Eukarya the chimera: eukaryotes, a secondary innovation of the two domains of life?

Sagan, 1967, On the origin of mitosing cells, J. Theor. Biol., 14, 255, 10.1016/0022-5193(67)90079-3 Martijn, 2018, Deep mitochondrial origin outside the sampled alphaproteobacteria, Nature, 557, 101, 10.1038/s41586-018-0059-5 Wang, 2015, An integrated phylogenomic approach toward pinpointing the origin of mitochondria, Sci. Rep., 5, 7949, 10.1038/srep07949 Woese, 1977, Phylogenetic structure of the prokaryotic domain: The primary kingdoms, Proc. Natl. Acad. Sci. U. S. A., 74, 5088, 10.1073/pnas.74.11.5088 Lake, 1984, Eocytes: a new ribosome structure indicates a kingdom with a close relationship to eukaryotes, Proc. Natl. Acad. Sci. U. S. A., 81, 3786, 10.1073/pnas.81.12.3786 Hartman, 2002, The origin of the eukaryotic cell: A genomic investigation, Proc. Natl. Acad. Sci. U. S. A., 99, 1420, 10.1073/pnas.032658599 Yutin, 2012, Archaeal origin of tubulin, Biol. Direct, 7, 10, 10.1186/1745-6150-7-10 Ettema, 2011, An actin-based cytoskeleton in archaea, Mol. Microbiol., 80, 1052, 10.1111/j.1365-2958.2011.07635.x Samson, 2008, A role for the ESCRT system in cell division in Archaea, Science, 322, 1710, 10.1126/science.1165322 Imachi, 2020, Isolation of an archaeon at the prokaryote–eukaryote interface, Nature, 577, 519, 10.1038/s41586-019-1916-6 Zaremba-Niedzwiedzka, 2017, Asgard archaea illuminate the origin of eukaryotic cellular complexity, Nature, 541, 353, 10.1038/nature21031 Klinger, 2016, Tracing the archaeal origins of eukaryotic membrane-trafficking system building blocks, Mol. Biol. Evol., 33, 1528, 10.1093/molbev/msw034 Spang, 2015, Complex archaea that bridge the gap between prokaryotes and eukaryotes, Nature, 521, 173, 10.1038/nature14447 Hug, 2016, A new view of the tree of life, Nat. Microbiol., 1, 16048, 10.1038/nmicrobiol.2016.48 Eme, 2017, Archaea and the origin of eukaryotes, Nat. Rev. Microbiol., 15, 711, 10.1038/nrmicro.2017.133 Makarova, 2005, Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell, Nucleic Acids Res., 33, 4626, 10.1093/nar/gki775 Pittis, 2016, Late acquisition of mitochondria by a host with chimaeric prokaryotic ancestry, Nature, 531, 101, 10.1038/nature16941 Ku, 2015, Endosymbiotic gene transfer from prokaryotic pangenomes: Inherited chimerism in eukaryotes, Proc. Natl. Acad. Sci. U. S. A., 112, 10139, 10.1073/pnas.1421385112 Thiergart, 2012, An evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin, Genome Biol. Evol., 4, 466, 10.1093/gbe/evs018 Gray, 1999, Mitochondrial evolution, Science, 283, 1476, 10.1126/science.283.5407.1476 Gabaldón, 2018, Relative timing of mitochondrial endosymbiosis and the ‘pre-mitochondrial symbioses’ hypothesis, IUBMB Life, 70, 1188, 10.1002/iub.1950 Timmis, 2004, Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes, Nat. Rev. Genet., 5, 123, 10.1038/nrg1271 Vosseberg, 2021, Timing the origin of eukaryotic cellular complexity with ancient duplications, Nat. Ecol. Evol., 5, 92, 10.1038/s41559-020-01320-z Koonin, 2010, The origin and early evolution of eukaryotes in the light of phylogenomics, Genome Biol., 11, 209, 10.1186/gb-2010-11-5-209 Pisani, 2007, Supertrees disentangle the chimerical origin of eukaryotic genomes, Mol. Biol. Evol., 24, 1752, 10.1093/molbev/msm095 Esser, 2004, A Genome Phylogeny for Mitochondria Among α-Proteobacteria and a Predominantly Eubacterial Ancestry of Yeast Nuclear Genes, Mol. Biol. Evol., 21, 1643, 10.1093/molbev/msh160 Gabaldón, 2007, From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism, PLoS Comput. Biol., 3, 10.1371/journal.pcbi.0030219 Gabaldón, 2004, Shaping the mitochondrial proteome, Biochim. Biophys. Acta (Bioenergetics), 1659, 212, 10.1016/j.bbabio.2004.07.011 