-G) are the products of an ancient gene duplication, which appears to predate the divergence of all extant organismal lineages. Thus, it should be possible to root a universal phylogeny based on either protein using the second protein as an outgroup. This approach was originally taken independently with two separate gene duplication pairs, (i) the regulatory and catalytic subunits of the proton ATPases and (ii) the protein synthesis elongation factors EF-Tu and EF-G. Questions about the orthology of the ATPase genes have obscured the former results, and the elongation factor data have been criticized for inadequate taxonomic representation and alignment errors. We have expanded the latter analysis using a broad representation of taxa from all three domains of life. All phylogenetic methods used strongly place the root of the universal tree between two highly distinct groups, the archaeons/eukaryotes and the eubacteria. We also find that a combined data set of EF-Tu and EF-G sequences favors placement of the eukaryotes within the Archaea, as the sister group to the Crenarchaeota. This relationship is supported by bootstrap values of 60-89% with various distance and maximum likelihood methods, while unweighted parsimony gives 58% support for archaeal monophyly.}, } @article {pmid8742637, year = {1996}, author = {Iwabe, N and Kuma, K and Miyata, T}, title = {Evolution of gene families and relationship with organismal evolution: rapid divergence of tissue-specific genes in the early evolution of chordates.}, journal = {Molecular biology and evolution}, volume = {13}, number = {3}, pages = {483-493}, doi = {10.1093/oxfordjournals.molbev.a025609}, pmid = {8742637}, issn = {0737-4038}, mesh = {Animals ; Arthropods/classification/genetics ; *Biological Evolution ; Chordata, Nonvertebrate/classification/*genetics ; *Genes ; *Genetic Variation ; Humans ; Molecular Sequence Data ; Multigene Family ; Organ Specificity ; Phylogeny ; Proteins/genetics ; Vertebrates/classification/genetics ; }, abstract = {To determine a possible relationship between organismal and molecular evolution, the divergence patterns of gene families were examined by taking special notice of functional difference, tissue distribution, and intracellular localization of the members. A phylogenetic analysis of 25 different gene families revealed interesting patterns of divergence of these families: Most gene duplications giving rise to different functions antedate the vertebrates-arthropods separation. On the other hand, in a group of members carrying virtually identical function to one another but differing in tissue distribution (tissue-specific isoform), most gene duplications have occurred independently in each of vertebrates and arthropods after the separation of the two animal groups. In family members encoding molecules localizing in cell compartments (compartmentalized isoforms), the gene duplications antedate the animals-fungi separation. In the cases of the Ca2+ pump and rab subfamilies, the compartmentalized isoforms were shown to have diverged during the early evolution of eukaryotes. A phylogenetic analysis of the tissue-specific isoforms from 26 different subfamilies revealed extensive gene duplications and rapid rates of amino acid substitutions in the early evolution of chordates before the separation of fishes and tetrapods. On the contrary, the genetic variations are relatively low in the later period. This pattern of evolution observed at the molecular level is correlated well with that of tissue evolution based on fossil evidence and morphological data, and thus evolution at the two levels may be related.}, } @article {pmid8781286, year = {1996}, author = {Hashimoto, T and Hasegawa, M}, title = {Origin and early evolution of eukaryotes inferred from the amino acid sequences of translation elongation factors 1alpha/Tu and 2/G.}, journal = {Advances in biophysics}, volume = {32}, number = {}, pages = {73-120}, doi = {10.1016/0065-227x(96)84742-3}, pmid = {8781286}, issn = {0065-227X}, mesh = {Amino Acid Sequence ; Animals ; Archaea ; Bacteria ; Drosophila melanogaster ; Eukaryota ; Eukaryotic Cells ; *Evolution, Molecular ; Fungi ; Humans ; Molecular Sequence Data ; Peptide Elongation Factor 1 ; Peptide Elongation Factor 2 ; Peptide Elongation Factor G ; Peptide Elongation Factor Tu/*chemistry ; Peptide Elongation Factors/*chemistry ; *Phylogeny ; Plants ; Sequence Homology, Amino Acid ; }, } @article {pmid8721999, year = {1995}, author = {Bachellerie, JP and Nicoloso, M and Qu, LH and Michot, B and Caizergues-Ferrer, M and Cavaille, J and Renalier, MH}, title = {Novel intron-encoded small nucleolar RNAs with long sequence complementarities to mature rRNAs involved in ribosome biogenesis.}, journal = {Biochemistry and cell biology = Biochimie et biologie cellulaire}, volume = {73}, number = {11-12}, pages = {835-843}, doi = {10.1139/o95-091}, pmid = {8721999}, issn = {0829-8211}, mesh = {Animals ; Base Sequence ; Cell Nucleolus/*genetics ; Genetic Code ; *Introns ; Mice ; Molecular Sequence Data ; RNA, Ribosomal/*genetics ; RNA, Small Nuclear/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {Recently, several new snoRNAs encoded in introns of genes coding for ribosomal, ribosome-associated, or nucleolar proteins have been discovered. We are presently studying four of these intronic snoRNAs. Three of them, U20, U21, and U24, are closely related to each other on a structural basis. They are included in genes encoding nucleolin and ribosomal proteins L5 and L7a, respectively, in warm-blooded vertebrates. These three metabolically stable snoRNAs interact with nucleolar protein fibrillarin. In addition, they display common features that make them strikingly related to snoRNA U14. U14 contains two tracts of complementarity to 18S rRNA, which are required for the production of 18S rRNA. U20 displays a 21 nucleotide (nt) long complementarity to 18S rRNA. U21 contains a 13 nt complementarity to an invariant sequence in eukaryotic 28S rRNA. U24 has two separate 12 nt long complementarities to a highly conserved tract of 28S rRNA. Phylogenetic evidences support the fundamental importance of the pairings of these three snoRNAs to pre-rRNA, which could be involved in a control of pre-rRNA folding during preribosome assembly. By transfection of mouse cells, we have also analyzed the processing of U20 and found that the -cis acting signals for its processing from intronic RNA are restricted to the mature snoRNA sequence. Finally, we have documented changes of host genes for these three intronic snoRNAs during the evolution of eukaryotes.}, } @article {pmid8577841, year = {1995}, author = {Mitchison, TJ}, title = {Evolution of a dynamic cytoskeleton.