@article {pmid39689855,
year = {2024},
author = {Belyaev, AO and Karpov, SA and Keeling, PJ and Tikhonenkov, DV},
title = {The nature of 'jaws': a new predatory representative of Provora and the ultrastructure of nibbling protists.},
journal = {Open biology},
volume = {14},
number = {12},
pages = {240158},
doi = {10.1098/rsob.240158},
pmid = {39689855},
issn = {2046-2441},
support = {//Russian Science Foundation/ ; },
mesh = {*Phylogeny ; Flagella/ultrastructure ; Eukaryota/ultrastructure/genetics ; Stramenopiles/ultrastructure/genetics ; Organelles/ultrastructure ; },
abstract = {The recently discovered Provora supergroup has primarily been examined to determine their phylogenomic position in the eukaryotic tree. Their morphology is more poorly studied, and here we focus on their cellular organization and how it compares with that of other supergroups. These small eukaryovorous flagellates exhibit several ultrastructural features that are also found in a subset of taxa from a wide variety of deep-branching lineages (Stramenopiles, Alveolata, Hemimastigophora, Malawimonadidae, Discoba and Metamonada), including vesicles beneath the plasmalemma, two opposing vanes on the flagella, a ventral feeding groove and a fibrillar system resembling the excavate type. Additionally, we identified four main microtubular roots (r1-r4) and a singlet root between r1 and r2, which support the strong feeding apparatus resembling 'jaws'. Their unique extrusive organelles (ampulosomes) have a similar organization to Hemimastigophora extrusomes, but most of their cell characteristics most closely resemble features of the TSAR + Haptista grouping. We also describe a new species, Nibbleromonas piranha sp. nov., and highlight features of its feeding behaviour, which can be so aggressive as to result in cannibalism.},
}

*Phylogeny
Flagella/ultrastructure
Eukaryota/ultrastructure/genetics
Stramenopiles/ultrastructure/genetics
Organelles/ultrastructure

@article {pmid39656733,
year = {2024},
author = {Abu-Elmakarem, H and Taerum, SJ and Petitjean, C and Kotyk, M and Kay, C and Čepička, I and Bass, D and Gile, GH and Williams, TA},
title = {Transcriptome and Evolutionary Analysis of Pseudotrichomonas keilini, a Free-Living Anaerobic Eukaryote.},
journal = {Genome biology and evolution},
volume = {16},
number = {12},
pages = {},
pmid = {39656733},
issn = {1759-6653},
support = {22-22538S//Czech Science Foundation/ ; DEB-2045329//US National Science foundation/ ; GBMF9741//Gordon and Betty Moore Foundation/ ; },
mesh = {*Transcriptome ; Anaerobiosis ; *Phylogeny ; *Evolution, Molecular ; Parabasalidea/genetics ; Biological Evolution ; },
abstract = {The early evolution of eukaryotes and their adaptations to low-oxygen environments are fascinating open questions in biology. Genome-scale data from novel eukaryotes, and particularly from free-living lineages, are the key to answering these questions. The Parabasalia are a major group of anaerobic eukaryotes that form the most speciose lineage of Metamonada. The most well-studied are parasitic parabasalids, including Trichomonas vaginalis and Tritrichomonas foetus, but very little genome-scale data are available for free-living members of the group. Here, we sequenced the transcriptome of Pseudotrichomonas keilini, a free-living parabasalian. Comparative genomic analysis indicated that P. keilini possesses a metabolism and gene complement that are in many respects similar to its parasitic relative T. vaginalis and that in the time since their most recent common ancestor, it is the T. vaginalis lineage that has experienced more genomic change, likely due to the transition to a parasitic lifestyle. Features shared between P. keilini and T. vaginalis include a hydrogenosome (anaerobic mitochondrial homolog) that we predict to function much as in T. vaginalis and a complete glycolytic pathway that is likely to represent one of the primary means by which P. keilini obtains ATP. Phylogenomic analysis indicates that P. keilini branches within a clade of endobiotic parabasalids, consistent with the hypothesis that different parabasalid lineages evolved toward parasitic or free-living lifestyles from an endobiotic, anaerobic, or microaerophilic common ancestor.},
}

*Transcriptome
Anaerobiosis
*Phylogeny
*Evolution, Molecular
Parabasalidea/genetics
Biological Evolution

@article {pmid39585925,
year = {2024},
author = {Richards, TA and Eme, L and Archibald, JM and Leonard, G and Coelho, SM and de Mendoza, A and Dessimoz, C and Dolezal, P and Fritz-Laylin, LK and Gabaldón, T and Hampl, V and Kops, GJPL and Leger, MM and Lopez-Garcia, P and McInerney, JO and Moreira, D and Muñoz-Gómez, SA and Richter, DJ and Ruiz-Trillo, I and Santoro, AE and Sebé-Pedrós, A and Snel, B and Stairs, CW and Tromer, EC and van Hooff, JJE and Wickstead, B and Williams, TA and Roger, AJ and Dacks, JB and Wideman, JG},
title = {Reconstructing the last common ancestor of all eukaryotes.},
journal = {PLoS biology},
volume = {22},
number = {11},
pages = {e3002917},
pmid = {39585925},
issn = {1545-7885},
mesh = {*Eukaryota/genetics ; *Phylogeny ; Eukaryotic Cells/metabolism ; Evolution, Molecular ; Genomics/methods ; Biological Evolution ; },
abstract = {Understanding the origin of eukaryotic cells is one of the most difficult problems in all of biology. A key challenge relevant to the question of eukaryogenesis is reconstructing the gene repertoire of the last eukaryotic common ancestor (LECA). As data sets grow, sketching an accurate genomics-informed picture of early eukaryotic cellular complexity requires provision of analytical resources and a commitment to data sharing. Here, we summarise progress towards understanding the biology of LECA and outline a community approach to inferring its wider gene repertoire. Once assembled, a robust LECA gene set will be a useful tool for evaluating alternative hypotheses about the origin of eukaryotes and understanding the evolution of traits in all descendant lineages, with relevance in diverse fields such as cell biology, microbial ecology, biotechnology, agriculture, and medicine. In this Consensus View, we put forth the status quo and an agreed path forward to reconstruct LECA's gene content.},
}

*Eukaryota/genetics
*Phylogeny
Eukaryotic Cells/metabolism
Evolution, Molecular
Genomics/methods
Biological Evolution

@article {pmid39543792,
year = {2024},
author = {Jacobs, HT and Rustin, P and Bénit, P and Davidi, D and Terzioglu, M},
title = {Mitochondria: great balls of fire.},
journal = {The FEBS journal},
volume = {291},
number = {24},
pages = {5327-5341},
pmid = {39543792},
issn = {1742-4658},
support = {ALTF 1146-2018//European Molecular Biology Organization/ ; 324730//Research Council of Finland/ ; n/a//Edmond de Rothschild Foundation/ ; LT000232/2019-L//Human Frontier Science Program/ ; },
mesh = {*Mitochondria/metabolism ; Animals ; Humans ; Mitochondrial Dynamics ; Homeostasis ; Hot Temperature ; Biological Evolution ; },
abstract = {Recent experimental studies indicate that mitochondria in mammalian cells are maintained at temperatures of at least 50 °C. While acknowledging the limitations of current experimental methods and their interpretation, we here consider the ramifications of this finding for cellular functions and for evolution. We consider whether mitochondria as heat-producing organelles had a role in the origin of eukaryotes and in the emergence of homeotherms. The homeostatic responses of mitochondrial temperature to externally applied heat imply the existence of a molecular heat-sensing system in mitochondria. While current findings indicate high temperatures for the innermost compartments of mitochondria, those of the mitochondrial surface and of the immediately surrounding cytosol remain to be determined. We ask whether some aspects of mitochondrial dynamics and motility could reflect changes in the supply and demand for mitochondrial heat, and whether mitochondrial heat production could be a factor in diseases and immunity.},
}

*Mitochondria/metabolism
Animals
Humans
Mitochondrial Dynamics
Homeostasis
Hot Temperature
Biological Evolution

@article {pmid39543208,
year = {2024},
author = {Zhou, X and Zhang, N and Gong, J and Zhang, K and Chen, P and Cheng, X and Ye, BC and Zhao, G and Jing, X and Li, X},
title = {In vivo assembly of complete eukaryotic nucleosomes and (H3-H4)-only non-canonical nucleosomal particles in the model bacterium Escherichia coli.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1510},
pmid = {39543208},
issn = {2399-3642},
mesh = {*Nucleosomes/metabolism ; *Escherichia coli/genetics/metabolism ; *Histones/metabolism/genetics ; },
abstract = {As a fundamental unit for packaging genomic DNA into chromatin, the eukaryotic nucleosome core comprises a canonical octamer with two copies for each histone, H2A, H2B, H3, and H4, wrapped around with 147 base pairs of DNA. While H3 and H4 share structure-fold with archaeal histone-like proteins, the eukaryotic nucleosome core and the complete nucleosome (the core plus H1 histone) are unique to eukaryotes. To explore whether the eukaryotic nucleosome can assemble in prokaryotes and to reconstruct the possible route for its emergence in eukaryogenesis, we developed an in vivo system for assembly of nucleosomes in the model bacterium, Escherichia coli, and successfully reconstituted the core nucleosome, the complete nucleosome, and unexpectedly the non-canonical (H3-H4)4 octasome. The core and complete nucleosomes assembled in E. coli exhibited footprints typical of eukaryotic hosts after in situ micrococcal nuclease digestion. Additionally, they caused condensation of E. coli nucleoid. We also demonstrated the stable formation of non-canonical (H3-H4)2 tetrasome and (H3-H4)4 octasomes in vivo, which are suggested to be 'fossil complex' that marks the intermediate in the progressive development of eukaryotic nucleosome. The study presents a unique platform in a bacterium for in vivo assembly and studying the properties of non-canonical variants of nucleosome.},
}

*Nucleosomes/metabolism
*Escherichia coli/genetics/metabolism
*Histones/metabolism/genetics

@article {pmid39506510,
year = {2024},
author = {Sterner, EG and Cote-L'Heureux, A and Maurer-Alcalá, XX and Katz, LA},
title = {Diverse Genome Structures among Eukaryotes May Have Arisen in Response to Genetic Conflict.},
journal = {Genome biology and evolution},
volume = {16},
number = {11},
pages = {},
pmid = {39506510},
issn = {1759-6653},
support = {R15 HG010409/HG/NHGRI NIH HHS/United States ; OCE-1924570//NSF/ ; R15HG010409/GF/NIH HHS/United States ; },
mesh = {*Eukaryota/genetics ; *Genome ; *Evolution, Molecular ; Aneuploidy ; Chromatin/genetics ; Eukaryotic Cells/metabolism ; },
abstract = {In contrast to the typified view of genome cycling only between haploidy and diploidy, there is evidence from across the tree of life of genome dynamics that alter both copy number (i.e. ploidy) and chromosome complements. Here, we highlight examples of such processes, including endoreplication, aneuploidy, inheritance of extrachromosomal DNA, and chromatin extrusion. Synthesizing data on eukaryotic genome dynamics in diverse extant lineages suggests the possibility that such processes were present before the last eukaryotic common ancestor. While present in some prokaryotes, these features appear exaggerated in eukaryotes where they are regulated by eukaryote-specific innovations including the nucleus, complex cytoskeleton, and synaptonemal complex. Based on these observations, we propose a model by which genome conflict drove the transformation of genomes during eukaryogenesis: from the origin of eukaryotes (i.e. first eukaryotic common ancestor) through the evolution of last eukaryotic common ancestor.},
}

*Eukaryota/genetics
*Genome
*Evolution, Molecular
Aneuploidy
Chromatin/genetics
Eukaryotic Cells/metabolism

@article {pmid39418309,
year = {2024},
author = {More, KJ and Kaufman, JGG and Dacks, JB and Manna, PT},
title = {Evolutionary origins of the lysosome-related organelle sorting machinery reveal ancient homology in post-endosome trafficking pathways.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {43},
pages = {e2403601121},
pmid = {39418309},
issn = {1091-6490},
support = {207455/Z/17/Z//Wellcome Trust (WT)/ ; 101030247//European Commission (EC)/ ; RES0043758//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; /WT_/Wellcome Trust/United Kingdom ; RES0046091//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; },
mesh = {*Lysosomes/metabolism ; *Protein Transport ; *Evolution, Molecular ; Phylogeny ; Endosomes/metabolism ; Eukaryota/metabolism/genetics ; Organelles/metabolism ; Biological Evolution ; },
abstract = {The major organelles of the endomembrane system were in place by the time of the last eukaryotic common ancestor (LECA) (~1.5 billion years ago). Their acquisitions were defining milestones during eukaryogenesis. Comparative cell biology and evolutionary analyses show multiple instances of homology in the protein machinery controlling distinct interorganelle trafficking routes. Resolving these homologous relationships allows us to explore processes underlying the emergence of additional, distinct cellular compartments, infer ancestral states predating LECA, and explore the process of eukaryogenesis itself. Here, we undertake a molecular evolutionary analysis (including providing a transcriptome of the jakobid flagellate Reclinomonas americana), exploring the origins of the machinery responsible for the biogenesis of lysosome-related organelles (LROs), the Biogenesis of LRO Complexes (BLOCs 1,2, and 3). This pathway has been studied only in animals and is not considered a feature of the basic eukaryotic cell plan. We show that this machinery is present across the eukaryotic tree of life and was likely in place prior to LECA, making it an underappreciated facet of eukaryotic cellular organisation. Moreover, we resolve multiple points of ancient homology between all three BLOCs and other post-endosomal retrograde trafficking machinery (BORC, CCZ1 and MON1 proteins, and an unexpected relationship with the "homotypic fusion and vacuole protein sorting" (HOPS) and "Class C core vacuole/endosomal tethering" (CORVET) complexes), offering a mechanistic and evolutionary unification of these trafficking pathways. Overall, this study provides a comprehensive account of the rise of the LROs biogenesis machinery from before the LECA to current eukaryotic diversity, integrating it into the larger mechanistic framework describing endomembrane evolution.},
}

*Lysosomes/metabolism
*Protein Transport
*Evolution, Molecular
Phylogeny
Endosomes/metabolism
Eukaryota/metabolism/genetics
Organelles/metabolism
Biological Evolution