Roger, 2017, The origin and diversification of mitochondria, Curr. Biol., 27, R1177, 10.1016/j.cub.2017.09.015 Hofstatter, 2021, Complex evolution of the mismatch repair system in eukaryotes is illuminated by novel archaeal genomes, J. Mol. Evol., 89, 12, 10.1007/s00239-020-09979-5 Wong, 2020, Microbial dark matter filling the niche in hypersaline microbial mats, Microbiome, 8, 135, 10.1186/s40168-020-00910-0 Bulzu, 2019, Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche, Nat. Microbiol., 4, 1129, 10.1038/s41564-019-0404-y Fournier, 2018, A briefly argued case that Asgard Archaea are part of the eukaryote tree, Front. Microbiol., 9, 1896, 10.3389/fmicb.2018.01896 Dacks, 2007, Evolution of the eukaryotic membrane-trafficking system: origin, tempo and mode, J. Cell Sci., 120, 2977, 10.1242/jcs.013250 Sacher, 2008, The TRAPP complex: insights into its architecture and function, Traffic, 9, 2032, 10.1111/j.1600-0854.2008.00833.x Podar, 2008, The prokaryotic V4R domain is the likely ancestor of a key component of the eukaryotic vesicle transport system, Biol. Direct, 3, 2, 10.1186/1745-6150-3-2 Barlowe, 1994, COPII: A membrane coat formed by Sec proteins that drive vesicle budding from the endoplasmic reticulum, Cell, 77, 895, 10.1016/0092-8674(94)90138-4 Jahn, 2012, Molecular machines governing exocytosis of synaptic vesicles, Nature, 490, 201, 10.1038/nature11320 Neveu, 2020, Prototypic SNARE proteins are encoded in the genomes of Heimdallarchaeota, potentially bridging the gap between the prokaryotes and eukaryotes, Curr. Biol., 30, 2468, 10.1016/j.cub.2020.04.060 Olmos, 2016, The ESCRT machinery: new roles at new holes, Curr. Opin. Cell Biol., 38, 1, 10.1016/j.ceb.2015.12.001 McCullough, 2018, Structures, functions, and dynamics of ESCRT-III/Vps4 membrane remodeling and fission complexes, Annu. Rev. Cell Biol., 34, 85, 10.1146/annurev-cellbio-100616-060600 Leung, 2008, Evolution of the multivesicular body ESCRT machinery; retention across the eukaryotic lineage, Traffic, 9, 1698, 10.1111/j.1600-0854.2008.00797.x Hurley, 2010, The ESCRT complexes, Crit. Rev. Biochem. Mol. Biol., 45, 463, 10.3109/10409238.2010.502516 Raiborg, 2009, The ESCRT machinery in endosomal sorting of ubiquitylated membrane proteins, Nature, 458, 445, 10.1038/nature07961 Lu, 2020, Coevolution of eukaryote-like Vps4 and ESCRT-III subunits in the Asgard Archaea, mBio, 11, e00417, 10.1128/mBio.00417-20 Gunning, 2015, The evolution of compositionally and functionally distinct actin filaments, J. Cell Sci., 128, 2009, 10.1242/jcs.165563 Downing, 1998, Tubulin and microtubule structure, Curr. Opin. Cell Biol., 10, 16, 10.1016/S0955-0674(98)80082-3 Akıl, 2018, Genomes of Asgard archaea encode profilins that regulate actin, Nature, 562, 439, 10.1038/s41586-018-0548-6 Akıl, 2020, Insights into the evolution of regulated actin dynamics via characterization of primitive gelsolin/cofilin proteins from Asgard archaea, Proc. Natl. Acad. Sci. U. S. A., 117, 19904, 10.1073/pnas.2009167117 Akıl, 2021, Mythical origins of the actin cytoskeleton, Curr. Opin. Cell Biol., 68, 55, 10.1016/j.ceb.2020.08.011 Stairs, 2020, The archaeal roots of the eukaryotic dynamic actin cytoskeleton, Curr. Biol., 30, R521, 10.1016/j.cub.2020.02.074 Liao, 2021, Cell division in the archaeon Haloferax volcanii relies on two FtsZ proteins with distinct functions in division ring assembly and constriction, Nat. Microbiol., 6, 594, 10.1038/s41564-021-00894-z Liao, 2018, Archaeal cell biology: diverse functions of tubulin-like cytoskeletal proteins at the cell envelope, Emerg. Top. Life Sci., 2, 547, 10.1042/ETLS20180026 Duggin, 2015, CetZ tubulin-like proteins control archaeal cell shape, Nature, 519, 362, 10.1038/nature13983 