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {349}, number = {1329}, pages = {299-304}, doi = {10.1098/rstb.1995.0117}, pmid = {8577841}, issn = {0962-8436}, mesh = {*Actins ; Adenosine Triphosphate/metabolism ; Animals ; *Cytoskeleton ; Eukaryotic Cells ; *Evolution, Molecular ; Humans ; Microtubules ; *Models, Biological ; *Tubulin/metabolism ; }, abstract = {Actin filaments and microtubules form the cytoskeleton of all eukaryotic cells, and they are responsible for organizing the cytoplasm and supporting motile processes. Both polymers are highly dynamic, and their polymerization dynamics are central to their organization. Though their evolutionary origins appear to be distinct, actin and tubulin have a similar mechanism for promoting polymerization dynamics in which the energy of nucleotide triphosphate hydrolysis during polymerization is used to weaken the bonds between subunits, thus promoting subsequent depolymerization. The evolutionary origins of actin and tubulin are unclear. It is likely that motile mechanisms driven by reversible polymerization, termed thermal ratchets, are older than those based on ATPase motor proteins. Such mechanisms are still important in modern eukaryotes, and may have powered early versions of the critical motile processes of phagocytosis and chromosome segregation in primitive cells. Thus evolution of dynamic cytoskeletal polymers may have been one of the earliest and most important steps leading to the evolution of eukaryotes. Plausible evolutionary pathways can be constructed leading from simple enzymes to dynamic cytoskeletal polymers.}, } @article {pmid8577835, year = {1995}, author = {Bird, A and Tweedie, S}, title = {Transcriptional noise and the evolution of gene number.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {349}, number = {1329}, pages = {249-253}, doi = {10.1098/rstb.1995.0109}, pmid = {8577835}, issn = {0962-8436}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Biological Evolution ; DNA/metabolism ; Eukaryotic Cells ; Evolution, Molecular ; *Genes ; Genome ; Humans ; Invertebrates/genetics ; Methylation ; *Models, Biological ; Models, Genetic ; Prokaryotic Cells ; *Transcription, Genetic ; Vertebrates/genetics ; }, abstract = {Several proposals are made to explain the apparent increase in complexity of certain lineages during evolution. The proposals (not made in this order) are: (1) that gene number is a valid measure of biological complexity; (2) that gene number has not increased continuously during evolution, but has risen in discrete steps; (3) that two of the biggest steps occurred at the transition from prokaryotes to eukaryotes and the transition from invertebrates to vertebrates; (4) that these steps were made possible by 'systemic' changes in the way that genetic information is managed in the genome; (5) that the ability to silence inappropriate promoters is the primary limitation on gene number; (6) that the invention of nucleosomes (and perhaps the nuclear membrane) facilitated the evolution of eukaryotes from prokaryotic ancestors; (7) that the spread of low density methylation throughout the genome facilitated the evolution of vertebrates from invertebrate ancestors.}, } @article {pmid7651339, year = {1995}, author = {Müller, F and Krüger, D and Sattlegger, E and Hoffmann, B and Ballario, P and Kanaan, M and Barthelmess, IB}, title = {The cpc-2 gene of Neurospora crassa encodes a protein entirely composed of WD-repeat segments that is involved in general amino acid control and female fertility.}, journal = {Molecular & general genetics : MGG}, volume = {248}, number = {2}, pages = {162-173}, pmid = {7651339}, issn = {0026-8925}, mesh = {Amino Acid Sequence ; Amino Acids/*metabolism ; Base Sequence ; Cloning, Molecular ; Conserved Sequence ; Fungal Proteins/chemistry/*genetics/physiology ; GTP-Binding Proteins/chemistry/genetics ; Gene Expression Regulation, Fungal ; *Genes, Fungal ; Genetic Complementation Test ; Molecular Sequence Data ; Mutation ; Neurospora crassa/*genetics/physiology ; Ornithine Carbamoyltransferase/genetics/metabolism ; RNA, Messenger/genetics ; Repetitive Sequences, Nucleic Acid ; Sequence Homology, Amino Acid ; Transcription, Genetic/genetics ; Transformation, Genetic ; }, abstract = {Phenotypic and molecular studies of the mutation U142 indicate that the cpc-2+ gene is required to activate general amino acid control under conditions of amino acid limitation in the vegetative growth phase, and for formation of protoperithecia in preparation for the sexual phase of the life cycle of Neurospora crassa. The cpc-2 gene was cloned by complementation of the cpc-2 mutation in a his-2ts bradytrophic background. Genomic and cDNA sequence analysis indicated a 1636 bp long open reading frame interrupted by four introns. The deduced 316 amino acid polypeptide reveals 70% positional identity over its full length with G-protein beta-subunit-related polypeptides found in humans, rat (RACK1), chicken, tobacco and Chlamydomonas. With the exception of RACK1 the function of these proteins is obscure. All are entirely made up of seven WD-repeats. Expression studies of cpc-2 revealed one abundant transcript in the wild type; in the mutant its level is drastically reduced. In mutant cells transformed with the complementing sequence, the transcript level, enzyme regulation and female fertility are restored. In the wild type the cpc-2 transcript is down-regulated under conditions of amino acid limitation. With cpc-2 a new element involved in general amino acid control has been identified, indicating a function for a WD-repeat protein that belongs to a class that is conserved throughout the evolution of eukaryotes.}, } @article {pmid7732579, year = {1995}, author = {Bird, AP}, title = {Gene number, noise reduction and biological complexity.}, journal = {Trends in genetics : TIG}, volume = {11}, number = {3}, pages = {94-100}, doi = {10.1016/S0168-9525(00)89009-5}, pmid = {7732579}, issn = {0168-9525}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Binding Sites ; Biological Evolution ; DNA/genetics/metabolism ; Eukaryota/genetics ; Eukaryotic Cells ; Fungi/genetics ; Gene Expression Regulation ; *Genes ; *Genome ; Invertebrates/genetics ; Methylation ; Multigene Family ; Prokaryotic Cells ; Regulatory Sequences, Nucleic Acid ; Transcription Factors/metabolism ; Transcription, Genetic ; Vertebrates/genetics ; }, abstract = {Preliminary estimates suggest that gene number, and hence biological complexity, increased suddenly at two periods of macroevolutionary change (the origin of eukaryotes and the origin of vertebrates), but otherwise remained relatively constant. As the genome is in constant flux, what normally constrains the number of different genes that an organism can retain? Here, I suggest that an important limitation on gene number is the efficiency of mechanisms that reduce transcriptional background noise. The appearance of both eukaryotes and vertebrates coincided with novel mechanisms of noise reduction.}, } @article {pmid7815931, year = {1994}, author = {Pawlowski, J and Bolivar, I and Guiard-Maffia, J and Gouy, M}, title = {Phylogenetic position of foraminifera inferred from LSU rRNA gene sequences.