@article {pmid37276405,
year = {2023},
author = {Kumar, P and Babu, KSD and Singh, AK and Singh, DK and Nalli, A and Mukul, SJ and Roy, A and Mazeed, M and Raman, B and Kruparani, SP and Siddiqi, I and Sankaranarayanan, R},
title = {Distinct localization of chiral proofreaders resolves organellar translation conflict in plants.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {24},
pages = {e2219292120},
doi = {10.1073/pnas.2219292120},
pmid = {37276405},
issn = {1091-6490},
abstract = {Plants have two endosymbiotic organelles originated from two bacterial ancestors. The transition from an independent bacterium to a successful organelle would have required extensive rewiring of biochemical networks for its integration with archaeal host. Here, using Arabidopsis as a model system, we show that plant D-aminoacyl-tRNA deacylase 1 (DTD1), of bacterial origin, is detrimental to organellar protein synthesis owing to its changed tRNA recognition code. Plants survive this conflict by spatially restricting the conflicted DTD1 to the cytosol. In addition, plants have targeted archaeal DTD2 to both the organelles as it is compatible with their translation machinery due to its strict D-chiral specificity and lack of tRNA determinants. Intriguingly, plants have confined bacterial-derived DTD1 to work in archaeal-derived cytosolic compartment whereas archaeal DTD2 is targeted to bacterial-derived organelles. Overall, the study provides a remarkable example of the criticality of optimization of biochemical networks for survival and evolution of plant mitochondria and chloroplast.},
}

@article {pmid37254790,
year = {2023},
author = {López-García, P and Moreira, D},
title = {The symbiotic origin of the eukaryotic cell.},
journal = {Comptes rendus biologies},
volume = {346},
number = {},
pages = {55-73},
doi = {10.5802/crbiol.118},
pmid = {37254790},
issn = {1768-3238},
abstract = {Eukaryogenesis represented a major evolutionary transition that led to the emergence of complex cells from simpler ancestors. For several decades, the most accepted scenario involved the evolution of an independent lineage of proto-eukaryotes endowed with an endomembrane system, including a nuclear compartment, a developed cytoskeleton and phagocytosis, which engulfed the alphaproteobacterial ancestor of mitochondria. However, the recent discovery by metagenomic and cultural approaches of Asgard archaea, which harbour many genes in common with eukaryotes and are their closest relatives in phylogenomic trees, rather supports scenarios based on the symbiosis of one Asgard-like archaeon and one or more bacteria at the origin of the eukaryotic cell. Here, we review the recent discoveries that led to this conceptual shift, briefly evoking current models of eukaryogenesis and the challenges ahead to discriminate between them and to establish a detailed, plausible scenario that accounts for the evolution of eukaryotic traits from those of their prokaryotic ancestors.},
}

@article {pmid37236370,
year = {2023},
author = {Řezanka, T and Kyselová, L and Murphy, DJ},
title = {Archaeal lipids.},
journal = {Progress in lipid research},
volume = {91},
number = {},
pages = {101237},
doi = {10.1016/j.plipres.2023.101237},
pmid = {37236370},
issn = {1873-2194},
abstract = {The major archaeal membrane glycerolipids are distinguished from those of bacteria and eukaryotes by the contrasting stereochemistry of their glycerol backbones, and by the use of ether-linked isoprenoid-based alkyl chains rather than ester-linked fatty acyl chains for their hydrophobic moieties. These fascinating compounds play important roles in the extremophile lifestyles of many species, but are also present in the growing numbers of recently discovered mesophilic archaea. The past decade has witnessed significant advances in our understanding of archaea in general and their lipids in particular. Much of the new information has come from the ability to screen large microbial populations via environmental metagenomics, which has revolutionised our understanding of the extent of archaeal biodiversity that is coupled with a strict conservation of their membrane lipid compositions. Significant additional progress has come from new culturing and analytical techniques that are gradually enabling archaeal physiology and biochemistry to be studied in real time. These studies are beginning to shed light on the much-discussed and still-controversial process of eukaryogenesis, which probably involved both bacterial and archaeal progenitors. Puzzlingly, although eukaryotes retain many attributes of their putative archaeal ancestors, their lipid compositions only reflect their bacterial progenitors. Finally, elucidation of archaeal lipids and their metabolic pathways have revealed potentially interesting applications that have opened up new frontiers for biotechnological exploitation of these organisms. This review is concerned with the analysis, structure, function, evolution and biotechnology of archaeal lipids and their associated metabolic pathways.},
}

@article {pmid37226840,
year = {2023},
author = {Spitzer, J},
title = {Physicochemical origins of prokaryotic and eukaryotic organisms.},
journal = {The Journal of physiology},
volume = {},
number = {},
pages = {},
doi = {10.1113/JP284428},
pmid = {37226840},
issn = {1469-7793},
abstract = {figure legend The continuity of Earth's chemical and Darwinian evolutions. Microbial life on Earth was created by diurnal (cycling) forces and gradients arising from the rotation of the Sun-irradiated Earth. On a colloidal level, prokaryotic life emerged from carbonaceous, geochemical inclusions in the sediments of Usiglio-type pools, which were cyclically energized by chemical reactions and tidal phase separations ("purifications"). Fusions and rehydrations of prokaryotes (natural genetic engineering) initiated the evolution of eukaryotes during the Precambrian supereon. This article is protected by copyright. All rights reserved.},
}

@article {pmid37127702,
year = {2023},
author = {Krupovic, M and Dolja, VV and Koonin, EV},
title = {The virome of the last eukaryotic common ancestor and eukaryogenesis.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {37127702},
issn = {2058-5276},
abstract = {All extant eukaryotes descend from the last eukaryotic common ancestor (LECA), which is thought to have featured complex cellular organization. To gain insight into LECA biology and eukaryogenesis-the origin of the eukaryotic cell, which remains poorly understood-we reconstructed the LECA virus repertoire. We compiled an inventory of eukaryotic hosts of all major virus taxa and reconstructed the LECA virome by inferring the origins of these groups of viruses. The origin of the LECA virome can be traced back to a small set of bacterial-not archaeal-viruses. This provenance of the LECA virome is probably due to the bacterial origin of eukaryotic membranes, which is most compatible with two endosymbiosis events in a syntrophic model of eukaryogenesis. In the first endosymbiosis, a bacterial host engulfed an Asgard archaeon, preventing archaeal viruses from entry owing to a lack of archaeal virus receptors on the external membranes.},
}

@article {pmid37105243,
year = {2023},
author = {Su, H and Xu, J and Li, J and Yi, Z},
title = {Four ciliate-specific expansion events occurred during actin gene family evolution of eukaryotes.},
journal = {Molecular phylogenetics and evolution},
volume = {184},
number = {},
pages = {107789},
doi = {10.1016/j.ympev.2023.107789},
pmid = {37105243},
issn = {1095-9513},
mesh = {*Actins/genetics ; Phylogeny ; Multigene Family ; Transcriptome ; *Ciliophora/genetics ; Evolution, Molecular ; },
abstract = {Actin gene family is a divergent and ancient eukaryotic cellular cytoskeletal gene family, and participates in many essential cellular processes. Ciliated protists offer us an excellent opportunity to investigate gene family evolution, since their gene families evolved faster in ciliates than in other eukaryotes. Nonetheless, actin gene family is well studied in few model ciliate species but little is known about its evolutionary patterns in ciliates. Here, we analyzed the evolutionary pattern of eukaryotic actin gene family based on genomes/transcriptomes of 36 species covering ten ciliate classes, as well as those of nine non-ciliate eukaryotic species. Results showed: (1) Except for conventional actins and actin-related proteins (Arps) shared by various eukaryotes, at least four ciliate-specific subfamilies occurred during evolution of actin gene family. Expansions of Act2 and ArpC were supposed to have happened in the ciliate common ancestor, while expansions of ActI and ActII may have occurred in the ancestor of Armophorea, Muranotrichea, and Spirotrichea. (2) The number of actin isoforms varied greatly among ciliate species. Environmental adaptability, whole genome duplication (WGD) or segmental duplication events, distinct spatial and temporal patterns of expression might play driving forces for the variation of isoform numbers. (3) The 'birth and death' model of evolution could explain the evolution of actin gene family in ciliates. And actin genes have been generally under strong negative selection to maintain protein structures and physiological functions. Collectively, we provided meaningful information for understanding the evolution of eukaryotic actin gene family.},
}

*Actins/genetics
Phylogeny
Multigene Family
Transcriptome
*Ciliophora/genetics
Evolution, Molecular

@article {pmid37071674,
year = {2023},
author = {Libby, E and Kempes, CP and Okie, JG},
title = {Metabolic compatibility and the rarity of prokaryote endosymbioses.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {17},
pages = {e2206527120},
pmid = {37071674},
issn = {1091-6490},
mesh = {Phylogeny ; *Symbiosis/genetics ; *Prokaryotic Cells/metabolism ; Eukaryota/genetics ; Eukaryotic Cells/metabolism ; Biological Evolution ; },
abstract = {The evolution of the mitochondria was a significant event that gave rise to the eukaryotic lineage and most large complex life. Central to the origins of the mitochondria was an endosymbiosis between prokaryotes. Yet, despite the potential benefits that can stem from a prokaryotic endosymbiosis, their modern occurrence is exceptionally rare. While many factors may contribute to their rarity, we lack methods for estimating the extent to which they constrain the appearance of a prokaryotic endosymbiosis. Here, we address this knowledge gap by examining the role of metabolic compatibility between a prokaryotic host and endosymbiont. We use genome-scale metabolic flux models from three different collections (AGORA, KBase, and CarveMe) to assess the viability, fitness, and evolvability of potential prokaryotic endosymbioses. We find that while more than half of host-endosymbiont pairings are metabolically viable, the resulting endosymbioses have reduced growth rates compared to their ancestral metabolisms and are unlikely to gain mutations to overcome these fitness differences. In spite of these challenges, we do find that they may be more robust in the face of environmental perturbations at least in comparison with the ancestral host metabolism lineages. Our results provide a critical set of null models and expectations for understanding the forces that shape the structure of prokaryotic life.},
}

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

@article {pmid36965057,
year = {2023},
author = {Speijer, D},
title = {How mitochondria showcase evolutionary mechanisms and the importance of oxygen.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {45},
number = {6},
pages = {e2300013},
doi = {10.1002/bies.202300013},
pmid = {36965057},
issn = {1521-1878},
mesh = {*Biological Evolution ; *Oxygen/metabolism ; Eukaryota/metabolism ; Bacteria/genetics/metabolism ; Mitochondria/metabolism ; },
abstract = {Darwinian evolution can be simply stated: natural selection of inherited variations increasing differential reproduction. However, formulated thus, links with biochemistry, cell biology, ecology, and population dynamics remain unclear. To understand interactive contributions of chance and selection, higher levels of biological organization (e.g., endosymbiosis), complexities of competing selection forces, and emerging biological novelties (such as eukaryotes or meiotic sex), we must analyze actual examples. Focusing on mitochondria, I will illuminate how biology makes sense of life's evolution, and the concepts involved. First, looking at the bacterium - mitochondrion transition: merging with an archaeon, it lost its independence, but played a decisive role in eukaryogenesis, as an extremely efficient aerobic ATP generator and internal ROS source. Second, surveying later mitochondrion adaptations and diversifications illustrates concepts such as constructive neutral evolution, dynamic interactions between endosymbionts and hosts, the contingency of life histories, and metabolic reprogramming. Without oxygen, mitochondria disappear; with (intermittent) oxygen diversification occurs in highly complex ways, especially upon (temporary) phototrophic substrate supply. These expositions show the Darwinian model to be a highly fruitful paradigm.},
}

*Biological Evolution
*Oxygen/metabolism
Eukaryota/metabolism
Bacteria/genetics/metabolism
Mitochondria/metabolism

@article {pmid36921606,
year = {2023},
author = {Muñoz-Gómez, SA and Cadena, LR and Gardiner, AT and Leger, MM and Sheikh, S and Connell, LB and Bilý, T and Kopejtka, K and Beatty, JT and Koblížek, M and Roger, AJ and Slamovits, CH and Lukeš, J and Hashimi, H},
title = {Intracytoplasmic-membrane development in alphaproteobacteria involves the homolog of the mitochondrial crista-developing protein Mic60.},
journal = {Current biology : CB},
volume = {33},
number = {6},
pages = {1099-1111.e6},
doi = {10.1016/j.cub.2023.02.059},
pmid = {36921606},
issn = {1879-0445},
mesh = {*Mitochondrial Proteins/metabolism ; *Alphaproteobacteria/genetics/metabolism ; Mitochondrial Membranes/metabolism ; Mitochondria/metabolism ; Biological Evolution ; },
abstract = {Mitochondrial cristae expand the surface area of respiratory membranes and ultimately allow for the evolutionary scaling of respiration with cell volume across eukaryotes. The discovery of Mic60 homologs among alphaproteobacteria, the closest extant relatives of mitochondria, suggested that cristae might have evolved from bacterial intracytoplasmic membranes (ICMs). Here, we investigated the predicted structure and function of alphaproteobacterial Mic60, and a protein encoded by an adjacent gene Orf52, in two distantly related purple alphaproteobacteria, Rhodobacter sphaeroides and Rhodopseudomonas palustris. In addition, we assessed the potential physical interactors of Mic60 and Orf52 in R. sphaeroides. We show that the three α helices of mitochondrial Mic60's mitofilin domain, as well as its adjacent membrane-binding amphipathic helix, are present in alphaproteobacterial Mic60. The disruption of Mic60 and Orf52 caused photoheterotrophic growth defects, which are most severe under low light conditions, and both their disruption and overexpression led to enlarged ICMs in both studied alphaproteobacteria. We also found that alphaproteobacterial Mic60 physically interacts with BamA, the homolog of Sam50, one of the main physical interactors of eukaryotic Mic60. This interaction, responsible for making contact sites at mitochondrial envelopes, has been conserved in modern alphaproteobacteria despite more than a billion years of evolutionary divergence. Our results suggest a role for Mic60 in photosynthetic ICM development and contact site formation at alphaproteobacterial envelopes. Overall, we provide support for the hypothesis that mitochondrial cristae evolved from alphaproteobacterial ICMs and have therefore improved our understanding of the nature of the mitochondrial ancestor.},
}

*Mitochondrial Proteins/metabolism
*Alphaproteobacteria/genetics/metabolism
Mitochondrial Membranes/metabolism
Mitochondria/metabolism
Biological Evolution