@article {pmid39333491,
year = {2024},
author = {Jing, X and Zhang, N and Zhou, X and Chen, P and Gong, J and Zhang, K and Wu, X and Cai, W and Ye, BC and Hao, P and Zhao, GP and Yang, S and Li, X},
title = {Creating a bacterium that forms eukaryotic nucleosome core particles.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8283},
pmid = {39333491},
issn = {2041-1723},
mesh = {*Nucleosomes/metabolism/ultrastructure ; *Escherichia coli/metabolism/genetics ; *Histones/metabolism/genetics ; *Microscopy, Atomic Force ; DNA, Bacterial/metabolism/genetics ; Chromosomes, Bacterial/metabolism/genetics ; Green Fluorescent Proteins/metabolism/genetics ; Eukaryotic Cells/metabolism ; },
abstract = {The nucleosome is one of the hallmarks of eukaryotes, a dynamic platform that supports many critical functions in eukaryotic cells. Here, we engineer the in vivo assembly of the nucleosome core in the model bacterium Escherichia coli. We show that bacterial chromosome DNA and eukaryotic histones can assemble in vivo to form nucleosome complexes with many features resembling those found in eukaryotes. The formation of nucleosomes in E. coli was visualized with atomic force microscopy and using tripartite split green fluorescent protein. Under a condition that moderate histones expression was induced at 1 µM IPTG, the nucleosome-forming bacterium is viable and has sustained growth for at least 110 divisions in longer-term growth experiments. It exhibits stable nucleosome formation, a consistent transcriptome across passages, and reduced growth fitness under stress conditions. In particular, the nucleosome arrays in E. coli genic regions have profiles resembling those in eukaryotic cells. The observed compatibility between the eukaryotic nucleosome and the bacterial chromosome machinery may reflect a prerequisite for bacteria-archaea union, providing insight into eukaryogenesis and the origin of the nucleosome.},
}

*Nucleosomes/metabolism/ultrastructure
*Escherichia coli/metabolism/genetics
*Histones/metabolism/genetics
*Microscopy, Atomic Force
DNA, Bacterial/metabolism/genetics
Chromosomes, Bacterial/metabolism/genetics
Green Fluorescent Proteins/metabolism/genetics
Eukaryotic Cells/metabolism

@article {pmid39321796,
year = {2024},
author = {Cadena, LR and Hammond, M and Tesařová, M and Chmelová, Ľ and Svobodová, M and Durante, IM and Yurchenko, V and Lukeš, J},
title = {A novel nabelschnur protein regulates segregation of the kinetoplast DNA in Trypanosoma brucei.},
journal = {Current biology : CB},
volume = {34},
number = {20},
pages = {4803-4812.e3},
doi = {10.1016/j.cub.2024.08.044},
pmid = {39321796},
issn = {1879-0445},
mesh = {*Trypanosoma brucei brucei/genetics/metabolism ; *DNA, Kinetoplast/metabolism/genetics ; *Protozoan Proteins/metabolism/genetics ; DNA Replication ; },
abstract = {The acquisition of mitochondria was imperative for initiating eukaryogenesis and thus is a characteristic feature of eukaryotic cells.[1][,][2] The parasitic protist Trypanosoma brucei contains a singular mitochondrion with a unique mitochondrial genome, termed the kinetoplast DNA (kDNA).[3] Replication of the kDNA occurs during the G1 phase of the cell cycle, prior to the start of nuclear DNA replication.[4] Although numerous proteins have been functionally characterized and identified as vital components of kDNA replication and division, the molecular mechanisms governing this highly precise process remain largely unknown.[5][,][6] One division-related and morphologically characteristic structure that remains most enigmatic is the "nabelschnur," an undefined, filament-resembling structure observed by electron microscopy between segregating daughter kDNA networks.[7][,][8][,][9] To date, only one protein, TbLAP1, an M17 family leucyl aminopeptidase metalloprotease, is known to localize to the nabelschnur.[9] While screening proteins from the T. brucei MitoTag project,[10] we identified a previously uncharacterized protein with an mNeonGreen signal localizing to the kDNA as well as forming a point of connection between dividing kDNAs. Here, we demonstrate that this kDNA-associated protein, named TbNAB70, indeed localizes to the nabelschnur and plays an essential role in the segregation of newly replicated kDNAs and subsequent cytokinesis in T. brucei.},
}

*Trypanosoma brucei brucei/genetics/metabolism
*DNA, Kinetoplast/metabolism/genetics
*Protozoan Proteins/metabolism/genetics
DNA Replication

@article {pmid39261613,
year = {2024},
author = {Vosseberg, J and van Hooff, JJE and Köstlbacher, S and Panagiotou, K and Tamarit, D and Ettema, TJG},
title = {The emerging view on the origin and early evolution of eukaryotic cells.},
journal = {Nature},
volume = {633},
number = {8029},
pages = {295-305},
pmid = {39261613},
issn = {1476-4687},
mesh = {Animals ; Archaea/classification/cytology ; Bacteria/classification/cytology/metabolism ; *Biological Evolution ; *Eukaryota/classification/cytology/metabolism ; *Eukaryotic Cells/cytology/metabolism ; Mitochondria/metabolism ; Phylogeny ; Prokaryotic Cells/cytology/metabolism/classification ; *Symbiosis ; *Models, Biological ; },
abstract = {The origin of the eukaryotic cell, with its compartmentalized nature and generally large size compared with bacterial and archaeal cells, represents a cornerstone event in the evolution of complex life on Earth. In a process referred to as eukaryogenesis, the eukaryotic cell is believed to have evolved between approximately 1.8 and 2.7 billion years ago from its archaeal ancestors, with a symbiosis with a bacterial (proto-mitochondrial) partner being a key event. In the tree of life, the branch separating the first from the last common ancestor of all eukaryotes is long and lacks evolutionary intermediates. As a result, the timing and driving forces of the emergence of complex eukaryotic features remain poorly understood. During the past decade, environmental and comparative genomic studies have revealed vital details about the identity and nature of the host cell and the proto-mitochondrial endosymbiont, enabling a critical reappraisal of hypotheses underlying the symbiotic origin of the eukaryotic cell. Here we outline our current understanding of the key players and events underlying the emergence of cellular complexity during the prokaryote-to-eukaryote transition and discuss potential avenues of future research that might provide new insights into the enigmatic origin of the eukaryotic cell.},
}

Animals
Archaea/classification/cytology
Bacteria/classification/cytology/metabolism
*Biological Evolution
*Eukaryota/classification/cytology/metabolism
*Eukaryotic Cells/cytology/metabolism
Mitochondria/metabolism
Phylogeny
Prokaryotic Cells/cytology/metabolism/classification
*Symbiosis
*Models, Biological

@article {pmid39189742,
year = {2024},
author = {Wurzbacher, CE and Hammer, J and Haufschild, T and Wiegand, S and Kallscheuer, N and Jogler, C},
title = {"Candidatus Uabimicrobium helgolandensis"-a planctomycetal bacterium with phagocytosis-like prey cell engulfment, surface-dependent motility, and cell division.},
journal = {mBio},
volume = {15},
number = {10},
pages = {e0204424},
pmid = {39189742},
issn = {2150-7511},
support = {AWI_BAH_o4//Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (AWI)/ ; EXC 2051 - Project-ID 390713860//German Research foundation/ ; SFB 1076 - Project Number 218627073//German Research foundation/ ; Project-ID 239748522 - CRC 1127 ChemBioSys//German Research foundation/ ; //Studienstiftung des Deutschen Volkes (Studienstiftung)/ ; //Landesgraduiertenstipendium/ ; //Jena School for Microbial Communications/ ; },
mesh = {*Phagocytosis ; *Cell Division ; Phylogeny ; Planctomycetales/genetics/classification/physiology/isolation & purification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The unique cell biology presented by members of the phylum Planctomycetota has puzzled researchers ever since their discovery. Initially thought to have eukaryotic-like features, their traits are now recognized as exceptional but distinctly bacterial. However, recently discovered strains again added novel and stunning aspects to the planctomycetal cell biology-shapeshifting by members of the "Saltatorellus" clade to an extent that is unprecedented in any other bacterial phylum, and phagocytosis-like cell engulfment in the bacterium "Candidatus Uabimicrobium amorphum." These recent additions to the phylum Planctomycetota indicate hitherto unexplored members with unique cell biology, which we aimed to make accessible for further investigations. Targeting bacteria with features like "Ca. U. amorphum", we first studied both the morphology and behavior of this microorganism in more detail. While similar to eukaryotic amoeboid organisms at first sight, we found "Ca. U. amorphum" to be rather distinct in many regards. Presenting a detailed description of "Ca. U. amorphum," we furthermore found this organism to divide in a fashion that has never been described in any other organism. Employing the obtained knowledge, we isolated a second "bacterium of prey" from the harbor of Heligoland Island (North Sea, Germany). Our isolate shares key features with "Ca. U. amorphum": phagocytosis-like cell engulfment, surface-dependent motility, and the same novel mode of cell division. Being related to "Ca. U. amorphum" within genus thresholds, we propose the name "Ca. Uabimicrobium helgolandensis" for this strain.IMPORTANCE"Candidatus Uabimicrobium helgolandensis" HlEnr_7 adds to the explored bacterial biodiversity with its phagocytosis-like uptake of prey bacteria. Enrichment of this strain indicates that there might be "impossible" microbes out there, missed by metagenomic analyses. Such organisms have the potential to challenge our understanding of nature. For example, the origin of eukaryotes remains enigmatic, with a contentious debate surrounding both the mitochondrial host entity and the moment of uptake. Currently, favored models involve a proteobacterium as the mitochondrial progenitor and an Asgard archaeon as the fusion partner. Models in which a eukaryotic ancestor engulfed the mitochondrial ancestor via phagocytosis had been largely rejected due to bioenergetic constraints. Thus, the phagocytosis-like abilities of planctomycetal bacteria might influence the debate, demonstrating that prey engulfment is possible in a prokaryotic cellular framework.},
}

*Phagocytosis
*Cell Division
Phylogeny
Planctomycetales/genetics/classification/physiology/isolation & purification
RNA, Ribosomal, 16S/genetics

@article {pmid39153248,
year = {2024},
author = {Bickel, B and Giraud, AL and Zuberbühler, K and van Schaik, CP},
title = {Language follows a distinct mode of extra-genomic evolution.},
journal = {Physics of life reviews},
volume = {50},
number = {},
pages = {211-225},
doi = {10.1016/j.plrev.2024.08.003},
pmid = {39153248},
issn = {1873-1457},
mesh = {Humans ; *Language ; Biological Evolution ; Animals ; Genomics/methods ; Cultural Evolution ; Genome ; },
abstract = {As one of the most specific, yet most diverse of human behaviors, language is shaped by both genomic and extra-genomic evolution. Sharing methods and models between these modes of evolution has significantly advanced our understanding of language and inspired generalized theories of its evolution. Progress is hampered, however, by the fact that the extra-genomic evolution of languages, i.e. linguistic evolution, maps only partially to other forms of evolution. Contrasting it with the biological evolution of eukaryotes and the cultural evolution of technology as the best understood models, we show that linguistic evolution is special by yielding a stationary dynamic rather than stable solutions, and that this dynamic allows the use of language change for social differentiation while maintaining its global adaptiveness. Linguistic evolution furthermore differs from technological evolution by requiring vertical transmission, allowing the reconstruction of phylogenies; and it differs from eukaryotic biological evolution by foregoing a genotype vs phenotype distinction, allowing deliberate and biased change. Recognising these differences will improve our empirical tools and open new avenues for analyzing how linguistic, cultural, and biological evolution interacted with each other when language emerged in the hominin lineage. Importantly, our framework will help to cope with unprecedented scientific and ethical challenges that presently arise from how rapid cultural evolution impacts language, most urgently from interventional clinical tools for language disorders, potential epigenetic effects of technology on language, artificial intelligence and linguistic communicators, and global losses of linguistic diversity and identity. Beyond language, the distinctions made here allow identifying variation in other forms of biological and cultural evolution, developing new perspectives for empirical research.},
}

Humans
*Language
Biological Evolution
Animals
Genomics/methods
Cultural Evolution
Genome

@article {pmid39129173,
year = {2024},
author = {Motomura, K and Bekker, A and Ikehara, M and Sano, T and Lin, Y and Kiyokawa, S},
title = {Lateral redox variability in ca. 1.9 Ga marine environments indicated by organic carbon and nitrogen isotope compositions.},
journal = {Geobiology},
volume = {22},
number = {4},
pages = {e12614},
doi = {10.1111/gbi.12614},
pmid = {39129173},
issn = {1472-4669},
mesh = {*Oxidation-Reduction ; *Nitrogen Isotopes/analysis ; *Carbon Isotopes/analysis ; Geologic Sediments/chemistry ; Canada ; Carbon/analysis ; },
abstract = {The stepwise oxygenation of Earth's surficial environment is thought to have shaped the evolutionary history of life. Microfossil records and molecular clocks suggest eukaryotes appeared during the Paleoproterozoic, perhaps shortly after the Great Oxidation Episode at ca. 2.43 Ga. The mildly oxygenated atmosphere and surface oceans likely contributed to the early evolution of eukaryotes. However, the principal trigger for the eukaryote appearance and a potential factor for their delayed expansion (i.e., intermediate ocean redox conditions until the Neoproterozoic) remain poorly understood, largely owing to a lack of constraints on marine and terrestrial nutrient cycling. Here, we analyzed redox-sensitive element contents and organic carbon and nitrogen isotope compositions of relatively low metamorphic-grade (greenschist facies) black shales preserved in the Flin Flon Belt of central Canada to examine open-marine redox conditions and biological activity around the ca. 1.9 Ga Flin Flon oceanic island arc. The black shale samples were collected from the Reed Lake area in the eastern part of the Flin Flon Belt, and the depositional site was likely distal from the Archean cratons. The black shales have low Al/Ti ratios and are slightly depleted in light rare-earth elements relative to the post-Archean average shale, which is consistent with a limited contribution from felsic igneous rocks in Archean upper continental crust. Redox conditions have likely varied between suboxic and euxinic at the depositional site of the studied section, as suggested by variable U/Al and Mo/Al ratios. Organic carbon and nitrogen isotope compositions of the black shales are approximately -23‰ and +13.7‰, respectively, and these values are systematically higher than those of broadly coeval continental margin deposits (approximately -30‰ for δ[13]Corg and +5‰ for δ[15]Nbulk). These elevated values are indicative of high productivity that led to enhanced denitrification (i.e., a high denitrification rate relative to nitrogen influx at the depositional site). Similar geochemical patterns have also been observed in the modern Peruvian oxygen minimum zone where dissolved nitrogen compounds are actively lost from the reservoir via denitrification and anammox, but the large nitrate reservoir of the deep ocean prevents exhaustion of the surface nitrate pool. Nitrogen must have been widely bioavailable in the ca. 1.9 Ga oceans, and its supply to upwelling zones must have supported habitable environments for eukaryotes, even in the middle of oceans around island arcs.},
}

*Oxidation-Reduction
*Nitrogen Isotopes/analysis
*Carbon Isotopes/analysis
Geologic Sediments/chemistry
Canada
Carbon/analysis