}, journal = {Molecular biology and evolution}, volume = {11}, number = {6}, pages = {929-938}, doi = {10.1093/oxfordjournals.molbev.a040174}, pmid = {7815931}, issn = {0737-4038}, mesh = {Animals ; Base Sequence ; Cloning, Molecular ; Consensus Sequence ; DNA, Protozoan/genetics/isolation & purification ; DNA, Ribosomal/*genetics ; Eukaryota/*genetics ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal/*genetics ; Rats/genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {A 5'-terminal region of 1600-1800 base pairs was amplified, cloned, and sequenced in the large subunit rDNA (LSU rDNA) of four species of foraminifera. These sequences were compared with the homologous regions of 16 eukaryotic taxa in order to establish the phylogenetic position of foraminifera. Analysis of 610 unambiguously aligned bases shows that foraminifera branch closely to plasmodial and cellular slime molds in the middle of the eukaryotic tree--that is, much earlier than suggested by the fossil record. These data, the first DNA sequences reported for foraminifera, will help analyze this class of protists and the early evolution of eukaryotes.}, } @article {pmid7953533, year = {1994}, author = {Sidow, A and Thomas, WK}, title = {A molecular evolutionary framework for eukaryotic model organisms.}, journal = {Current biology : CB}, volume = {4}, number = {7}, pages = {596-603}, doi = {10.1016/s0960-9822(00)00131-7}, pmid = {7953533}, issn = {0960-9822}, mesh = {Amino Acid Sequence ; Animal Population Groups/*genetics ; Animals ; Fungal Proteins/genetics ; Fungi/*genetics ; *Genes ; Genes, Fungal ; Genes, Plant ; Genetic Markers ; Humans ; Likelihood Functions ; *Models, Biological ; Molecular Sequence Data ; Multigene Family ; *Phylogeny ; Plant Proteins/genetics ; Plants/*genetics ; Polymerase Chain Reaction ; RNA Polymerase II/genetics ; RNA Polymerase III/genetics ; RNA, Fungal/genetics ; RNA, Plant/genetics ; RNA, Ribosomal, 18S/*genetics ; }, abstract = {BACKGROUND: Implicit in the characterization of a model organism is the hope that insights into its biology can be extended to other species. For this hope to be fulfilled, the phylogenetic position of the model organism within a larger evolutionary framework must be known. We focus here on major model organisms of developmental genetics and cell biology. We first consider the positions of the nematode Caenorhabditis elegans and the arthropod Drosophila melanogaster within a phylogeny of the major advanced metazoan groups. Then we consider the evolutionary relationships between fungi (represented by Saccharomyces cerevisiae and Schizosaccharomyces pombe), plants, and animals.

RESULTS: We show, by a direct comparison with small subunit ribosomal RNA (18 S rRNA), that RNA polymerase II is an appropriate molecule for addressing the phylogenetic branchings in the early evolution of eukaryotes. The results from the analyses of newly determined and previously published sequences of the two largest subunits of RNA polymerase II suggest the following. Firstly, that plants and animals share a last common ancestor that excludes fungi, the lineage of which originated earlier. Secondly, that the lineage leading to the nematode Caenorhabditis elegans diverged earlier from the Metazoa than the lineages of arthropods, deuterostomes, annelids and molluscs. Finally, that deuterostomes arose from within protostomes.

CONCLUSIONS: RNA polymerase II is well-suited for the elucidation of the evolutionary relationships among eukaryotes. We emphasize the implications of our results for other biological disciplines in addition to molecular evolution, as a phylogenetic framework allows predictions and inferences to be made about the existence of fundamental biological mechanisms elucidated in model organisms.}, } @article {pmid8186465, year = {1994}, author = {Gibbons, BH and Asai, DJ and Tang, WJ and Hays, TS and Gibbons, IR}, title = {Phylogeny and expression of axonemal and cytoplasmic dynein genes in sea urchins.}, journal = {Molecular biology of the cell}, volume = {5}, number = {1}, pages = {57-70}, pmid = {8186465}, issn = {1059-1524}, support = {GM-30401/GM/NIGMS NIH HHS/United States ; GM-44757/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Cilia/*chemistry ; Consensus Sequence ; Cytoplasm/*chemistry ; Dictyostelium/genetics ; Drosophila melanogaster/genetics ; Dyneins/*genetics ; Embryo, Nonmammalian/chemistry/ultrastructure ; Gene Expression Regulation ; *Genes ; Molecular Sequence Data ; *Multigene Family ; *Phylogeny ; Sea Urchins/embryology/*genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity ; }, abstract = {Transcripts approximately 14.5 kilobases in length from 14 different genes that encode for dynein heavy chains have been identified in poly(A)+ RNA from sea urchin embryos. Analysis of the changes in level of these dynein transcripts in response to deciliation, together with their sequence relatedness, suggests that 11 or more of these genes encode dynein isoforms that participate in regeneration of external cilia on the embryo, whereas the single gene whose deduced sequence closely resembles that of cytoplasmic dynein in other organisms appears not to be involved in this regeneration. The four consensus motifs for phosphate binding found previously in the beta heavy chain of sea urchin dynein are present in all five additional isoforms for which extended sequences have been obtained, suggesting that these sites play a significant role in dynein function. Sequence analysis of a approximately 400 amino acid region encompassing the putative hydrolytic ATP-binding site shows that the dynein genes fall into at least six distinct classes. Most of these classes in sea urchin have a high degree of sequence identity with one of the dynein heavy chain genes identified in Drosophila, indicating that the radiation of the dynein gene family into the present classes occurred at an early stage in the evolution of eukaryotes. Evolutionary changes in cytoplasmic dynein have been more constrained than those in the axonemal dyneins.}, } @article {pmid8121287, year = {1994}, author = {Hashimoto, T and Nakamura, Y and Nakamura, F and Shirakura, T and Adachi, J and Goto, N and Okamoto, K and Hasegawa, M}, title = {Protein phylogeny gives a robust estimation for early divergences of eukaryotes: phylogenetic place of a mitochondria-lacking protozoan, Giardia lamblia.