@article {pmid36792581,
year = {2023},
author = {Filée, J and Becker, HF and Mellottee, L and Eddine, RZ and Li, Z and Yin, W and Lambry, JC and Liebl, U and Myllykallio, H},
title = {Bacterial origins of thymidylate metabolism in Asgard archaea and Eukarya.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {838},
pmid = {36792581},
issn = {2041-1723},
mesh = {*Archaea/metabolism ; *Eukaryota/genetics/metabolism ; Phylogeny ; Thymidylate Synthase/genetics/metabolism ; Bacteria/genetics/metabolism ; Amino Acids/metabolism ; Folic Acid/metabolism ; DNA/metabolism ; },
abstract = {Asgard archaea include the closest known archaeal relatives of eukaryotes. Here, we investigate the evolution and function of Asgard thymidylate synthases and other folate-dependent enzymes required for the biosynthesis of DNA, RNA, amino acids and vitamins, as well as syntrophic amino acid utilization. Phylogenies of Asgard folate-dependent enzymes are consistent with their horizontal transmission from various bacterial groups. We experimentally validate the functionality of thymidylate synthase ThyX of the cultured 'Candidatus Prometheoarchaeum syntrophicum'. The enzyme efficiently uses bacterial-like folates and is inhibited by mycobacterial ThyX inhibitors, even though the majority of experimentally tested archaea are known to use carbon carriers distinct from bacterial folates. Our phylogenetic analyses suggest that the eukaryotic thymidylate synthase, required for de novo DNA synthesis, is not closely related to archaeal enzymes and might have been transferred from bacteria to protoeukaryotes during eukaryogenesis. Altogether, our study suggests that the capacity of eukaryotic cells to duplicate their genetic material is a sum of archaeal (replisome) and bacterial (thymidylate synthase) characteristics. We also propose that recent prevalent lateral gene transfer from bacteria has markedly shaped the metabolism of Asgard archaea.},
}

*Archaea/metabolism
*Eukaryota/genetics/metabolism
Phylogeny
Thymidylate Synthase/genetics/metabolism
Bacteria/genetics/metabolism
Amino Acids/metabolism
Folic Acid/metabolism
DNA/metabolism

@article {pmid36752808,
year = {2023},
author = {Bremer, N and Tria, FDK and Skejo, J and Martin, WF},
title = {The Ancestral Mitotic State: Closed Orthomitosis With Intranuclear Spindles in the Syncytial Last Eukaryotic Common Ancestor.},
journal = {Genome biology and evolution},
volume = {15},
number = {3},
pages = {},
pmid = {36752808},
issn = {1759-6653},
mesh = {*Eukaryota/genetics ; *Eukaryotic Cells ; Mitosis ; Cell Nucleus ; Cytosol ; },
abstract = {All eukaryotes have linear chromosomes that are distributed to daughter nuclei during mitotic division, but the ancestral state of nuclear division in the last eukaryotic common ancestor (LECA) is so far unresolved. To address this issue, we have employed ancestral state reconstructions for mitotic states that can be found across the eukaryotic tree concerning the intactness of the nuclear envelope during mitosis (open or closed), the position of spindles (intranuclear or extranuclear), and the symmetry of spindles being either axial (orthomitosis) or bilateral (pleuromitosis). The data indicate that the LECA possessed closed orthomitosis with intranuclear spindles. Our reconstruction is compatible with recent findings indicating a syncytial state of the LECA, because it decouples three main processes: chromosome division, chromosome partitioning, and cell division (cytokinesis). The possession of closed mitosis using intranuclear spindles adds to the number of cellular traits that can now be attributed to LECA, providing insights into the lifestyle of this otherwise elusive biological entity at the origin of eukaryotic cells. Closed mitosis in a syncytial eukaryotic common ancestor would buffer mutations arising at the origin of mitotic division by allowing nuclei with viable chromosome sets to complement defective nuclei via mRNA in the cytosol.},
}

*Eukaryota/genetics
*Eukaryotic Cells
Mitosis
Cell Nucleus
Cytosol

@article {pmid36692278,
year = {2022},
author = {Forterre, P and Gaïa, M},
title = {[Viruses and the evolution of modern eukaryotic cells].},
journal = {Medecine sciences : M/S},
volume = {38},
number = {12},
pages = {990-998},
doi = {10.1051/medsci/2022164},
pmid = {36692278},
issn = {1958-5381},
mesh = {Humans ; *Eukaryotic Cells ; Phylogeny ; *Viruses/genetics ; Eukaryota/genetics ; Cell Nucleus ; Evolution, Molecular ; Biological Evolution ; },
abstract = {It is now well accepted that viruses have played an important role in the evolution of modern eukaryotes. In this review, we suggest that interactions between ancient eukaryoviruses and proto-eukaryotes also played a major role in eukaryogenesis. We discuss phylogenetic analyses that highlight the viral origin of several key proteins in the molecular biology of eukaryotes. We also discuss recent observations that, by analogy, could suggest a viral origin of the cellular nucleus. Finally, we hypothesize that mechanisms of cell differentiation in multicellular organisms might have originated from mechanisms implemented by viruses to transform infected cells into virocells.},
}

Humans
*Eukaryotic Cells
Phylogeny
*Viruses/genetics
Eukaryota/genetics
Cell Nucleus
Evolution, Molecular
Biological Evolution

@article {pmid36672768,
year = {2022},
author = {Santos, FB and Del-Bem, LE},
title = {The Evolution of tRNA Copy Number and Repertoire in Cellular Life.},
journal = {Genes},
volume = {14},
number = {1},
pages = {},
pmid = {36672768},
issn = {2073-4425},
mesh = {Animals ; *Anticodon ; *DNA Copy Number Variations ; RNA, Transfer/genetics ; RNA ; Eukaryota/genetics ; Archaea/genetics ; },
abstract = {tRNAs are universal decoders that bridge the gap between transcriptome and proteome. They can also be processed into small RNA fragments with regulatory functions. In this work, we show that tRNA copy number is largely controlled by genome size in all cellular organisms, in contrast to what is observed for protein-coding genes that stop expanding between ~20,000 and ~35,000 loci per haploid genome in eukaryotes, regardless of genome size. Our analyses indicate that after the bacteria/archaea split, the tRNA gene pool experienced the evolution of increased anticodon diversity in the archaeal lineage, along with a tRNA gene size increase and mature tRNA size decrease. The evolution and diversification of eukaryotes from archaeal ancestors involved further expansion of the tRNA anticodon repertoire, additional increase in tRNA gene size and decrease in mature tRNA length, along with an explosion of the tRNA gene copy number that emerged coupled with accelerated genome size expansion. Our findings support the notion that macroscopic eukaryotes with a high diversity of cell types, such as land plants and vertebrates, independently evolved a high diversity of tRNA anticodons along with high gene redundancy caused by the expansion of the tRNA copy number. The results presented here suggest that the evolution of tRNA genes played important roles in the early split between bacteria and archaea, and in eukaryogenesis and the later emergence of complex eukaryotes, with potential implications in protein translation and gene regulation through tRNA-derived RNA fragments.},
}

Animals
*Anticodon
*DNA Copy Number Variations
RNA, Transfer/genetics
RNA
Eukaryota/genetics
Archaea/genetics

@article {pmid36631250,
year = {2023},
author = {Vosseberg, J and Stolker, D and von der Dunk, SHA and Snel, B},
title = {Integrating Phylogenetics With Intron Positions Illuminates the Origin of the Complex Spliceosome.},
journal = {Molecular biology and evolution},
volume = {40},
number = {1},
pages = {},
pmid = {36631250},
issn = {1537-1719},
mesh = {*Spliceosomes/genetics ; Introns ; Phylogeny ; *RNA Splicing ; Eukaryota/genetics ; Evolution, Molecular ; },
abstract = {Eukaryotic genes are characterized by the presence of introns that are removed from pre-mRNA by a spliceosome. This ribonucleoprotein complex is comprised of multiple RNA molecules and over a hundred proteins, which makes it one of the most complex molecular machines that originated during the prokaryote-to-eukaryote transition. Previous works have established that these introns and the spliceosomal core originated from self-splicing introns in prokaryotes. Yet, how the spliceosomal core expanded by recruiting many additional proteins remains largely elusive. In this study, we use phylogenetic analyses to infer the evolutionary history of 145 proteins that we could trace back to the spliceosome in the last eukaryotic common ancestor. We found that an overabundance of proteins derived from ribosome-related processes was added to the prokaryote-derived core. Extensive duplications of these proteins substantially increased the complexity of the emerging spliceosome. By comparing the intron positions between spliceosomal paralogs, we infer that most spliceosomal complexity postdates the spread of introns through the proto-eukaryotic genome. The reconstruction of early spliceosomal evolution provides insight into the driving forces behind the emergence of complexes with many proteins during eukaryogenesis.},
}

*Spliceosomes/genetics
Introns
Phylogeny
*RNA Splicing
Eukaryota/genetics
Evolution, Molecular

@article {pmid36599981,
year = {2023},
author = {Otsuka, S and Tempkin, JOB and Zhang, W and Politi, AZ and Rybina, A and Hossain, MJ and Kueblbeck, M and Callegari, A and Koch, B and Morero, NR and Sali, A and Ellenberg, J},
title = {A quantitative map of nuclear pore assembly reveals two distinct mechanisms.},
journal = {Nature},
volume = {613},
number = {7944},
pages = {575-581},
pmid = {36599981},
issn = {1476-4687},
support = {P41 GM109824/GM/NIGMS NIH HHS/United States ; R01 GM112108/GM/NIGMS NIH HHS/United States ; R01 GM083960/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; Interphase ; Mitosis ; *Nuclear Pore/chemistry/metabolism ; *Nuclear Pore Complex Proteins/chemistry/metabolism ; Spectrometry, Fluorescence ; },
abstract = {Understanding how the nuclear pore complex (NPC) is assembled is of fundamental importance to grasp the mechanisms behind its essential function and understand its role during the evolution of eukaryotes[1-4]. There are at least two NPC assembly pathways-one during the exit from mitosis and one during nuclear growth in interphase-but we currently lack a quantitative map of these events. Here we use fluorescence correlation spectroscopy calibrated live imaging of endogenously fluorescently tagged nucleoporins to map the changes in the composition and stoichiometry of seven major modules of the human NPC during its assembly in single dividing cells. This systematic quantitative map reveals that the two assembly pathways have distinct molecular mechanisms, in which the order of addition of two large structural components, the central ring complex and nuclear filaments are inverted. The dynamic stoichiometry data was integrated to create a spatiotemporal model of the NPC assembly pathway and predict the structures of postmitotic NPC assembly intermediates.},
}

Humans
Interphase
Mitosis
*Nuclear Pore/chemistry/metabolism
*Nuclear Pore Complex Proteins/chemistry/metabolism
Spectrometry, Fluorescence

@article {pmid36569058,
year = {2022},
author = {Li, R and Song, X and Gao, S and Peng, S},
title = {Analysis on the interactions between the first introns and other introns in mitochondrial ribosomal protein genes.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1091698},
pmid = {36569058},
issn = {1664-302X},
abstract = {It is realized that the first intron plays a key role in regulating gene expression, and the interactions between the first introns and other introns must be related to the regulation of gene expression. In this paper, the sequences of mitochondrial ribosomal protein genes were selected as the samples, based on the Smith-Waterman method, the optimal matched segments between the first intron and the reverse complementary sequences of other introns of each gene were obtained, and the characteristics of the optimal matched segments were analyzed. The results showed that the lengths and the ranges of length distributions of the optimal matched segments are increased along with the evolution of eukaryotes. For the distributions of the optimal matched segments with different GC contents, the peak values are decreased along with the evolution of eukaryotes, but the corresponding GC content of the peak values are increased along with the evolution of eukaryotes, it means most introns of higher organisms interact with each other though weak bonds binding. By comparing the lengths and matching rates of optimal matched segments with those of siRNA and miRNA, it is found that some optimal matched segments may be related to non-coding RNA with special biological functions, just like siRNA and miRNA, they may play an important role in the process of gene expression and regulation. For the relative position of the optimal matched segments, the peaks of relative position distributions of optimal matched segments are increased during the evolution of eukaryotes, and the positions of the first two peaks exhibit significant conservatism.},
}

@article {pmid36562617,
year = {2023},
author = {Spang, A},
title = {Is an archaeon the ancestor of eukaryotes?.},
journal = {Environmental microbiology},
volume = {25},
number = {4},
pages = {775-779},
doi = {10.1111/1462-2920.16323},
pmid = {36562617},
issn = {1462-2920},
mesh = {*Archaea/genetics ; *Eukaryota/genetics ; Phylogeny ; Biological Evolution ; Eukaryotic Cells ; },
abstract = {The origin of complex cellular life is a key puzzle in evolutionary research, which has broad implications for various neighbouring scientific disciplines. Naturally, views on this topic vary widely depending on the world view and context from which this topic is approached. In the following, I will share my perspective about our current scientific knowledge on the origin of eukaryotic cells, that is, eukaryogenesis, from a biological point of view focusing on the question as to whether an archaeon was the ancestor of eukaryotes.},
}

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

@article {pmid36533149,
year = {2022},
author = {Guglielmini, J and Gaia, M and Da Cunha, V and Criscuolo, A and Krupovic, M and Forterre, P},
title = {Viral origin of eukaryotic type IIA DNA topoisomerases.},
journal = {Virus evolution},
volume = {8},
number = {2},
pages = {veac097},
pmid = {36533149},
issn = {2057-1577},
abstract = {Type II DNA topoisomerases of the family A (Topo IIAs) are present in all Bacteria (DNA gyrase) and eukaryotes. In eukaryotes, they play a major role in transcription, DNA replication, chromosome segregation, and modulation of chromosome architecture. The origin of eukaryotic Topo IIA remains mysterious since they are very divergent from their bacterial homologs and have no orthologs in Archaea. Interestingly, eukaryotic Topo IIAs have close homologs in viruses of the phylum Nucleocytoviricota, an expansive assemblage of large and giant viruses formerly known as the nucleocytoplasmic large DNA viruses. Topo IIAs are also encoded by some bacterioviruses of the class Caudoviricetes (tailed bacteriophages). To elucidate the origin of the eukaryotic Topo IIA, we performed in-depth phylogenetic analyses on a dataset combining viral and cellular Topo IIA homologs. Topo IIAs encoded by Bacteria and eukaryotes form two monophyletic groups nested within Topo IIA encoded by Caudoviricetes and Nucleocytoviricota, respectively. Importantly, Nucleocytoviricota remained well separated from eukaryotes after removing both Bacteria and Caudoviricetes from the data set, indicating that the separation of Nucleocytoviricota and eukaryotes is probably not due to long-branch attraction artifact. The topologies of our trees suggest that the eukaryotic Topo IIA was probably acquired from an ancestral member of the Nucleocytoviricota of the class Megaviricetes, before the emergence of the last eukaryotic common ancestor (LECA). This result further highlights a key role of these viruses in eukaryogenesis and suggests that early proto-eukaryotes used a Topo IIB instead of a Topo IIA for solving their DNA topological problems.},
}