@article {pmid39128722,
year = {2024},
author = {Carilo, I and Senju, Y and Yokoyama, T and Robinson, RC},
title = {Intercompatibility of eukaryotic and Asgard archaea ribosome-translocon machineries.},
journal = {The Journal of biological chemistry},
volume = {300},
number = {9},
pages = {107673},
pmid = {39128722},
issn = {1083-351X},
mesh = {*Ribosomes/metabolism ; *Endoplasmic Reticulum/metabolism ; *Archaeal Proteins/metabolism/genetics ; Membrane Proteins/metabolism/genetics ; Archaea/metabolism/genetics ; Protein Transport ; Eukaryota/metabolism/genetics ; Phylogeny ; Protein Sorting Signals/physiology ; Eukaryotic Cells/metabolism ; },
abstract = {In all domains of life, the ribosome-translocon complex inserts nascent transmembrane proteins into, and processes and transports signal peptide-containing proteins across, membranes. Eukaryotic translocons are anchored in the endoplasmic reticulum, while the prokaryotic complexes reside in cell membranes. Phylogenetic analyses indicate the inheritance of eukaryotic Sec61/oligosaccharyltransferase/translocon-associated protein translocon subunits from an Asgard archaea ancestor. However, the mechanism for translocon migration from a peripheral membrane to an internal cellular compartment (the proto-endoplasmic reticulum) during eukaryogenesis is unknown. Here we show compatibility between the eukaryotic ribosome-translocon complex and Asgard signal peptides and transmembrane proteins. We find that Asgard translocon proteins from Candidatus Prometheoarchaeum syntrophicum strain Candidatus Prometheoarchaeum syntrophicum strain MK-D1, a Lokiarchaeon confirmed to contain no internal cellular membranes, are targeted to the eukaryotic endoplasmic reticulum on ectopic expression. Furthermore, we show that the cytoplasmic domain of Candidatus Prometheoarchaeum syntrophicum strain MK-D1 oligosaccharyltransferase 1 (ribophorin I) can interact with eukaryotic ribosomes. Our data indicate that the location of existing ribosome-translocon complexes, at the protein level, determines the future placement of yet-to-be-translated translocon subunits. This principle predicts that during eukaryogenesis, under positive selection pressure, the relocation of a few translocon complexes to the proto-endoplasmic reticulum will have contributed to propagating the new translocon location, leading to their loss from the cell membrane.},
}

*Ribosomes/metabolism
*Endoplasmic Reticulum/metabolism
*Archaeal Proteins/metabolism/genetics
Membrane Proteins/metabolism/genetics
Archaea/metabolism/genetics
Protein Transport
Eukaryota/metabolism/genetics
Phylogeny
Protein Sorting Signals/physiology
Eukaryotic Cells/metabolism

@article {pmid39085194,
year = {2024},
author = {Valentin-Alvarado, LE and Appler, KE and De Anda, V and Schoelmerich, MC and West-Roberts, J and Kivenson, V and Crits-Christoph, A and Ly, L and Sachdeva, R and Greening, C and Savage, DF and Baker, BJ and Banfield, JF},
title = {Asgard archaea modulate potential methanogenesis substrates in wetland soil.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6384},
pmid = {39085194},
issn = {2041-1723},
support = {LI-SIAME-00002001//Simons Foundation/ ; },
mesh = {*Wetlands ; *Methane/metabolism ; *Soil Microbiology ; *Archaea/genetics/metabolism ; *Carbon Cycle ; *Soil/chemistry ; Phylogeny ; Genome, Archaeal ; Oxidation-Reduction ; },
abstract = {The roles of Asgard archaea in eukaryogenesis and marine biogeochemical cycles are well studied, yet their contributions in soil ecosystems remain unknown. Of particular interest are Asgard archaeal contributions to methane cycling in wetland soils. To investigate this, we reconstructed two complete genomes for soil-associated Atabeyarchaeia, a new Asgard lineage, and a complete genome of Freyarchaeia, and predicted their metabolism in situ. Metatranscriptomics reveals expression of genes for [NiFe]-hydrogenases, pyruvate oxidation and carbon fixation via the Wood-Ljungdahl pathway. Also expressed are genes encoding enzymes for amino acid metabolism, anaerobic aldehyde oxidation, hydrogen peroxide detoxification and carbohydrate breakdown to acetate and formate. Overall, soil-associated Asgard archaea are predicted to include non-methanogenic acetogens, highlighting their potential role in carbon cycling in terrestrial environments.},
}

*Wetlands
*Methane/metabolism
*Soil Microbiology
*Archaea/genetics/metabolism
*Carbon Cycle
*Soil/chemistry
Phylogeny
Genome, Archaeal
Oxidation-Reduction

@article {pmid39081798,
year = {2024},
author = {Nakagawa, S and Imachi, H and Shimamura, S and Yanaka, S and Yagi, H and Yagi-Utsumi, M and Sakai, H and Kato, S and Ohkuma, M and Kato, K and Takai, K},
title = {Characterization of protein glycosylation in an Asgard archaeon.},
journal = {BBA advances},
volume = {6},
number = {},
pages = {100118},
pmid = {39081798},
issn = {2667-1603},
abstract = {Archaeal cells are typically enveloped by glycosylated S-layer proteins. Archaeal protein glycosylation provides valuable insights not only into their adaptation to their niches but also into their evolutionary trajectory. Notably, thermophilic Thermoproteota modify proteins with N-glycans that include two GlcNAc units at the reducing end, resembling the "core structure" preserved across eukaryotes. Recently, Asgard archaea, now classified as members of the phylum Promethearchaeota, have offered unprecedented opportunities for understanding the role of archaea in eukaryogenesis. Despite the presence of genes indicative of protein N-glycosylation in this archaeal group, these have not been experimentally investigated. Here we performed a glycoproteome analysis of the firstly isolated Asgard archaeon Promethearchaeum syntrophicum. Over 700 different proteins were identified through high-resolution LC-MS/MS analysis, however, there was no evidence of either the presence or glycosylation of putative S-layer proteins. Instead, N-glycosylation in this archaeon was primarily observed in an extracellular solute-binding protein, possibly related to chemoreception or transmembrane transport of oligopeptides. The glycan modification occurred on an asparagine residue located within the conserved N-X-S/T sequon, consistent with the pattern found in other archaea, bacteria, and eukaryotes. Unexpectedly, three structurally different N-glycans lacking the conventional core structure were identified in this archaeon, presenting unique compositions that included atypical sugars. Notably, one of these sugars was likely HexNAc modified with a threonine residue, similar to modifications previously observed in mesophilic methanogens within the Methanobacteriati. Our findings advance our understanding of Asgard archaea physiology and evolutionary dynamics.},
}

@article {pmid39012914,
year = {2024},
author = {Hernández Sánchez-Rebato, M and Schubert, V and White, CI},
title = {Meiotic double-strand break repair DNA synthesis tracts in Arabidopsis thaliana.},
journal = {PLoS genetics},
volume = {20},
number = {7},
pages = {e1011197},
pmid = {39012914},
issn = {1553-7404},
mesh = {*Arabidopsis/genetics ; *DNA Breaks, Double-Stranded ; *Meiosis/genetics ; DNA Repair/genetics ; Endodeoxyribonucleases/genetics/metabolism ; Arabidopsis Proteins/genetics/metabolism ; Chromosomes, Plant/genetics ; Meiotic Prophase I/genetics ; Crossing Over, Genetic ; DNA Replication/genetics ; },
abstract = {We report here the successful labelling of meiotic prophase I DNA synthesis in the flowering plant, Arabidopsis thaliana. Incorporation of the thymidine analogue, EdU, enables visualisation of the footprints of recombinational repair of programmed meiotic DNA double-strand breaks (DSB), with ~400 discrete, SPO11-dependent, EdU-labelled chromosomal foci clearly visible at pachytene and later stages of meiosis. This number equates well with previous estimations of 200-300 DNA double-strand breaks per meiosis in Arabidopsis, confirming the power of this approach to detect the repair of most or all SPO11-dependent meiotic DSB repair events. The chromosomal distribution of these DNA-synthesis foci accords with that of early recombination markers and MLH1, which marks Class I crossover sites. Approximately 10 inter-homologue cross-overs (CO) have been shown to occur in each Arabidopsis male meiosis and, athough very probably under-estimated, an equivalent number of inter-homologue gene conversions (GC) have been described. Thus, at least 90% of meiotic recombination events, and very probably more, have not previously been accessible for analysis. Visual examination of the patterns of the foci on the synapsed pachytene chromosomes corresponds well with expectations from the different mechanisms of meiotic recombination and notably, no evidence for long Break-Induced Replication DNA synthesis tracts was found. Labelling of meiotic prophase I, SPO11-dependent DNA synthesis holds great promise for further understanding of the molecular mechanisms of meiotic recombination, at the heart of reproduction and evolution of eukaryotes.},
}

*Arabidopsis/genetics
*DNA Breaks, Double-Stranded
*Meiosis/genetics
DNA Repair/genetics
Endodeoxyribonucleases/genetics/metabolism
Arabidopsis Proteins/genetics/metabolism
Chromosomes, Plant/genetics
Meiotic Prophase I/genetics
Crossing Over, Genetic
DNA Replication/genetics

@article {pmid38995044,
year = {2024},
author = {Ewerling, A and May-Simera, HL},
title = {Evolutionary trajectory for nuclear functions of ciliary transport complex proteins.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {88},
number = {3},
pages = {e0000624},
pmid = {38995044},
issn = {1098-5557},
support = {GRK2526/1 - Projectnr. 407023052//Deutsche Forschungsgemeinschaft (DFG)/ ; },
mesh = {*Cilia/metabolism ; Animals ; Humans ; *Cell Nucleus/metabolism ; Evolution, Molecular ; Nuclear Pore Complex Proteins/metabolism ; Biological Evolution ; Eukaryota/metabolism/genetics ; },
abstract = {SUMMARYCilia and the nucleus were two defining features of the last eukaryotic common ancestor. In early eukaryotic evolution, these structures evolved through the diversification of a common membrane-coating ancestor, the protocoatomer. While in cilia, the descendants of this protein complex evolved into parts of the intraflagellar transport complexes and BBSome, the nucleus gained its selectivity by recruiting protocoatomer-like proteins to the nuclear envelope to form the selective nuclear pore complexes. Recent studies show a growing number of proteins shared between the proteomes of the respective organelles, and it is currently unknown how ciliary transport proteins could acquire nuclear functions and vice versa. The nuclear functions of ciliary proteins are still observable today and remain relevant for the understanding of the disease mechanisms behind ciliopathies. In this work, we review the evolutionary history of cilia and nucleus and their respective defining proteins and integrate current knowledge into theories for early eukaryotic evolution. We postulate a scenario where both compartments co-evolved and that fits current models of eukaryotic evolution, explaining how ciliary proteins and nucleoporins acquired their dual functions.},
}

*Cilia/metabolism
Animals
Humans
*Cell Nucleus/metabolism
Evolution, Molecular
Nuclear Pore Complex Proteins/metabolism
Biological Evolution
Eukaryota/metabolism/genetics

@article {pmid38967402,
year = {2024},
author = {Hoshino, Y and Gaucher, EA},
title = {Impact of steroid biosynthesis on the aerobic adaptation of eukaryotes.},
journal = {Geobiology},
volume = {22},
number = {4},
pages = {e12612},
pmid = {38967402},
issn = {1472-4669},
support = {R01 AR069137/AR/NIAMS NIH HHS/United States ; MURI W911NF-16-1-0372//Department of Defense/ ; 2032315//National Science Foundation/ ; R01AR069137/NH/NIH HHS/United States ; RGP0041//Human Frontier Science Program/ ; //German Research Foundation Priority program 2237/ ; },
mesh = {*Steroids/biosynthesis/metabolism ; *Eukaryota/metabolism/genetics ; Aerobiosis ; Biological Evolution ; Adaptation, Physiological ; },
abstract = {Steroids are indispensable components of the eukaryotic cellular membrane and the acquisition of steroid biosynthesis was a key factor that enabled the evolution of eukaryotes. The polycyclic carbon structures of steroids can be preserved in sedimentary rocks as chemical fossils for billions of years and thus provide invaluable clues to trace eukaryotic evolution from the distant past. Steroid biosynthesis consists of (1) the production of protosteroids and (2) the subsequent modifications toward "modern-type" steroids such as cholesterol and stigmasterol. While protosteroid biosynthesis requires only two genes for the cyclization of squalene, complete modification of protosteroids involves ~10 additional genes. Eukaryotes universally possess at least some of those additional genes and thus produce modern-type steroids as major final products. The geological biomarker records suggest a prolonged period of solely protosteroid production in the mid-Proterozoic before the advent of modern-type steroids in the Neoproterozoic. It has been proposed that mid-Proterozoic protosteroids were produced by hypothetical stem-group eukaryotes that presumably possessed genes only for protosteroid production, even though in modern environments protosteroid production as a final product is found exclusively in bacteria. The host identity of mid-Proterozoic steroid producers is crucial for understanding the early evolution of eukaryotes. In this perspective, we discuss how geological biomarker data and genetic data complement each other and potentially provide a more coherent scenario for the evolution of steroids and associated early eukaryotes. We further discuss the potential impacts that steroids had on the evolution of aerobic metabolism in eukaryotes, which may have been an important factor for the eventual ecological dominance of eukaryotes in many modern environments.},
}

*Steroids/biosynthesis/metabolism
*Eukaryota/metabolism/genetics
Aerobiosis
Biological Evolution
Adaptation, Physiological

@article {pmid38951509,
year = {2024},
author = {Bastiaanssen, C and Bobadilla Ugarte, P and Kim, K and Finocchio, G and Feng, Y and Anzelon, TA and Köstlbacher, S and Tamarit, D and Ettema, TJG and Jinek, M and MacRae, IJ and Joo, C and Swarts, DC and Wu, F},
title = {RNA-guided RNA silencing by an Asgard archaeal Argonaute.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {5499},
pmid = {38951509},
issn = {2041-1723},
support = {32370003//National Natural Science Foundation of China (National Science Foundation of China)/ ; 682509//Consejo Nacional de Ciencia y Tecnología (CONCYT)/ ; ERC Consolidator grant (819299)//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; ERC-2020-STG 948783//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; Frontier 10-10//Ewha Womans University (Ewha)/ ; ALTF 76-2022//European Molecular Biology Organization (EMBO)/ ; },
mesh = {*Argonaute Proteins/metabolism/genetics ; Humans ; RNA Interference ; Archaea/genetics/metabolism ; RNA, Small Interfering/metabolism/genetics ; Archaeal Proteins/metabolism/genetics ; Cryoelectron Microscopy ; MicroRNAs/genetics/metabolism ; Evolution, Molecular ; Phylogeny ; },
abstract = {Argonaute proteins are the central effectors of RNA-guided RNA silencing pathways in eukaryotes, playing crucial roles in gene repression and defense against viruses and transposons. Eukaryotic Argonautes are subdivided into two clades: AGOs generally facilitate miRNA- or siRNA-mediated silencing, while PIWIs generally facilitate piRNA-mediated silencing. It is currently unclear when and how Argonaute-based RNA silencing mechanisms arose and diverged during the emergence and early evolution of eukaryotes. Here, we show that in Asgard archaea, the closest prokaryotic relatives of eukaryotes, an evolutionary expansion of Argonaute proteins took place. In particular, a deep-branching PIWI protein (HrAgo1) encoded by the genome of the Lokiarchaeon 'Candidatus Harpocratesius repetitus' shares a common origin with eukaryotic PIWI proteins. Contrasting known prokaryotic Argonautes that use single-stranded DNA as guides and/or targets, HrAgo1 mediates RNA-guided RNA cleavage, and facilitates gene silencing when expressed in human cells and supplied with miRNA precursors. A cryo-EM structure of HrAgo1, combined with quantitative single-molecule experiments, reveals that the protein displays structural features and target-binding modes that are a mix of those of eukaryotic AGO and PIWI proteins. Thus, this deep-branching archaeal PIWI may have retained an ancestral molecular architecture that preceded the functional and mechanistic divergence of eukaryotic AGOs and PIWIs.},
}