}, journal = {Molecular biology and evolution}, volume = {11}, number = {1}, pages = {65-71}, doi = {10.1093/oxfordjournals.molbev.a040093}, pmid = {8121287}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; Base Composition ; Base Sequence ; Biological Evolution ; DNA Primers/genetics ; DNA, Protozoan/genetics ; Entamoeba histolytica/genetics ; Euglena gracilis/genetics ; Giardia lamblia/*genetics ; Molecular Sequence Data ; Peptide Elongation Factor 1 ; Peptide Elongation Factors/genetics ; *Phylogeny ; Plasmodium falciparum/genetics ; Protozoan Proteins/*genetics ; }, abstract = {A partial nucleotide sequence of the mRNA encoding a major part of elongation factor 1 alpha (EF1 alpha) from a mitochondria-lacking protozoan, Giardia lamblia, was reported, and the phylogenetic relationship among lower eukaryotes was inferred by the maximum-likelihood and maximum-parsimony methods of protein phylogeny. Both the methods consistently demonstrated that, G. lamblia among the four protozoan species being analyzed, is the earliest offshoot of the eukaryotic tree. Although the Giardia EF1 alpha gene showed an extremely high G+C content as compared with those of other protozoa, it was concentrated only at the third codon positions, resulting in no remarkable differences of amino acid frequencies vis-à-vis those of other species. This clearly suggests (a) that the amino acid frequencies of conservative proteins are free from the drastic bias of genome G+C content, which is a serious problem in the widely used tree of ribosomal RNA, and (b) that protein phylogeny gives a robust estimation for the early divergences in the evolution of eukaryotes.}, } @article {pmid8408041, year = {1993}, author = {Schneider, A and McNally, KP and Agabian, N}, title = {Splicing and 3'-processing of the tyrosine tRNA of Trypanosoma brucei.}, journal = {The Journal of biological chemistry}, volume = {268}, number = {29}, pages = {21868-21874}, pmid = {8408041}, issn = {0021-9258}, support = {AI21975/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; DNA, Protozoan ; Introns ; Molecular Sequence Data ; Nucleic Acid Conformation ; *RNA Processing, Post-Transcriptional ; *RNA Splicing ; RNA, Protozoan/chemistry/*genetics ; RNA, Transfer, Tyr/chemistry/*genetics ; Trypanosoma brucei brucei/*metabolism ; }, abstract = {Trypanosoma brucei belongs to a family of protozoa that is characterized as having diverged early in the evolution of eukaryotes. Many unusual forms of RNA processing have been discovered in these cells, one of which is trans-splicing, and, although a great number of genes have been sequenced, no evidence for cis-splicing has yet been found. This study shows that tRNA(Tyr) of T. brucei contains an 11-nucleotide intron. tRNA of the size predicted for unspliced precursor was detected by Northern analysis using an oligonucleotide probe complementary to the putative intervening region. Direct sequence analysis of mature tRNA(Tyr) showed that the predicted intron region is absent from this form of the molecule. Mutated versions of the gene encoding tRNA(Tyr) were introduced into trypanosomes by DNA transformation and shown to be expressed in vivo. Introduction into the genome of a tRNA(Tyr) gene containing an amber suppressor mutation led to a significant accumulation of unspliced precursor molecules. Analysis of the tRNA(Tyr) species from both the wild type and transformed cells revealed unspliced and spliced processing intermediates. The relative abundance of each of these intermediates suggests that 3'-processing and splicing occur independently and that, in the wild type, splicing tends to precede 3'-processing and CCA addition.}, } @article {pmid8372230, year = {1993}, author = {Hasegawa, M}, title = {[Phylogenetic place of Archaebacteria and the origin of eukaryotes].}, journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme}, volume = {38}, number = {10}, pages = {1546-1555}, pmid = {8372230}, issn = {0039-9450}, mesh = {Animals ; Archaea/*genetics ; *Genes, Overlapping ; Peptide Elongation Factor 1 ; Peptide Elongation Factor 2 ; Peptide Elongation Factor G ; Peptide Elongation Factor Tu ; Peptide Elongation Factors ; *Phylogeny ; RNA, Ribosomal, 5S ; }, } @article {pmid8472892, year = {1993}, author = {Herscovics, A and Orlean, P}, title = {Glycoprotein biosynthesis in yeast.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {7}, number = {6}, pages = {540-550}, doi = {10.1096/fasebj.7.6.8472892}, pmid = {8472892}, issn = {0892-6638}, support = {GM-31265/GM/NIGMS NIH HHS/United States ; GM-46220/GM/NIGMS NIH HHS/United States ; }, mesh = {Carbohydrate Metabolism ; Fungal Proteins/*biosynthesis/metabolism ; Glycoproteins/*biosynthesis/metabolism ; Glycosylation ; Glycosylphosphatidylinositols/metabolism ; Mannose/metabolism ; Saccharomyces cerevisiae/*metabolism ; }, abstract = {Many proteins in the yeast Saccharomyces cerevisiae are modified by the attachment of N-linked saccharides to asparagine, of O-linked mannose glycans to serine or threonine, and of glycosylphosphoinositol membrane anchors. The biosynthetic events leading to these modifications are coupled to the secretory pathway. Early stages of N-linked glycosylation and the formation of glycosylphosphoinositol anchors have been conserved through evolution of eukaryotes. Studies of yeast offer a variety of genetic and molecular biological approaches, which have led to the isolation of different glycosylation mutants and of genes for enzymes involved in glycosylation. Yeast mutants are useful to identify biosynthetic intermediates, to establish whether a given enzyme is essential for viability, and to determine how cellular functions are affected when glycosylation is perturbed. Yeast glycosylation mutants and genes can be used to identify their counterparts in other eukaryotes.}, } @article {pmid8315658, year = {1993}, author = {Hasegawa, M and Hashimoto, T and Adachi, J and Iwabe, N and Miyata, T}, title = {Early branchings in the evolution of eukaryotes: ancient divergence of entamoeba that lacks mitochondria revealed by protein sequence data.}, journal = {Journal of molecular evolution}, volume = {36}, number = {4}, pages = {380-388}, pmid = {8315658}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animal Population Groups/classification/genetics ; Animals ; Archaea/classification/genetics ; DNA, Ribosomal/genetics ; Entamoeba/*genetics ; *Eukaryotic Cells ; Fungi/classification/genetics ; Likelihood Functions ; Mitochondria ; Peptide Elongation Factor 1 ; Peptide Elongation Factors/*genetics ; *Phylogeny ; Plants/classification/genetics ; Protozoan Proteins/*genetics ; Species Specificity ; }, abstract = {Phylogenetic analyses of ribosomal RNA sequences have played an important role in the study of early evolution of life. However, Loomis and Smith suggested that the ribosomal RNA tree is sometimes misleading--especially when G+C content differs widely among lineages--and that a protein tree from amino acid sequences may be more reliable. In this study, we analyzed amino acid sequence data of elongation factor-1 alpha by a maximum likelihood method to clarify branching orders in the early evolution of eukaryotes. Contrary to Sogin et al.'s tree of small-subunit ribosomal RNA, a protozoan species, Entamoeba histolytica, that lacks mitochondria was shown to have diverged from the line leading to eukaryotes with mitochondria before the latter separated into several kingdoms. This indicates that Entamoeba is a living relic of the earliest phase of eukaryotic evolution before the symbiosis of protomitochondria occurred. Furthermore, this suggests that, among eukaryotic kingdoms with mitochondria, Fungi is the closest relative of Animalia, and that a cellular slime mold, Dictyostelium discoideum, had not diverged from the line leading to Plantae-Fungi-Animalia before these three kingdoms separated.