It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea. Here, I argue that these analyses are not reliable, and I critically discuss archaeal ancestor scenarios, as well as fusion scenarios for the origin of eukaryotes. Based on recognized evolutionary trends toward reduction in archaea and toward complexity in eukarya, I suggest that their last common ancestor was more complex than modern archaea but simpler than modern eukaryotes (the bug in-between scenario). I propose that the ancestors of archaea (and bacteria) escaped protoeukaryotic predators by invading high temperature biotopes, triggering their reductive evolution toward the “prokaryotic” phenotype (the thermoreduction hypothesis). Intriguingly, whereas archaea and eukarya share many basic features at the molecular level, the archaeal mobilome resembles more the bacterial than the eukaryotic one. I suggest that selection of different parts of the ancestral virosphere at the onset of the three domains played a critical role in shaping their respective biology. Eukarya probably evolved toward complexity with the help of retroviruses and large DNA viruses, whereas similar selection pressure (thermoreduction) could explain why the archaeal and bacterial mobilomes somehow resemble each other. 1. Introduction Archaea have been confused with bacteria, under the term prokaryotes, until their originality was finally recognized by 16S rRNA cataloguing [1]. Archaea were previously “hidden before our eyes”, strikingly resembling bacteria under the light and electron microscopes. Archaea and bacteria are also quite similar at the genomic level, with small circular genomes, compact gene organization, and functionally related genes organized into operons. At the same time, archaea, unlike bacteria, exhibit a lot of “eukaryotic features” at the molecular level [2–6]. It is often assumed that archaea resemble eukarya when their informational systems (DNA replication, transcription, and translation) are considered but resemble bacteria in terms of their operational systems. This is clearly not the case, since many archaeal operational systems (such as ATP production, protein secretion, cell division and vesicles formation, and protein modification machinery) also use proteins that have only eukaryotic homologues or that are more similar to their eukaryotic rather than to their bacterial homologues [7–14]. The bacterial-like features of some archaeal metabolic pathways could be mostly due to lateral gene
References
[1]
C. R. Woese and G. E. Fox, “Phylogenetic structure of the prokaryotic domain: the primary kingdoms,” Proceedings of the National Academy of Sciences of the United States of America, vol. 74, no. 11, pp. 5088–5090, 1977.
[2]
W. Zillig, “Comparative biochemistry of Archaea and Bacteria,” Current Opinion in Genetics & Development, vol. 1, no. 4, pp. 544–551, 1991.
[3]
G. Olsen and C. R. Woese, “Archaeal genomics: an overview,” Cell, vol. 89, no. 7, pp. 991–994, 1997.
[4]
P. Forterre, “Archaea: what can we learn from their sequences?” Current Opinion in Genetics and Development, vol. 7, no. 6, pp. 764–770, 1997.
[5]
R. Garrett and H. P. Klenk, Archaea, Blackwell, Oxford, UK, 2007.
[6]
C. Brochier-Armanet, P. Forterre, and S. Gribaldo, “Phylogeny and evolution of the Archaea: one hundred genomes later,” Current Opinion in Microbiology, vol. 14, no. 3, pp. 274–281, 2011.
[7]
G. Grüber and V. Marshansky, “New insights into structure-function relationships between archeal ATP synthase (A1A0) and vacuolar type ATPase (V1V0),” BioEssays, vol. 30, no. 11-12, pp. 1096–1109, 2008.
[8]
B. Van den Berg, W. M. Clemons Jr., I. Collinson et al., “X-ray structure of a protein-conducting channel,” Nature, vol. 427, no. 6969, pp. 36–44, 2004.
[9]
X. Wang and J. Lutkenhaus, “FtsZ ring: the eubacterial division apparatus conserved in archaebacteria,” Molecular Microbiology, vol. 21, no. 2, pp. 313–319, 1996.
[10]
E. Gérard, B. Labedan, and P. Forterre, “Isolation of a minD-like gene in the hyperthermophilic archaeon pyrococcus AL585, and phylogenetic characterization of related proteins in the three domains of life,” Gene, vol. 222, no. 1, pp. 99–106, 1998.
[11]
K. S. Makarova, N. Yutin, S. D. Bell, and E. V. Koonin, “Evolution of diverse cell division and vesicle formation systems in Archaea,” Nature Reviews Microbiology, vol. 8, no. 10, pp. 731–741, 2010.