*Argonaute Proteins/metabolism/genetics
Humans
RNA Interference
Archaea/genetics/metabolism
RNA, Small Interfering/metabolism/genetics
Archaeal Proteins/metabolism/genetics
Cryoelectron Microscopy
MicroRNAs/genetics/metabolism
Evolution, Molecular
Phylogeny

@article {pmid38866018,
year = {2024},
author = {Greening, C and Cabotaje, PR and Valentin Alvarado, LE and Leung, PM and Land, H and Rodrigues-Oliveira, T and Ponce-Toledo, RI and Senger, M and Klamke, MA and Milton, M and Lappan, R and Mullen, S and West-Roberts, J and Mao, J and Song, J and Schoelmerich, M and Stairs, CW and Schleper, C and Grinter, R and Spang, A and Banfield, JF and Berggren, G},
title = {Minimal and hybrid hydrogenases are active from archaea.},
journal = {Cell},
volume = {187},
number = {13},
pages = {3357-3372.e19},
pmid = {38866018},
issn = {1097-4172},
mesh = {*Archaea/genetics/enzymology ; Archaeal Proteins/metabolism/chemistry/genetics ; Genome, Archaeal ; *Hydrogen/metabolism ; *Hydrogenase/metabolism/genetics/chemistry ; Iron-Sulfur Proteins/metabolism/genetics/chemistry ; Models, Molecular ; *Phylogeny ; Protein Structure, Tertiary ; },
abstract = {Microbial hydrogen (H2) cycling underpins the diversity and functionality of diverse anoxic ecosystems. Among the three evolutionarily distinct hydrogenase superfamilies responsible, [FeFe] hydrogenases were thought to be restricted to bacteria and eukaryotes. Here, we show that anaerobic archaea encode diverse, active, and ancient lineages of [FeFe] hydrogenases through combining analysis of existing and new genomes with extensive biochemical experiments. [FeFe] hydrogenases are encoded by genomes of nine archaeal phyla and expressed by H2-producing Asgard archaeon cultures. We report an ultraminimal hydrogenase in DPANN archaea that binds the catalytic H-cluster and produces H2. Moreover, we identify and characterize remarkable hybrid complexes formed through the fusion of [FeFe] and [NiFe] hydrogenases in ten other archaeal orders. Phylogenetic analysis and structural modeling suggest a deep evolutionary history of hybrid hydrogenases. These findings reveal new metabolic adaptations of archaea, streamlined H2 catalysts for biotechnological development, and a surprisingly intertwined evolutionary history between the two major H2-metabolizing enzymes.},
}

*Archaea/genetics/enzymology
Archaeal Proteins/metabolism/chemistry/genetics
Genome, Archaeal
*Hydrogen/metabolism
*Hydrogenase/metabolism/genetics/chemistry
Iron-Sulfur Proteins/metabolism/genetics/chemistry
Models, Molecular
*Phylogeny
Protein Structure, Tertiary

@article {pmid38813783,
year = {2024},
author = {Wolyniak, MJ and Frazier, RH and Gemborys, PK and Loehr, HE},
title = {Malate dehydrogenase: a story of diverse evolutionary radiation.},
journal = {Essays in biochemistry},
volume = {68},
number = {2},
pages = {213-220},
pmid = {38813783},
issn = {1744-1358},
support = {//Hampden-Sydney College Office of Undergraduate Research/ ; },
mesh = {*Malate Dehydrogenase/metabolism/genetics ; *Evolution, Molecular ; Bacteria/enzymology/genetics ; Phylogeny ; Archaea/genetics/enzymology ; Symbiosis ; Humans ; Eukaryota/enzymology/genetics ; Gene Transfer, Horizontal ; },
abstract = {Malate dehydrogenase (MDH) is a ubiquitous enzyme involved in cellular respiration across all domains of life. MDH's ubiquity allows it to act as an excellent model for considering the history of life and how the rise of aerobic respiration and eukaryogenesis influenced this evolutionary process. Here, we present the diversity of the MDH family of enzymes across bacteria, archaea, and eukarya, the relationship between MDH and lactate dehydrogenase (LDH) in the formation of a protein superfamily, and the connections between MDH and endosymbiosis in the formation of mitochondria and chloroplasts. The development of novel and powerful DNA sequencing techniques has challenged some of the conventional wisdom underlying MDH evolution and suggests a history dominated by gene duplication, horizontal gene transfer, and cryptic endosymbiosis events and adaptation to a diverse range of environments across all domains of life over evolutionary time. The data also suggest a superfamily of proteins that do not share high levels of sequential similarity but yet retain strong conservation of core function via key amino acid residues and secondary structural components. As DNA sequencing and 'big data' analysis techniques continue to improve in the life sciences, it is likely that the story of MDH will continue to refine as more examples of superfamily diversity are recovered from nature and analyzed.},
}

*Malate Dehydrogenase/metabolism/genetics
*Evolution, Molecular
Bacteria/enzymology/genetics
Phylogeny
Archaea/genetics/enzymology
Symbiosis
Humans
Eukaryota/enzymology/genetics
Gene Transfer, Horizontal

@article {pmid38748857,
year = {2024},
author = {Cezanne, A and Foo, S and Kuo, YW and Baum, B},
title = {The Archaeal Cell Cycle.},
journal = {Annual review of cell and developmental biology},
volume = {40},
number = {1},
pages = {1-23},
doi = {10.1146/annurev-cellbio-111822-120242},
pmid = {38748857},
issn = {1530-8995},
support = {203276/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Archaea/metabolism/genetics ; *Cell Cycle/genetics ; *DNA Replication ; Cell Division ; Archaeal Proteins/metabolism ; },
abstract = {Since first identified as a separate domain of life in the 1970s, it has become clear that archaea differ profoundly from both eukaryotes and bacteria. In this review, we look across the archaeal domain and discuss the diverse mechanisms by which archaea control cell cycle progression, DNA replication, and cell division. While the molecular and cellular processes archaea use to govern these critical cell biological processes often differ markedly from those described in bacteria and eukaryotes, there are also striking similarities that highlight both unique and common principles of cell cycle control across the different domains of life. Since much of the eukaryotic cell cycle machinery has its origins in archaea, exploration of the mechanisms of archaeal cell division also promises to illuminate the evolution of the eukaryotic cell cycle.},
}

*Archaea/metabolism/genetics
*Cell Cycle/genetics
*DNA Replication
Cell Division
Archaeal Proteins/metabolism

@article {pmid38674651,
year = {2024},
author = {Zhu, P and Hou, J and Xiong, Y and Xie, R and Wang, Y and Wang, F},
title = {Expanded Archaeal Genomes Shed New Light on the Evolution of Isoprenoid Biosynthesis.},
journal = {Microorganisms},
volume = {12},
number = {4},
pages = {},
pmid = {38674651},
issn = {2076-2607},
support = {42230401//National Natural Science Foundation of China/ ; WH510244001//Shanghai Jiao Tong University 2030 Project/ ; 2023M742235//China Postdoctoral Science Foundation/ ; },
abstract = {Isoprenoids and their derivatives, essential for all cellular life on Earth, are particularly crucial in archaeal membrane lipids, suggesting that their biosynthesis pathways have ancient origins and play pivotal roles in the evolution of early life. Despite all eukaryotes, archaea, and a few bacterial lineages being known to exclusively use the mevalonate (MVA) pathway to synthesize isoprenoids, the origin and evolutionary trajectory of the MVA pathway remain controversial. Here, we conducted a thorough comparison and phylogenetic analysis of key enzymes across the four types of MVA pathway, with the particular inclusion of metagenome assembled genomes (MAGs) from uncultivated archaea. Our findings support an archaeal origin of the MVA pathway, likely postdating the divergence of Bacteria and Archaea from the Last Universal Common Ancestor (LUCA), thus implying the LUCA's enzymatic inability for isoprenoid biosynthesis. Notably, the Asgard archaea are implicated in playing central roles in the evolution of the MVA pathway, serving not only as putative ancestors of the eukaryote- and Thermoplasma-type routes, but also as crucial mediators in the gene transfer to eukaryotes, possibly during eukaryogenesis. Overall, this study advances our understanding of the origin and evolutionary history of the MVA pathway, providing unique insights into the lipid divide and the evolution of early life.},
}

@article {pmid38502495,
year = {2024},
author = {Maréchal, E},
title = {How Did Thylakoids Emerge in Cyanobacteria, and How Were the Primary Chloroplast and Chromatophore Acquired?.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2776},
number = {},
pages = {3-20},
pmid = {38502495},
issn = {1940-6029},
mesh = {Thylakoids/metabolism ; Chloroplasts/genetics/metabolism ; Photosynthesis/genetics ; *Cyanobacteria/genetics/metabolism ; Eukaryota ; *Chromatophores ; Symbiosis/genetics ; },
abstract = {The emergence of thylakoid membranes in cyanobacteria is a key event in the evolution of all oxygenic photosynthetic cells, from prokaryotes to eukaryotes. Recent analyses show that they could originate from a unique lipid phase transition rather than from a supposed vesicular budding mechanism. Emergence of thylakoids coincided with the great oxygenation event, more than two billion years ago. The acquisition of semi-autonomous organelles, such as the mitochondrion, the chloroplast, and, more recently, the chromatophore, is a critical step in the evolution of eukaryotes. They resulted from primary endosymbiotic events that seem to share general features, i.e., an acquisition of a bacterium/cyanobacteria likely via a phagocytic membrane, a genome reduction coinciding with an escape of genes from the organelle to the nucleus, and, finally, the appearance of an active system translocating nuclear-encoded proteins back to the organelles. An intense mobilization of foreign genes of bacterial origin, via horizontal gene transfers, plays a critical role. Some third partners, like Chlamydia, might have facilitated the transition from cyanobacteria to the early chloroplast. This chapter further details our current understanding of primary endosymbiosis, focusing on primary chloroplasts, thought to have appeared over a billion years ago, and the chromatophore, which appeared around a hundred years ago.},
}

Thylakoids/metabolism
Chloroplasts/genetics/metabolism
Photosynthesis/genetics
*Cyanobacteria/genetics/metabolism
Eukaryota
*Chromatophores
Symbiosis/genetics

@article {pmid38498818,
year = {2024},
author = {Bozdag, GO and Szeinbaum, N and Conlin, PL and Chen, K and Fos, SM and Garcia, A and Penev, PI and Schaible, GA and Trubl, G},
title = {Chapter 5: Major Biological Innovations in the History of Life on Earth.},
journal = {Astrobiology},
volume = {24},
number = {S1},
pages = {S107-S123},
pmid = {38498818},
issn = {1557-8070},
support = {R35 GM138030/GM/NIGMS NIH HHS/United States ; },
mesh = {Phylogeny ; *Biological Evolution ; *Earth, Planet ; Oxygen ; Photosynthesis ; },
abstract = {All organisms living on Earth descended from a single, common ancestral population of cells, known as LUCA-the last universal common ancestor. Since its emergence, the diversity and complexity of life have increased dramatically. This chapter focuses on four key biological innovations throughout Earth's history that had a significant impact on the expansion of phylogenetic diversity, organismal complexity, and ecospace habitation. First is the emergence of the last universal common ancestor, LUCA, which laid the foundation for all life-forms on Earth. Second is the evolution of oxygenic photosynthesis, which resulted in global geochemical and biological transformations. Third is the appearance of a new type of cell-the eukaryotic cell-which led to the origin of a new domain of life and the basis for complex multicellularity. Fourth is the multiple independent origins of multicellularity, resulting in the emergence of a new level of complex individuality. A discussion of these four key events will improve our understanding of the intertwined history of our planet and its inhabitants and better inform the extent to which we can expect life at different degrees of diversity and complexity elsewhere.},
}

Phylogeny
*Biological Evolution
*Earth, Planet
Oxygen
Photosynthesis

@article {pmid38472392,
year = {2024},
author = {Tran, LT and Akıl, C and Senju, Y and Robinson, RC},
title = {The eukaryotic-like characteristics of small GTPase, roadblock and TRAPPC3 proteins from Asgard archaea.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {273},
pmid = {38472392},
issn = {2399-3642},
support = {JPMJCR19S5//MEXT | JST | Core Research for Evolutional Science and Technology (CREST)/ ; JP20H00476//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP19K23727//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP23K05718//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP23H04423//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; GBMF9743//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; GBMF9743//Simons Foundation/ ; },
mesh = {*Monomeric GTP-Binding Proteins/chemistry ; Archaea/metabolism ; Protein Transport ; },
abstract = {Membrane-enclosed organelles are defining features of eukaryotes in distinguishing these organisms from prokaryotes. Specification of distinct membranes is critical to assemble and maintain discrete compartments. Small GTPases and their regulators are the signaling molecules that drive membrane-modifying machineries to the desired location. These signaling molecules include Rab and Rag GTPases, roadblock and longin domain proteins, and TRAPPC3-like proteins. Here, we take a structural approach to assess the relatedness of these eukaryotic-like proteins in Asgard archaea, the closest known prokaryotic relatives to eukaryotes. We find that the Asgard archaea GTPase core domains closely resemble eukaryotic Rabs and Rags. Asgard archaea roadblock, longin and TRAPPC3 domain-containing proteins form dimers similar to those found in the eukaryotic TRAPP and Ragulator complexes. We conclude that the emergence of these protein architectures predated eukaryogenesis, however further adaptations occurred in proto-eukaryotes to allow these proteins to regulate distinct internal membranes.},
}

*Monomeric GTP-Binding Proteins/chemistry
Archaea/metabolism
Protein Transport

@article {pmid38449346,
year = {2024},
author = {Speijer, D},
title = {How mitochondrial cristae illuminate the important role of oxygen during eukaryogenesis.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {46},
number = {5},
pages = {e2300193},
doi = {10.1002/bies.202300193},
pmid = {38449346},
issn = {1521-1878},
mesh = {*Oxygen/metabolism ; *Mitochondria/metabolism/genetics ; *Mitochondrial Membranes/metabolism ; Animals ; Eukaryota/metabolism/genetics ; Adenosine Triphosphate/metabolism ; Biological Evolution ; Eukaryotic Cells/metabolism ; },
abstract = {Inner membranes of mitochondria are extensively folded, forming cristae. The observed overall correlation between efficient eukaryotic ATP generation and the area of internal mitochondrial inner membranes both in unicellular organisms and metazoan tissues seems to explain why they evolved. However, the crucial use of molecular oxygen (O2) as final acceptor of the electron transport chain is still not sufficiently appreciated. O2 was an essential prerequisite for cristae development during early eukaryogenesis and could be the factor allowing cristae retention upon loss of mitochondrial ATP generation. Here I analyze illuminating bacterial and unicellular eukaryotic examples. I also discuss formative influences of intracellular O2 consumption on the evolution of the last eukaryotic common ancestor (LECA). These considerations bring about an explanation for the many genes coming from other organisms than the archaeon and bacterium merging at the start of eukaryogenesis.},
}

*Oxygen/metabolism
*Mitochondria/metabolism/genetics
*Mitochondrial Membranes/metabolism
Animals
Eukaryota/metabolism/genetics
Adenosine Triphosphate/metabolism
Biological Evolution
Eukaryotic Cells/metabolism