}, } @article {pmid8445484, year = {1993}, author = {Cotton, DW}, title = {Intimate relations: the serial endosymbiotic theory of the origin of eukaryotes.}, journal = {The Journal of pathology}, volume = {169}, number = {2}, pages = {189-190}, doi = {10.1002/path.1711690203}, pmid = {8445484}, issn = {0022-3417}, mesh = {Animals ; Autoimmune Diseases ; *Biological Evolution ; Eukaryotic Cells/*physiology ; Host-Parasite Interactions ; Models, Biological ; Organelles/physiology ; Parasites/physiology ; *Symbiosis ; }, } @article {pmid1621096, year = {1992}, author = {Rivera, MC and Lake, JA}, title = {Evidence that eukaryotes and eocyte prokaryotes are immediate relatives.}, journal = {Science (New York, N.Y.)}, volume = {257}, number = {5066}, pages = {74-76}, doi = {10.1126/science.1621096}, pmid = {1621096}, issn = {0036-8075}, mesh = {Amino Acid Sequence ; Bacteria/*genetics ; Base Sequence ; *Biological Evolution ; DNA, Bacterial/genetics ; Humans ; Models, Molecular ; Molecular Sequence Data ; Peptide Elongation Factor 1 ; Peptide Elongation Factor G ; Peptide Elongation Factor Tu/chemistry/*genetics ; Peptide Elongation Factors/*genetics ; Peptide Initiation Factors/*genetics ; Phylogeny ; Plants/genetics ; Prokaryotic Initiation Factor-2 ; Protein Conformation ; Saccharomyces cerevisiae/genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {The phylogenetic origin of eukaryotes has been unclear because eukaryotic nuclear genes have diverged substantially from prokaryotic ones. The genes coding for elongation factor EF-1 alpha were compared among various organisms. The EF-1 alpha sequences of eukaryotes contained an 11-amino acid segment that was also found in eocytes (extremely thermophilic, sulfur-metabolizing bacteria) but that was absent in all other bacteria. The related (paralogous) genes encoding elongation factor EF-2 and initiation factor IF-2 also lacked the 11-amino acid insert. These data imply that the eocytes are the closest surviving relatives (sister taxon) of the eukaryotes.}, } @article {pmid1640383, year = {1992}, author = {Siddall, ME and Hong, H and Desser, SS}, title = {Phylogenetic analysis of the Diplomonadida (Wenyon, 1926) Brugerolle, 1975: evidence for heterochrony in protozoa and against Giardia lamblia as a "missing link".}, journal = {The Journal of protozoology}, volume = {39}, number = {3}, pages = {361-367}, doi = {10.1111/j.1550-7408.1992.tb01465.x}, pmid = {1640383}, issn = {0022-3921}, mesh = {Animals ; *Biological Evolution ; Diplomonadida/classification/*genetics ; Giardia lamblia/classification/*genetics ; Phylogeny ; }, abstract = {A suite of 23 ultrastructural characters was used in a phylogenetic analysis of the protozoan order Diplomonadida. A single most parsimonious solution was found, with a length of 38 transformations and a consistency index of 0.84. The cladogram supports previous hypotheses of the relationships of the genera in the suborder Diplomonadina, as well as the inclusion of the genera Enteromonas and Trimitus in the order. Heterochrony is suggested in the change to binary axial symmetry, as hypermorphosis resulting from delayed cytokinesis in the ancestor. Hypotheses regarding a pivotal position for Giardia lamblia in the evolution of eukaryotes are inconsistent with the phylogeny proposed here.}, } @article {pmid1585174, year = {1992}, author = {Knoll, AH}, title = {The early evolution of eukaryotes: a geological perspective.}, journal = {Science (New York, N.Y.)}, volume = {256}, number = {5057}, pages = {622-627}, doi = {10.1126/science.1585174}, pmid = {1585174}, issn = {0036-8075}, mesh = {*Biological Evolution ; Cyanobacteria ; Eukaryota ; *Eukaryotic Cells ; Fossils ; Geological Phenomena ; *Geology ; Mitochondria ; Phylogeny ; }, abstract = {Molecular phylogenies of eukaryotic organisms imply patterns of biological and environmental history that can be tested against the geological record. As predicted by sequence comparisons, Precambrian rocks show evidence of episodic increases in biological diversity and atmospheric oxygen concentrations. Nonetheless, complete integration of the two records remains elusive and may require that the earliest macroscopic organisms be recognized as extinct experiments in eukaryotic multicellularity.}, } @article {pmid1382081, year = {1992}, author = {Chevrier, V and Komesli, S and Schmit, AC and Vantard, M and Lambert, AM and Job, D}, title = {A monoclonal antibody, raised against mammalian centrosomes and screened by recognition of plant microtubule organizing centers, identifies a pericentriolar component in different cell types.}, journal = {Journal of cell science}, volume = {101 (Pt 4)}, number = {}, pages = {823-835}, doi = {10.1242/jcs.101.4.823}, pmid = {1382081}, issn = {0021-9533}, mesh = {Animals ; Antibodies, Monoclonal/*immunology ; Antibody Specificity ; Cattle ; Cell Line ; Centrioles/chemistry/*immunology ; Epitopes ; HeLa Cells ; Humans ; Immunoblotting ; Microscopy, Immunoelectron ; Microtubule Proteins/analysis/immunology ; Microtubules/*immunology ; Spindle Apparatus/immunology ; Thymus Gland/chemistry/ultrastructure ; Zea mays/chemistry/*immunology/ultrastructure ; }, abstract = {We have used monoclonal antibodies raised against isolated native calf thymus centrosomes to probe the structure and composition of the pericentriolar material. To distinguish prospective antibodies as specific to conserved elements of this material, we screened clones by their identification of microtubule organizing centers (MTOCs) in different animal and plant cells. Among the clonal antibodies that reacted with MTOCs in both plant and mammalian cells, we describe one (mAb 6C6) that was found to immunostain centrosomes in a variety of bovine and human cells. In cycling cells this signal persisted through the entire cell cycle. Microscopy showed that the mAb 6C6 antigen was a component of the pericentriolar material and this was confirmed by biochemical analysis of centrosomes. Using immunoblot analysis of protein fractions derived from purified components of centrosomes, we have characterized the mAb 6C6 antigen as a 180 kDa polypeptide. We conclude that we have identified a protein component permanently associated with the pericentriolar material. Surprisingly, monoclonal antibody 6C6 also stained other mitotic organelles in mammalian cells, in a cell-cycle-dependent manner. During prometaphase and metaphase the antibody stained both centrosomes and kinetochores. At the onset of anaphase the kinetochore-specific staining dissociated from chromosomes and was subsequently redistributed onto a newly characterized organelle, the telophase disc while the centrosomal stain remained intact. It is not known if the 180 kDa centrosomal protein itself redistributes during mitosis, or if the pattern observed represents other antigens with shared epitopes. The pericentriolar material is thought to be composed of conserved elements, which appeared very early during the evolution of eukaryotes. Our results strongly suggest that mAb 6C6 identifies one of these elements.