@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},
mesh = {Humans ; *Nuclear Pore/metabolism ; *Cell Nucleus/metabolism ; Nuclear Pore Complex Proteins/chemistry ; Mitosis ; Interphase ; Nuclear Envelope/metabolism ; },
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.},
}

Humans
*Nuclear Pore/metabolism
*Cell Nucleus/metabolism
Nuclear Pore Complex Proteins/chemistry
Mitosis
Interphase
Nuclear Envelope/metabolism

@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 {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.},
}

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

@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},
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.},
}

Animals
*Gene Duplication
Phylogeny
Synteny
*Eukaryota
Sequence Alignment

@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.},
}

Animals
Pseudogenes
Phylogeny
Open Reading Frames
Genome
*Trypanosoma brucei brucei/genetics
*Parasites/genetics

@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.},
}

Archaea
Bacteria
*Chlamydomonas reinhardtii/genetics
*Flagella/metabolism

@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.},
}

*Eukaryota/genetics
*Eukaryotic Cells
Guanosine Triphosphate
Likelihood Functions
Phylogeny

@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.},
}

*Biological Evolution
*Eukaryota
Phylogeny
Symbiosis

@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},
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.},
}

*Microalgae/metabolism
Sirolimus/metabolism
Signal Transduction
Photosynthesis
Eukaryota

@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.},
}

*Archaea/genetics
Bacteria/genetics
Evolution, Molecular
*Gene Transfer, Horizontal
Phylogeny

@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.},
}

Chromosomes
*Crossing Over, Genetic/genetics
Eukaryota/genetics
Genome
Meiosis
*RNA, Circular
Selection, Genetic

@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.},
}

Cytoplasm/genetics
*Eukaryota/genetics
Genome
*Inheritance Patterns
Symbiosis

@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},
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.},
}

Active Transport, Cell Nucleus
*Biological Phenomena
Nuclear Envelope/metabolism
*Nuclear Pore/metabolism
Nuclear Pore Complex Proteins/metabolism
Plant Breeding
Plants/metabolism

@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.},
}

Bacteria
*Gammaproteobacteria
Host Adaptation
*Legionella/genetics
Virulence Factors

@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 {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.},
}

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

@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.},
}

*Archaea/genetics
*Eukaryota
Phylogeny

@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 = {R01 GM067862/GM/NIGMS NIH HHS/United States ; R35 GM139607/GM/NIGMS NIH HHS/United States ; 1R35GM139607/NH/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.},
}

Animals
Cell Nucleus/genetics
DNA, Mitochondrial/genetics
*Drosophila/genetics
Epistasis, Genetic
*Genome, Mitochondrial
Mitochondria/genetics

@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 = {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.},
}

Alleles
Diploidy
Genotype
*Genotyping Techniques
*High-Throughput Nucleotide Sequencing/methods
*Plants/genetics
*Polyploidy

@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.},
}

*Escherichia coli Proteins/genetics
*Eukaryota/genetics/metabolism
Evolution, Molecular
Membrane Transport Proteins/genetics/metabolism
Mitochondria/genetics/metabolism
Mitochondrial Proteins/genetics/metabolism
Protein Transport

@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.},
}

*Archaea/genetics/metabolism
*Eukaryota/genetics
Eukaryotic Cells/metabolism
Phylogeny

@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.},
}

*Biological Evolution
Eukaryota/genetics
*Eukaryotic Cells/metabolism
Phylogeny
Prokaryotic Cells/metabolism
Symbiosis

@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},
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.},
}

Algorithms
*Evolution, Molecular
Gene Duplication
*Gene Transfer, Horizontal
Genome
Phylogeny
Symbiosis/genetics

@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.},
}

Animals
*DNA Transposable Elements
*Evolution, Molecular
Humans
Plants/genetics

@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.},
}

Archaea/genetics
*Biological Evolution
*Eukaryota/genetics
Eukaryotic Cells
Phylogeny
Prokaryotic Cells

@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.},
}

Cell Nucleus/*genetics
Chloroplasts/*genetics
Endophytes/genetics
*Gene Transfer, Horizontal
Genome
Mitochondria/*genetics
Plants/genetics
Plastids/genetics

@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.},
}

Archaea/*classification
Biological Evolution
Eukaryota
*Genome, Archaeal
Metagenomics
*Phylogeny

@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.},
}

Animals
*Biological Evolution
Eukaryota/*genetics
*Genes, gag
Retroelements/*genetics
Selection, Genetic

@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.},
}

Animals
*Biological Evolution
Cell Survival/physiology
DNA, Mitochondrial/*physiology
Eukaryota/genetics/*growth & development
Eukaryotic Cells/*physiology
*Evolution, Molecular
Humans
Mitochondria/physiology
Time Factors

@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.},
}

*Archaea/genetics
Biological Evolution
*Eukaryota
Eukaryotic Cells
Evolution, Molecular
Phylogeny