@article {pmid38436469,
year = {2024},
author = {van der Gulik, PTS and Hoff, WD and Speijer, D},
title = {The contours of evolution: In defence of Darwin's tree of life paradigm.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {46},
number = {5},
pages = {e2400012},
doi = {10.1002/bies.202400012},
pmid = {38436469},
issn = {1521-1878},
mesh = {Animals ; *Biological Evolution ; *Gene Transfer, Horizontal ; *Phylogeny ; },
abstract = {Both the concept of a Darwinian tree of life (TOL) and the possibility of its accurate reconstruction have been much criticized. Criticisms mostly revolve around the extensive occurrence of lateral gene transfer (LGT), instances of uptake of complete organisms to become organelles (with the associated subsequent gene transfer to the nucleus), as well as the implications of more subtle aspects of the biological species concept. Here we argue that none of these criticisms are sufficient to abandon the valuable TOL concept and the biological realities it captures. Especially important is the need to conceptually distinguish between organismal trees and gene trees, which necessitates incorporating insights of widely occurring LGT into modern evolutionary theory. We demonstrate that all criticisms, while based on important new findings, do not invalidate the TOL. After considering the implications of these new insights, we find that the contours of evolution are best represented by a TOL.},
}

Animals
*Biological Evolution
*Gene Transfer, Horizontal
*Phylogeny

@article {pmid38391233,
year = {2024},
author = {Charles-Orszag, A and Petek-Seoane, NA and Mullins, RD},
title = {Archaeal actins and the origin of a multi-functional cytoskeleton.},
journal = {Journal of bacteriology},
volume = {206},
number = {3},
pages = {e0034823},
pmid = {38391233},
issn = {1098-5530},
support = {//Howard Hughes Medical Institute (HHMI)/ ; },
mesh = {*Actins/metabolism ; *Archaea/genetics/metabolism ; Cytoskeleton/metabolism ; Bacteria/metabolism ; Biological Evolution ; },
abstract = {Actin and actin-like proteins form filamentous polymers that carry out important cellular functions in all domains of life. In this review, we sketch a map of the function and regulation of actin-like proteins across bacteria, archaea, and eukarya, marking some of the terra incognita that remain in this landscape. We focus particular attention on archaea because mapping the structure and function of cytoskeletal systems across this domain promises to help us understand the evolutionary relationship between the (mostly) mono-functional actin-like filaments found in bacteria and the multi-functional actin cytoskeletons that characterize eukaryotic cells.},
}

*Actins/metabolism
*Archaea/genetics/metabolism
Cytoskeleton/metabolism
Bacteria/metabolism
Biological Evolution

@article {pmid38335232,
year = {2024},
author = {von der Dunk, SHA and Hogeweg, P and Snel, B},
title = {Intracellular signaling in proto-eukaryotes evolves to alleviate regulatory conflicts of endosymbiosis.},
journal = {PLoS computational biology},
volume = {20},
number = {2},
pages = {e1011860},
pmid = {38335232},
issn = {1553-7358},
mesh = {*Biological Evolution ; *Symbiosis/genetics ; Eukaryotic Cells/metabolism ; Prokaryotic Cells/metabolism ; Eukaryota/genetics ; Phylogeny ; },
abstract = {The complex eukaryotic cell resulted from a merger between simpler prokaryotic cells, yet the role of the mitochondrial endosymbiosis with respect to other eukaryotic innovations has remained under dispute. To investigate how the regulatory challenges associated with the endosymbiotic state impacted genome and network evolution during eukaryogenesis, we study a constructive computational model where two simple cells are forced into an obligate endosymbiosis. Across multiple in silico evolutionary replicates, we observe the emergence of different mechanisms for the coordination of host and symbiont cell cycles, stabilizing the endosymbiotic relationship. In most cases, coordination is implicit, without signaling between host and symbiont. Signaling only evolves when there is leakage of regulatory products between host and symbiont. In the fittest evolutionary replicate, the host has taken full control of the symbiont cell cycle through signaling, mimicking the regulatory dominance of the nucleus over the mitochondrion that evolved during eukaryogenesis.},
}

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

@article {pmid38307786,
year = {2024},
author = {Muñoz-Gómez, SA},
title = {The energetic costs of cellular complexity in evolution.},
journal = {Trends in microbiology},
volume = {32},
number = {8},
pages = {746-755},
doi = {10.1016/j.tim.2024.01.003},
pmid = {38307786},
issn = {1878-4380},
mesh = {*Energy Metabolism ; *Biological Evolution ; Evolution, Molecular ; },
abstract = {The evolutionary history of cells has been marked by drastic increases in complexity. Some hypothesize that such cellular complexification requires a massive energy flux as the origin of new features is hypothetically more energetically costly than their evolutionary maintenance. However, it remains unclear how increases in cellular complexity demand more energy. I propose that the early evolution of new genes with weak functions imposes higher energetic costs by overexpression before their functions are evolutionarily refined. In the long term, the accumulation of new genes deviates resources away from growth and reproduction. Accrued cellular complexity further requires additional infrastructure for its maintenance. Altogether, this suggests that larger and more complex cells are defined by increased survival but lower reproductive capacity.},
}

*Energy Metabolism
*Biological Evolution
Evolution, Molecular

@article {pmid38307322,
year = {2024},
author = {Biran, A and Santos, TCB and Dingjan, T and Futerman, AH},
title = {The Sphinx and the egg: Evolutionary enigmas of the (glyco)sphingolipid biosynthetic pathway.},
journal = {Biochimica et biophysica acta. Molecular and cell biology of lipids},
volume = {1869},
number = {3},
pages = {159462},
doi = {10.1016/j.bbalip.2024.159462},
pmid = {38307322},
issn = {1879-2618},
mesh = {*Sphingolipids/metabolism ; *Biosynthetic Pathways ; Metabolic Networks and Pathways ; Eukaryota/metabolism ; Endoplasmic Reticulum/metabolism ; },
abstract = {In eukaryotes, the de novo synthesis of sphingolipids (SLs) consists of multiple sequential steps which are compartmentalized between the endoplasmic reticulum and the Golgi apparatus. Studies over many decades have identified the enzymes in the pathway, their localization, topology and an array of regulatory mechanisms. However, little is known about the evolutionary forces that underly the generation of this complex pathway or of its anteome, i.e., the metabolic pathways that converge on the SL biosynthetic pathway and are essential for its activity. After briefly describing the pathway, we discuss the mechanisms by which the enzymes of the SL biosynthetic pathway are targeted to their different subcellular locations, how the pathway per se may have evolved, including its compartmentalization, and the relationship of the pathway to eukaryogenesis. We discuss the circular interdependence of the evolution of the SL pathway, and comment on whether current Darwinian evolutionary models are able to provide genuine mechanistic insight into how the pathway came into being.},
}

*Sphingolipids/metabolism
*Biosynthetic Pathways
Metabolic Networks and Pathways
Eukaryota/metabolism
Endoplasmic Reticulum/metabolism

@article {pmid38228651,
year = {2024},
author = {Krishnan, N and Csiszár, V and Móri, TF and Garay, J},
title = {Genesis of ectosymbiotic features based on commensalistic syntrophy.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {1366},
pmid = {38228651},
issn = {2045-2322},
support = {955708//Horizon 2020/ ; 125569//NKFIH/ ; },
mesh = {Humans ; Phylogeny ; *Symbiosis ; *Eukaryota ; Mitochondria ; Biological Evolution ; },
abstract = {The symbiogenetic origin of eukaryotes with mitochondria is considered a major evolutionary transition. The initial interactions and conditions of symbiosis, along with the phylogenetic affinity of the host, are widely debated. Here, we focus on a possible evolutionary path toward an association of individuals of two species based on unidirectional syntrophy. With the backing of a theoretical model, we hypothesize that the first step in the evolution of such symbiosis could be the appearance of a linking structure on the symbiont's membrane, using which it forms an ectocommensalism with its host. We consider a commensalistic model based on the syntrophy hypothesis in the framework of coevolutionary dynamics and mutant invasion into a monomorphic resident system (evolutionary substitution). We investigate the ecological and evolutionary stability of the consortium (or symbiotic merger), with vertical transmissions playing a crucial role. The impact of the 'effectiveness of vertical transmission' on the dynamics is also analyzed. We find that the transmission of symbionts and the additional costs incurred by the mutant determine the conditions of fixation of the consortia. Additionally, we observe that small and highly metabolically active symbionts are likely to form the consortia.},
}

Humans
Phylogeny
*Symbiosis
*Eukaryota
Mitochondria
Biological Evolution

@article {pmid38225278,
year = {2024},
author = {Lu, Z and Xia, R and Zhang, S and Pan, J and Liu, Y and Wolf, YI and Koonin, EV and Li, M},
title = {Evolution of optimal growth temperature in Asgard archaea inferred from the temperature dependence of GDP binding to EF-1A.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {515},
pmid = {38225278},
issn = {2041-1723},
mesh = {*Archaea/growth & development ; Phylogeny ; Temperature ; *Guanosine Diphosphate/metabolism ; *Peptide Elongation Factor 1/metabolism ; },
abstract = {The archaeal ancestor of eukaryotes apparently belonged to the phylum Asgardarchaeota, but the ecology and evolution of Asgard archaea are poorly understood. The optimal GDP-binding temperature of a translation elongation factor (EF-1A or EF-Tu) has been previously shown to correlate with the optimal growth temperature of diverse prokaryotes. Here, we reconstruct ancestral EF-1A sequences and experimentally measure the optimal GDP-binding temperature of EF-1A from ancient and extant Asgard archaea, to infer the evolution of optimal growth temperatures in Asgardarchaeota. Our results suggest that the Asgard ancestor of eukaryotes was a moderate thermophile, with an optimal growth temperature around 53 °C. The origin of eukaryotes appears to coincide with a transition from thermophilic to mesophilic lifestyle during the evolution of Asgard archaea.},
}

*Archaea/growth & development
Phylogeny
Temperature
*Guanosine Diphosphate/metabolism
*Peptide Elongation Factor 1/metabolism

@article {pmid38219525,
year = {2024},
author = {Romero, H and Aguilar, PS and Graña, M and Langleib, M and Gudiño, V and Podbilewicz, B},
title = {Membrane fusion and fission during eukaryogenesis.},
journal = {Current opinion in cell biology},
volume = {86},
number = {},
pages = {102321},
doi = {10.1016/j.ceb.2023.102321},
pmid = {38219525},
issn = {1879-0410},
mesh = {Phylogeny ; *Membrane Fusion ; *Prokaryotic Cells/metabolism ; Eukaryotic Cells/metabolism ; Eukaryota ; Biological Evolution ; },
abstract = {All eukaryotes can be traced back to a single shared ancestral lineage that emerged from interactions between different prokaryotic cells. Current models of eukaryogenesis describe various selective forces and evolutionary mechanisms that contributed to the formation of eukaryotic cells. Central to this process were significant changes in cellular structure, resulting in the configuration of a new cell type characterized by internal membrane compartments. Additionally, eukaryogenesis results in a life cycle that relies on cell-cell fusion. We discuss the potential roles of proteins involved in remodeling cellular membranes, highlighting two critical stages in the evolution of eukaryotes: the internalization of symbiotic partners and a scenario wherein the emergence of sexual reproduction is linked to a polyploid ancestor generated by cell-cell fusion.},
}

Phylogeny
*Membrane Fusion
*Prokaryotic Cells/metabolism
Eukaryotic Cells/metabolism
Eukaryota
Biological Evolution

@article {pmid38179456,
year = {2023},
author = {Medina-Chávez, NO and Torres-Cerda, A and Chacón, JM and Harcombe, WR and De la Torre-Zavala, S and Travisano, M},
title = {Disentangling a metabolic cross-feeding in a halophilic archaea-bacteria consortium.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1276438},
pmid = {38179456},
issn = {1664-302X},
abstract = {Microbial syntrophy, a cooperative metabolic interaction among prokaryotes, serves a critical role in shaping communities, due to the auxotrophic nature of many microorganisms. Syntrophy played a key role in the evolution of life, including the hypothesized origin of eukaryotes. In a recent exploration of the microbial mats within the exceptional and uniquely extreme Cuatro Cienegas Basin (CCB), a halophilic isolate, designated as AD140, emerged as a standout due to its distinct growth pattern. Subsequent genome sequencing revealed AD140 to be a co-culture of a halophilic archaeon from the Halorubrum genus and a marine halophilic bacterium, Marinococcus luteus, both occupying the same ecological niche. This intriguing coexistence hints at an early-stage symbiotic relationship that thrives on adaptability. By delving into their metabolic interdependence through genomic analysis, this study aims to uncover shared characteristics that enhance their symbiotic association, offering insights into the evolution of halophilic microorganisms and their remarkable adaptations to high-salinity environments.},
}

@article {pmid38113835,
year = {2023},
author = {Whelan, TA and Fast, NM},
title = {Exploring the highly reduced spliceosome of Pseudoloma neurophilia.},
journal = {Current biology : CB},
volume = {33},
number = {24},
pages = {R1280-R1281},
doi = {10.1016/j.cub.2023.10.034},
pmid = {38113835},
issn = {1879-0445},
mesh = {*Spliceosomes/genetics/metabolism ; Introns/genetics ; RNA Splicing ; RNA, Small Nuclear/genetics/metabolism ; *Microsporidia/genetics/metabolism ; },
abstract = {Spliceosomal introns evolved early in eukaryogenesis, originating from self-splicing group II introns that invaded the proto-eukaryotic genome[1]. Elements of these ribozymes, now called snRNAs (U1, U2, U4, U5, U6), were co-opted to excise these invasive elements. Prior to eukaryotic diversification, the spliceosome is predicted to have accumulated hundreds of proteins[2]. This early complexification has obscured our understanding of spliceosomal evolution. Reduced systems with few introns and tiny spliceosomes give insights into the plasticity of the splicing reaction and provide an opportunity to study the evolution of the spliceosome[3][,][4]. Microsporidia are intracellular parasites possessing extremely reduced genomes that have lost many, and in some instances all, introns[5]. In the purportedly intron-lacking genome of the microsporidian Pseudoloma neurophilia[6], we identified two introns that are spliced at high levels. Furthermore, with only 14 predicted proteins, the P. neurophilia spliceosome could be the smallest known. Intriguingly, the few proteins retained are divergent compared to canonical orthologs. Even the central spliceosomal protein Prp8, which originated from the proteinaceous component of group II introns, is extremely divergent. This is unusual given that Prp8 is highly conserved across eukaryotes, including other microsporidia. All five P. neurophilia snRNAs are present, and all but U2 have diverged extensively, likely resulting from the loss of interacting proteins. Despite this divergence, U1 and U2 are predicted to pair with intron sequences more extensively than previously described. The P. neurophilia spliceosome is retained to splice a mere two introns and, with few proteins and reliance on RNA-RNA interactions, could function in a manner more reminiscent of presumed ancestral splicing.},
}

*Spliceosomes/genetics/metabolism
Introns/genetics
RNA Splicing
RNA, Small Nuclear/genetics/metabolism
*Microsporidia/genetics/metabolism