}, } @article {pmid1339595, year = {1992}, author = {Perasso, R and Baroin-Tourancheau, A}, title = {[Eukaryogenesis: a model derivated from ribosomal RNA molecular phylogenise].}, journal = {Comptes rendus des seances de la Societe de biologie et de ses filiales}, volume = {186}, number = {6}, pages = {656-665}, pmid = {1339595}, issn = {0037-9026}, mesh = {Base Sequence ; *Eukaryotic Cells ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 28S/*genetics ; }, abstract = {We have undertaken the construction of a broad molecular phylogeny of protists through the comparison of 28S rRNA molecules. The sequences from several major protistan phyla were aligned and combined with a broad database of metazoans, metaphytes, fungi and bacteria and we have derived dendrograms from both distance matrix and parsimony methods. In agreement with classical systematics, a number of monophyletic groups separated by large evolutionary distances were observed (those of the ciliates, the chlorophytes, etc.). From this analysis, several inferences on the eukaryogenesis can be made among which the ancient origin of the cytoskeleton, the late occurrence of the chloroplastic endosymbiosis and the simultaneous emergence of the triploblastic and diploblastic metazoan patterns.}, } @article {pmid1822277, year = {1991}, author = {Sogin, ML}, title = {Early evolution and the origin of eukaryotes.}, journal = {Current opinion in genetics & development}, volume = {1}, number = {4}, pages = {457-463}, doi = {10.1016/s0959-437x(05)80192-3}, pmid = {1822277}, issn = {0959-437X}, support = {GM32964/GM/NIGMS NIH HHS/United States ; }, mesh = {Animal Population Groups/classification/*genetics ; Animals ; Bacteria/classification/genetics ; *Biological Evolution ; Cell Nucleus ; DNA, Ribosomal/genetics ; Fungi/classification/*genetics ; Genetic Code ; Genome ; Models, Biological ; Phylogeny ; Plants/classification/*genetics ; Proteins/genetics ; RNA, Ribosomal/genetics ; Symbiosis ; }, abstract = {Our understanding of evolutionary relationships in the eukaryotic world has been revolutionized by molecular systematics. Phylogenies based upon comparisons of rRNAs define five major eukaryotic assemblages plus a series of paraphyletic protist lineages. Comparison of conserved genes that were duplicated prior to the divergence of eubacteria, archaebacteria, and eukaryotes, positions the root of the universal tree within the eubacterial line of descent. In this review a novel model is presented which uses the rRNA and protein based phylogenies to describe the evolutionary origins of eukaryotes.}, } @article {pmid1672285, year = {1991}, author = {Kotula, L and Laury-Kleintop, LD and Showe, L and Sahr, K and Linnenbach, AJ and Forget, B and Curtis, PJ}, title = {The exon-intron organization of the human erythrocyte alpha-spectrin gene.}, journal = {Genomics}, volume = {9}, number = {1}, pages = {131-140}, doi = {10.1016/0888-7543(91)90230-c}, pmid = {1672285}, issn = {0888-7543}, support = {CA10815/CA/NCI NIH HHS/United States ; DK19482/DK/NIDDK NIH HHS/United States ; HL33884/HL/NHLBI NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; Erythrocytes/*metabolism ; *Exons ; Genes ; Humans ; *Introns ; Molecular Sequence Data ; Polymorphism, Restriction Fragment Length ; RNA Splicing ; Repetitive Sequences, Nucleic Acid ; Restriction Mapping ; Sequence Homology, Nucleic Acid ; Spectrin/*genetics ; }, abstract = {The human erythrocyte alpha-spectrin gene which spans 80 kbp has been cloned from human genomic DNA as overlapping lambda recombinants. The exon-intron junctions were identified and the exons mapped. The gene is encoded by 52 exons whose sizes range from 684 bp to the smallest of 18 bp. The donor and acceptor splice site sequences match the splice site consensus sequences, with the exception of one splice site where a donor sequence begins with -GC. The size and location of exons do not correlate with the 106-amino-acid repeat, except in three locations where the surrounding codons are conserved as well. The lack of correspondence between exons and 106-amino-acid repeat is interpreted to reflect the appearance of a spectrin-like gene from a minigene early in the evolution of eukaryotes. Since current evidence indicates that introns were present in genes before the divergence of prokaryotes and eukaryotes, it is possible that the original distribution of introns within the minigene has been lost by the random deletion of introns from the spectrin gene.}, } @article {pmid2111857, year = {1990}, author = {van Daal, A and White, EM and Elgin, SC and Gorovsky, MA}, title = {Conservation of intron position indicates separation of major and variant H2As is an early event in the evolution of eukaryotes.}, journal = {Journal of molecular evolution}, volume = {30}, number = {5}, pages = {449-455}, pmid = {2111857}, issn = {0022-2844}, support = {GM21793/GM/NIGMS NIH HHS/United States ; GM31532/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; *Biological Evolution ; Chickens ; DNA/analysis ; Drosophila/*genetics ; Eukaryotic Cells ; *Genetic Variation ; *Histones/*genetics ; *Introns ; Molecular Sequence Data ; Tetrahymena/*genetics ; }, abstract = {Genomic clones of Drosophila and Tetrahymena histone H2A variants were isolated using the corresponding cDNA clones (van Daal et al. 1988; White et al. 1988). The site corresponding to the initiation of transcription was defined by primer extension for both Drosophila and Tetrahymena genomic sequences. The sequences of the genomic clones revealed the presence of introns in each of the genes. The Drosophila gene has three introns: one immediately following the initiation codon, one between amino acids 26 and 27 (gln and phe), and one between amino acids 64 and 65 (glu and val). The Tetrahymena gene has two introns, the positions of which are identical to the first two introns of the Drosophila gene. The chicken H2A.F variant gene has been recently sequenced and it contains four introns (Dalton et al. 1989). The first three of these are in the same positions as the introns in the Drosophila gene. The fourth intron interrupts amino acid 108 (gly). In all cases the sizes and the sequences of the introns are divergent. However, the fact that they are in conserved positions suggests that at least two of the introns were present in the ancestral gene. A phylogenetic tree constructed from the sequences of the variant and major cell cycle-regulated histone H2A proteins from several species indicates that the H2A variant proteins are evolutionarily separate and distinct from the major cell cycle-regulated histone H2A proteins. The ancestral H2A gene must have duplicated and diverged before fungi and ciliates diverged from the rest of the eukaryote lineage. In addition, it appears that the variant histone H2A proteins analyzed here are more conserved than the major histone H2A proteins.