Serial endosymbiosis or singular event at the origin of eukaryotes?

Journal of Theoretical Biology - Tập 434 - Trang 58-67 - 2017
Nick Lane1
1Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, United Kingdom

Tài liệu tham khảo

Allen, 1993, Control of gene expression by redox potential and the requirement for chloroplast and mitochondrial genomes, J. Theor. Biol., 165, 609, 10.1006/jtbi.1993.1210 Allen, 2003, The function of genomes in bioenergetic organelles, Philos. Trans. R. Soc. B, 358, 19, 10.1098/rstb.2002.1191 Allen, 2017, The CoRR hypothesis for genes in organelles, J. Theor. Biol., 10.1016/j.jtbi.2017.04.008 Amend, 2001, Energetics of overall metabolic reactions of thermophilic and hyperthermophilic archaea and bacteria, FEMS Microbiol. Rev., 25, 175, 10.1111/j.1574-6976.2001.tb00576.x Angert, 2012, DNA replication and genomic architecture of very large bacteria, Annu. Rev. Microbiol., 66, 197, 10.1146/annurev-micro-090110-102827 Archibald, 2009, The puzzle of plastid evolution, Curr. Biol., 19, R81, 10.1016/j.cub.2008.11.067 Archibald, 2015, Endosymbiosis and eukaryotic cell evolution, Curr. Biol., 25, R911, 10.1016/j.cub.2015.07.055 Barry, 2006, DNA replication in the archaea, Microbiol. Mol. Biol. Rev., 70, 876, 10.1128/MMBR.00029-06 Blackstone, 2013, Genetic and energetic aspects of conflict and conflict mediation, Philos. Trans. R. Soc. B, 368, 10.1098/rstb.2012.0266 Booth, 2015, Eukaryogenesis, how special really?, Proc. Natl. Acad. Sci. USA., 112, 10278, 10.1073/pnas.1421376112 Boyle, 2013, Nitrogen cycle feedbacks as a control on euxinia in the mid-Proterozoic ocean, Nat. Commun., 4, 1533, 10.1038/ncomms2511 Brocchieri, 2005, Protein length in eukaryotic and prokaryotic proteomes, Nucleic Acids Res, 33, 3390, 10.1093/nar/gki615 Canfield, 1998, A new model for proterozoic ocean chemistry, Nature, 396, 450, 10.1038/24839 Carvalho-Santos, 2011, Tracing the origins of centrioles, cilia, and flagella, J. Cell Biol., 194, 165, 10.1083/jcb.201011152 Cavalier-Smith, 1987, Eukaryotes with no mitochondria, Nature, 326, 332, 10.1038/326332a0 Cavalier-Smith, 1989, Archaebacteria and archezoa, Nature, 339, 100, 10.1038/339100a0 Cavalier-Smith, 2002, The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa, Int. J. Syst. Evol. Microbiol., 52, 297, 10.1099/00207713-52-2-297 Cavalier-Smith, 2014, The neomuran revolution and phagotrophic origin of eukaryotes and cilia in light of intracellular coevolution and a revised tree of life, Cold Spring Harbor Perspect. Biol., 6, 10.1101/cshperspect.a016006 Cloud, 1965, Significance of the Gunflint (Precambrian) microflora, Science, 148, 27, 10.1126/science.148.3666.27 Crick, 1958, On protein synthesis, Symp. Soc. Exp. Biol., 12, 138 Crick, 1968, The origin of the genetic code, J. Mol. Biol., 38, 367, 10.1016/0022-2836(68)90392-6 Daniels, 1968, Starvation effects on the ultrastructure of amoeba mitochondria, Z. Zellforsch., 91, 159, 10.1007/BF00364307 Dodd, 2017, Evidence for early life in Earth's oldest hydrothermal vent precipitates, Nature, 543, 60, 10.1038/nature21377 Dinman, 2009, The eukaryotic ribosome: current status and challenges, J. Biol. Chem., 284, 11761, 10.1074/jbc.R800074200 Dobell, 1914, Cytological