@article {pmid38103995,
year = {2024},
author = {Yu, Y and Li, YP and Ren, K and Hao, X and Fru, EC and Rønn, R and Rivera, WL and Becker, K and Feng, R and Yang, J and Rensing, C},
title = {A brief history of metal recruitment in protozoan predation.},
journal = {Trends in microbiology},
volume = {32},
number = {5},
pages = {465-476},
doi = {10.1016/j.tim.2023.11.008},
pmid = {38103995},
issn = {1878-4380},
mesh = {*Metals/metabolism ; *Phagocytosis ; *Dictyostelium/metabolism/physiology ; Biological Evolution ; Acanthamoeba ; Animals ; Phagosomes/metabolism ; Zinc/metabolism ; Metalloids/metabolism ; Copper/metabolism ; Biological Availability ; Mitochondria/metabolism ; },
abstract = {Metals and metalloids are used as weapons for predatory feeding by unicellular eukaryotes on prokaryotes. This review emphasizes the role of metal(loid) bioavailability over the course of Earth's history, coupled with eukaryogenesis and the evolution of the mitochondrion to trace the emergence and use of the metal(loid) prey-killing phagosome as a feeding strategy. Members of the genera Acanthamoeba and Dictyostelium use metals such as zinc (Zn) and copper (Cu), and possibly metalloids, to kill their bacterial prey after phagocytosis. We provide a potential timeline on when these capacities first evolved and how they correlate with perceived changes in metal(loid) bioavailability through Earth's history. The origin of phagotrophic eukaryotes must have postdated the Great Oxidation Event (GOE) in agreement with redox-dependent modification of metal(loid) bioavailability for phagotrophic poisoning. However, this predatory mechanism is predicted to have evolved much later - closer to the origin of the multicellular metazoans and the evolutionary development of the immune systems.},
}

*Metals/metabolism
*Phagocytosis
*Dictyostelium/metabolism/physiology
Biological Evolution
Acanthamoeba
Animals
Phagosomes/metabolism
Zinc/metabolism
Metalloids/metabolism
Copper/metabolism
Biological Availability
Mitochondria/metabolism

@article {pmid38060007,
year = {2023},
author = {Romei, M and Carpentier, M and Chomilier, J and Lecointre, G},
title = {Origins and Functional Significance of Eukaryotic Protein Folds.},
journal = {Journal of molecular evolution},
volume = {91},
number = {6},
pages = {854-864},
pmid = {38060007},
issn = {1432-1432},
support = {IPV program of Sorbonne University, PhD grant//Sorbonne Université/ ; },
mesh = {Animals ; Phylogeny ; *Bacteria/genetics ; *Archaea/genetics ; Proteins ; Eukaryota/genetics ; Biological Evolution ; },
abstract = {Folds are the architecture and topology of a protein domain. Categories of folds are very few compared to the astronomical number of sequences. Eukaryotes have more protein folds than Archaea and Bacteria. These folds are of two types: shared with Archaea and/or Bacteria on one hand and specific to eukaryotic clades on the other hand. The first kind of folds is inherited from the first endosymbiosis and confirms the mixed origin of eukaryotes. In a dataset of 1073 folds whose presence or absence has been evidenced among 210 species equally distributed in the three super-kingdoms, we have identified 28 eukaryotic folds unambiguously inherited from Bacteria and 40 eukaryotic folds unambiguously inherited from Archaea. Compared to previous studies, the repartition of informational function is higher than expected for folds originated from Bacteria and as high as expected for folds inherited from Archaea. The second type of folds is specifically eukaryotic and associated with an increase of new folds within eukaryotes distributed in particular clades. Reconstructed ancestral states coupled with dating of each node on the tree of life provided fold appearance rates. The rate is on average twice higher within Eukaryota than within Bacteria or Archaea. The highest rates are found in the origins of eukaryotes, holozoans, metazoans, metazoans stricto sensu, and vertebrates: the roots of these clades correspond to bursts of fold evolution. We could correlate the functions of some of the fold synapomorphies within eukaryotes with significant evolutionary events. Among them, we find evidence for the rise of multicellularity, adaptive immune system, or virus folds which could be linked to an ecological shift made by tetrapods.},
}

Animals
Phylogeny
*Bacteria/genetics
*Archaea/genetics
Proteins
Eukaryota/genetics
Biological Evolution

@article {pmid38046947,
year = {2023},
author = {Pollard, TD and Korn, ED},
title = {Discovery of the first unconventional myosin: Acanthamoeba myosin-I.},
journal = {Frontiers in physiology},
volume = {14},
number = {},
pages = {1324623},
pmid = {38046947},
issn = {1664-042X},
abstract = {Having characterized actin from Acanthamoeba castellanii (Weihing and Korn, Biochemistry, 1971, 10, 590-600) and knowing that myosin had been isolated from the slime mold Physarum (Hatano and Tazawa, Biochim. Biophys. Acta, 1968, 154, 507-519; Adelman and Taylor, Biochemistry, 1969, 8, 4976-4988), we set out in 1969 to find myosin in Acanthamoeba. We used K-EDTA-ATPase activity to assay myosin, because it is a unique feature of muscle myosins. After slightly less than 3 years, we purified a K-EDTA ATPase that interacted with actin. Actin filaments stimulated the Mg-ATPase activity of the crude enzyme, but this was lost with further purification. Recombining fractions from the column where this activity was lost revealed a "cofactor" that allowed actin filaments to stimulate the Mg-ATPase of the purified enzyme. The small size of the heavy chain and physical properties of the purified myosin were unprecedented, so many were skeptical, assuming that our myosin was a proteolytic fragment of a larger myosin similar to muscle or Physarum myosin. Subsequently our laboratories confirmed that Acanthamoeba myosin-I is a novel unconventional myosin that interacts with membrane lipids (Adams and Pollard, Nature, 1989, 340 (6234), 565-568) and that the cofactor is a myosin heavy chain kinase (Maruta and Korn, J. Biol. Chem., 1977, 252, 8329-8332). Phylogenetic analysis (Odronitz and Kollmar, Genome Biology, 2007, 8, R196) later established that class I myosin was the first myosin to appear during the evolution of eukaryotes.},
}

@article {pmid38018971,
year = {2023},
author = {Baum, B and Spang, A},
title = {On the origin of the nucleus: a hypothesis.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {87},
number = {4},
pages = {e0018621},
pmid = {38018971},
issn = {1098-5557},
support = {/WT_/Wellcome Trust/United Kingdom ; 222460/WT_/Wellcome Trust/United Kingdom ; 947317/ERC_/European Research Council/International ; MC_UP_1201/27/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Phylogeny ; *Eukaryotic Cells ; *Genome, Archaeal ; Archaea/genetics ; Bacteria/genetics ; Biological Evolution ; },
abstract = {SUMMARYIn this hypothesis article, we explore the origin of the eukaryotic nucleus. In doing so, we first look afresh at the nature of this defining feature of the eukaryotic cell and its core functions-emphasizing the utility of seeing the eukaryotic nucleoplasm and cytoplasm as distinct regions of a common compartment. We then discuss recent progress in understanding the evolution of the eukaryotic cell from archaeal and bacterial ancestors, focusing on phylogenetic and experimental data which have revealed that many eukaryotic machines with nuclear activities have archaeal counterparts. In addition, we review the literature describing the cell biology of representatives of the TACK and Asgardarchaeaota - the closest known living archaeal relatives of eukaryotes. Finally, bringing these strands together, we propose a model for the archaeal origin of the nucleus that explains much of the current data, including predictions that can be used to put the model to the test.},
}

Phylogeny
*Eukaryotic Cells
*Genome, Archaeal
Archaea/genetics
Bacteria/genetics
Biological Evolution

@article {pmid37978174,
year = {2023},
author = {Mahendrarajah, TA and Moody, ERR and Schrempf, D and Szánthó, LL and Dombrowski, N and Davín, AA and Pisani, D and Donoghue, PCJ and Szöllősi, GJ and Williams, TA and Spang, A},
title = {ATP synthase evolution on a cross-braced dated tree of life.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {7456},
pmid = {37978174},
issn = {2041-1723},
support = {BB/N000919/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Phylogeny ; *Bacteria/genetics ; *Archaea/genetics ; Mitochondria/genetics ; Adenosine Triphosphate ; Evolution, Molecular ; Eukaryota/genetics ; Biological Evolution ; },
abstract = {The timing of early cellular evolution, from the divergence of Archaea and Bacteria to the origin of eukaryotes, is poorly constrained. The ATP synthase complex is thought to have originated prior to the Last Universal Common Ancestor (LUCA) and analyses of ATP synthase genes, together with ribosomes, have played a key role in inferring and rooting the tree of life. We reconstruct the evolutionary history of ATP synthases using an expanded taxon sampling set and develop a phylogenetic cross-bracing approach, constraining equivalent speciation nodes to be contemporaneous, based on the phylogenetic imprint of endosymbioses and ancient gene duplications. This approach results in a highly resolved, dated species tree and establishes an absolute timeline for ATP synthase evolution. Our analyses show that the divergence of ATP synthase into F- and A/V-type lineages was a very early event in cellular evolution dating back to more than 4 Ga, potentially predating the diversification of Archaea and Bacteria. Our cross-braced, dated tree of life also provides insight into more recent evolutionary transitions including eukaryogenesis, showing that the eukaryotic nuclear and mitochondrial lineages diverged from their closest archaeal (2.67-2.19 Ga) and bacterial (2.58-2.12 Ga) relatives at approximately the same time, with a slightly longer nuclear stem-lineage.},
}

Phylogeny
*Bacteria/genetics
*Archaea/genetics
Mitochondria/genetics
Adenosine Triphosphate
Evolution, Molecular
Eukaryota/genetics
Biological Evolution

@article {pmid37939146,
year = {2023},
author = {Garcia, PS and Barras, F and Gribaldo, S},
title = {Components of iron-Sulfur cluster assembly machineries are robust phylogenetic markers to trace the origin of mitochondria and plastids.},
journal = {PLoS biology},
volume = {21},
number = {11},
pages = {e3002374},
pmid = {37939146},
issn = {1545-7885},
mesh = {Phylogeny ; *Iron-Sulfur Proteins/genetics/metabolism ; Plastids/genetics/metabolism ; Mitochondria/genetics/metabolism ; Iron/metabolism ; Sulfur/metabolism ; },
abstract = {Establishing the origin of mitochondria and plastids is key to understand 2 founding events in the origin and early evolution of eukaryotes. Recent advances in the exploration of microbial diversity and in phylogenomics approaches have indicated a deep origin of mitochondria and plastids during the diversification of Alphaproteobacteria and Cyanobacteria, respectively. Here, we strongly support these placements by analyzing the machineries for assembly of iron-sulfur ([Fe-S]) clusters, an essential function in eukaryotic cells that is carried out in mitochondria by the ISC machinery and in plastids by the SUF machinery. We assessed the taxonomic distribution of ISC and SUF in representatives of major eukaryotic supergroups and analyzed the phylogenetic relationships with their prokaryotic homologues. Concatenation datasets of core ISC proteins show an early branching of mitochondria within Alphaproteobacteria, right after the emergence of Magnetococcales. Similar analyses with the SUF machinery place primary plastids as sister to Gloeomargarita within Cyanobacteria. Our results add to the growing evidence of an early emergence of primary organelles and show that the analysis of essential machineries of endosymbiotic origin provide a robust signal to resolve ancient and fundamental steps in eukaryotic evolution.},
}

Phylogeny
*Iron-Sulfur Proteins/genetics/metabolism
Plastids/genetics/metabolism
Mitochondria/genetics/metabolism
Iron/metabolism
Sulfur/metabolism

@article {pmid37840457,
year = {2024},
author = {Câmara, AS and Kubalová, I and Schubert, V},
title = {Helical chromonema coiling is conserved in eukaryotes.},
journal = {The Plant journal : for cell and molecular biology},
volume = {118},
number = {5},
pages = {1284-1300},
doi = {10.1111/tpj.16484},
pmid = {37840457},
issn = {1365-313X},
support = {Schu 762/11-1//Deutsche Forschungsgemeinschaft/ ; SO 2132/1-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Chromatin/genetics/metabolism ; Eukaryota/genetics ; Chromatids/genetics/metabolism ; Meiosis ; Mitosis ; Animals ; Chromosomes, Plant/genetics ; Plants/genetics ; },
abstract = {Efficient chromatin condensation is required to transport chromosomes during mitosis and meiosis, forming daughter cells. While it is well accepted that these processes follow fundamental rules, there has been a controversial debate for more than 140 years on whether the higher-order chromatin organization in chromosomes is evolutionarily conserved. Here, we summarize historical and recent investigations based on classical and modern methods. In particular, classical light microscopy observations based on living, fixed, and treated chromosomes covering a wide range of plant and animal species, and even in single-cell eukaryotes suggest that the chromatids of large chromosomes are formed by a coiled chromatin thread, named the chromonema. More recently, these findings were confirmed by electron and super-resolution microscopy, oligo-FISH, molecular interaction data, and polymer simulation. Altogether, we describe common and divergent features of coiled chromonemata in different species. We hypothesize that chromonema coiling in large chromosomes is a fundamental feature established early during the evolution of eukaryotes to handle increasing genome sizes.},
}

*Chromatin/genetics/metabolism
Eukaryota/genetics
Chromatids/genetics/metabolism
Meiosis
Mitosis
Animals
Chromosomes, Plant/genetics
Plants/genetics

@article {pmid37803921,
year = {2024},
author = {Weston, EJ and Eglit, Y and Simpson, AGB},
title = {Kaonashia insperata gen. et sp. nov., a eukaryotrophic flagellate, represents a novel major lineage of heterotrophic stramenopiles.},
journal = {The Journal of eukaryotic microbiology},
volume = {71},
number = {1},
pages = {e13003},
doi = {10.1111/jeu.13003},
pmid = {37803921},
issn = {1550-7408},
support = {298366-2019//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Phylogeny ; *Stramenopiles/genetics ; DNA, Ribosomal/genetics ; *Diatoms/genetics ; Cryptophyta/genetics ; },
abstract = {Eukaryotrophic protists are ecologically significant and possess characteristics key to understanding the evolution of eukaryotes; however, they remain poorly studied, due partly to the complexities of maintaining predator-prey cultures. Kaonashia insperata, gen. nov., et sp. nov., is a free-swimming biflagellated eukaryotroph with a conspicuous ventral groove, a trait observed in distantly related lineages across eukaryote diversity. Di-eukaryotic (predator-prey) cultures of K. insperata with three marine algae (Isochrysis galbana, Guillardia theta, and Phaeodactylum tricornutum) were established by single-cell isolation. Growth trials showed that the studied K. insperata clone grew particularly well on G. theta, reaching a peak abundance of 1.0 × 10[5] ± 4.0 × 10[4] cells ml[-1] . Small-subunit ribosomal DNA phylogenies infer that K. insperata is a stramenopile with moderate support; however, it does not fall within any well-defined phylogenetic group, including environmental sequence clades (e.g. MASTs), and its specific placement remains unresolved. Electron microscopy shows traits consistent with stramenopile affinity, including mastigonemes on the anterior flagellum and tubular mitochondrial cristae. Kaonashia insperata may represent a novel major lineage within stramenopiles, and be important for understanding the evolutionary history of the group. While heterotrophic stramenopile flagellates are considered to be predominantly bacterivorous, eukaryotrophy may be relatively widespread amongst this assemblage.},
}