@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.},
}

Basal Bodies
*Biological Evolution
Cell Movement
Centromere
*Eukaryotic Cells
Flagella
Genome, Mitochondrial
Genome, Plastid
Microbial Consortia
Organelles/genetics
*Prokaryotic Cells
*Symbiosis

@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.},
}

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

@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 ; },
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 {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},
support = {R15 HG010409/HG/NHGRI NIH HHS/United States ; },
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.},
}

*DNA Transposable Elements
Epigenesis, Genetic
Eukaryota/*genetics
*Evolution, Molecular
*Models, Genetic

@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.},
}

Aquatic Organisms/*classification/ultrastructure
*Biodiversity
Curacao
Eukaryota/*classification/ultrastructure
Microscopy, Electron, Transmission
Seawater/*parasitology
Species Specificity

@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.},
}

Animals
*Autotrophic Processes
Bacteria, Anaerobic/genetics/*metabolism
Cell Nucleus/genetics/*metabolism
Eukaryota/genetics/*metabolism
Humans
Phylogeny
Plants/genetics/*metabolism
Russia
*Symbiosis
Translating

@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.},
}

Bacteria/*chemistry/genetics
Biological Evolution
Eukaryota/*chemistry/genetics
Lipid Droplets/*chemistry
Organelles
Plastids
Symbiosis

@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.},
}

Archaea/classification/genetics
*Biological Evolution
*Eukaryota/classification/genetics
Research/trends

@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.},
}

*Archaea/genetics
*Eukaryota
Geologic Sediments
Phylogeny
RNA, Ribosomal, 16S/genetics
Salinity

@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.},
}

Archaea/genetics
*Biological Evolution
*Eukaryota/genetics
Eukaryotic Cells
Phylogeny
Prokaryotic Cells
Symbiosis

@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.},
}

Animals
*Biological Evolution
Eukaryota/classification/genetics/metabolism
History, 20th Century
History, 21st Century
Humans
Phylogeny
RNA/physiology
Telomerase/*chemistry/*physiology
Telomere/metabolism

@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.},
}

Animals
Conserved Sequence
DNA Repair/*genetics
Eukaryota/*genetics
*Evolution, Molecular
Humans
Introns/genetics
Phylogeny

@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.},
}

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

@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.},
}

Archaea/classification/*genetics
Geologic Sediments/microbiology
In Situ Hybridization, Fluorescence/*methods
Microscopy, Fluorescence
Oligonucleotide Probes/*genetics
Phylogeny

@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 ; U01 HL116321/HL/NHLBI 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 {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.},
}

Archaea/genetics/metabolism
*Biological Evolution
DNA, Mitochondrial/genetics
Eukaryota/*genetics/*physiology
Gene Deletion
Mitochondria/genetics/*physiology

@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.},
}

*Archaea/classification/genetics/growth & development/metabolism
*Biodiversity
*Biological Evolution
*Ecology
Energy Metabolism
Environmental Microbiology
Genetic Variation
Genome, Archaeal
Phylogeny

@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.},
}

*Biological Evolution
Eukaryotic Cells/*physiology
Extracellular Space/*physiology
*Microbial Interactions
Models, Biological
Phagocytosis
Prokaryotic Cells/*physiology
Symbiosis

@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.},
}

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

@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 {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.},
}

Amino Acids/metabolism
Archaea/*enzymology
Carbon Cycle
Ecosystem
Fatty Acids/metabolism
Genomics
Geologic Sediments/*chemistry
*Metagenome
Peptides/metabolism
*Phylogeny

@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},
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.},
}

Animals
*Autophagy
*Drug Resistance, Neoplasm
*Homeostasis
Humans
Lysosomes/*pathology
Neoplasms/*pathology

@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.},
}

Cell Membrane/chemistry/*metabolism
Endoplasmic Reticulum/*metabolism
Lipid Metabolism
Lipids/*chemistry
Mitochondria/chemistry/*metabolism

@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.},
}

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

@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 ; },
}

*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.},
}

Anaerobiosis
Archaea/classification/*genetics/*metabolism
Carbon Cycle
Energy Metabolism
Fermentation
Genome, Archaeal
Geologic Sediments/microbiology
Metagenomics
Models, Biological
Oxidation-Reduction
Sulfides/metabolism

@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.},
}

*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

@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'.},
}

Eukaryota/cytology/genetics/*physiology
Genomics

@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.},
}

Archaea/*physiology
*Biological Evolution
DNA
Eukaryotic Cells/*physiology
Histones/*physiology
Mitochondria/physiology
Symbiosis

@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.},
}

*Biological Evolution
*Cell Nucleus
*Eukaryotic Cells
*Nuclear Pore
*Prokaryotic Cells