@article {pmid36472116,
year = {2022},
author = {Cahill, MA},
title = {Quo vadis PGRMC? Grand-Scale Biology in Human Health and Disease.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {27},
number = {11},
pages = {318},
doi = {10.31083/j.fbl2711318},
pmid = {36472116},
issn = {2768-6698},
mesh = {Animals ; Humans ; *Receptors, Progesterone/genetics/metabolism ; *Eukaryota ; Biology ; Mammals/metabolism ; Membrane Proteins/genetics ; },
abstract = {The title usage of Latin Quo vadis 'where are you going' extends the question Unde venisti from where 'did you come?' posed in the accompanying paper and extends consideration of how ancient eukaryotic and eumetazoan functions of progesterone receptor membrane component (PGRMC) proteins (PGRMC1 and PGRMC2 in mammals) could influence modern human health and disease. This paper attempts to extrapolate to modern biology in terms of extensions of hypothetical ancestral functional states from early eukaryotes and the last eumetazoan common ancestor (LEUMCA), to relativize human metabolic physiology and disease. As novel cell types and functional specializations appeared in bilaterian animals, PGRMC functions are hypothesized to have continued to be part of the toolkit used to develop new cell types and manage increasingly complex tasks such as nerve-gut-microbiome neuronal and hormonal communication. A critical role of PGRMC (as one component of a new eumetazoan genetic machinery) is proposed in LEUMCA endocrinology, neurogenesis, and nerve-gut communication with possible involvement in circadian nicotinamide adenine dinucleotide synthesis. This model would explain the contribution of PGRMC to metabolic and differentiation/behavioral changes observed in age-related diseases like diabetes, cancer and perhaps aging itself. Consistent with proposed key regulation of neurogenesis in the LEUMCA, it is argued that Alzheimer's disease is the modern pathology that most closely reflects the suite of functions related to PGRMC biology, with the 'usual suspect' pathologies possibly being downstream of PGRMC1. Hopefully, these thoughts help to signpost directions for future research.},
}

Animals
Humans
*Receptors, Progesterone/genetics/metabolism
*Eukaryota
Biology
Mammals/metabolism
Membrane Proteins/genetics

@article {pmid36472108,
year = {2022},
author = {Cahill, MA},
title = {Unde venisti PGRMC? Grand-Scale Biology from Early Eukaryotes and Eumetazoan Animal Origins.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {27},
number = {11},
pages = {317},
doi = {10.31083/j.fbl2711317},
pmid = {36472108},
issn = {2768-6698},
mesh = {Animals ; Humans ; *Eukaryota ; *Proteomics ; Epigenesis, Genetic ; Receptors, Progesterone/metabolism ; Glycolysis ; Heme/metabolism ; Mammals/metabolism ; Membrane Proteins/genetics/metabolism ; },
abstract = {The title usage of Unde venisti 'from where have you come' is from a now dead language (Latin) that foundationally influenced modern English (not the major influence, but an essential formative one). This is an apt analogy for how both the ancient eukaryotic and eumetazoan functions of PGRMC proteins (PGRMC1 and PGRMC2 in mammals) probably influence modern human biology: via a formative trajectory from an evolutionarily foundational fulcrum. There is an arguable probability, although not a certainty, that PGRMC-like proteins were involved in eukaryogenesis. If so, then the proto-eukaryotic ancestral protein is modelled as having initiated the oxygen-induced and CYP450 (Cytochrome P450)-mediated synthesis of sterols in the endoplasmic reticulum to regulate proto-mitochondrial activity and heme homeostasis, as well as having enabled sterol transport between endoplasmic reticulum (ER) and mitochondria membranes involving the actin cytoskeleton, transport of heme from mitochondria, and possibly the regulation/origins of mitosis/meiosis. Later, during animal evolution, the last eumetazoan common ancestor (LEUMCA) acquired PGRMC phosphorylated tyrosines coincidentally with the gastrulation organizer, Netrin/deleted in colorectal carcinoma (DCC) signaling, muscle fibers, synapsed neurons, and neural recovery via a sleep-like process. Modern PGRMC proteins regulate multiple functions, including CYP450-mediated steroidogenesis, membrane trafficking, heme homeostasis, glycolysis/Warburg effect, fatty acid metabolism, mitochondrial regulation, and genomic CpG epigenetic regulation of gene expression. The latter imposes the system of differentiation status-sensitive cell-type specific proteomic complements in multi-tissued descendants of the LEUMCA. This paper attempts to trace PGRMC functions through time, proposing that key functions were involved in early eukaryotes, and were later added upon in the LEUMCA. An accompanying paper considers the implications of this awareness for human health and disease.},
}

Animals
Humans
*Eukaryota
*Proteomics
Epigenesis, Genetic
Receptors, Progesterone/metabolism
Glycolysis
Heme/metabolism
Mammals/metabolism
Membrane Proteins/genetics/metabolism

@article {pmid36461738,
year = {2023},
author = {Ponlachantra, K and Suginta, W and Robinson, RC and Kitaoku, Y},
title = {AlphaFold2: A versatile tool to predict the appearance of functional adaptations in evolution: Profilin interactions in uncultured Asgard archaea: Profilin interactions in uncultured Asgard archaea.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {45},
number = {2},
pages = {e2200119},
doi = {10.1002/bies.202200119},
pmid = {36461738},
issn = {1521-1878},
mesh = {*Archaea/metabolism ; *Profilins/genetics/metabolism ; Actins ; Phylogeny ; Furylfuramide/metabolism ; Eukaryota/metabolism ; },
abstract = {The release of AlphaFold2 (AF2), a deep-learning-aided, open-source protein structure prediction program, from DeepMind, opened a new era of molecular biology. The astonishing improvement in the accuracy of the structure predictions provides the opportunity to characterize protein systems from uncultured Asgard archaea, key organisms in evolutionary biology. Despite the accumulation in metagenomics-derived Asgard archaea eukaryotic-like protein sequences, limited structural and biochemical information have restricted the insight in their potential functions. In this review, we focus on profilin, an actin-dynamics regulating protein, which in eukaryotes, modulates actin polymerization through (1) direct actin interaction, (2) polyproline binding, and (3) phospholipid binding. We assess AF2-predicted profilin structures in their potential abilities to participate in these activities. We demonstrate that AF2 is a powerful new tool for understanding the emergence of biological functional traits in evolution.},
}

*Archaea/metabolism
*Profilins/genetics/metabolism
Actins
Phylogeny
Furylfuramide/metabolism
Eukaryota/metabolism

@article {pmid36399624,
year = {2022},
author = {Field, MC and Rout, MP},
title = {Coatomer in the universe of cellular complexity.},
journal = {Molecular biology of the cell},
volume = {33},
number = {14},
pages = {},
pmid = {36399624},
issn = {1939-4586},
support = {P41 GM109824/GM/NIGMS NIH HHS/United States ; R01 CA228351/CA/NCI NIH HHS/United States ; R01 GM112108/GM/NIGMS NIH HHS/United States ; 204697/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Eukaryotic Cells/metabolism ; *Eukaryota/genetics ; Biological Evolution ; COP-Coated Vesicles ; Endosomal Sorting Complexes Required for Transport/metabolism ; },
abstract = {Eukaryotic cells possess considerable internal complexity, differentiating them from prokaryotes. Eukaryogenesis, an evolutionary transitional period culminating in the last eukaryotic common ancestor (LECA), marked the origin of the eukaryotic endomembrane system. LECA is reconstructed as possessing intracellular complexity akin to modern eukaryotes. Construction of endomembrane compartments involved three key gene families: coatomer, BAR-domain proteins, and ESCRT. Each has a distinct evolutionary origin, but of these coatomer and BAR proteins are eukaryote specific, while ESCRT has more ancient origins. We discuss the structural motifs defining these three membrane-coating complexes and suggest that compared with BAR and ESCRT, the coatomer architecture had a unique ability to be readily and considerably modified, unlocking functional diversity and enabling the development of the eukaryotic cell.},
}

*Eukaryotic Cells/metabolism
*Eukaryota/genetics
Biological Evolution
COP-Coated Vesicles
Endosomal Sorting Complexes Required for Transport/metabolism

@article {pmid36373631,
year = {2023},
author = {Mencía, M},
title = {Acid digestion and symbiont: Proton sharing at the origin of mitochondriogenesis?: Proton production by a symbiotic bacterium may have been the origin of two hallmark eukaryotic features, acid digestion and mitochondria: Proton production by a symbiotic bacterium may have been the origin of two hallmark eukaryotic features, acid digestion and mitochondria.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {45},
number = {1},
pages = {e2200136},
doi = {10.1002/bies.202200136},
pmid = {36373631},
issn = {1521-1878},
mesh = {*Protons ; Phylogeny ; *Eukaryota ; Symbiosis ; Bacteria ; Mitochondria ; Digestion ; Biological Evolution ; },
abstract = {The initial relationships between organisms leading to endosymbiosis and the first eukaryote are currently a topic of hot debate. Here, I present a theory that offers a gradual scenario in which the origins of phagocytosis and mitochondria are intertwined in such a way that the evolution of one would not be possible without the other. In this scenario, the premitochondrial bacterial symbiont became initially associated with a protophagocytic host on the basis of cooperation to kill prey with symbiont-produced toxins and reactive oxygen species (ROS). Subsequently, the cooperation was focused on the digestion stage, through the acidification of the protophagocytic cavities via exportation of protons produced by the aerobic respiration of the symbiont. The host gained an improved phagocytic capacity and the symbiont received organic compounds from prey. As the host gradually lost its membrane energetics to develop lysosomal digestion, respiration was centralized in the premitochondrial symbiont for energy production for the consortium.},
}

*Protons
Phylogeny
*Eukaryota
Symbiosis
Bacteria
Mitochondria
Digestion
Biological Evolution

@article {pmid36366773,
year = {2023},
author = {van der Gulik, PTS and Hoff, WD and Speijer, D},
title = {Renewing Linnaean taxonomy: a proposal to restructure the highest levels of the Natural System.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {98},
number = {2},
pages = {584-602},
doi = {10.1111/brv.12920},
pmid = {36366773},
issn = {1469-185X},
mesh = {*Eukaryota ; *Biodiversity ; Phylogeny ; },
abstract = {During the last century enormous progress has been made in the understanding of biological diversity, involving a dramatic shift from macroscopic to microscopic organisms. The question now arises as to whether the Natural System introduced by Carl Linnaeus, which has served as the central system for organizing biological diversity, can accommodate the great expansion of diversity that has been discovered. Important discoveries regarding biological diversity have not been fully integrated into a formal, coherent taxonomic system. In addition, because of taxonomic challenges and conflicts, various proposals have been made to abandon key aspects of the Linnaean system. We review the current status of taxonomy of the living world, focussing on groups at the taxonomic level of phylum and above. We summarize the main arguments against and in favour of abandoning aspects of the Linnaean system. Based on these considerations, we conclude that retaining the Linnaean Natural System provides important advantages. We propose a relatively small number of amendments for extending this system, particularly to include the named rank of world (Latin alternative mundis) formally to include non-cellular entities (viruses), and the named rank of empire (Latin alternative imperium) to accommodate the depth of diversity in (unicellular) eukaryotes that has been uncovered. We argue that in the case of both the eukaryotic domain and the viruses the cladistic approach intrinsically fails. However, the resulting semi-cladistic system provides a productive way forward that can help resolve taxonomic challenges. The amendments proposed allow us to: (i) retain named taxonomic levels and the three-domain system, (ii) improve understanding of the main eukaryotic lineages, and (iii) incorporate viruses into the Natural System. Of note, the proposal described herein is intended to serve as the starting point for a broad scientific discussion regarding the modernization of the Linnaean system.},
}

*Eukaryota
*Biodiversity
Phylogeny

@article {pmid36355038,
year = {2022},
author = {Raval, PK and Garg, SG and Gould, SB},
title = {Endosymbiotic selective pressure at the origin of eukaryotic cell biology.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
pmid = {36355038},
issn = {2050-084X},
mesh = {*Eukaryotic Cells/physiology ; *Symbiosis/genetics ; Biological Evolution ; Eukaryota/genetics ; Archaea/genetics ; Cell Nucleus ; Meiosis ; Biology ; Phylogeny ; },
abstract = {The dichotomy that separates prokaryotic from eukaryotic cells runs deep. The transition from pro- to eukaryote evolution is poorly understood due to a lack of reliable intermediate forms and definitions regarding the nature of the first host that could no longer be considered a prokaryote, the first eukaryotic common ancestor, FECA. The last eukaryotic common ancestor, LECA, was a complex cell that united all traits characterising eukaryotic biology including a mitochondrion. The role of the endosymbiotic organelle in this radical transition towards complex life forms is, however, sometimes questioned. In particular the discovery of the asgard archaea has stimulated discussions regarding the pre-endosymbiotic complexity of FECA. Here we review differences and similarities among models that view eukaryotic traits as isolated coincidental events in asgard archaeal evolution or, on the contrary, as a result of and in response to endosymbiosis. Inspecting eukaryotic traits from the perspective of the endosymbiont uncovers that eukaryotic cell biology can be explained as having evolved as a solution to housing a semi-autonomous organelle and why the addition of another endosymbiont, the plastid, added no extra compartments. Mitochondria provided the selective pressures for the origin (and continued maintenance) of eukaryotic cell complexity. Moreover, they also provided the energetic benefit throughout eukaryogenesis for evolving thousands of gene families unique to eukaryotes. Hence, a synthesis of the current data lets us conclude that traits such as the Golgi apparatus, the nucleus, autophagosomes, and meiosis and sex evolved as a response to the selective pressures an endosymbiont imposes.},
}

*Eukaryotic Cells/physiology
*Symbiosis/genetics
Biological Evolution
Eukaryota/genetics
Archaea/genetics
Cell Nucleus
Meiosis
Biology
Phylogeny

@article {pmid36313567,
year = {2022},
author = {Cellier, MFM},
title = {Nramp: Deprive and conquer?.},
journal = {Frontiers in cell and developmental biology},
volume = {10},
number = {},
pages = {988866},
pmid = {36313567},
issn = {2296-634X},
abstract = {Solute carriers 11 (Slc11) evolved from bacterial permease (MntH) to eukaryotic antibacterial defense (Nramp) while continuously mediating proton (H[+])-dependent manganese (Mn[2+]) import. Also, Nramp horizontal gene transfer (HGT) toward bacteria led to mntH polyphyly. Prior demonstration that evolutionary rate-shifts distinguishing Slc11 from outgroup carriers dictate catalytic specificity suggested that resolving Slc11 family tree may provide a function-aware phylogenetic framework. Hence, MntH C (MC) subgroups resulted from HGTs of prototype Nramp (pNs) parologs while archetype Nramp (aNs) correlated with phagocytosis. PHI-Blast based taxonomic profiling confirmed MntH B phylogroup is confined to anaerobic bacteria vs. MntH A (MA)'s broad distribution; suggested niche-related spread of MC subgroups; established that MA-variant MH, which carries 'eukaryotic signature' marks, predominates in archaea. Slc11 phylogeny shows MH is sister to Nramp. Site-specific analysis of Slc11 charge network known to interact with the protonmotive force demonstrates sequential rate-shifts that recapitulate Slc11 evolution. 3D mapping of similarly coevolved sites across Slc11 hydrophobic core revealed successive targeting of discrete areas. The data imply that pN HGT could advantage recipient bacteria for H[+]-dependent Mn[2+] acquisition and Alphafold 3D models suggest conformational divergence among MC subgroups. It is proposed that Slc11 originated as a bacterial stress resistance function allowing Mn[2+]-dependent persistence in conditions adverse for growth, and that archaeal MH could contribute to eukaryogenesis as a Mn[2+] sequestering defense perhaps favoring intracellular growth-competent bacteria.},
}