}, } @article {pmid2683414, year = {1989}, author = {Nebert, DW and Nelson, DR and Feyereisen, R}, title = {Evolution of the cytochrome P450 genes.}, journal = {Xenobiotica; the fate of foreign compounds in biological systems}, volume = {19}, number = {10}, pages = {1149-1160}, doi = {10.3109/00498258909043167}, pmid = {2683414}, issn = {0049-8254}, mesh = {Animals ; *Biological Evolution ; Cytochrome P-450 Enzyme System/biosynthesis/*genetics ; Gene Expression Regulation, Enzymologic ; *Genes ; Multigene Family ; Plants/genetics ; }, abstract = {1. The P450 gene superfamily is presently known to contain more than 78 members, divided into 14 families. 2. The superfamily has undergone divergent evolution, and the ancestral gene is probably more than 2 billion years old. 3. The recent 'burst' in new P450 genes, particularly in the II family during the past 800 million years, appears to be the result of 'animal-plant warfare'. 4. Due to the presence or absence of a particular P450 gene in one species but not the other, it may not be correct to extrapolate toxicity or cancer data from rodent to human. 5. Increases in the P450 gene product (enzyme induction) almost always reflect an elevated rate in gene transcription, although there are several exceptions. 6. The mechanisms of P450 gene regulation (induction) by classes of inducers might become better understood through the comparison of different phyla that differ in response to a particular class of inducers. 7. Amongst several carefully selected phyla, delineation between which electron donor (presence of Fe2S2 protein or NADPH-P450 oxidoreductase, or both) interacts with P450 may provide valuable information about the evolution of eukaryotes from prokaryotes.}, } @article {pmid2528146, year = {1989}, author = {Gogarten, JP and Kibak, H and Dittrich, P and Taiz, L and Bowman, EJ and Bowman, BJ and Manolson, MF and Poole, RJ and Date, T and Oshima, T and Konishi, J and Denda, K and Yoshida, M}, title = {Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {86}, number = {17}, pages = {6661-6665}, pmid = {2528146}, issn = {0027-8424}, support = {GM-28703/GM/NIGMS NIH HHS/United States ; RR-08132/RR/NCRR NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Archaea/enzymology/*genetics ; Bacteria/*genetics ; *Biological Evolution ; Eukaryotic Cells/enzymology ; Gram-Negative Chemolithotrophic Bacteria/enzymology/*genetics ; Macromolecular Substances ; Molecular Sequence Data ; Phylogeny ; Proton-Translocating ATPases/*genetics ; Sequence Homology, Nucleic Acid ; Vacuoles/*enzymology ; }, abstract = {Active transport across the vacuolar components of the eukaryotic endomembrane system is energized by a specific vacuolar H+-ATPase. The amino acid sequences of the 70- and 60-kDa subunits of the vacuolar H+-ATPase are approximately equal to 25% identical to the beta and alpha subunits, respectively, of the eubacterial-type F0F1-ATPases. We now report that the same vacuolar H+-ATPase subunits are approximately equal to 50% identical to the alpha and beta subunits, respectively, of the sulfur-metabolizing Sulfolobus acidocaldarius, an archaebacterium (Archaeobacterium). Moreover, the homologue of an 88-amino acid stretch near the amino-terminal end of the 70-kDa subunit is absent from the F0F1-ATPase beta subunit but is present in the alpha subunit of Sulfolobus. Since the two types of subunits (alpha and beta subunits; 60- and 70-kDa subunits) are homologous to each other, they must have arisen by a gene duplication that occurred prior to the last common ancestor of the eubacteria, eukaryotes, and Sulfolobus. Thus, the phylogenetic tree of the subunits can be rooted at the site where the gene duplication occurred. The inferred evolutionary tree contains two main branches: a eubacterial branch and an eocyte branch that gave rise to Sulfolobus and the eukaryotic host cell. The implication is that the vacuolar H+-ATPase of eukaryotes arose by the internalization of the plasma membrane H+-ATPase of an archaebacterial-like ancestral cell.}, } @article {pmid3146644, year = {1988}, author = {Qi, GR and Cao, GJ and Jiang, P and Feng, XL and Gu, XR}, title = {Studies on the sites expressing evolutionary changes in the structure of eukaryotic 5S ribosomal RNA.}, journal = {Journal of molecular evolution}, volume = {27}, number = {4}, pages = {336-340}, pmid = {3146644}, issn = {0022-2844}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 5S/*genetics ; Species Specificity ; }, abstract = {We have determined the complete sequences of 5S rRNAs from a lamprey (Lampetra reissneri), a lancelet (Branchiostoma belcheri), silkworms (Philosamia cynthia ricini, Bombyx mori, Antheraea pernyi), and a silkworm hybrid (artificially fertilized hybrid species of Philosamia cynthia ricini male x Bombyx mori female), as well as those of cotton seeds (Gossypium hirsutum L.). Having compared more than 170 eukaryotic 5S rRNAs of which seven sequences have been determined by our group as mentioned above, we have found that the "evolutionary sites" that exist at special locations in these structures are closely related to the evolution of eukaryotes. The changes proceed step by step in an orderly way, i.e., the change in nucleotide residues of the "evolutionary sites" depends on the order of the evolution of the species and shows group-specific patterns.}, } @article {pmid3549607, year = {1987}, author = {Corliss, JO}, title = {Protistan phylogeny and eukaryogenesis.}, journal = {International review of cytology}, volume = {100}, number = {}, pages = {319-370}, doi = {10.1016/s0074-7696(08)61703-9}, pmid = {3549607}, issn = {0074-7696}, mesh = {Animals ; Eukaryota/classification/cytology/*genetics ; *Phylogeny ; Species Specificity ; }, } @article {pmid3300813, year = {1987}, author = {Szathmáry, E}, title = {Early evolution of microtubules and undulipodia.