Phylogeny
*Stramenopiles/genetics
DNA, Ribosomal/genetics
*Diatoms/genetics
Cryptophyta/genetics

@article {pmid37765506,
year = {2023},
author = {Wegner, L and Porth, ML and Ehlers, K},
title = {Multicellularity and the Need for Communication-A Systematic Overview on (Algal) Plasmodesmata and Other Types of Symplasmic Cell Connections.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {18},
pages = {},
pmid = {37765506},
issn = {2223-7747},
support = {EH 372/1-1//Deutsche Forschungsgemeinschaft/ ; },
abstract = {In the evolution of eukaryotes, the transition from unicellular to simple multicellular organisms has happened multiple times. For the development of complex multicellularity, characterized by sophisticated body plans and division of labor between specialized cells, symplasmic intercellular communication is supposed to be indispensable. We review the diversity of symplasmic connectivity among the eukaryotes and distinguish between distinct types of non-plasmodesmatal connections, plasmodesmata-like structures, and 'canonical' plasmodesmata on the basis of developmental, structural, and functional criteria. Focusing on the occurrence of plasmodesmata (-like) structures in extant taxa of fungi, brown algae (Phaeophyceae), green algae (Chlorophyta), and streptophyte algae, we present a detailed critical update on the available literature which is adapted to the present classification of these taxa and may serve as a tool for future work. From the data, we conclude that, actually, development of complex multicellularity correlates with symplasmic connectivity in many algal taxa, but there might be alternative routes. Furthermore, we deduce a four-step process towards the evolution of canonical plasmodesmata and demonstrate similarity of plasmodesmata in streptophyte algae and land plants with respect to the occurrence of an ER component. Finally, we discuss the urgent need for functional investigations and molecular work on cell connections in algal organisms.},
}

@article {pmid37727796,
year = {2023},
author = {Craig, JM and Kumar, S and Hedges, SB},
title = {The origin of eukaryotes and rise in complexity were synchronous with the rise in oxygen.},
journal = {Frontiers in bioinformatics},
volume = {3},
number = {},
pages = {1233281},
pmid = {37727796},
issn = {2673-7647},
support = {R01 GM126567/GM/NIGMS NIH HHS/United States ; R35 GM139540/GM/NIGMS NIH HHS/United States ; },
abstract = {The origin of eukaryotes was among the most important events in the history of life, spawning a new evolutionary lineage that led to all complex multicellular organisms. However, the timing of this event, crucial for understanding its environmental context, has been difficult to establish. The fossil and biomarker records are sparse and molecular clocks have thus far not reached a consensus, with dates spanning 2.1-0.91 billion years ago (Ga) for critical nodes. Notably, molecular time estimates for the last common ancestor of eukaryotes are typically hundreds of millions of years younger than the Great Oxidation Event (GOE, 2.43-2.22 Ga), leading researchers to question the presumptive link between eukaryotes and oxygen. We obtained a new time estimate for the origin of eukaryotes using genetic data of both archaeal and bacterial origin, the latter rarely used in past studies. We also avoided potential calibration biases that may have affected earlier studies. We obtained a conservative interval of 2.2-1.5 Ga, with an even narrower core interval of 2.0-1.8 Ga, for the origin of eukaryotes, a period closely aligned with the rise in oxygen. We further reconstructed the history of biological complexity across the tree of life using three universal measures: cell types, genes, and genome size. We found that the rise in complexity was temporally consistent with and followed a pattern similar to the rise in oxygen. This suggests a causal relationship stemming from the increased energy needs of complex life fulfilled by oxygen.},
}

@article {pmid37713454,
year = {2023},
author = {Porter, SM and Riedman, LA},
title = {Frameworks for Interpreting the Early Fossil Record of Eukaryotes.},
journal = {Annual review of microbiology},
volume = {77},
number = {},
pages = {173-191},
doi = {10.1146/annurev-micro-032421-113254},
pmid = {37713454},
issn = {1545-3251},
mesh = {*Eukaryota/genetics ; *Fossils ; Eukaryotic Cells ; Paleontology ; Ecology ; },
abstract = {The origin of modern eukaryotes is one of the key transitions in life's history, and also one of the least understood. Although the fossil record provides the most direct view of this process, interpreting the fossils of early eukaryotes and eukaryote-grade organisms is not straightforward. We present two end-member models for the evolution of modern (i.e., crown) eukaryotes-one in which modern eukaryotes evolved early, and another in which they evolved late-and interpret key fossils within these frameworks, including where they might fit in eukaryote phylogeny and what they may tell us about the evolution of eukaryotic cell biology and ecology. Each model has different implications for understanding the rise of complex life on Earth, including different roles of Earth surface oxygenation, and makes different predictions that future paleontological studies can test.},
}

*Eukaryota/genetics
*Fossils
Eukaryotic Cells
Paleontology
Ecology

@article {pmid37699353,
year = {2023},
author = {Donoghue, PCJ and Kay, C and Spang, A and Szöllősi, G and Nenarokova, A and Moody, ERR and Pisani, D and Williams, TA},
title = {Defining eukaryotes to dissect eukaryogenesis.},
journal = {Current biology : CB},
volume = {33},
number = {17},
pages = {R919-R929},
doi = {10.1016/j.cub.2023.07.048},
pmid = {37699353},
issn = {1879-0445},
support = {BB/T012773/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Eukaryota/genetics ; Phylogeny ; *Eukaryotic Cells ; Biological Evolution ; Dissent and Disputes ; },
abstract = {The origin of eukaryotes is among the most contentious debates in evolutionary biology, attracting multiple seemingly incompatible theories seeking to explain the sequence in which eukaryotic characteristics were acquired. Much of the controversy arises from differing views on the defining characteristics of eukaryotes. We argue that eukaryotes should be defined phylogenetically, and that doing so clarifies where competing hypotheses of eukaryogenesis agree and how we may test among aspects of disagreement. Some hypotheses make predictions about the phylogenetic origins of eukaryotic genes and are distinguishable on that basis. However, other hypotheses differ only in the order of key evolutionary steps, like mitochondrial endosymbiosis and nuclear assembly, which cannot currently be distinguished phylogenetically. Stages within eukaryogenesis may be made identifiable through the absolute dating of gene duplicates that map to eukaryotic traits, such as in genes of host or mitochondrial origin that duplicated and diverged functionally prior to emergence of the last eukaryotic common ancestor. In this way, it may finally be possible to distinguish heat from light in the debate over eukaryogenesis.},
}

*Eukaryota/genetics
Phylogeny
*Eukaryotic Cells
Biological Evolution
Dissent and Disputes

@article {pmid37666024,
year = {2023},
author = {Field, MC},
title = {Deviating from the norm: Nuclear organisation in trypanosomes.},
journal = {Current opinion in cell biology},
volume = {85},
number = {},
pages = {102234},
doi = {10.1016/j.ceb.2023.102234},
pmid = {37666024},
issn = {1879-0410},
support = {204697/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Nuclear Pore Complex Proteins ; Evolution, Molecular ; Nuclear Envelope/metabolism ; Nuclear Pore/metabolism ; *Trypanosoma/metabolism ; Lamins/metabolism ; Cell Nucleus/metabolism ; Nuclear Lamina/metabolism ; },
abstract = {At first glance the nucleus is a highly conserved organelle. Overall nuclear morphology, the octagonal nuclear pore complex, the presence of peripheral heterochromatin and the nuclear envelope appear near constant features right down to the ultrastructural level. New work is revealing significant compositional divergence within these nuclear structures and their associated functions, likely reflecting adaptations and distinct mechanisms between eukaryotic lineages and especially the trypanosomatids. While many examples of mechanistic divergence currently lack obvious functional interpretations, these studies underscore the malleability of nuclear architecture. I will discuss some recent findings highlighting these facets within trypanosomes, together with the underlying evolutionary framework and make a call for the exploration of nuclear function in non-canonical experimental organisms.},
}

*Nuclear Pore Complex Proteins
Evolution, Molecular
Nuclear Envelope/metabolism
Nuclear Pore/metabolism
*Trypanosoma/metabolism
Lamins/metabolism
Cell Nucleus/metabolism
Nuclear Lamina/metabolism

@article {pmid37632100,
year = {2023},
author = {Gaïa, M and Forterre, P},
title = {From Mimivirus to Mirusvirus: The Quest for Hidden Giants.},
journal = {Viruses},
volume = {15},
number = {8},
pages = {},
pmid = {37632100},
issn = {1999-4915},
mesh = {*Mimiviridae/genetics ; Eukaryota ; *Giant Viruses/genetics ; },
abstract = {Our perception of viruses has been drastically evolving since the inception of the field of virology over a century ago. In particular, the discovery of giant viruses from the Nucleocytoviricota phylum marked a pivotal moment. Their previously concealed diversity and abundance unearthed an unprecedented complexity in the virus world, a complexity that called for new definitions and concepts. These giant viruses underscore the intricate interactions that unfold over time between viruses and their hosts, and are themselves suspected to have played a significant role as a driving force in the evolution of eukaryotes since the dawn of this cellular domain. Whether they possess exceptional relationships with their hosts or whether they unveil the actual depths of evolutionary connections between viruses and cells otherwise hidden in smaller viruses, the attraction giant viruses exert on the scientific community and beyond continues to grow. Yet, they still hold surprises. Indeed, the recent identification of mirusviruses connects giant viruses to herpesviruses, each belonging to distinct viral realms. This discovery substantially broadens the evolutionary landscape of Nucleocytoviricota. Undoubtedly, the years to come will reveal their share of surprises.},
}

*Mimiviridae/genetics
Eukaryota
*Giant Viruses/genetics

@article {pmid37606230,
year = {2023},
author = {Yubuki, N and Torruella, G and Galindo, LJ and Heiss, AA and Ciobanu, MC and Shiratori, T and Ishida, KI and Blaz, J and Kim, E and Moreira, D and López-García, P and Eme, L},
title = {Molecular and morphological characterization of four new ancyromonad genera and proposal for an updated taxonomy of the Ancyromonadida.},
journal = {The Journal of eukaryotic microbiology},
volume = {70},
number = {6},
pages = {e12997},
doi = {10.1111/jeu.12997},
pmid = {37606230},
issn = {1550-7408},
mesh = {Phylogeny ; Sequence Analysis, DNA ; *Eukaryota ; RNA, Ribosomal, 18S/genetics ; Microscopy, Electron ; },
abstract = {Ancyromonads are small biflagellated protists with a bean-shaped morphology. They are cosmopolitan in marine, freshwater, and soil environments, where they attach to surfaces while feeding on bacteria. These poorly known grazers stand out by their uncertain phylogenetic position in the tree of eukaryotes, forming a deep-branching "orphan" lineage that is considered key to a better understanding of the early evolution of eukaryotes. Despite their ecological and evolutionary interest, only limited knowledge exists about their true diversity. Here, we aimed to characterize ancyromonads better by integrating environmental surveys with behavioral observation and description of cell morphology, for which sample isolation and culturing are indispensable. We studied 18 ancyromonad strains, including 14 new isolates and seven new species. We described three new and genetically divergent genera: Caraotamonas, Nyramonas, and Olneymonas, together encompassing four species. The remaining three new species belong to the already-known genera Fabomonas and Ancyromonas. We also raised Striomonas, formerly a subgenus of Nutomonas, to full genus status, on morphological and phylogenetic grounds. We studied the morphology of diverse ancyromonads under light and electron microscopy and carried out molecular phylogenetic analyses, also including 18S rRNA gene sequences from several environmental surveys. Based on these analyses, we have updated the taxonomy of Ancyromonadida.},
}

Phylogeny
Sequence Analysis, DNA
*Eukaryota
RNA, Ribosomal, 18S/genetics
Microscopy, Electron

@article {pmid37558594,
year = {2023},
author = {van Hooff, JJE},
title = {Towards unraveling the origins of eukaryotic nuclear genome organization.},
journal = {Trends in cell biology},
volume = {33},
number = {10},
pages = {820-823},
doi = {10.1016/j.tcb.2023.07.008},
pmid = {37558594},
issn = {1879-3088},
mesh = {Humans ; *Eukaryota/genetics ; *Archaea/genetics ; Phylogeny ; Eukaryotic Cells/metabolism ; Prokaryotic Cells/metabolism ; },
abstract = {With 3D genome mapping maturing over the past decade, studies exposed the differences between eukaryotic and prokaryotic genome organization. This raises the question of how the complex eukaryotic genome organization originated. Here, I explore potential pathways to answering this question, guided by our changing understanding of the origins of eukaryotes.},
}

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

@article {pmid37553111,
year = {2023},
author = {Hernández, G and Vazquez-Pianzola, P},
title = {eIF4E as a molecular wildcard in metazoans RNA metabolism.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {98},
number = {6},
pages = {2284-2306},
doi = {10.1111/brv.13005},
pmid = {37553111},
issn = {1469-185X},
mesh = {Humans ; Animals ; *Drosophila melanogaster/genetics ; *Eukaryotic Initiation Factor-4E/genetics/chemistry/metabolism ; RNA, Messenger/genetics/metabolism ; RNA/metabolism ; },
abstract = {The evolutionary origin of eukaryotes spurred the transition from prokaryotic-like translation to a more sophisticated, eukaryotic translation. During this process, successive gene duplication of a single, primordial eIF4E gene encoding the mRNA cap-binding protein eukaryotic translation initiation factor 4E (eIF4E) gave rise to a plethora of paralog genes across eukaryotes that underwent further functional diversification in RNA metabolism. The ability to take different roles is due to eIF4E promiscuity in binding many partner proteins, rendering eIF4E a highly versatile and multifunctional player that functions as a molecular wildcard. Thus, in metazoans, eIF4E paralogs are involved in various processes, including messenger RNA (mRNA) processing, export, translation, storage, and decay. Moreover, some paralogs display differential expression in tissues and developmental stages and show variable biochemical properties. In this review, we discuss recent advances shedding light on the functional diversification of eIF4E in metazoans. We emphasise humans and two phylogenetically distant species which have become paradigms for studies on development, namely the fruit fly Drosophila melanogaster and the roundworm Caenorhabditis elegans.},
}

Humans
Animals
*Drosophila melanogaster/genetics
*Eukaryotic Initiation Factor-4E/genetics/chemistry/metabolism
RNA, Messenger/genetics/metabolism
RNA/metabolism