@article {pmid36221007,
year = {2023},
author = {Nachmias, D and Melnikov, N and Zorea, A and Sharon, M and Yemini, R and De-Picchoto, Y and Tsirkas, I and Aharoni, A and Frohn, B and Schwille, P and Zarivach, R and Mizrahi, I and Elia, N},
title = {Asgard ESCRT-III and VPS4 reveal conserved chromatin binding properties of the ESCRT machinery.},
journal = {The ISME journal},
volume = {17},
number = {1},
pages = {117-129},
pmid = {36221007},
issn = {1751-7370},
mesh = {Animals ; Humans ; *Endosomal Sorting Complexes Required for Transport/genetics/chemistry/metabolism ; Saccharomyces cerevisiae/metabolism ; Archaea/genetics ; Chromatin/genetics/metabolism ; Mammals ; Adenosine Triphosphatases/genetics/metabolism ; *Saccharomyces cerevisiae Proteins/chemistry/genetics/metabolism ; },
abstract = {The archaeal Asgard superphylum currently stands as the most promising prokaryotic candidate, from which eukaryotic cells emerged. This unique superphylum encodes for eukaryotic signature proteins (ESP) that could shed light on the origin of eukaryotes, but the properties and function of these proteins is largely unresolved. Here, we set to understand the function of an Asgard archaeal protein family, namely the ESCRT machinery, that is conserved across all domains of life and executes basic cellular eukaryotic functions, including membrane constriction during cell division. We find that ESCRT proteins encoded in Loki archaea, express in mammalian and yeast cells, and that the Loki ESCRT-III protein, CHMP4-7, resides in the eukaryotic nucleus in both organisms. Moreover, Loki ESCRT-III proteins associated with chromatin, recruited their AAA-ATPase VPS4 counterpart to organize in discrete foci in the mammalian nucleus, and directly bind DNA. The human ESCRT-III protein, CHMP1B, exhibited similar nuclear properties and recruited both human and Asgard VPS4s to nuclear foci, indicating interspecies interactions. Mutation analysis revealed a role for the N terminal region of ESCRT-III in mediating these phenotypes in both human and Asgard ESCRTs. These findings suggest that ESCRT proteins hold chromatin binding properties that were highly preserved through the billion years of evolution separating Asgard archaea and humans. The conserved chromatin binding properties of the ESCRT membrane remodeling machinery, reported here, may have important implications for the origin of eukaryogenesis.},
}

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 {pmid36194551,
year = {2022},
author = {Gäbelein, CG and Reiter, MA and Ernst, C and Giger, GH and Vorholt, JA},
title = {Engineering Endosymbiotic Growth of E. coli in Mammalian Cells.},
journal = {ACS synthetic biology},
volume = {11},
number = {10},
pages = {3388-3396},
pmid = {36194551},
issn = {2161-5063},
mesh = {Animals ; Humans ; *Symbiosis ; *Escherichia coli/genetics ; HeLa Cells ; Biological Evolution ; Bacteria ; Amino Acids, Aromatic ; Mammals ; },
abstract = {Endosymbioses are cellular mergers in which one cell lives within another cell and have led to major evolutionary transitions, most prominently to eukaryogenesis. Generation of synthetic endosymbioses aims to provide a defined starting point for studying fundamental processes in emerging endosymbiotic systems and enable the engineering of cells with novel properties. Here, we tested the potential of different bacteria for artificial endosymbiosis in mammalian cells. To this end, we adopted the fluidic force microscopy technology to inject diverse bacteria directly into the cytosol of HeLa cells and examined the endosymbiont-host interactions by real-time fluorescence microscopy. Among them, Escherichia coli grew exponentially within the cytoplasm, however, at a faster pace than its host cell. To slow down the intracellular growth of E. coli, we introduced auxotrophies in E. coli and demonstrated that the intracellular growth rate can be reduced by limiting the uptake of aromatic amino acids. In consequence, the survival of the endosymbiont-host pair was prolonged. The presented experimental framework enables studying endosymbiotic candidate systems at high temporal resolution and at the single cell level. Our work represents a starting point for engineering a stable, vertically inherited endosymbiosis.},
}

Animals
Humans
*Symbiosis
*Escherichia coli/genetics
HeLa Cells
Biological Evolution
Bacteria
Amino Acids, Aromatic
Mammals

@article {pmid36125740,
year = {2022},
author = {Forterre, P},
title = {Archaea: A Goldmine for Molecular Biologists and Evolutionists.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2522},
number = {},
pages = {1-21},
pmid = {36125740},
issn = {1940-6029},
mesh = {*Archaea/genetics ; Bacteria/genetics ; *Biological Evolution ; Eukaryota/genetics ; Genome, Archaeal ; RNA, Ribosomal, 16S ; },
abstract = {The rebuttal of the prokaryote-eukaryote dichotomy and the elaboration of the three domains concept by Carl Woese and colleagues has been a breakthrough in biology. With the methodologies available at this time, they have shown that a single molecule, the 16S ribosomal RNA, could reveal the global organization of the living world. Later on, mining archaeal genomes led to major discoveries in archaeal molecular biology, providing a third model for comparative molecular biology. These analyses revealed the strong eukaryal flavor of the basic molecular fabric of Archaea and support rooting the universal tree between Bacteria and Arcarya (the clade grouping Archaea and Eukarya). However, in contradiction with this conclusion, it remains to understand why the archaeal and bacterial mobilomes are so similar and so different from the eukaryal one. These last years, the number of recognized archaea lineages (phyla?) has exploded. The archaeal nomenclature is now in turmoil and debates about the nature of the last universal common ancestor, the last archaeal common ancestor, and the topology of the tree of life are still going on. Interestingly, the expansion of the archaeal eukaryome, especially in the Asgard archaea, has provided new opportunities to study eukaryogenesis. In recent years, the application to Archaea of the new methodologies described in the various chapters of this book have opened exciting avenues to study the molecular biology and the physiology of these fascinating microorganisms.},
}

*Archaea/genetics
Bacteria/genetics
*Biological Evolution
Eukaryota/genetics
Genome, Archaeal
RNA, Ribosomal, 16S

@article {pmid36103518,
year = {2022},
author = {Tricou, T and Tannier, E and de Vienne, DM},
title = {Ghost lineages can invalidate or even reverse findings regarding gene flow.},
journal = {PLoS biology},
volume = {20},
number = {9},
pages = {e3001776},
pmid = {36103518},
issn = {1545-7885},
mesh = {*Biological Evolution ; *Gene Flow ; Genome ; Phylogeny ; },
abstract = {Introgression, endosymbiosis, and gene transfer, i.e., horizontal gene flow (HGF), are primordial sources of innovation in all domains of life. Our knowledge on HGF relies on detection methods that exploit some of its signatures left on extant genomes. One of them is the effect of HGF on branch lengths of constructed phylogenies. This signature has been formalized in statistical tests for HGF detection and used for example to detect massive adaptive gene flows in malaria vectors or to order evolutionary events involved in eukaryogenesis. However, these studies rely on the assumption that ghost lineages (all unsampled extant and extinct taxa) have little influence. We demonstrate here with simulations and data reanalysis that when considering the more realistic condition that unsampled taxa are legion compared to sampled ones, the conclusion of these studies become unfounded or even reversed. This illustrates the necessity to recognize the existence of ghosts in evolutionary studies.},
}

*Biological Evolution
*Gene Flow
Genome
Phylogeny

@article {pmid36045281,
year = {2022},
author = {Akıl, C and Tran, LT and Orhant-Prioux, M and Baskaran, Y and Senju, Y and Takeda, S and Chotchuang, P and Muengsaen, D and Schulte, A and Manser, E and Blanchoin, L and Robinson, RC},
title = {Structural and biochemical evidence for the emergence of a calcium-regulated actin cytoskeleton prior to eukaryogenesis.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {890},
pmid = {36045281},
issn = {2399-3642},
mesh = {Actin Cytoskeleton/metabolism ; *Actins/metabolism ; Archaea/metabolism ; *Calcium/metabolism ; Gelsolin/chemistry/metabolism ; },
abstract = {Charting the emergence of eukaryotic traits is important for understanding the characteristics of organisms that contributed to eukaryogenesis. Asgard archaea and eukaryotes are the only organisms known to possess regulated actin cytoskeletons. Here, we determined that gelsolins (2DGels) from Lokiarchaeota (Loki) and Heimdallarchaeota (Heim) are capable of regulating eukaryotic actin dynamics in vitro and when expressed in eukaryotic cells. The actin filament severing and capping, and actin monomer sequestering, functionalities of 2DGels are strictly calcium controlled. We determined the X-ray structures of Heim and Loki 2DGels bound actin monomers. Each structure possesses common and distinct calcium-binding sites. Loki2DGel has an unusual WH2-like motif (LVDV) between its two gelsolin domains, in which the aspartic acid coordinates a calcium ion at the interface with actin. We conclude that the calcium-regulated actin cytoskeleton predates eukaryogenesis and emerged in the predecessors of the last common ancestor of Loki, Heim and Thorarchaeota.},
}

Actin Cytoskeleton/metabolism
*Actins/metabolism
Archaea/metabolism
*Calcium/metabolism
Gelsolin/chemistry/metabolism

@article {pmid36040076,
year = {2022},
author = {Kontou, A and Herman, EK and Field, MC and Dacks, JB and Koumandou, VL},
title = {Evolution of factors shaping the endoplasmic reticulum.},
journal = {Traffic (Copenhagen, Denmark)},
volume = {23},
number = {9},
pages = {462-473},
pmid = {36040076},
issn = {1600-0854},
support = {204697/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Endoplasmic Reticulum/metabolism ; *Eukaryotic Cells ; Protein Transport ; },
abstract = {Endomembrane system compartments are significant elements in virtually all eukaryotic cells, supporting functions including protein synthesis, post-translational modifications and protein/lipid targeting. In terms of membrane area the endoplasmic reticulum (ER) is the largest intracellular organelle, but the origins of proteins defining the organelle and the nature of lineage-specific modifications remain poorly studied. To understand the evolution of factors mediating ER morphology and function we report a comparative genomics analysis of experimentally characterized ER-associated proteins involved in maintaining ER structure. We find that reticulons, REEPs, atlastins, Ufe1p, Use1p, Dsl1p, TBC1D20, Yip3p and VAPs are highly conserved, suggesting an origin at least as early as the last eukaryotic common ancestor (LECA), although many of these proteins possess additional non-ER functions in modern eukaryotes. Secondary losses are common in individual species and in certain lineages, for example lunapark is missing from the Stramenopiles and the Alveolata. Lineage-specific innovations include protrudin, Caspr1, Arl6IP1, p180, NogoR, kinectin and CLIMP-63, which are restricted to the Opisthokonta. Hence, much of the machinery required to build and maintain the ER predates the LECA, but alternative strategies for the maintenance and elaboration of ER shape and function are present in modern eukaryotes. Moreover, experimental investigations for ER maintenance factors in diverse eukaryotes are expected to uncover novel mechanisms.},
}

*Endoplasmic Reticulum/metabolism
*Eukaryotic Cells
Protein Transport

@article {pmid36028415,
year = {2022},
author = {Obado, SO and Rout, MP and Field, MC},
title = {Sending the message: specialized RNA export mechanisms in trypanosomes.},
journal = {Trends in parasitology},
volume = {38},
number = {10},
pages = {854-867},
pmid = {36028415},
issn = {1471-5007},
support = {P41 GM109824/GM/NIGMS NIH HHS/United States ; R01 AI140429/AI/NIAID NIH HHS/United States ; R01 GM112108/GM/NIGMS NIH HHS/United States ; 204697/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Active Transport, Cell Nucleus/genetics ; Animals ; Cell Nucleus/genetics/metabolism ; *RNA/genetics/metabolism ; RNA, Messenger/genetics ; *Trypanosoma/genetics/metabolism ; },
abstract = {Export of RNA from the nucleus is essential for all eukaryotic cells and has emerged as a major step in the control of gene expression. mRNA molecules are required to complete a complex series of processing events and pass a quality control system to protect the cytoplasm from the translation of aberrant proteins. Many of these events are highly conserved across eukaryotes, reflecting their ancient origin, but significant deviation from a canonical pathway as described from animals and fungi has emerged in the trypanosomatids. With significant implications for the mechanisms that control gene expression and hence differentiation, responses to altered environments and fitness as a parasite, these deviations may also reveal additional, previously unsuspected, mRNA export pathways.},
}

Active Transport, Cell Nucleus/genetics
Animals
Cell Nucleus/genetics/metabolism
*RNA/genetics/metabolism
RNA, Messenger/genetics
*Trypanosoma/genetics/metabolism

@article {pmid35994648,
year = {2022},
author = {Colnaghi, M and Lane, N and Pomiankowski, A},
title = {Repeat sequences limit the effectiveness of lateral gene transfer and favored the evolution of meiotic sex in early eukaryotes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {35},
pages = {e2205041119},
pmid = {35994648},
issn = {1091-6490},
mesh = {Computer Simulation ; *DNA Repeat Expansion/genetics ; *Eukaryota/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal/genetics ; Genome/genetics ; *Meiosis/genetics ; Mutation ; Mutation Accumulation ; Phylogeny ; Prokaryotic Cells ; },
abstract = {The transition from prokaryotic lateral gene transfer to eukaryotic meiotic sex is poorly understood. Phylogenetic evidence suggests that it was tightly linked to eukaryogenesis, which involved an unprecedented rise in both genome size and the density of genetic repeats. Expansion of genome size raised the severity of Muller's ratchet, while limiting the effectiveness of lateral gene transfer (LGT) at purging deleterious mutations. In principle, an increase in recombination length combined with higher rates of LGT could solve this problem. Here, we show using a computational model that this solution fails in the presence of genetic repeats prevalent in early eukaryotes. The model demonstrates that dispersed repeat sequences allow ectopic recombination, which leads to the loss of genetic information and curtails the capacity of LGT to prevent mutation accumulation. Increasing recombination length in the presence of repeat sequences exacerbates the problem. Mutational decay can only be resisted with homology along extended sequences of DNA. We conclude that the transition to homologous pairing along linear chromosomes was a key innovation in meiotic sex, which was instrumental in the expansion of eukaryotic genomes and morphological complexity.},
}

Computer Simulation
*DNA Repeat Expansion/genetics
*Eukaryota/genetics
*Evolution, Molecular
*Gene Transfer, Horizontal/genetics
Genome/genetics
*Meiosis/genetics
Mutation
Mutation Accumulation
Phylogeny
Prokaryotic Cells