[12]
N. Yutin, M. Y. Wolf, Y. I. Wolf, and E. V. Koonin, “The origins of phagocytosis and eukaryogenesis,” Biology Direct, vol. 4, p. 9, 2009.
[13]
N. Yutin and E. V. Koonin, “Archaeal origin of tubulin,” Biology Direct, vol. 7, p. 10, 2012.
[14]
T. Nunoura, Y. Takaki, J. Kakuta et al., “Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group,” Nucleic Acids Research, vol. 39, no. 8, pp. 3204–3223, 2011.
[15]
F. M. Cohan and A. F. Koeppel, “The origins of ecological diversity in prokaryotes,” Current Biology, vol. 18, no. 21, pp. R1024–R1034, 2008.
[16]
J. Armengaud, B. Fernandez, V. Chaumont et al., “Identification, purification, and characterization of an eukaryotic-like phosphopantetheine adenylyltransferase (coenzyme A biosynthetic pathway) in the hyperthermophilic archaeon Pyrococcus abyssi,” Journal of Biological Chemistry, vol. 278, no. 33, pp. 31078–31087, 2003.
[17]
T. Sato and H. Atomi, “Novel metabolic pathways in Archaea,” Current Opinion in Microbiology, vol. 14, no. 3, pp. 307–314, 2011.
[18]
J. Lombard, P. López-García, and D. Moreira, “Phylogenomic investigation of phospholipid synthesis in archaea,” Archaea, vol. 2012, Article ID 630910, 13 pages, 2012.
[19]
C. Brochier-Armanet, S. Gribaldo, and P. Forterre, “A DNA topoisomerase IB in Thaumarchaeota testifies for the presence of this enzyme in the last common ancestor of Archaea and Eucarya,” Biology Direct, vol. 3, p. 54, 2008.
[20]
E. V. Koonin, “The origin and early evolution of eukaryotes in the light of phylogenomics,” Genome Biology, vol. 11, no. 5, p. 209, 2010.
[21]
J. Martijn and T. J. Ettema, “From archaeon to eukaryote: the evolutionary dark ages of the eukaryotic cell,” Biochemical Society Transactions, vol. 41, no. 1, pp. 451–457, 2013.
[22]
J. Lombard, P. López-García, and D. Moreira, “The early evolution of lipid membranes and the three domains of life,” Nature Reviews Microbiology, vol. 10, no. 7, pp. 507–515, 2012.
[23]
E. V. Koonin and Y. I. Wolf, “Evolution of microbes and viruses: a paradigm shift in evolutionary biology?” Frontiers in Cellular and Infection Microbiology, vol. 2, p. 119, 2012.
[24]
M. Pina, A. Bize, P. Forterre, and D. Prangishvili, “The archeoviruses,” FEMS Microbiology Reviews, vol. 35, no. 6, pp. 1035–1054, 2011.
[25]
M. Krupovic, D. Prangishvili, R. W. Hendrix, and D. H. Bamford, “Genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere,” Microbiology and Molecular Biology Reviews, vol. 75, no. 4, pp. 610–635, 2011.
[26]
N. G. Abrescia, D. H. Bamford, J. M. Grimes, and D. I. Stuart, “Structure unifies the viral universe,” Annual Review of Biochemistry, vol. 81, pp. 795–822, 2012.
[27]
M. Krupovi？, P. Forterre, and D. H. Bamford, “Comparative analysis of the mosaic genomes of tailed archaeal viruses and proviruses suggests common themes for virion architecture and assembly with tailed viruses of bacteria,” Journal of Molecular Biology, vol. 397, no. 1, pp. 144–160, 2010.
[28]
N. S. Atanasova, E. Roine, A. Oren, D. H. Bamford, and H. M. Oksanen, “Global network of specific virus-host interactions in hypersaline environments,” Environmental Microbiology, vol. 14, no. 2, pp. 426–440, 2012.
[29]
M. Krupovic, A. Spang, S. Gribaldo, P. Forterre, and C. Schleper, “A thaumarchaeal provirus testifies for an ancient association of tailed viruses with archaea,” Biochemical Society Transactions, vol. 39, no. 1, pp. 82–88, 2011.