studies on three species of Amoeba—A. lacertae Hartmann, A. glebae n.sp., A. fluvialis n.sp, Arch. Protistenk., 34, 139 Elliott, 2015, What's in a genome? The C-value enigma and the evolution of eukaryotic genome content, Philos. Trans. R. Soc. B, 370, 10.1098/rstb.2014.0331 Embley, 2006, Eukaryotic evolution, changes and challenges, Nature, 440, 623, 10.1038/nature04546 Errington, 2013, l-form bacteria, cell walls and the origins of life, Open Biol, 3, 10.1098/rsob.120143 Fritz-Laylin, 2010, The genome of Naegleria gruberi illuminates early eukaryotic versatility, Cell, 140, 631, 10.1016/j.cell.2010.01.032 Garg, 2016, Mitochondria, the cell cycle, and the origin of sex, via a syncytial eukaryotic common ancestor, Genome Biol. Evol., 8, 1950, 10.1093/gbe/evw136 Gerschman, 1954, Oxygen poisoning and X-irradiation: a mechanism in common, Science, 119, 623, 10.1126/science.119.3097.623 Gibor, 1964, Plastids and mitochondria: inheritable systems, Science, 145, 890, 10.1126/science.145.3635.890 Griese, 2011, Ploidy in cyanobacteria, FEMS Microbiol. Lett., 323, 124, 10.1111/j.1574-6968.2011.02368.x Hadjivasiliou, 2012, Selection for mitonuclear co-adaptation could favour the evolution of two sexes, Proc. R. Soc. B, 279, 1865, 10.1098/rspb.2011.1871 Hadjivasiliou, 2013, Dynamics of mitochondrial inheritance in the evolution of binary mating types and two sexes, Proc. R. Soc. B, 280, 10.1098/rspb.2013.1920 Harold, 2014 Karnkowska, 2016, A eukaryote without a mitochondrial genome, Curr. Biol., 26, 1274, 10.1016/j.cub.2016.03.053 Keeling, 1998, A kingdom's progress: Archezoa and the origin of eukaryotes, BioEssays, 20, 87, 10.1002/(SICI)1521-1878(199801)20:1<87::AID-BIES12>3.0.CO;2-4 Knoll, 2006, Eukaryotic organisms in Proterozoic oceans, Philos. Trans. R. Soc. B., 361, 1023, 10.1098/rstb.2006.1843 Knoll, 2016, Life: the first two billion years, Philos. Trans. R. Soc. B, 371, 10.1098/rstb.2015.0493 Koonin, 2004, A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes, Genome Biol., 5, R7, 10.1186/gb-2004-5-2-r7 Koonin, 2010, The origin and early evolution of eukaryotes in the light phylogenomics, Genome Biol., 11, 209, 10.1186/gb-2010-11-5-209 Koonin, 2012 Koonin, 2015, Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier?, Philos. Trans. R. Soc. B, 370, 10.1098/rstb.2014.0333 Lane, 2002 Lane, 2005 Lane, 2011, Energetics and genetics across the prokaryote-eukaryote divide, Biol. Direct, 6, 35, 10.1186/1745-6150-6-35 Lane, 2014, Bioenergetic constraints on the evolution of complex life, Cold Spring Harbor Perspect. Biol., 6, 10.1101/cshperspect.a015982 Lane, 2015 Lane, 2010, The energetics of genome complexity, Nature, 467, 929, 10.1038/nature09486 Lane, 2015, Eukaryotes really are special, and mitochondria are why, Proc. Natl. Acad. Sci. USA, 112, E4823, 10.1073/pnas.1509237112 Lane, 2016, Mitochondria, complexity, and evolutionary deficit spending, Proc. Natl. Acad. Sci. USA, 113, E666, 10.1073/pnas.1522213113 Lindmark, 1973, Hydrogenosome, a cytoplasmic organelle of the anaerobic flagellate, Tritrichomonas foetus, and its role in pyruvate metabolism, J. Biol. Chem., 248, 7724, 10.1016/S0021-9258(19)43249-3 Lovelock, 1974, Atmospheric homeostasis by and