@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 {pmid35761090,
year = {2022},
author = {Banciu, HL and Gridan, IM and Zety, AV and Baricz, A},
title = {Asgard archaea in saline environments.},
journal = {Extremophiles : life under extreme conditions},
volume = {26},
number = {2},
pages = {21},
pmid = {35761090},
issn = {1433-4909},
mesh = {*Archaea ; Eukaryotic Cells/metabolism ; *Genome, Archaeal ; Metagenome ; Phylogeny ; },
abstract = {Members of candidate Asgardarchaeota superphylum appear to share numerous eukaryotic-like attributes thus being broadly explored for their relevance to eukaryogenesis. On the contrast, the ecological roles of Asgard archaea remains understudied. Asgard archaea have been frequently associated to low-oxygen aquatic sedimentary environments worldwide spanning a broad but not extreme salinity range. To date, the available information on diversity and potential biogeochemical roles of Asgardarchaeota mostly sourced from marine habitats and to a much lesser extend from true saline environments (i.e., > 3% w/v total salinity). Here, we provide an overview on diversity and ecological implications of Asgard archaea distributed across saline environments and briefly explore their metagenome-resolved potential for osmoadaptation. Loki-, Thor- and Heimdallarchaeota are the dominant Asgard clades in saline habitats where they might employ anaerobic/microaerophilic organic matter degradation and autotrophic carbon fixation. Homologs of primary solute uptake ABC transporters seemingly prevail in Thorarchaeota, whereas those putatively involved in trehalose and ectoine biosynthesis were mostly inferred in Lokiarchaeota. We speculate that Asgardarchaeota might adopt compatible solute-accumulating ('salt-out') strategy as response to salt stress. Our current understanding on the distribution, ecology and salt-adaptive strategies of Asgardarchaeota in saline environments are, however, limited by insufficient sampling and incompleteness of the available metagenome-assembled genomes. Extensive sampling combined with 'omics'- and cultivation-based approaches seem, therefore, crucial to gain deeper knowledge on this particularly intriguing archaeal lineage.},
}

*Archaea
Eukaryotic Cells/metabolism
*Genome, Archaeal
Metagenome
Phylogeny

@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 {pmid35662005,
year = {2022},
author = {Kumar, P and Bhatnagar, A and Sankaranarayanan, R},
title = {Chiral proofreading during protein biosynthesis and its evolutionary implications.},
journal = {FEBS letters},
volume = {596},
number = {13},
pages = {1615-1627},
doi = {10.1002/1873-3468.14419},
pmid = {35662005},
issn = {1873-3468},
mesh = {Amino Acids/metabolism ; Glycine/metabolism ; *Protein Biosynthesis ; RNA, Transfer/genetics/metabolism ; RNA, Transfer, Amino Acyl/chemistry/metabolism ; *RNA, Transfer, Gly/metabolism ; },
abstract = {Homochirality of biomacromolecules is a prerequisite for their proper functioning and hence essential for all life forms. This underscores the role of cellular chiral checkpoints in enforcing homochirality during protein biosynthesis. d-Aminoacyl-tRNA deacylase (DTD) is an enzyme that performs 'chirality-based proofreading' to remove d-amino acids mistakenly attached to tRNAs, thus recycling them for further rounds of translation. Paradoxically, owing to its l-chiral rejection mode of action, DTD can remove glycine as well, which is an achiral amino acid. However, this activity is modulated by discriminator base (N73) in tRNA, a unique element that protects the cognate Gly-tRNA[Gly] . Here, we review our recent work showing various aspects of DTD and tRNA[Gly] coevolution and its key role in maintaining proper translation surveillance in both bacteria and eukaryotes. Moreover, we also discuss two major optimization events on DTD and tRNA that resolved compatibility issues among the archaeal and the bacterial translation apparatuses. Importantly, such optimizations are necessary for the emergence of mitochondria and successful eukaryogenesis.},
}

Amino Acids/metabolism
Glycine/metabolism
*Protein Biosynthesis
RNA, Transfer/genetics/metabolism
RNA, Transfer, Amino Acyl/chemistry/metabolism
*RNA, Transfer, Gly/metabolism

@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 {pmid35642316,
year = {2022},
author = {Bremer, N and Tria, FDK and Skejo, J and Garg, SG and Martin, WF},
title = {Ancestral State Reconstructions Trace Mitochondria But Not Phagocytosis to the Last Eukaryotic Common Ancestor.},
journal = {Genome biology and evolution},
volume = {14},
number = {6},
pages = {},
pmid = {35642316},
issn = {1759-6653},
mesh = {Animals ; *Biological Evolution ; *Eukaryota/genetics ; Eukaryotic Cells/physiology ; Mitochondria/genetics ; Phagocytosis/physiology ; Phylogeny ; Symbiosis/genetics ; },
abstract = {Two main theories have been put forward to explain the origin of mitochondria in eukaryotes: phagotrophic engulfment (undigested food) and microbial symbiosis (physiological interactions). The two theories generate mutually exclusive predictions about the order in which mitochondria and phagocytosis arose. To discriminate the alternatives, we have employed ancestral state reconstructions (ASR) for phagocytosis as a trait, phagotrophy as a feeding habit, the presence of mitochondria, the presence of plastids, and the multinucleated organization across major eukaryotic lineages. To mitigate the bias introduced by assuming a particular eukaryotic phylogeny, we reconstructed the appearance of these traits across 1789 different rooted gene trees, each having species from opisthokonts, mycetozoa, hacrobia, excavate, archeplastida, and Stramenopiles, Alveolates and Rhizaria. The trees reflect conflicting relationships and different positions of the root. We employed a novel phylogenomic test that summarizes ASR across trees which reconstructs a last eukaryotic common ancestor that possessed mitochondria, was multinucleated, lacked plastids, and was non-phagotrophic as well as non-phagocytic. This indicates that both phagocytosis and phagotrophy arose subsequent to the origin of mitochondria, consistent with findings from comparative physiology. Furthermore, our ASRs uncovered multiple origins of phagocytosis and of phagotrophy across eukaryotes, indicating that, like wings in animals, these traits are useful but neither ancestral nor homologous across groups. The data indicate that mitochondria preceded the origin of phagocytosis, such that phagocytosis cannot have been the mechanism by which mitochondria were acquired.},
}

Animals
*Biological Evolution
*Eukaryota/genetics
Eukaryotic Cells/physiology
Mitochondria/genetics
Phagocytosis/physiology
Phylogeny
Symbiosis/genetics

@article {pmid35633668,
year = {2022},
author = {Bell, PJL},
title = {Eukaryogenesis: The Rise of an Emergent Superorganism.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {858064},
pmid = {35633668},
issn = {1664-302X},
abstract = {Although it is widely taught that all modern life descended via modification from a last universal common ancestor (LUCA), this dominant paradigm is yet to provide a generally accepted explanation for the chasm in design between prokaryotic and eukaryotic cells. Counter to this dominant paradigm, the viral eukaryogenesis (VE) hypothesis proposes that the eukaryotes originated as an emergent superorganism and thus did not evolve from LUCA via descent with incremental modification. According to the VE hypothesis, the eukaryotic nucleus descends from a viral factory, the mitochondrion descends from an enslaved alpha-proteobacteria and the cytoplasm and plasma membrane descend from an archaeal host. A virus initiated the eukaryogenesis process by colonising an archaeal host to create a virocell that had its metabolism reprogrammed to support the viral factory. Subsequently, viral processes facilitated the entry of a bacterium into the archaeal cytoplasm which was also eventually reprogrammed to support the viral factory. As the viral factory increased control of the consortium, the archaeal genome was lost, the bacterial genome was greatly reduced and the viral factory eventually evolved into the nucleus. It is proposed that the interaction between these three simple components generated a superorganism whose emergent properties allowed the evolution of eukaryotic complexity. If the radical tenets of the VE hypothesis are ultimately accepted, current biological paradigms regarding viruses, cell theory, LUCA and the universal Tree of Life (ToL) should be fundamentally altered or completely abandoned.},
}

@article {pmid35589959,
year = {2022},
author = {Vosseberg, J and Schinkel, M and Gremmen, S and Snel, B},
title = {The spread of the first introns in proto-eukaryotic paralogs.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {476},
pmid = {35589959},
issn = {2399-3642},
mesh = {*Eukaryota/genetics ; Eukaryotic Cells ; *Evolution, Molecular ; Humans ; Introns/genetics ; Spliceosomes/genetics ; },
abstract = {Spliceosomal introns are a unique feature of eukaryotic genes. Previous studies have established that many introns were present in the protein-coding genes of the last eukaryotic common ancestor (LECA). Intron positions shared between genes that duplicated before LECA could in principle provide insight into the emergence of the first introns. In this study we use ancestral intron position reconstructions in two large sets of duplicated families to systematically identify these ancient paralogous intron positions. We found that 20-35% of introns inferred to have been present in LECA were shared between paralogs. These shared introns, which likely preceded ancient duplications, were wide spread across different functions, with the notable exception of nuclear transport. Since we observed a clear signal of pervasive intron loss prior to LECA, it is likely that substantially more introns were shared at the time of duplication than we can detect in LECA. The large extent of shared introns indicates an early origin of introns during eukaryogenesis and suggests an early origin of a nuclear structure, before most of the other complex eukaryotic features were established.},
}

*Eukaryota/genetics
Eukaryotic Cells
*Evolution, Molecular
Humans
Introns/genetics
Spliceosomes/genetics

@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 {pmid35449457,
year = {2022},
author = {Mills, DB and Boyle, RA and Daines, SJ and Sperling, EA and Pisani, D and Donoghue, PCJ and Lenton, TM},
title = {Eukaryogenesis and oxygen in Earth history.},
journal = {Nature ecology & evolution},
volume = {6},
number = {5},
pages = {520-532},
pmid = {35449457},
issn = {2397-334X},
support = {BB/T012773/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Archaea ; *Atmosphere ; Eukaryota ; Fossils ; Humans ; Hypoxia ; *Oxygen/metabolism ; },
abstract = {The endosymbiotic origin of mitochondria during eukaryogenesis has long been viewed as an adaptive response to the oxygenation of Earth's surface environment, presuming a fundamentally aerobic lifestyle for the free-living bacterial ancestors of mitochondria. This oxygen-centric view has been robustly challenged by recent advances in the Earth and life sciences. While the permanent oxygenation of the atmosphere above trace concentrations is now thought to have occurred 2.2 billion years ago, large parts of the deep ocean remained anoxic until less than 0.5 billion years ago. Neither fossils nor molecular clocks correlate the origin of mitochondria, or eukaryogenesis more broadly, to either of these planetary redox transitions. Instead, mitochondria-bearing eukaryotes are consistently dated to between these two oxygenation events, during an interval of pervasive deep-sea anoxia and variable surface-water oxygenation. The discovery and cultivation of the Asgard archaea has reinforced metabolic evidence that eukaryogenesis was initially mediated by syntrophic H2 exchange between an archaeal host and an α-proteobacterial symbiont living under anoxia. Together, these results temporally, spatially and metabolically decouple the earliest stages of eukaryogenesis from the oxygen content of the surface ocean and atmosphere. Rather than reflecting the ancestral metabolic state, obligate aerobiosis in eukaryotes is most probably derived, having only become globally widespread over the past 1 billion years as atmospheric oxygen approached modern levels.},
}

Archaea
*Atmosphere
Eukaryota
Fossils
Humans
Hypoxia
*Oxygen/metabolism

@article {pmid35394422,
year = {2022},
author = {Meyer, BH and Adam, PS and Wagstaff, BA and Kolyfetis, GE and Probst, AJ and Albers, SV and Dorfmueller, HC},
title = {Agl24 is an ancient archaeal homolog of the eukaryotic N-glycan chitobiose synthesis enzymes.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
pmid = {35394422},
issn = {2050-084X},
support = {/WT_/Wellcome Trust/United Kingdom ; 105606/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Archaea/genetics ; Disaccharides ; *Eukaryota ; Phylogeny ; Polysaccharides ; },
abstract = {Protein N-glycosylation is a post-translational modification found in organisms of all domains of life. The crenarchaeal N-glycosylation begins with the synthesis of a lipid-linked chitobiose core structure, identical to that in Eukaryotes, although the enzyme catalyzing this reaction remains unknown. Here, we report the identification of a thermostable archaeal β-1,4-N-acetylglucosaminyltransferase, named archaeal glycosylation enzyme 24 (Agl24), responsible for the synthesis of the N-glycan chitobiose core. Biochemical characterization confirmed its function as an inverting β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol glycosyltransferase. Substitution of a conserved histidine residue, found also in the eukaryotic and bacterial homologs, demonstrated its functional importance for Agl24. Furthermore, bioinformatics and structural modeling revealed similarities of Agl24 to the eukaryotic Alg14/13 and a distant relation to the bacterial MurG, which are catalyzing the same or a similar reaction, respectively. Phylogenetic analysis of Alg14/13 homologs indicates that they are ancient in Eukaryotes, either as a lateral transfer or inherited through eukaryogenesis.},
}

*Archaea/genetics
Disaccharides
*Eukaryota
Phylogeny
Polysaccharides

@article {pmid35333570,
year = {2022},
author = {Akıl, C and Ali, S and Tran, LT and Gaillard, J and Li, W and Hayashida, K and Hirose, M and Kato, T and Oshima, A and Fujishima, K and Blanchoin, L and Narita, A and Robinson, RC},
title = {Structure and dynamics of Odinarchaeota tubulin and the implications for eukaryotic microtubule evolution.},
journal = {Science advances},
volume = {8},
number = {12},
pages = {eabm2225},
pmid = {35333570},
issn = {2375-2548},
mesh = {Eukaryota/metabolism ; *Eukaryotic Cells/metabolism ; Guanosine Triphosphate/metabolism ; Microtubules/metabolism ; *Tubulin/chemistry ; },
abstract = {Tubulins are critical for the internal organization of eukaryotic cells, and understanding their emergence is an important question in eukaryogenesis. Asgard archaea are the closest known prokaryotic relatives to eukaryotes. Here, we elucidated the apo and nucleotide-bound x-ray structures of an Asgard tubulin from hydrothermal living Odinarchaeota (OdinTubulin). The guanosine 5'-triphosphate (GTP)-bound structure resembles a microtubule protofilament, with GTP bound between subunits, coordinating the "+" end subunit through a network of water molecules and unexpectedly by two cations. A water molecule is located suitable for GTP hydrolysis. Time course crystallography and electron microscopy revealed conformational changes on GTP hydrolysis. OdinTubulin forms tubules at high temperatures, with short curved protofilaments coiling around the tubule circumference, more similar to FtsZ, rather than running parallel to its length, as in microtubules. Thus, OdinTubulin represents an evolutionary stage intermediate between prokaryotic FtsZ and eukaryotic microtubule-forming tubulins.},
}

Eukaryota/metabolism
*Eukaryotic Cells/metabolism
Guanosine Triphosphate/metabolism
Microtubules/metabolism
*Tubulin/chemistry

@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 {pmid35275997,
year = {2022},
author = {Jüttner, M and Ferreira-Cerca, S},
title = {Looking through the Lens of the Ribosome Biogenesis Evolutionary History: Possible Implications for Archaeal Phylogeny and Eukaryogenesis.},
journal = {Molecular biology and evolution},
volume = {39},
number = {4},
pages = {},
pmid = {35275997},
issn = {1537-1719},
mesh = {*Archaea/genetics ; Biological Evolution ; Eukaryota/genetics ; *Genome, Archaeal ; Phylogeny ; Ribosomes/genetics ; },
abstract = {Our understanding of microbial diversity and its evolutionary relationships has increased substantially over the last decade. Such an understanding has been greatly fueled by culture-independent metagenomics analyses. However, the outcome of some of these studies and their biological and evolutionary implications, such as the origin of the eukaryotic lineage from the recently discovered archaeal Asgard superphylum, is debated. The sequences of the ribosomal constituents are amongst the most used phylogenetic markers. However, the functional consequences underlying the analysed sequence diversity and their putative evolutionary implications are essentially not taken into consideration. Here, we propose to exploit additional functional hallmarks of ribosome biogenesis to help disentangle competing evolutionary hypotheses. Using selected examples, such as the multiple origins of halophily in archaea or the evolutionary relationship between the Asgard archaea and Eukaryotes, we illustrate and discuss how function-aware phylogenetic framework can contribute to refining our understanding of archaeal phylogeny and the origin of eukaryotic cells.},
}