@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.},
}

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

@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.},
}

Algorithms
Animals
Evolution, Molecular
Gene Transfer, Horizontal
Humans
*Multigene Family
Phylogeny

@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.},
}

Archaea/genetics/metabolism
*Biological Evolution
Eukaryotic Cells/metabolism
Mitochondria/*genetics
*Phylogeny
Prokaryotic Cells/metabolism
Symbiosis/*genetics

@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.},
}

Biological Evolution
Blastocystis/cytology/enzymology/genetics/*metabolism
Diatoms/cytology/enzymology/genetics/*metabolism
Energy Metabolism
Genome, Mitochondrial
*Glycolysis
Mitochondria/genetics/*metabolism
Symbiosis
Transformation, Genetic

@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.},
}

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

@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.},
}

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

@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.},
}

Chimera/*genetics/*metabolism
*Databases, Genetic
Eukaryotic Cells/*physiology
*Evolution, Molecular
*Phylogeny

@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.},
}

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

@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.},
}

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

@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.},
}

Alveolata/classification/*genetics
*Evolution, Molecular
*Genome, Mitochondrial
Phylogeny

@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.},
}

AMP-Activated Protein Kinases/chemistry/*metabolism
Adenine Nucleotides/metabolism
Animals
Binding Sites
Biological Evolution
*Energy Metabolism
Glucose/*metabolism
Humans

@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.},
}

Animals
Anthozoa/*physiology
Biological Evolution
Dinoflagellida/*physiology
*Symbiosis

@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.},
}

Archaea/*genetics
*Biological Evolution
Eukaryota/*genetics
Pharmacogenomic Variants

@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.},
}

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

@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.},
}

Cyanobacteria/classification/*genetics/*physiology
Diatoms/*microbiology
Evolution, Molecular
Genomics
Phylogeny
Symbiosis/genetics/*physiology

@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.},
}

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

@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.},
}

Animals
*Biological Evolution
Gastrointestinal Tract/anatomy & histology
Isoptera/anatomy & histology
*Phylogeny
*Symbiosis

@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.},
}

Bacteria/genetics
Eukaryotic Cells
Interspersed Repetitive Sequences
*Introns
RNA, Catalytic/genetics
Spliceosomes

@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.},
}

*Biological Evolution
Energy Metabolism
Genome, Mitochondrial
*Mitochondria
*Models, Biological
Phagocytosis
Phylogeny

@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.},
}

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

@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.},
}

*Biological Evolution
Earth, Planet
*Eukaryota
*Prokaryotic Cells

@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.},
}

Animals
Archaea/classification/cytology
*Biological Evolution
Biological Transport
Coated Vesicles/chemistry/*genetics/metabolism
Eukaryotic Cells/classification/*cytology/metabolism
Humans
Membrane Proteins/genetics/metabolism

@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.},
}

Adaptation, Biological
Animals
Eukaryotic Cells/cytology/*physiology
*Evolution, Molecular
Fungi/genetics
Humans
*Metagenomics
Phylogeny
Rho Guanine Nucleotide Exchange Factors/*genetics
Signal Transduction
Vertebrates/genetics

@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.},
}

*Biological Evolution
Energy Metabolism
Eukaryota/*cytology
Genomics
Membranes/metabolism
Organelles
Organogenesis/*genetics
Symbiosis/*genetics

@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.},
}

Actins/genetics/*metabolism
Archaea/genetics/*metabolism
Archaeal Proteins/genetics/*metabolism
Cytoskeleton
Phylogeny
Pyrobaculum/genetics/metabolism

@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.},
}

Archaea/genetics
Bacteria/genetics
Bayes Theorem
Eukaryota/genetics
*Evolution, Molecular
*Genome
Mitochondria
*Models, Genetic
*Phylogeny
*Proteome

@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.},
}

Animals
Cytochrome P-450 Enzyme System/*metabolism
Fungi/metabolism
Mitochondria/enzymology/*metabolism
Plants/metabolism

@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.},
}

Animals
Glyceraldehyde-3-Phosphate Dehydrogenases/genetics/*metabolism
Humans
Mitochondria/genetics/metabolism
Phylogeny
Plastids/enzymology
Symbiosis/genetics/physiology

@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.},
}

Bacterial Proteins/metabolism
Cell Compartmentation/*genetics
Chlamydia/genetics
Eukaryota/genetics
*Evolution, Molecular
*Nuclear Envelope
Phylogeny
Tubulin/genetics/metabolism
Ubiquitin/genetics/metabolism
Verrucomicrobia/genetics

@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.},
}

Animals
Humans
RNA-Binding Proteins/*chemistry/*metabolism

@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 ; R00 GM108865/GM/NIGMS NIH HHS/United States ; K99 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.},
}

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

@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.},
}

Archaea/*genetics
Bacteria/*genetics
Eukaryota/*genetics
*Evolution, Molecular