[30]
M. K. Pietil？, N. S. Atanasova, V. Manole et al., “Virion architecture unifies globally distributed pleolipoviruses infecting halophilic archaea,” Journal of Virology, vol. 86, no. 9, pp. 5067–5079, 2012.
[31]
J. Filée, P. Siguier, and M. Chandler, “Insertion sequence diversity in archaea,” Microbiology and Molecular Biology Reviews, vol. 71, no. 1, pp. 121–157, 2007.
[32]
N. Soler, M. Gaudin, E. Marguet, and P. Forterre, “Plasmids, viruses and virus-like membrane vesicles from Thermococcales,” Biochemical Society Transactions, vol. 39, no. 1, pp. 36–44, 2011.
[33]
M. Krupovic, M. Gonnet, W. B. Hania, P. Forterre, and G. Erauso, “Insights into dynamics of mobile genetic elements in hyperthermophilic environments from five new Thermococcus plasmids,” PLoS One, vol. 8, no. 1, Article ID e49044, 2013.
[34]
B. O. Greve, S. Jensen, K. Brügger, W. Zillig, and R. A. Garrett, “Genomic comparison of archaeal conjugative plasmids from Sulfolobus,” Archaea, vol. 1, no. 4, pp. 231–239, 2004.
[35]
B. Greve, S. Jensen, H. Phan et al., “Novel RepA-MCM proteins encoded in plasmids pTAU4, pORA1 and pTIK4 from Sulfolobus neozealandicus,” Archaea, vol. 1, no. 5, pp. 319–325, 2005.
[36]
D. Cortez, S. Quevillon-Cheruel, S. Gribaldo et al., “Evidence for a Xer/dif system for chromosome resolution in archaea,” PLoS Genetics, vol. 6, no. 10, Article ID e1001166, 2010.
[37]
N. Soler, A. Justome, S. Quevillon-Cheruel et al., “The rolling-circle plasmid pTN1 from the hyperthermophilic archaeon Thermococcus nautilus,” Molecular Microbiology, vol. 66, no. 2, pp. 357–370, 2007.
[38]
P. Forterre, “Evolution, viral,” in Encyclopedia of Microbiology, M. Schaechter, Ed., pp. 370–389, Elsevier, New York, NY, USA, 3rd edition, 2009.
[39]
A. K. Kalliomaa-Sanford, F. A. Rodriguez-Casta？eda, B. N. McLeod et al., “Chromosome segregation in Archaea mediated by a hybrid DNA partition machine,” Proceedings of the National Academy of Sciences of the United States of America, vol. 109, no. 10, pp. 3754–3579, 2012.
[40]
P. Forterre, “Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: a hypothesis for the origin of cellular domain,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 10, pp. 3669–3674, 2006.
[41]
R. Sorek, C. M. Lawrence, and B. Wiedenheft, “CRISPR-mediated adaptive immune systems in Bacteria and Archaea,” Annual Review of Biochemistry, vol. 82, pp. 237–266, 2013.
[42]
K. S. Makarova, Y. I. Wolf, and E. V. Koonin, “Comparative genomics of defense systems in archaea and bacteria,” Nucleic Acids Research, vol. 41, no. 8, pp. 4360–4377, 2013.
[43]
K. S. Makarova, Y. I. Wolf, J. van der Oost, and E. V. Koonin, “Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements,” Biology Direct, vol. 4, p. 29, 2009.
[44]
A. M. Poole and D. Penny, “Evaluating hypotheses for the origin of eukaryotes,” BioEssays, vol. 29, no. 1, pp. 74–84, 2007.
[45]
S. Gribaldo, A. M. Poole, V. Daubin, P. Forterre, and C. Brochier-Armanet, “The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?” Nature Reviews Microbiology, vol. 8, no. 10, pp. 743–752, 2010.
[46]
P. Forterre, “A new fusion hypothesis for the origin of Eukarya: better than previous ones, but probably also wrong,” Research in Microbiology, vol. 162, no. 1, pp. 77–91, 2011.
[47]
N. Yutin, K. S. Makarova, S. L. Mekhedov, Y. I. Wolf, and E. V. Koonin, “The deep archaeal roots of eukaryotes,” Molecular Biology and Evolution, vol. 25, no. 8, pp. 1619–1630, 2008.