*Archaea/genetics
Biological Evolution
Eukaryota/genetics
*Genome, Archaeal
Phylogeny
Ribosomes/genetics

@article {pmid35218347,
year = {2022},
author = {Spang, A and Mahendrarajah, TA and Offre, P and Stairs, CW},
title = {Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere.},
journal = {Genome biology and evolution},
volume = {14},
number = {6},
pages = {},
pmid = {35218347},
issn = {1759-6653},
mesh = {*Archaea ; Biological Evolution ; Eukaryota ; Phylogeny ; *Viruses/genetics ; },
abstract = {The tree of life (TOL) is a powerful framework to depict the evolutionary history of cellular organisms through time, from our microbial origins to the diversification of multicellular eukaryotes that shape the visible biosphere today. During the past decades, our perception of the TOL has fundamentally changed, in part, due to profound methodological advances, which allowed a more objective approach to studying organismal and viral diversity and led to the discovery of major new branches in the TOL as well as viral lineages. Phylogenetic and comparative genomics analyses of these data have, among others, revolutionized our understanding of the deep roots and diversity of microbial life, the origin of the eukaryotic cell, eukaryotic diversity, as well as the origin, and diversification of viruses. In this review, we provide an overview of some of the recent discoveries on the evolutionary history of cellular organisms and their viruses and discuss a variety of complementary techniques that we consider crucial for making further progress in our understanding of the TOL and its interconnection with the virosphere.},
}

*Archaea
Biological Evolution
Eukaryota
Phylogeny
*Viruses/genetics

@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 {pmid35150280,
year = {2022},
author = {Da Cunha, V and Gaia, M and Ogata, H and Jaillon, O and Delmont, TO and Forterre, P},
title = {Giant Viruses Encode Actin-Related Proteins.},
journal = {Molecular biology and evolution},
volume = {39},
number = {2},
pages = {},
pmid = {35150280},
issn = {1537-1719},
mesh = {Actins/genetics ; Eukaryota/genetics ; Eukaryotic Cells ; Evolution, Molecular ; *Giant Viruses/genetics ; Phylogeny ; },
abstract = {The emergence of the eukaryotic cytoskeleton is a critical yet puzzling step of eukaryogenesis. Actin and actin-related proteins (ARPs) are ubiquitous components of this cytoskeleton. The gene repertoire of the Last Eukaryotic Common Ancestor (LECA) would have therefore harbored both actin and various ARPs. Here, we report the presence and expression of actin-related genes in viral genomes (viractins) of some Imitervirales, a viral order encompassing the giant Mimiviridae. Phylogenetic analyses suggest an early recruitment of an actin-related gene by viruses from ancient protoeukaryotic hosts before the emergence of modern eukaryotes, possibly followed by a back transfer that gave rise to eukaryotic actins. This supports a coevolutionary scenario between pre-LECA lineages and their viruses, which could have contributed to the emergence of the modern eukaryotic cytoskeleton.},
}

Actins/genetics
Eukaryota/genetics
Eukaryotic Cells
Evolution, Molecular
*Giant Viruses/genetics
Phylogeny

@article {pmid35084524,
year = {2022},
author = {La, SR and Ndhlovu, A and Durand, PM},
title = {The Ancient Origins of Death Domains Support the 'Original Sin' Hypothesis for the Evolution of Programmed Cell Death.},
journal = {Journal of molecular evolution},
volume = {90},
number = {1},
pages = {95-113},
pmid = {35084524},
issn = {1432-1432},
mesh = {Apoptosis ; *Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; Caspases/genetics/metabolism ; Death Domain ; Evolution, Molecular ; *Genome, Archaeal/genetics ; Peptide Hydrolases/genetics/metabolism ; Phylogeny ; },
abstract = {The discovery of caspase homologs in bacteria highlighted the relationship between programmed cell death (PCD) evolution and eukaryogenesis. However, the origin of PCD genes in prokaryotes themselves (bacteria and archaea) is poorly understood and a source of controversy. Whether archaea also contain C14 peptidase enzymes and other death domains is largely unknown because of a historical dearth of genomic data. Archaeal genomic databases have grown significantly in the last decade, which allowed us to perform a detailed comparative study of the evolutionary histories of PCD-related death domains in major archaeal phyla, including the deepest branching phyla of Candidatus Aenigmarchaeota, Candidatus Woesearchaeota, and Euryarchaeota. We identified death domains associated with executioners of PCD, like the caspase homologs of the C14 peptidase family, in 321 archaea sequences. Of these, 15.58% were metacaspase type I orthologues and 84.42% were orthocaspases. Maximum likelihood phylogenetic analyses revealed a scattered distribution of orthocaspases and metacaspases in deep-branching bacteria and archaea. The tree topology was incongruent with the prokaryote 16S phylogeny suggesting a common ancestry of PCD genes in prokaryotes and subsequent massive horizontal gene transfer coinciding with the divergence of archaea and bacteria. Previous arguments for the origin of PCD were philosophical in nature with two popular propositions being the "addiction" and 'original sin' hypotheses. Our data support the 'original sin' hypothesis, which argues for a pleiotropic origin of the PCD toolkit with pro-life and pro-death functions tracing back to the emergence of cellular life-the Last Universal Common Ancestor State.},
}

Apoptosis
*Archaea/genetics/metabolism
Bacteria/genetics/metabolism
Caspases/genetics/metabolism
Death Domain
Evolution, Molecular
*Genome, Archaeal/genetics
Peptide Hydrolases/genetics/metabolism
Phylogeny

@article {pmid35027725,
year = {2022},
author = {Muñoz-Gómez, SA and Susko, E and Williamson, K and Eme, L and Slamovits, CH and Moreira, D and López-García, P and Roger, AJ},
title = {Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria.},
journal = {Nature ecology & evolution},
volume = {6},
number = {3},
pages = {253-262},
pmid = {35027725},
issn = {2397-334X},
mesh = {*Alphaproteobacteria/genetics/metabolism ; Metagenome ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins ; Phylogeny ; },
abstract = {Determining the phylogenetic origin of mitochondria is key to understanding the ancestral mitochondrial symbiosis and its role in eukaryogenesis. However, the precise evolutionary relationship between mitochondria and their closest bacterial relatives remains hotly debated. The reasons include pervasive phylogenetic artefacts as well as limited protein and taxon sampling. Here we developed a new model of protein evolution that accommodates both across-site and across-branch compositional heterogeneity. We applied this site-and-branch-heterogeneous model (MAM60 + GFmix) to a considerably expanded dataset that comprises 108 mitochondrial proteins of alphaproteobacterial origin, and novel metagenome-assembled genomes from microbial mats, microbialites and sediments. The MAM60 + GFmix model fits the data much better and agrees with analyses of compositionally homogenized datasets with conventional site-heterogenous models. The consilience of evidence thus suggests that mitochondria are sister to the Alphaproteobacteria to the exclusion of MarineProteo1 and Magnetococcia. We also show that the ancestral presence of the crista-developing mitochondrial contact site and cristae organizing system (a mitofilin-domain-containing Mic60 protein) in mitochondria and the Alphaproteobacteria only supports their close relationship.},
}

*Alphaproteobacteria/genetics/metabolism
Metagenome
Mitochondria/genetics/metabolism
Mitochondrial Proteins
Phylogeny

@article {pmid35027677,
year = {2022},
author = {Wu, F and Speth, DR and Philosof, A and Crémière, A and Narayanan, A and Barco, RA and Connon, SA and Amend, JP and Antoshechkin, IA and Orphan, VJ},
title = {Unique mobile elements and scalable gene flow at the prokaryote-eukaryote boundary revealed by circularized Asgard archaea genomes.},
journal = {Nature microbiology},
volume = {7},
number = {2},
pages = {200-212},
pmid = {35027677},
issn = {2058-5276},
mesh = {Archaea/*genetics ; Archaeal Proteins/genetics ; Bacteria/genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; *Gene Flow ; *Genome, Archaeal ; Metagenomics ; Phylogeny ; Prokaryotic Cells/*metabolism ; },
abstract = {Eukaryotic genomes are known to have garnered innovations from both archaeal and bacterial domains but the sequence of events that led to the complex gene repertoire of eukaryotes is largely unresolved. Here, through the enrichment of hydrothermal vent microorganisms, we recovered two circularized genomes of Heimdallarchaeum species that belong to an Asgard archaea clade phylogenetically closest to eukaryotes. These genomes reveal diverse mobile elements, including an integrative viral genome that bidirectionally replicates in a circular form and aloposons, transposons that encode the 5,000 amino acid-sized proteins Otus and Ephialtes. Heimdallaechaeal mobile elements have garnered various genes from bacteria and bacteriophages, likely playing a role in shuffling functions across domains. The number of archaea- and bacteria-related genes follow strikingly different scaling laws in Asgard archaea, exhibiting a genome size-dependent ratio and a functional division resembling the bacteria- and archaea-derived gene repertoire across eukaryotes. Bacterial gene import has thus likely been a continuous process unaltered by eukaryogenesis and scaled up through genome expansion. Our data further highlight the importance of viewing eukaryogenesis in a pan-Asgard context, which led to the proposal of a conceptual framework, that is, the Heimdall nucleation-decentralized innovation-hierarchical import model that accounts for the emergence of eukaryotic complexity.},
}

Archaea/*genetics
Archaeal Proteins/genetics
Bacteria/genetics
Eukaryota/*genetics
*Evolution, Molecular
*Gene Flow
*Genome, Archaeal
Metagenomics
Phylogeny
Prokaryotic Cells/*metabolism

@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 {pmid35012979,
year = {2022},
author = {Bellinger, MR and Wei, J and Hartmann, U and Cadiou, H and Winklhofer, M and Banks, MA},
title = {Conservation of magnetite biomineralization genes in all domains of life and implications for magnetic sensing.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {3},
pages = {},
pmid = {35012979},
issn = {1091-6490},
mesh = {Animals ; Biological Evolution ; Biomineralization/*genetics ; Ferrosoferric Oxide/*chemistry ; Genomics ; *Magnetic Phenomena ; Magnetosomes/genetics ; Salmon ; },
abstract = {Animals use geomagnetic fields for navigational cues, yet the sensory mechanism underlying magnetic perception remains poorly understood. One idea is that geomagnetic fields are physically transduced by magnetite crystals contained inside specialized receptor cells, but evidence for intracellular, biogenic magnetite in eukaryotes is scant. Certain bacteria produce magnetite crystals inside intracellular compartments, representing the most ancient form of biomineralization known and having evolved prior to emergence of the crown group of eukaryotes, raising the question of whether magnetite biomineralization in eukaryotes and prokaryotes might share a common evolutionary history. Here, we discover that salmonid olfactory epithelium contains magnetite crystals arranged in compact clusters and determine that genes differentially expressed in magnetic olfactory cells, contrasted to nonmagnetic olfactory cells, share ancestry with an ancient prokaryote magnetite biomineralization system, consistent with exaptation for use in eukaryotic magnetoreception. We also show that 11 prokaryote biomineralization genes are universally present among a diverse set of eukaryote taxa and that nine of those genes are present within the Asgard clade of archaea Lokiarchaeota that affiliates with eukaryotes in phylogenomic analysis. Consistent with deep homology, we present an evolutionary genetics hypothesis for magnetite formation among eukaryotes to motivate convergent approaches for examining magnetite-based magnetoreception, molecular origins of matrix-associated biomineralization processes, and eukaryogenesis.},
}

Animals
Biological Evolution
Biomineralization/*genetics
Ferrosoferric Oxide/*chemistry
Genomics
*Magnetic Phenomena
Magnetosomes/genetics
Salmon

@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 {pmid34949483,
year = {2022},
author = {Cohen, PA and Kodner, RB},
title = {The earliest history of eukaryotic life: uncovering an evolutionary story through the integration of biological and geological data.},
journal = {Trends in ecology & evolution},
volume = {37},
number = {3},
pages = {246-256},
doi = {10.1016/j.tree.2021.11.005},
pmid = {34949483},
issn = {1872-8383},
mesh = {Biological Evolution ; *Ecosystem ; *Eukaryota/genetics ; Eukaryotic Cells ; Fossils ; Geology ; Phylogeny ; },
abstract = {While there is significant data on eukaryogenesis and the early development of the eukaryotic lineage, major uncertainties regarding their origins and evolution remain, including questions of taxonomy, timing, and paleoecology. Here we examine the origin and diversification of the eukaryotes in the Proterozoic Eon as viewed through fossils, organic biomarkers, molecular clocks, phylogenies, and redox proxies. Our interpretation of the integration of these data suggest that eukaryotes were likely aerobic and established in Proterozoic ecosystems. We argue that we must closely examine and integrate both biological and geological evidence and examine points of agreement and contention to gain new insights into the true origin and early evolutionary history of this vastly important group.},
}

Biological Evolution
*Ecosystem
*Eukaryota/genetics
Eukaryotic Cells
Fossils
Geology
Phylogeny

@article {pmid34863611,
year = {2022},
author = {Nobs, SJ and MacLeod, FI and Wong, HL and Burns, BP},
title = {Eukarya the chimera: eukaryotes, a secondary innovation of the two domains of life?.},
journal = {Trends in microbiology},
volume = {30},
number = {5},
pages = {421-431},
doi = {10.1016/j.tim.2021.11.003},
pmid = {34863611},
issn = {1878-4380},
mesh = {Archaea/genetics ; Bacteria/genetics ; *Biological Evolution ; *Eukaryota/genetics ; Eukaryotic Cells ; Phylogeny ; },
abstract = {One of the most significant events in the evolution of life is the origin of the eukaryotic cell, an increase in cellular complexity that occurred approximately 2 billion years ago. Ground-breaking research has centered around unraveling the characteristics of the Last Eukaryotic Common Ancestor (LECA) and the nuanced archaeal and bacterial contributions in eukaryogenesis, resulting in fundamental changes in our understanding of the Tree of Life. The archaeal and bacterial roles are covered by theories of endosymbiogenesis wherein an ancestral host archaeon and a bacterial endosymbiont merged to create a new complex cell type - Eukarya - and its mitochondrion. Eukarya is often regarded as a unique and distinct domain due to complex innovations not found in archaea or bacteria, despite housing a chimeric genome containing genes of both archaeal and bacterial origin. However, the discovery of complex cell machineries in recently described Asgard archaeal lineages, and the growing support for diverse bacterial gene transfers prior to and during the time of LECA, is redefining our understanding of eukaryogenesis. Indeed, the uniqueness of Eukarya, as a domain, is challenged. It is likely that many microbial syntrophies, encompassing a 'microbial village', were required to 'raise' a eukaryote during the process of eukaryogenesis.},
}