Brueckner, 2020, Bacterial genes outnumber archaeal genes in eukaryotic genomes, Genome Biol. Evol., 12, 282, 10.1093/gbe/evaa047 Fournier, 2015, Ancient horizontal gene transfer and the last common ancestors, BMC Evol. Biol., 15, 70, 10.1186/s12862-015-0350-0 Nelson-Sathi, 2015, Origins of major archaeal clades correspond to gene acquisitions from bacteria, Nature, 517, 77, 10.1038/nature13805 Méheust, 2018, Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution, Genome Biol., 19, 75, 10.1186/s13059-018-1454-9 Rivera, 1998, Genomic evidence for two functionally distinct gene classes, Proc. Natl. Acad. Sci. U. S. A., 95, 6239, 10.1073/pnas.95.11.6239 Mans, 2004, Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex, Cell Cycle, 3, 1625, 10.4161/cc.3.12.1316 DeGrasse, 2009, Evidence for a shared nuclear pore complex architecture that is conserved from the last common eukaryotic ancestor*, Mol. Cell Proteom., 8, 2119, 10.1074/mcp.M900038-MCP200 Yutin, 2009, The origins of phagocytosis and eukaryogenesis, Biol. Direct, 4, 9, 10.1186/1745-6150-4-9 Weller, 2002, Identification of a DNA nonhomologous end-joining complex in bacteria, Science, 297, 1686, 10.1126/science.1074584 Koumandou, 2013, Molecular paleontology and complexity in the last eukaryotic common ancestor, Crit. Rev. Biochem. Mol. Biol., 48, 373, 10.3109/10409238.2013.821444 Lane, 2010, The energetics of genome complexity, Nature, 467, 929, 10.1038/nature09486 Lane, 2014, Bioenergetic constraints on the evolution of complex life, Cold Spring Harb. Perspect. Biol., 6, 10.1101/cshperspect.a015982 Spang, 2019, Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism, Nat. Microbiol., 4, 1138, 10.1038/s41564-019-0406-9 López-García, 2020, The Syntrophy hypothesis for the origin of eukaryotes revisited, Nat. Microbiol., 5, 655, 10.1038/s41564-020-0710-4 López-García, 2020, Cultured Asgard archaea shed light on eukaryogenesis, Cell, 181, 232, 10.1016/j.cell.2020.03.058 Jeong, 2019, Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation, Sci. Rep., 9, 5953, 10.1038/s41598-019-42227-5 Caro-Quintero, 2015, Inter-phylum HGT has shaped the metabolism of many mesophilic and anaerobic bacteria, ISME J., 9, 958, 10.1038/ismej.2014.193 Hug, 2018, It takes a village: microbial communities thrive through interactions and metabolic handoffs, mSystems, 3, 10.1128/mSystems.00152-17 Beraldi-Campesi, 2013, Early life on land and the first terrestrial ecosystems, Ecol. Process., 2, 1, 10.1186/2192-1709-2-1 Javaux, 2018, The Paleoproterozoic fossil record: Implications for the evolution of the biosphere during Earth’s middle-age, Earth Sci. Rev., 176, 68, 10.1016/j.earscirev.2017.10.001 Betts, 2018, Integrated genomic and fossil evidence illuminates life’s early evolution and eukaryote origin, Nat. Ecol. Evol., 2, 1556, 10.1038/s41559-018-0644-x Jain, 2003, Horizontal gene transfer accelerates genome innovation and evolution, Mol. Biol. Evol., 20, 1598, 10.1093/molbev/msg154 David, 2011, Rapid evolutionary innovation during an Archaean genetic expansion, Nature, 469, 93, 10.1038/nature09649 Fuchsman, 2017, Effect of the environment on horizontal gene transfer between bacteria and archaea, PeerJ, 5, 10.7717/peerj.3865 Jahnert, 2012, Characteristics, distribution and morphogenesis of subtidal microbial systems in Shark Bay, Australia, Mar. Geol., 303–306, 115, 10.1016/j.margeo.2012.02.009 Wong, 2018, Disentangling the drivers of functional complexity at the metagenomic level in Shark Bay microbial mat microbiomes, ISME J., 12, 2619, 10.1038/s41396-018-0208-8 MacLeod, 2019, Asgard archaea: Diversity, function, and evolutionary implications in a range of microbiomes, AIMS Microbiol., 5, 48, 10.3934/microbiol.2019.1.48