@article {pmid37511529,
year = {2023},
author = {Kordiš, D and Turk, V},
title = {Origin and Early Diversification of the Papain Family of Cysteine Peptidases.},
journal = {International journal of molecular sciences},
volume = {24},
number = {14},
pages = {},
pmid = {37511529},
issn = {1422-0067},
support = {P1-0207, P1-0140, J1-2473//Slovenian Research Agency/ ; },
mesh = {*Papain/genetics/metabolism ; Cysteine/metabolism ; Evolution, Molecular ; Phylogeny ; Eukaryota/genetics ; Archaea/genetics ; *Cysteine Proteases/metabolism ; Peptide Hydrolases/metabolism ; },
abstract = {Peptidases of the papain family play a key role in protein degradation, regulated proteolysis, and the host-pathogen arms race. Although the papain family has been the subject of many studies, knowledge about its diversity, origin, and evolution in Eukaryota, Bacteria, and Archaea is limited; thus, we aimed to address these long-standing knowledge gaps. We traced the origin and expansion of the papain family with a phylogenomic analysis, using sequence data from numerous prokaryotic and eukaryotic proteomes, transcriptomes, and genomes. We identified the full complement of the papain family in all prokaryotic and eukaryotic lineages. Analysis of the papain family provided strong evidence for its early diversification in the ancestor of eukaryotes. We found that the papain family has undergone complex and dynamic evolution through numerous gene duplications, which produced eight eukaryotic ancestral paralogous C1A lineages during eukaryogenesis. Different evolutionary forces operated on C1A peptidases, including gene duplication, horizontal gene transfer, and gene loss. This study challenges the current understanding of the origin and evolution of the papain family and provides valuable insights into their early diversification. The findings of this comprehensive study provide guidelines for future structural and functional studies of the papain family.},
}

*Papain/genetics/metabolism
Cysteine/metabolism
Evolution, Molecular
Phylogeny
Eukaryota/genetics
Archaea/genetics
*Cysteine Proteases/metabolism
Peptide Hydrolases/metabolism

@article {pmid37507225,
year = {2023},
author = {Esposti, MD},
title = {Eukaryotes inherited inositol lipids from bacteria: implications for the models of eukaryogenesis.},
journal = {FEBS letters},
volume = {597},
number = {19},
pages = {2484-2496},
doi = {10.1002/1873-3468.14708},
pmid = {37507225},
issn = {1873-3468},
abstract = {The merger of two very different microbes, an anaerobic archaeon and an aerobic bacterium, led to the birth of eukaryotic cells. Current models hypothesize that an archaeon engulfed bacteria through external protrusions that then fused together forming the membrane organelles of eukaryotic cells, including mitochondria. Images of cultivated Lokiarchaea sustain this concept, first proposed in the inside-out model which assumes that the membrane traffic system of archaea drove the merging with bacterial cells through membrane expansions containing inositol lipids, considered to have evolved first in archaea. This assumption has been evaluated here in detail. The data indicate that inositol lipids first emerged in bacteria, not in archaea. The implications of this finding for the models of eukaryogenesis are discussed.},
}

@article {pmid37491455,
year = {2023},
author = {von der Dunk, SHA and Hogeweg, P and Snel, B},
title = {Obligate endosymbiosis enables genome expansion during eukaryogenesis.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {777},
pmid = {37491455},
issn = {2399-3642},
mesh = {Phylogeny ; *Eukaryotic Cells/metabolism ; *Symbiosis/genetics ; Biological Evolution ; Mitochondria/genetics ; },
abstract = {The endosymbiosis of an alpha-proteobacterium that gave rise to mitochondria was one of the key events in eukaryogenesis. One striking outcome of eukaryogenesis was a much more complex cell with a large genome. Despite the existence of many alternative hypotheses for this and other patterns potentially related to endosymbiosis, a constructive evolutionary model in which these hypotheses can be studied is still lacking. Here, we present a theoretical approach in which we focus on the consequences rather than the causes of mitochondrial endosymbiosis. Using a constructive evolutionary model of cell-cycle regulation, we find that genome expansion and genome size asymmetry arise from emergent host-symbiont cell-cycle coordination. We also find that holobionts with large host and small symbiont genomes perform best on long timescales and mimic the outcome of eukaryogenesis. By designing and studying a constructive evolutionary model of obligate endosymbiosis, we uncovered some of the forces that may drive the patterns observed in nature. Our results provide a theoretical foundation for patterns related to mitochondrial endosymbiosis, such as genome size asymmetry, and reveal evolutionary outcomes that have not been considered so far, such as cell-cycle coordination without direct communication.},
}

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

@article {pmid37442362,
year = {2023},
author = {Gollo, G},
title = {On the emergence of eukaryotes and other enigmas.},
journal = {Bio Systems},
volume = {231},
number = {},
pages = {104958},
doi = {10.1016/j.biosystems.2023.104958},
pmid = {37442362},
issn = {1872-8324},
mesh = {Male ; Humans ; *Eukaryota ; *Semen ; Biological Evolution ; Cell Nucleus ; Mitosis ; },
abstract = {The origin of eukaryotes is one of the most fundamental problems in the entire history of life. How did eukaryotes arise? Previous attempts to solve the problem are very far from an answer, at best they propose a solution to one of the various innovations that ended up culminating in eukaryotes. Based on a hypothetical-deductive methodology, as usual in evolutionary issues, I propose that eukaryotes emerged from the endosymbiotic association between a flagellate parasite and its host, of which the sperm is the main vestige. The hypothesis unifies the solution to the vast array of acquisitions shared by eukaryotes that differentiate them from other beings, remarkably cell nucleus, mitosis, meiosis and sexual reproduction. The solution has a deep impact on understanding the origin and functioning of all complex life forms.},
}

Male
Humans
*Eukaryota
*Semen
Biological Evolution
Cell Nucleus
Mitosis

@article {pmid37316666,
year = {2023},
author = {Eme, L and Tamarit, D and Caceres, EF and Stairs, CW and De Anda, V and Schön, ME and Seitz, KW and Dombrowski, N and Lewis, WH and Homa, F and Saw, JH and Lombard, J and Nunoura, T and Li, WJ and Hua, ZS and Chen, LX and Banfield, JF and John, ES and Reysenbach, AL and Stott, MB and Schramm, A and Kjeldsen, KU and Teske, AP and Baker, BJ and Ettema, TJG},
title = {Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes.},
journal = {Nature},
volume = {618},
number = {7967},
pages = {992-999},
pmid = {37316666},
issn = {1476-4687},
support = {/WT_/Wellcome Trust/United Kingdom ; 203276/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Archaea/classification/cytology/genetics ; *Eukaryota/classification/cytology/genetics ; Eukaryotic Cells/classification/cytology ; *Phylogeny ; Prokaryotic Cells/classification/cytology ; Datasets as Topic ; Gene Duplication ; Evolution, Molecular ; },
abstract = {In the ongoing debates about eukaryogenesis-the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors-members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes[1]. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved[2-4]. Here we analyse distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea and as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree and species tree reconciliation approaches, we show that analogous to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared with other archaea. Finally, we infer that the last common ancestor of Asgard archaea was probably a thermophilic chemolithotroph and that the lineage from which eukaryotes evolved adapted to mesophilic conditions and acquired the genetic potential to support a heterotrophic lifestyle. Our work provides key insights into the prokaryote-to-eukaryote transition and a platform for better understanding the emergence of cellular complexity in eukaryotic cells.},
}

*Archaea/classification/cytology/genetics
*Eukaryota/classification/cytology/genetics
Eukaryotic Cells/classification/cytology
*Phylogeny
Prokaryotic Cells/classification/cytology
Datasets as Topic
Gene Duplication
Evolution, Molecular

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

*Organelles/metabolism
Mitochondria/metabolism
RNA, Transfer, Amino Acyl/metabolism
Chloroplasts/metabolism
RNA, Transfer/metabolism
*Arabidopsis/genetics

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

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

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

*Archaea/chemistry/metabolism
*Membrane Lipids/metabolism
Bacteria/metabolism
Terpenes/metabolism
Ethers/chemistry/metabolism

@article {pmid37127702,
year = {2023},
author = {Krupovic, M and Dolja, VV and Koonin, EV},
title = {The virome of the last eukaryotic common ancestor and eukaryogenesis.},
journal = {Nature microbiology},
volume = {8},
number = {6},
pages = {1008-1017},
pmid = {37127702},
issn = {2058-5276},
support = {ZIA LM000073/ImNIH/Intramural NIH HHS/United States ; },
mesh = {*Eukaryota ; Eukaryotic Cells ; Virome ; Phylogeny ; Archaea/genetics ; Bacteria/genetics ; *Viruses/genetics ; },
abstract = {All extant eukaryotes descend from the last eukaryotic common ancestor (LECA), which is thought to have featured complex cellular organization. To gain insight into LECA biology and eukaryogenesis-the origin of the eukaryotic cell, which remains poorly understood-we reconstructed the LECA virus repertoire. We compiled an inventory of eukaryotic hosts of all major virus taxa and reconstructed the LECA virome by inferring the origins of these groups of viruses. The origin of the LECA virome can be traced back to a small set of bacterial-not archaeal-viruses. This provenance of the LECA virome is probably due to the bacterial origin of eukaryotic membranes, which is most compatible with two endosymbiosis events in a syntrophic model of eukaryogenesis. In the first endosymbiosis, a bacterial host engulfed an Asgard archaeon, preventing archaeal viruses from entry owing to a lack of archaeal virus receptors on the external membranes.},
}

*Eukaryota
Eukaryotic Cells
Virome
Phylogeny
Archaea/genetics
Bacteria/genetics
*Viruses/genetics

@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},
support = {101018894/ERC_/European Research Council/International ; },
mesh = {*Eukaryota/genetics ; *Eukaryotic Cells ; Mitosis ; Cell Nucleus ; Cytosol ; },
abstract = {All eukaryotes have linear chromosomes that are distributed to daughter nuclei during mitotic division, but the ancestral state of nuclear division in the last eukaryotic common ancestor (LECA) is so far unresolved. To address this issue, we have employed ancestral state reconstructions for mitotic states that can be found across the eukaryotic tree concerning the intactness of the nuclear envelope during mitosis (open or closed), the position of spindles (intranuclear or extranuclear), and the symmetry of spindles being either axial (orthomitosis) or bilateral (pleuromitosis). The data indicate that the LECA possessed closed orthomitosis with intranuclear spindles. Our reconstruction is compatible with recent findings indicating a syncytial state of the LECA, because it decouples three main processes: chromosome division, chromosome partitioning, and cell division (cytokinesis). The possession of closed mitosis using intranuclear spindles adds to the number of cellular traits that can now be attributed to LECA, providing insights into the lifestyle of this otherwise elusive biological entity at the origin of eukaryotic cells. Closed mitosis in a syncytial eukaryotic common ancestor would buffer mutations arising at the origin of mitotic division by allowing nuclei with viable chromosome sets to complement defective nuclei via mRNA in the cytosol.},
}

*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 GM083960/GM/NIGMS NIH HHS/United States ; R01 GM112108/GM/NIGMS NIH HHS/United States ; W 1261/FWF_/Austrian Science Fund FWF/Austria ; },
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 {pmid38818484,
year = {2022},
author = {Zhou, Z and Liu, Y and Anantharaman, K and Li, M},
title = {The expanding Asgard archaea invoke novel insights into Tree of Life and eukaryogenesis.},
journal = {mLife},
volume = {1},
number = {4},
pages = {374-381},
pmid = {38818484},
issn = {2770-100X},
abstract = {The division of organisms on the Tree of Life into either a three-domain (3D) tree or a two-domain (2D) tree has been disputed for a long time. Ever since the discovery of Archaea by Carl Woese in 1977 using 16S ribosomal RNA sequence as the evolutionary marker, there has been a great advance in our knowledge of not only the growing diversity of Archaea but also the evolutionary relationships between different lineages of living organisms. Here, we present this perspective to summarize the progress of archaeal diversity and changing notion of the Tree of Life. Meanwhile, we provide the latest progress in genomics/physiology-based discovery of Asgard archaeal lineages as the closest relative of Eukaryotes. Furthermore, we propose three major directions for future research on exploring the "next one" closest Eukaryote relative, deciphering the function of archaeal eukaryotic signature proteins and eukaryogenesis from both genomic and physiological aspects, and understanding the roles of horizontal gene transfer, viruses, and mobile elements in eukaryogenesis.},
}

@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},
support = {JPMJCR19S5//JST CREST/ ; //Moore-Simons Project/ ; GBMF9743//Origin of the Eukaryotic Cell/ ; //Vidyasirimedhi Institute of Science and Technology (VISTEC)/ ; },
mesh = {*Archaea/metabolism ; *Profilins/genetics/metabolism ; Actins ; Phylogeny ; Furylfuramide/metabolism ; Eukaryota/metabolism ; },
abstract = {The release of AlphaFold2 (AF2), a deep-learning-aided, open-source protein structure prediction program, from DeepMind, opened a new era of molecular biology. The astonishing improvement in the accuracy of the structure predictions provides the opportunity to characterize protein systems from uncultured Asgard archaea, key organisms in evolutionary biology. Despite the accumulation in metagenomics-derived Asgard archaea eukaryotic-like protein sequences, limited structural and biochemical information have restricted the insight in their potential functions. In this review, we focus on profilin, an actin-dynamics regulating protein, which in eukaryotes, modulates actin polymerization through (1) direct actin interaction, (2) polyproline binding, and (3) phospholipid binding. We assess AF2-predicted profilin structures in their potential abilities to participate in these activities. We demonstrate that AF2 is a powerful new tool for understanding the emergence of biological functional traits in evolution.},
}

*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},
support = {32070247//National Natural Science Foundation of China/ ; 2019M661344//China Postdoctoral Science Foundation/ ; //State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering in Fudan University/ ; },
mesh = {Animals ; *Gene Duplication ; Phylogeny ; Synteny ; *Eukaryota ; Sequence Alignment ; },
abstract = {MOTIVATION: Whole-genome duplication events have long been discovered throughout the evolution of eukaryotes, contributing to genome complexity and biodiversity and leaving traces in the descending organisms. Therefore, an accurate and rapid phylogenomic method is needed to identify the retained duplicated genes on various lineages across the target taxonomy.

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

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

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

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 = {R01 GM112108/GM/NIGMS NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R01 AI140429/AI/NIAID NIH HHS/United States ; P41 GM109824/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},
support = {BB/V003542/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/S003681/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {Computer Simulation ; *DNA Repeat Expansion/genetics ; *Eukaryota/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal/genetics ; Genome/genetics ; *Meiosis/genetics ; Mutation ; Mutation Accumulation ; Phylogeny ; Prokaryotic Cells ; },
abstract = {The transition from prokaryotic lateral gene transfer to eukaryotic meiotic sex is poorly understood. Phylogenetic evidence suggests that it was tightly linked to eukaryogenesis, which involved an unprecedented rise in both genome size and the density of genetic repeats. Expansion of genome size raised the severity of Muller's ratchet, while limiting the effectiveness of lateral gene transfer (LGT) at purging deleterious mutations. In principle, an increase in recombination length combined with higher rates of LGT could solve this problem. Here, we show using a computational model that this solution fails in the presence of genetic repeats prevalent in early eukaryotes. The model demonstrates that dispersed repeat sequences allow ectopic recombination, which leads to the loss of genetic information and curtails the capacity of LGT to prevent mutation accumulation. Increasing recombination length in the presence of repeat sequences exacerbates the problem. Mutational decay can only be resisted with homology along extended sequences of DNA. We conclude that the transition to homologous pairing along linear chromosomes was a key innovation in meiotic sex, which was instrumental in the expansion of eukaryotic genomes and morphological complexity.},
}

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