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

@article {pmid34830325,
year = {2021},
author = {Borao, S and Ayté, J and Hümmer, S},
title = {Evolution of the Early Spliceosomal Complex-From Constitutive to Regulated Splicing.},
journal = {International journal of molecular sciences},
volume = {22},
number = {22},
pages = {},
pmid = {34830325},
issn = {1422-0067},
mesh = {*Alternative Splicing ; Animals ; Base Sequence ; Evolution, Molecular ; Exons ; Humans ; Introns ; Mammals/*genetics/metabolism ; RNA Precursors/*genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Ribonucleoprotein, U1 Small Nuclear/genetics/metabolism ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Schizosaccharomyces/*genetics/metabolism ; Spliceosomes/chemistry/*genetics/metabolism ; Splicing Factor U2AF/genetics/metabolism ; },
abstract = {Pre-mRNA splicing is a major process in the regulated expression of genes in eukaryotes, and alternative splicing is used to generate different proteins from the same coding gene. Splicing is a catalytic process that removes introns and ligates exons to create the RNA sequence that codifies the final protein. While this is achieved in an autocatalytic process in ancestral group II introns in prokaryotes, the spliceosome has evolved during eukaryogenesis to assist in this process and to finally provide the opportunity for intron-specific splicing. In the early stage of splicing, the RNA 5' and 3' splice sites must be brought within proximity to correctly assemble the active spliceosome and perform the excision and ligation reactions. The assembly of this first complex, termed E-complex, is currently the least understood process. We focused in this review on the formation of the E-complex and compared its composition and function in three different organisms. We highlight the common ancestral mechanisms in S. cerevisiae, S. pombe, and mammals and conclude with a unifying model for intron definition in constitutive and regulated co-transcriptional splicing.},
}

*Alternative Splicing
Animals
Base Sequence
Evolution, Molecular
Exons
Humans
Introns
Mammals/*genetics/metabolism
RNA Precursors/*genetics/metabolism
RNA, Messenger/genetics/metabolism
Ribonucleoprotein, U1 Small Nuclear/genetics/metabolism
Saccharomyces cerevisiae/*genetics/metabolism
Saccharomyces cerevisiae Proteins/genetics/metabolism
Schizosaccharomyces/*genetics/metabolism
Spliceosomes/chemistry/*genetics/metabolism
Splicing Factor U2AF/genetics/metabolism

@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 {pmid34472688,
year = {2022},
author = {Kořený, L and Oborník, M and Horáková, E and Waller, RF and Lukeš, J},
title = {The convoluted history of haem biosynthesis.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {97},
number = {1},
pages = {141-162},
doi = {10.1111/brv.12794},
pmid = {34472688},
issn = {1469-185X},
mesh = {Biological Evolution ; *Eukaryota/genetics ; *Heme/genetics/metabolism ; Metabolic Networks and Pathways ; },
abstract = {The capacity of haem to transfer electrons, bind diatomic gases, and catalyse various biochemical reactions makes it one of the essential biomolecules on Earth and one that was likely used by the earliest forms of cellular life. Since the description of haem biosynthesis, our understanding of this multi-step pathway has been almost exclusively derived from a handful of model organisms from narrow taxonomic contexts. Recent advances in genome sequencing and functional studies of diverse and previously neglected groups have led to discoveries of alternative routes of haem biosynthesis that deviate from the 'classical' pathway. In this review, we take an evolutionarily broad approach to illuminate the remarkable diversity and adaptability of haem synthesis, from prokaryotes to eukaryotes, showing the range of strategies that organisms employ to obtain and utilise haem. In particular, the complex evolutionary histories of eukaryotes that involve multiple endosymbioses and horizontal gene transfers are reflected in the mosaic origin of numerous metabolic pathways with haem biosynthesis being a striking case. We show how different evolutionary trajectories and distinct life strategies resulted in pronounced tensions and differences in the spatial organisation of the haem biosynthesis pathway, in some cases leading to a complete loss of a haem-synthesis capacity and, rarely, even loss of a requirement for haem altogether.},
}

Biological Evolution
*Eukaryota/genetics
*Heme/genetics/metabolism
Metabolic Networks and Pathways

@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 {pmid34282823,
year = {2021},
author = {Makarov, AA and Padilla-Mejia, NE and Field, MC},
title = {Evolution and diversification of the nuclear pore complex.},
journal = {Biochemical Society transactions},
volume = {49},
number = {4},
pages = {1601-1619},
pmid = {34282823},
issn = {1470-8752},
support = {/WT_/Wellcome Trust/United Kingdom ; 204697/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; *Biological Evolution ; Biological Transport ; Membrane Proteins/metabolism ; Mitosis ; Nuclear Pore/*metabolism ; RNA, Messenger/metabolism ; },
abstract = {The nuclear pore complex (NPC) is responsible for transport between the cytoplasm and nucleoplasm and one of the more intricate structures of eukaryotic cells. Typically composed of over 300 polypeptides, the NPC shares evolutionary origins with endo-membrane and intraflagellar transport system complexes. The modern NPC was fully established by the time of the last eukaryotic common ancestor and, hence, prior to eukaryote diversification. Despite the complexity, the NPC structure is surprisingly flexible with considerable variation between lineages. Here, we review diversification of the NPC in major taxa in view of recent advances in genomic and structural characterisation of plant, protist and nucleomorph NPCs and discuss the implications for NPC evolution. Furthermore, we highlight these changes in the context of mRNA export and consider how this process may have influenced NPC diversity. We reveal the NPC as a platform for continual evolution and adaptation.},
}

Animals
*Biological Evolution
Biological Transport
Membrane Proteins/metabolism
Mitosis
Nuclear Pore/*metabolism
RNA, Messenger/metabolism

@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 {pmid34247240,
year = {2021},
author = {Vargová, R and Wideman, JG and Derelle, R and Klimeš, V and Kahn, RA and Dacks, JB and Eliáš, M},
title = {A Eukaryote-Wide Perspective on the Diversity and Evolution of the ARF GTPase Protein Family.},
journal = {Genome biology and evolution},
volume = {13},
number = {8},
pages = {},
pmid = {34247240},
issn = {1759-6653},
support = {R21 ES021028/ES/NIEHS NIH HHS/United States ; R35 GM122568/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Eukaryota/genetics ; Eukaryotic Cells ; Evolution, Molecular ; *GTP Phosphohydrolases/genetics ; Genome ; Phylogeny ; },
abstract = {The evolution of eukaryotic cellular complexity is interwoven with the extensive diversification of many protein families. One key family is the ARF GTPases that act in eukaryote-specific processes, including membrane traffic, tubulin assembly, actin dynamics, and cilia-related functions. Unfortunately, our understanding of the evolution of this family is limited. Sampling an extensive set of available genome and transcriptome sequences, we have assembled a data set of over 2,000 manually curated ARF family genes from 114 eukaryotic species, including many deeply diverged protist lineages, and carried out comprehensive molecular phylogenetic analyses. These reconstructed as many as 16 ARF family members present in the last eukaryotic common ancestor, nearly doubling the previously inferred ancient system complexity. Evidence for the wide occurrence and ancestral origin of Arf6, Arl13, and Arl16 is presented for the first time. Moreover, Arl17, Arl18, and SarB, newly described here, are absent from well-studied model organisms and as a result their function(s) remain unknown. Analyses of our data set revealed a previously unsuspected diversity of membrane association modes and domain architectures within the ARF family. We detail the step-wise expansion of the ARF family in the metazoan lineage, including discovery of several new animal-specific family members. Delving back to its earliest evolution in eukaryotes, the resolved relationship observed between the ARF family paralogs sets boundaries for scenarios of vesicle coat origins during eukaryogenesis. Altogether, our work fundamentally broadens the understanding of the diversity and evolution of a protein family underpinning the structural and functional complexity of the eukaryote cells.},
}

Animals
*Eukaryota/genetics
Eukaryotic Cells
Evolution, Molecular
*GTP Phosphohydrolases/genetics
Genome
Phylogeny

@article {pmid34229349,
year = {2021},
author = {Devos, DP},
title = {Reconciling Asgardarchaeota Phylogenetic Proximity to Eukaryotes and Planctomycetes Cellular Features in the Evolution of Life.},
journal = {Molecular biology and evolution},
volume = {38},
number = {9},
pages = {3531-3542},
pmid = {34229349},
issn = {1537-1719},
mesh = {Archaea/genetics ; Biological Evolution ; *Eukaryota/genetics ; Phylogeny ; *Planctomycetes ; },
abstract = {The relationship between the three domains of life-Archaea, Bacteria, and Eukarya-is one of Biology's greatest mysteries. Current favored models imply two ancestral domains, Bacteria and Archaea, with eukaryotes originating within Archaea. This type of models has been supported by the recent description of the Asgardarchaeota, the closest prokaryotic relatives of eukaryotes. However, there are many problems associated with any scenarios implying that eukaryotes originated from within the Archaea, including genome mosaicism, phylogenies, the cellular organization of the Archaea, and their ancestral character. By contrast, all models of eukaryogenesis fail to consider two relevant discoveries: the detection of membrane coat proteins, and of phagocytosis-related processes in Planctomycetes, which are among the bacteria with the most developed endomembrane system. Consideration of these often overlooked features and others found in Planctomycetes and related bacteria suggest an evolutionary model based on a single ancestral domain. In this model, the proximity of Asgard and eukaryotes is not rejected but instead, Asgard are considered as diverging away from a common ancestor instead of on the way toward the eukaryotic ancestor. This model based on a single ancestral domain solves most of the ambiguities associated with the ones based on two ancestral domains. The single-domain model is better suited to explain the origin and evolution of all three domains of life, blurring the distinctions between them. Support for this model as well as the opportunities that it presents not only for reinterpreting previous results, but also for planning future experiments, are explored.},
}

Archaea/genetics
Biological Evolution
*Eukaryota/genetics
Phylogeny
*Planctomycetes

@article {pmid34228793,
year = {2021},
author = {Zhang, S and Hama, Y and Mizushima, N},
title = {The evolution of autophagy proteins - diversification in eukaryotes and potential ancestors in prokaryotes.},
journal = {Journal of cell science},
volume = {134},
number = {13},
pages = {},
doi = {10.1242/jcs.233742},
pmid = {34228793},
issn = {1477-9137},
mesh = {Archaea/genetics ; Autophagy/genetics ; *Eukaryota/genetics ; Eukaryotic Cells ; Evolution, Molecular ; Phylogeny ; *Prokaryotic Cells ; },
abstract = {Autophagy is a degradative pathway for cytoplasmic constituents, and is conserved across eukaryotes. Autophagy-related (ATG) genes have undergone extensive multiplications and losses in different eukaryotic lineages, resulting in functional diversification and specialization. Notably, even though bacteria and archaea do not possess an autophagy pathway, they do harbor some remote homologs of Atg proteins, suggesting that preexisting proteins were recruited when the autophagy pathway developed during eukaryogenesis. In this Review, we summarize our current knowledge on the distribution of Atg proteins within eukaryotes and outline the major multiplication and loss events within the eukaryotic tree. We also discuss the potential prokaryotic homologs of Atg proteins identified to date, emphasizing the evolutionary relationships and functional differences between prokaryotic and eukaryotic proteins.},
}

Archaea/genetics
Autophagy/genetics
*Eukaryota/genetics
Eukaryotic Cells
Evolution, Molecular
Phylogeny
*Prokaryotic Cells

@article {pmid34217168,
year = {2021},
author = {Tan, DX},
title = {Genesis of the nucleus from bacterial sporulation: A simple hypothesis of eukaryotic origin.},
journal = {Neuro endocrinology letters},
volume = {42},
number = {2},
pages = {113-127},
pmid = {34217168},
issn = {2354-4716},
abstract = {The most complexed issue of eukaryogenesis is the origin of the nucleus. Many hypotheses have been forwarded to explain this. Most of them are complicated and intangible. Here, a new and relatively simple hypothesis to address this unresolved problem has been hypothesized. This hypothesis is denominated as "Theory of Nucleus Origin from Bacterial Sporulation" (TNOBS). The hypothesis points out that the nucleus may be derived from a bacterial endospore, particularly, when sporulation is arrested at stage 4 due to a gene mutation. At this stage, a double membrane structure containing a chromosome (foreospore) has developed, which is reminiscent of a nucleus. In addition to the forespore, the mother cell also contains an additional chromosome. This morphologically specific cell is referred as a proto-nucleate cell (PTC). The PTC requires additional energy to maintain their newly formed endomembrane compartment (protonucleus). This energy demand has the potential of driving the expression of genes for energy production from the cytosolic chromosome which finally evolves to mitochondria, whereas the forespore develops to the nucleus. This TNOBS considers the nucleus and mitochondrion having derived simultaneously in the same cell. Moreover, this scenario avoids the difficulty to explain how an α-proteobacterium (precursor of mitochondria) can be taken up by the host despite of lacking capacity for classic endocytosis. It is further suggested that PTC generation may not be an extremely rare event in nature due to the widely existing spore-forming bacteria and frequent mutations. TNOBS is comparably simple and may, in some of its principle traits, be even reproducible under laboratory conditions.},
}

@article {pmid34203645,
year = {2021},
author = {Almojil, D and Bourgeois, Y and Falis, M and Hariyani, I and Wilcox, J and Boissinot, S},
title = {The Structural, Functional and Evolutionary Impact of Transposable Elements in Eukaryotes.},
journal = {Genes},
volume = {12},
number = {6},
pages = {},
pmid = {34203645},
issn = {2073-4425},
mesh = {Animals ; *DNA Transposable Elements ; *Evolution, Molecular ; Humans ; Plants/genetics ; },
abstract = {Transposable elements (TEs) are nearly ubiquitous in eukaryotes. The increase in genomic data, as well as progress in genome annotation and molecular biology techniques, have revealed the vast number of ways mobile elements have impacted the evolution of eukaryotes. In addition to being the main cause of difference in haploid genome size, TEs have affected the overall organization of genomes by accumulating preferentially in some genomic regions, by causing structural rearrangements or by modifying the recombination rate. Although the vast majority of insertions is neutral or deleterious, TEs have been an important source of evolutionary novelties and have played a determinant role in the evolution of fundamental biological processes. TEs have been recruited in the regulation of host genes and are implicated in the evolution of regulatory networks. They have also served as a source of protein-coding sequences or even entire genes. The impact of TEs on eukaryotic evolution is only now being fully appreciated and the role they may play in a number of biological processes, such as speciation and adaptation, remains to be deciphered.},
}