for the biosphere: the Gaia hypothesis, Tellus, 26, 2, 10.3402/tellusa.v26i1-2.9731 Lynch, 2015, The bioenergetic costs of a gene, Proc. Natl. Acad. Sci. USA, 112, 15690, 10.1073/pnas.1514974112 Lynch, 2017, Membranes, energetics, and evolution across the prokaryote-eukaryote divide, eLife, 6, e20437, 10.7554/eLife.20437 Makarova, 2007, Evolutionary genomics of lactic acid bacteria, J. Bacteriol., 189, 1199, 10.1128/JB.01351-06 Mans, 2004, Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex, Cell Cycle, 3, 1612, 10.4161/cc.3.12.1316 Margulis, 2006, The phylogenetic tree topples, Am. Sci., 94, 194, 10.1511/2006.59.194 Margulis, 2007, Semes for analysis of evolution: de Duve's peroxysomes and Meyer's hydrogenosomes in the sulphurous Proterozoan eon, Nat. Rev. Genet., 8, 10.1038/nrg2071-c1 Margulis, 2005, Imperfections and oddities” in the origin of the nucleus, Paleobiology, 31, 175, 10.1666/0094-8373(2005)031[0175:IAOITO]2.0.CO;2 Margulis, 1997 Margulis, 2002 Martijn, 2013, From archaeon to eukaryote: the evolutionary dark ages of the eukaryotic cell, Biochem. Soc. Trans., 41, 451, 10.1042/BST20120292 Martin, 1999, Mosaic bacterial chromosomes: a challenge en route to a tree of genomes, BioEssays, 21, 99, 10.1002/(SICI)1521-1878(199902)21:2<99::AID-BIES3>3.0.CO;2-B Martin, 2006, Introns and the origin of nucleus–cytosol compartmentalization, Nature, 440, 41, 10.1038/nature04531 Martin, 1998, The hydrogen hypothesis for the first eukaryote, Nature, 392, 37, 10.1038/32096 Martin, 2016, Late mitochondrial origin is pure artefact, bioRxiv Martin, 2001, An overview of endosymbiotic models for the origins of eukaryotes, their ATP-producing organelles (mitochondria and hydrogenosomes), and their heterotrophic lifestyle, Biol. Chem., 382, 1521, 10.1515/BC.2001.187 Maynard Smith, 1995 McCutcheon, 2012, Extreme genome reduction in symbiotic bacteria, Nat. Rev. Microbiol., 10, 13, 10.1038/nrmicro2670 McCutcheon, 2011, An independent metabolic patchwork in the nested symbiosis of mealybugs, Curr. Biol., 21, 1366, 10.1016/j.cub.2011.06.051 McInerney, 2011, Planctomycetes and eukaryotes: a case of analogy not homology, BioEssays, 33, 810, 10.1002/bies.201100045 Mendell, 2008, Extreme polyploidy in a large bacterium, Proc. Natl. Acad. Sci. USA, 105, 6730, 10.1073/pnas.0707522105 Mentel, 2008, Energy metabolism among eukaryotic anaerobes in light of Proterozoic ocean chemistry, Philos. Trans. R. Soc. B., 363, 2717, 10.1098/rstb.2008.0031 Miller, 1953, A production of amino acids under possible primitive Earth conditions, Science, 117, 528, 10.1126/science.117.3046.528 Minerdi, 2002, Endosymbiotic bacteria in mycorrhizal fungi: from their morphology to genomic sequences, Plant Soil, 244, 211, 10.1023/A:1020211821753 Müller, 2012, Biochemistry and evolution of anaerobic energy metabolism in eukaryotes, Microbiol. Mol. Biol. Rev., 76, 444, 10.1128/MMBR.05024-11 Murphy, 2009, How mitochondria produce reactive oxygen species, Biochem. J., 417, 1, 10.1042/BJ20081386 Nývltová, 2015, Lateral gene transfer and gene duplication played a key role in the evolution of Mastigamoeba balamuthi hydrogenosomes, Mol. Biol. Evol., 32, 1039, 10.1093/molbev/msu408 Och, 2012, The Neoproterozoic