}, journal = {Bio Systems}, volume = {20}, number = {2}, pages = {115-131}, doi = {10.1016/0303-2647(87)90039-6}, pmid = {3300813}, issn = {0303-2647}, mesh = {*Biological Evolution ; *Cell Movement ; Cilia/*physiology ; Flagella/*physiology ; Microtubules/*physiology ; Models, Biological ; Spirochaeta/physiology ; }, abstract = {A critique of both autogeneous and symbiotic hypotheses for the origin of microtubules and cilia and eukaryotic flagella (undulipodia) is presented. It is proposed that spirochetes provided the ancient eukaryotic cell with microtubules twice; cytoplasmic microtubules originated from phagocytosed spirochetes whereas axopodial tubules of undulipodia were transformed from ectosymbiotic spirochetes. A role in transport for microtubules in spirochetes together with a detailed scenario by which free-living spirochetes attached as ectosymbionts and subsequently differentiated into undulipodia is outlined. A mechanism for the continuity of motility in the form of "training" of the novel microtubular axoneme by the ancient spirochete motility apparatus is proposed. Transitional states (missing links) are unlikely to have survived. Constraints regarding the nature of the host cell are discussed. A corresponding flowchart of the early evolution of eukaryotes is presented in which plastids and mitochondria are polyphyletic in their origins.}, } @article {pmid3541331, year = {1986}, author = {Seravin, LN}, title = {[The origin of the eukaryotic cell. IV. The general hypothesis of the autogenous origin of eukaryotes].}, journal = {Tsitologiia}, volume = {28}, number = {9}, pages = {899-910}, pmid = {3541331}, issn = {0041-3771}, mesh = {Aerobiosis ; Animals ; Biological Evolution ; Cell Membrane/ultrastructure ; Cells/*cytology ; Chloroplasts/ultrastructure ; DNA/genetics ; DNA, Bacterial/genetics ; Eukaryotic Cells/*cytology/metabolism ; Mitochondria/ultrastructure ; Mitosis ; Photosynthesis ; Prokaryotic Cells/cytology/metabolism ; }, abstract = {The general hypothesis of autogenous (non-symbiotic) origin of the eukaryotic cell summarises some hypotheses explaining possible ways of the origin of main components and organelles of such a cell (the primary unicellular protist). Six hypothesises are suggested. Arising of the eukaryotic surface membrane of protist (cell) as a result of modification of its lipidoacidic composition, when most of synblocks and ensembles of eukaryotic enzymes sink into the cytoplasm (due to membrane vesiculation). Establishment of eukaryotic cytoplasm on the basis of successive formation of two locomotory-supporting apparates: the primary one (microtrabecular system), and the second one (cytoskeleton). Arising of the nucleus from a polyheteronomous nucleoid of proeukaryotes. A combinatorical hypothesis of mitosis formation. Polyheteronucleoid hypothesis of the origin of the mitochondria and chloroplasts. Arising of the flagellum from the contractile tentacle-like organelle, whose axoneme is made of single microtubules. A close interrelation and interaction in the process of evolution is noted between surface membranes, the cytoplasm and the nucleus. In accord a principles of block-construction and heterochrony (see: Seravin, 1986r), the author explains the preservation of prokaryotic signs of organization in some components (and organelles) of eukaryotic cell (and protists).}, } @article {pmid556186, year = {1979}, author = {Anderson, KM and Bass, B and Saclarides, T}, title = {Cycloheximide insensitive nuclear protein synthesis partially suppressed by chloramphenicol: some possible implications in the evolution of eukaryotes.}, journal = {The International journal of biochemistry}, volume = {10}, number = {6}, pages = {523-527}, doi = {10.1016/0020-711x(79)90009-0}, pmid = {556186}, issn = {0020-711X}, mesh = {Animals ; Cell Line ; Cell Nucleus/drug effects/*metabolism ; Chloramphenicol/*metabolism ; Cricetinae ; Cycloheximide/*pharmacology ; Female ; Nucleoproteins/*biosynthesis ; Ovary ; Protein Biosynthesis/drug effects ; }, } @article {pmid132444, year = {1976}, author = {Goff, CG}, title = {Histones of Neurospora crassa.}, journal = {The Journal of biological chemistry}, volume = {251}, number = {13}, pages = {4131-4138}, pmid = {132444}, issn = {0021-9258}, mesh = {Amino Acids/analysis ; Animals ; Cattle ; Chromatin/analysis ; Chromosomes/analysis ; Electrophoresis, Polyacrylamide Gel ; Histones/*analysis/isolation & purification ; Mice ; Molecular Weight ; Neurospora/*analysis ; Neurospora crassa/*analysis ; Plants/analysis ; Species Specificity ; }, abstract = {Neurospora crassa chromatin isolated by a rapid method minimizing proteolytic degradation contains approximately one weight of acid-extractable basic protein per weight of DNA. This basic protein consists of five major polypeptide species which are similar in size to the histone proteins of higher eukaryotes and are present in approximately the same molar ratios. These five polypeptides have been purified by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. Their electrophoretic mobilities in polyacrylamide gels and their amino acid compositions indicate that they are histones homologous, although not identical, to the H1, H2A, H2B, H3, and H4 histones of mammals. The first 3 residues in the amino acid sequence of Neurospora H3 histone are identical to the first 3 residues in calf and pea H3; Neurospora H1, H2A, and H4 histones have blocked NH2 termini, like their mammalian counterparts. The finding of recognizable H1, H2A, H2B, H3, and H4 histones in Neurospora extends the range of eukaryotes now shown to contain a full complement of these strongly conserved chromosomal proteins, and supports the view that histones became involved in chromosome structure at a very early point in the evolution of eukaryotes.}, } @article {pmid4336057, year = {1972}, author = {Sonea, S}, title = {Bacterial plasmids instrumental in the origin of eukaryotes?.}, journal = {Revue canadienne de biologie}, volume = {31}, number = {1}, pages = {61-63}, pmid = {4336057}, issn = {0035-0915}, mesh = {Bacteria/*cytology ; *Cell Nucleus ; DNA, Bacterial/biosynthesis ; Diploidy ; *Genetics, Microbial ; Haploidy ; *Inclusion Bodies ; Symbiosis ; }, } @article {pmid5657061, year = {1968}, author = {Weyl, PK}, title = {Precambrian marine environment and the development of life.}, journal = {Science (New York, N.Y.)}, volume = {161}, number = {3837}, pages = {158-160}, doi = {10.1126/science.161.3837.158}, pmid = {5657061}, issn = {0036-8075}, mesh = {Eukaryota ; Marine Biology ; *Oceanography ; *Origin of Life ; Oxygen ; *Paleontology ; Photosynthesis ; }, abstract = {The tropical thermocline must have existed since the ocean's depth exceeded 300 meters. The density gradient in this layer concentrated organic aggregates formed abiologically near the surface of the sea, and the low rates of diflusion across this layer permitted the accumulation of oxygen once the layer was populated by blue-green algae; thus the evolution of eukaryotes became possible within the layer. Because of rapid mixing over the shelves, the eukaryotes were restricted initially to the thermocline over deep water. The shelves could not be permanently inhabited by organisms requiring respiration until the oxygen level of the atmosphere was adequate. At this stage, the swimming Metazoa of the thermocline could adapt to a benthic environment on the shelves by developing exoskeletons.}, }