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

@article {pmid34166615,
year = {2021},
author = {Liu, J and Tassinari, M and Souza, DP and Naskar, S and Noel, JK and Bohuszewicz, O and Buck, M and Williams, TA and Baum, B and Low, HH},
title = {Bacterial Vipp1 and PspA are members of the ancient ESCRT-III membrane-remodeling superfamily.},
journal = {Cell},
volume = {184},
number = {14},
pages = {3660-3673.e18},
pmid = {34166615},
issn = {1097-4172},
support = {MC_UP_1201/27/MRC_/Medical Research Council/United Kingdom ; 215553/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; 200074/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; 203276/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; BB/P001440/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/chemistry/isolation & purification/*metabolism/ultrastructure ; Cell Membrane/*metabolism ; Chickens ; Cryoelectron Microscopy ; Endosomal Sorting Complexes Required for Transport/chemistry/*metabolism ; Evolution, Molecular ; Heat-Shock Proteins/chemistry/*metabolism/ultrastructure ; Humans ; Models, Molecular ; *Multigene Family ; Nostoc/*metabolism ; Protein Structure, Secondary ; Sequence Homology, Amino Acid ; Thermodynamics ; },
abstract = {Membrane remodeling and repair are essential for all cells. Proteins that perform these functions include Vipp1/IM30 in photosynthetic plastids, PspA in bacteria, and ESCRT-III in eukaryotes. Here, using a combination of evolutionary and structural analyses, we show that these protein families are homologous and share a common ancient evolutionary origin that likely predates the last universal common ancestor. This homology is evident in cryo-electron microscopy structures of Vipp1 rings from the cyanobacterium Nostoc punctiforme presented over a range of symmetries. Each ring is assembled from rungs that stack and progressively tilt to form dome-shaped curvature. Assembly is facilitated by hinges in the Vipp1 monomer, similar to those in ESCRT-III proteins, which allow the formation of flexible polymers. Rings have an inner lumen that is able to bind and deform membranes. Collectively, these data suggest conserved mechanistic principles that underlie Vipp1, PspA, and ESCRT-III-dependent membrane remodeling across all domains of life.},
}

Amino Acid Sequence
Animals
Bacterial Proteins/chemistry/isolation & purification/*metabolism/ultrastructure
Cell Membrane/*metabolism
Chickens
Cryoelectron Microscopy
Endosomal Sorting Complexes Required for Transport/chemistry/*metabolism
Evolution, Molecular
Heat-Shock Proteins/chemistry/*metabolism/ultrastructure
Humans
Models, Molecular
*Multigene Family
Nostoc/*metabolism
Protein Structure, Secondary
Sequence Homology, Amino Acid
Thermodynamics

@article {pmid34131078,
year = {2021},
author = {Hoshino, Y and Gaucher, EA},
title = {Evolution of bacterial steroid biosynthesis and its impact on eukaryogenesis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {25},
pages = {},
pmid = {34131078},
issn = {1091-6490},
support = {R01 AR069137/AR/NIAMS NIH HHS/United States ; },
mesh = {Archaea/genetics ; Bacteria/genetics/*metabolism ; Bayes Theorem ; *Biosynthetic Pathways/genetics ; Cell Membrane/metabolism ; Eukaryotic Cells/*metabolism ; *Evolution, Molecular ; Genes, Bacterial ; Phylogeny ; Steroids/*biosynthesis ; },
abstract = {Steroids are components of the eukaryotic cellular membrane and have indispensable roles in the process of eukaryotic endocytosis by regulating membrane fluidity and permeability. In particular, steroids may have been a structural prerequisite for the acquisition of mitochondria via endocytosis during eukaryogenesis. While eukaryotes are inferred to have evolved from an archaeal lineage, there is little similarity between the eukaryotic and archaeal cellular membranes. As such, the evolution of eukaryotic cellular membranes has limited our understanding of eukaryogenesis. Despite evolving from archaea, the eukaryotic cellular membrane is essentially a fatty acid bacterial-type membrane, which implies a substantial bacterial contribution to the evolution of the eukaryotic cellular membrane. Here, we address the evolution of steroid biosynthesis in eukaryotes by combining ancestral sequence reconstruction and comprehensive phylogenetic analyses of steroid biosynthesis genes. Contrary to the traditional assumption that eukaryotic steroid biosynthesis evolved within eukaryotes, most steroid biosynthesis genes are inferred to be derived from bacteria. In particular, aerobic deltaproteobacteria (myxobacteria) seem to have mediated the transfer of key genes for steroid biosynthesis to eukaryotes. Analyses of resurrected steroid biosynthesis enzymes suggest that the steroid biosynthesis pathway in early eukaryotes may have been similar to the pathway seen in modern plants and algae. These resurrected proteins also experimentally demonstrate that molecular oxygen was required to establish the modern eukaryotic cellular membrane during eukaryogenesis. Our study provides unique insight into relationships between early eukaryotes and other bacteria in addition to the well-known endosymbiosis with alphaproteobacteria.},
}

Archaea/genetics
Bacteria/genetics/*metabolism
Bayes Theorem
*Biosynthetic Pathways/genetics
Cell Membrane/metabolism
Eukaryotic Cells/*metabolism
*Evolution, Molecular
Genes, Bacterial
Phylogeny
Steroids/*biosynthesis

@article {pmid34021750,
year = {2021},
author = {Wright, GSA},
title = {Bacterial Evolutionary Precursors of Eukaryotic Copper-Zinc Superoxide Dismutases.},
journal = {Molecular biology and evolution},
volume = {38},
number = {9},
pages = {3789-3803},
pmid = {34021750},
issn = {1537-1719},
support = {WRIGHT/OCT18/969-799/MNDA_/Motor Neurone Disease Association/United Kingdom ; },
mesh = {Bacteria/genetics/metabolism ; *Copper/metabolism ; *Eukaryota/metabolism ; Humans ; Superoxide Dismutase/chemistry/genetics/metabolism ; Zinc ; },
abstract = {Internalization of a bacteria by an archaeal cell expedited eukaryotic evolution. An important feature of the species that diversified into the great variety of eukaryotic life visible today was the ability to combat oxidative stress with a copper-zinc superoxide dismutase (CuZnSOD) enzyme activated by a specific, high-affinity copper chaperone. Adoption of a single protein interface that facilitates homodimerization and heterodimerization was essential; however, its evolution has been difficult to rationalize given the structural differences between bacterial and eukaryotic enzymes. In contrast, no consistent strategy for the maturation of periplasmic bacterial CuZnSODs has emerged. Here, 34 CuZnSODs are described that closely resemble the eukaryotic form but originate predominantly from aquatic bacteria. Crystal structures of a Bacteroidetes bacterium CuZnSOD portray both prokaryotic and eukaryotic characteristics and propose a mechanism for self-catalyzed disulfide maturation. Unification of a bacterial but eukaryotic-like CuZnSOD along with a ferredoxin-fold MXCXXC copper-binding domain within a single polypeptide created the advanced copper delivery system for CuZnSODs exemplified by the human copper chaperone for superoxide dismutase-1. The development of this system facilitated evolution of large and compartmentalized cells following endosymbiotic eukaryogenesis.},
}

Bacteria/genetics/metabolism
*Copper/metabolism
*Eukaryota/metabolism
Humans
Superoxide Dismutase/chemistry/genetics/metabolism
Zinc

@article {pmid34008202,
year = {2021},
author = {Speijer, D},
title = {Zombie ideas about early endosymbiosis: Which entry mechanisms gave us the "endo" in different endosymbionts?.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {43},
number = {7},
pages = {e2100069},
doi = {10.1002/bies.202100069},
pmid = {34008202},
issn = {1521-1878},
mesh = {Bacteria/genetics ; Biological Evolution ; Eukaryota ; *Eukaryotic Cells ; Phylogeny ; *Symbiosis ; },
abstract = {Recently, a review regarding the mechanics and evolution of mitochondrial fission appeared in Nature. Surprisingly, it stated authoritatively that the mitochondrial outer membrane, in contrast with the inner membrane of bacterial descent, was acquired from the host, presumably during uptake. However, it has been known for quite some time that this membrane was also derived from the Gram-negative, alpha-proteobacterium related precursor of present-day mitochondria. The zombie idea of the host membrane still surrounding the endosymbiont is not only wrong, but more importantly, might hamper the proper conception of possible scenarios of eukaryogenesis. Why? Because it steers the imagination not only with regard to possible uptake mechanisms, but also regarding what went on before. Here I critically discuss both the evidence for the continuity of the bacterial outer membrane, the reasons for the persistence of the erroneous host membrane hypothesis and the wider implications of these misconceptions for the ideas regarding events occurring during the first steps towards the evolution of the eukaryotes and later major eukaryotic differentiations. I will also highlight some of the latest insights regarding different instances of endosymbiont evolution.},
}

Bacteria/genetics
Biological Evolution
Eukaryota
*Eukaryotic Cells
Phylogeny
*Symbiosis

@article {pmid33984158,
year = {2021},
author = {Lineweaver, CH and Bussey, KJ and Blackburn, AC and Davies, PCW},
title = {Cancer progression as a sequence of atavistic reversions.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {43},
number = {7},
pages = {e2000305},
pmid = {33984158},
issn = {1521-1878},
support = {U54 CA217376/CA/NCI NIH HHS/United States ; U54-CA143682/CA/NCI NIH HHS/United States ; },
mesh = {*Biological Evolution ; Eukaryota ; Eukaryotic Cells ; Humans ; *Neoplasms/genetics ; Phenotype ; },
abstract = {It has long been recognized that cancer onset and progression represent a type of reversion to an ancestral quasi-unicellular phenotype. This general concept has been refined into the atavistic model of cancer that attempts to provide a quantitative analysis and testable predictions based on genomic data. Over the past decade, support for the multicellular-to-unicellular reversion predicted by the atavism model has come from phylostratigraphy. Here, we propose that cancer onset and progression involve more than a one-off multicellular-to-unicellular reversion, and are better described as a series of reversionary transitions. We make new predictions based on the chronology of the unicellular-eukaryote-to-multicellular-eukaryote transition. We also make new predictions based on three other evolutionary transitions that occurred in our lineage: eukaryogenesis, oxidative phosphorylation and the transition to adaptive immunity. We propose several modifications to current phylostratigraphy to improve age resolution to test these predictions. Also see the video abstract here: https://youtu.be/3unEu5JYJrQ.},
}

*Biological Evolution
Eukaryota
Eukaryotic Cells
Humans
*Neoplasms/genetics
Phenotype

@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 {pmid33892498,
year = {2021},
author = {Knopp, M and Stockhorst, S and van der Giezen, M and Garg, SG and Gould, SB},
title = {The Asgard Archaeal-Unique Contribution to Protein Families of the Eukaryotic Common Ancestor Was 0.3.},
journal = {Genome biology and evolution},
volume = {13},
number = {6},
pages = {},
pmid = {33892498},
issn = {1759-6653},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Eukaryota/*genetics ; *Multigene Family ; },
abstract = {The identification of the asgard archaea has fueled speculations regarding the nature of the archaeal host in eukaryogenesis and its level of complexity prior to endosymbiosis. Here, we analyzed the coding capacity of 150 eukaryotes, 1,000 bacteria, and 226 archaea, including the only cultured member of the asgard archaea. Clustering methods that consistently recover endosymbiotic contributions to eukaryotic genomes recover an asgard archaeal-unique contribution of a mere 0.3% to protein families present in the last eukaryotic common ancestor, while simultaneously suggesting that this group's diversity rivals that of all other archaea combined. The number of homologs shared exclusively between asgard archaea and eukaryotes is only 27 on average. This tiny asgard archaeal-unique contribution to the root of eukaryotic protein families questions claims that archaea evolved complexity prior to eukaryogenesis. Genomic and cellular complexity remains a eukaryote-specific feature and is best understood as the archaeal host's solution to housing an endosymbiont.},
}

Archaea/*genetics
Bacteria/*genetics
Eukaryota/*genetics
*Multigene Family

@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 {pmid33860546,
year = {2021},
author = {Brandeis, M},
title = {Were eukaryotes made by sex?: Sex might have been vital for merging endosymbiont and host genomes giving rise to eukaryotes.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {43},
number = {6},
pages = {e2000256},
doi = {10.1002/bies.202000256},
pmid = {33860546},
issn = {1521-1878},
mesh = {Archaea/genetics ; *Biological Evolution ; *Eukaryota/genetics ; Eukaryotic Cells ; Phylogeny ; Symbiosis/genetics ; },
abstract = {I hypothesize that the appearance of sex facilitated the merging of the endosymbiont and host genomes during early eukaryote evolution. Eukaryotes were formed by symbiosis between a bacterium that entered an archaeon, eventually giving rise to mitochondria. This entry was followed by the gradual transfer of most bacterial endosymbiont genes into the archaeal host genome. I argue that the merging of the mitochondrial genes into the host genome was vital for the evolution of genuine eukaryotes. At the time this process commenced it was unprecedented and required a novel mechanism. I suggest that this mechanism was meiotic sex, and that its appearance might have been THE crucial step that enabled the evolution of proper eukaryotes from early endosymbiont containing proto-eukaryotes. Sex might continue to be essential today for keeping genome insertions in check. Also see the video abstract here: https://youtu.be/aVMvWMpomac.},
}

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

@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 {pmid33812918,
year = {2021},
author = {Mikhailovsky, GE and Gordon, R},
title = {LUCA to LECA, the Lucacene: A model for the gigayear delay from the first prokaryote to eukaryogenesis.},
journal = {Bio Systems},
volume = {205},
number = {},
pages = {104415},
doi = {10.1016/j.biosystems.2021.104415},
pmid = {33812918},
issn = {1872-8324},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Biological Evolution ; Computer Simulation ; Eukaryota/*genetics ; *Gene Transfer, Horizontal ; *Models, Biological ; Mutation ; *Systems Biology ; Time Factors ; },
abstract = {It is puzzling why life on Earth consisted of prokaryotes for up to 2.5 ± 0.5 billion years (Gy) before the appearance of the first eukaryotes. This period, from LUCA (Last Universal Common Ancestor) to LECA (Last Eucaryotic Common Ancestor), we have named the Lucacene, to suggest all prokaryotic descendants of LUCA before the appearance of LECA. Here we present a simple model based on horizontal gene transfer (HGT). It is the process of HGT from Bacteria to Archaea and its reverse that we wish to simulate and estimate its duration until eukaryogenesis. Rough quantitation of its parameters shows that the model may explain the long duration of the Lucacene.},
}

Archaea/*genetics
Bacteria/*genetics
*Biological Evolution
Computer Simulation
Eukaryota/*genetics
*Gene Transfer, Horizontal
*Models, Biological
Mutation
*Systems Biology
Time Factors

@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 {pmid33621507,
year = {2021},
author = {Roger, AJ and Susko, E and Leger, MM},
title = {Evolution: Reconstructing the Timeline of Eukaryogenesis.},
journal = {Current biology : CB},
volume = {31},
number = {4},
pages = {R193-R196},
doi = {10.1016/j.cub.2020.12.035},
pmid = {33621507},
issn = {1879-0445},
mesh = {*Eukaryota/genetics ; *Eukaryotic Cells ; *Evolution, Molecular ; Humans ; *Phylogeny ; Time Factors ; },
abstract = {Timing the events in the evolution of eukaryotic cells is crucial to understanding this major transition. A recent study reconstructs the origins of thousands of gene families ancestral to eukaryotes and, using a controversial approach, aims to order the events of eukaryogenesis.},
}

*Eukaryota/genetics
*Eukaryotic Cells
*Evolution, Molecular
Humans
*Phylogeny
Time Factors

@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.},
}