oxygenation event: Environmental perturbations and biogeochemical cycling, Earth Sci. Rev., 110, 26, 10.1016/j.earscirev.2011.09.004 Patel, 2015, Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism, Nat. Chem., 7, 301, 10.1038/nchem.2202 Pittis, 2016, Late acquisition of mitochondria by a host with chimaeric prokaryotic ancestry, Nature, 531, 101, 10.1038/nature16941 Qiu, 2013, Assessing the bacterial contribution to the plastid proteome, Trends Plant Sci, 18, 680, 10.1016/j.tplants.2013.09.007 Radzvilavicius, 2015, Conflict and cooperation in eukaryogenesis: implications for the timing of endosymbiosis and the evolution of sex, J. R. Soc. Interface, 12, 10.1098/rsif.2015.0584 Sagan, 1967, On the origin of mitosing cells, J. Theor. Biol., 14, 225, 10.1016/0022-5193(67)90079-3 Schulz, 2006, The genus Thiomargarita, Prokaryotes, 6, 1156, 10.1007/0-387-30746-X_47 Schulz, 2001, Big bacteria, Annu. Rev. Microbiol., 55, 105, 10.1146/annurev.micro.55.1.105 Sousa, 2016, Lokiarchaeon is hydrogen dependent, Nat. Microbiol., 1, 16034, 10.1038/nmicrobiol.2016.34 Spang, 2015, Complex archaea that bridge the gap between prokaryotes and eukaryotes, Nature, 521, 173, 10.1038/nature14447 Staub, 2004, Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire, Bioessays, 26, 567, 10.1002/bies.20032 Vafai, 2012, Mitochondrial disorders as windows into an ancient organelle, Nature, 491, 374, 10.1038/nature11707 van der Giezen, 2013, Evolution: one thread to unite them all, Curr. Biol., 23, R679, 10.1016/j.cub.2013.06.048 Vellai, 1998, A new aspect to the origin and evolution of eukaryotes, J. Mol. Evol., 46, 499, 10.1007/PL00006331 von Dohlen, 2001, Mealybug beta-proteobacterial endosymbionts contain gamma-proteobacterial symbionts, Nature, 412, 433, 10.1038/35086563 Ward, 2009, Cytology of terminally differentiated Epulopiscium mother cells, DNA Cell. Biol., 28, 57, 10.1089/dna.2008.0801 Wallin, 1927 Wernegreen, 2012, Endosymbiosis, Curr. Biol., 22, R555, 10.1016/j.cub.2012.06.010 Wilson, 1925 Williams, 2013, An archaeal origin of eukaryotes supports only two primary domains of life, Nature, 504, 231, 10.1038/nature12779 Woese, 1967 Woese, 1977, Evolution phylogenetic structure of the prokaryotic domain: the primary kingdoms, Proc. Natl. Acad. Sci. USA, 74, 5088, 10.1073/pnas.74.11.5088 Wujek, 1979, Intracellular bacteria in the blue-green-alga Pleurocapsa minor, Trans. Am. Microsc. Soc., 98, 143, 10.2307/3225953 Yamaguchi, 2012, Prokaryote or eukaryote? A unique microorganism from the deep sea, J. Electron Microsc. (Tokyo)., 61, 423, 10.1093/jmicro/dfs062 Yutin, 2009, The origins of phagocytosis and eukaryogenesis, Biol. Direct, 4, 9, 10.1186/1745-6150-4-9 Zaremba-Niedzwiedzka, 2017, Asgard archaea illuminate the origin of eukaryotic cellular complexity, Nature, 10.1038/nature21031 Zouni, 2001, Crystal structure of photosystem II from Synechococcus elongatus at 3.8Å resolution, Nature, 409, 739, 10.1038/35055589 Zubacova, 2008, Comparative analysis of trichomonad genome sizes and karyotypes, Mol. Biochem. Parasitol., 161, 49, 10.1016/j.molbiopara.2008.06.004 Zuckerkandl, 1965, Molecules as documents of evolutionary history, J. Theor. Biol., 8, 357, 10.1016/0022-5193(65)90083-4