[48]
P. López-Gar？ia and D. Moreira, “Metabolic symbiosis at the origin of eukaryotes,” Trends in Biochemical Sciences, vol. 24, no. 3, pp. 88–93, 1999.
[49]
W. Martin and M. Müller, “The hydrogen hypothesis for the first eukaryote,” Nature, vol. 392, no. 6671, pp. 37–41, 1998.
[50]
C. G. Kurland, L. J. Collins, and D. Penny, “Genomics and the irreducible nature of eukaryote cells,” Science, vol. 312, no. 5776, pp. 1011–1014, 2006.
[51]
C. De Duve, “The origin of eukaryotes: a reappraisal,” Nature Reviews Genetics, vol. 8, no. 5, pp. 395–403, 2007.
[52]
T. Cavalier-Smith, “Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution,” Biology Direct, vol. 5, p. 7, 2010.
[53]
C. R. Woese, O. Kandler, and M. L. Wheelis, “Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya,” Proceedings of the National Academy of Sciences of the United States of America, vol. 87, no. 12, pp. 4576–4579, 1990.
[54]
B. El Yacoubi, I. Hatin, C. Deutsch et al., “Role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification,” EMBO Journal, vol. 30, no. 5, pp. 882–893, 2011.
[55]
C. J. Cox, P. G. Foster, R. P. Hirt, S. R. Harris, and T. M. Embley, “The archaebacterial origin of eukaryotes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 51, pp. 20356–20361, 2008.
[56]
A. Hecker, N. Leulliot, D. Gadelle et al., “An archaeal orthologue of the universal protein Kae1 is an iron metalloprotein which exhibits atypical DNA-binding properties and apurinic-endonuclease activity in vitro,” Nucleic Acids Research, vol. 35, no. 18, pp. 6042–6051, 2007.
[57]
A. M. Poole and N. Neumann, “Reconciling an archaeal origin of eukaryotes with engulfment: a biologically plausible update of the Eocyte hypothesis,” Research in Microbiology, vol. 162, no. 1, pp. 71–76, 2011.
[58]
P. G. Foster, C. J. Cox, and T. Martin Embley, “The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods,” Philosophical Transactions of the Royal Society B, vol. 364, no. 1527, pp. 2197–2207, 2009.
[59]
L. Guy and T. J. G. Ettema, “The archaeal 'TACK' superphylum and the origin of eukaryotes,” Trends in Microbiology, vol. 19, no. 12, pp. 580–587, 2011.
[60]
T. A. Williams, P. G. Foster, T. M. Nye, C. J. Cox, and T. M. Embley, “A congruent phylogenomic signal places eukaryotes within the Archaea,” Proceedings of the Royal Society B, vol. 279, no. 1749, pp. 4870–4879, 2012.
[61]
J. A. Lake, E. Henderson, M. Oakes, and M. W. Clark, “Eocytes: a new ribosome structure indicates a kingdom with a close relationship to eukaryotes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 81, no. 12, pp. 3786–3790, 1984.
[62]
C. P. Vivarès, M. Gouy, T. Thomarat, and G. Méténier, “Functional and evolutionary analysis of a eukaryotic parasitic genome,” Current Opinion in Microbiology, vol. 5, no. 5, pp. 499–505, 2002.
[63]
B. A. Curtis, G. Tanifuji, F. Burki et al., “Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs,” Nature, vol. 492, no. 7427, pp. 59–65, 2012.
[64]
U. Jahn, R. Summons, H. Sturt, E. Grosjean, and H. Huber, “Composition of the lipids of Nanoarchaeum equitans and their origin from its host Ignicoccus sp. strain KIN4/I,” Archives of Microbiology, vol. 182, no. 5, pp. 404–413, 2004.
[65]
P. Forterre, “The virocell concept and environmental microbiology,” The ISME Journal, vol. 7, no. 2, pp. 233–236, 2013.
[66]
S. Nelson-Sathi, T. Dagan, G. Landan et al., “Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea,” Proceedings of the National Academy of Sciences of the United States of America, vol. 109, no. 50, pp. 20537–20542, 2012.
[67]
P. López-García and D. Moreira, “Selective forces for the origin of the eukaryotic nucleus,” BioEssays, vol. 28, no. 5, pp. 525–533, 2006.
[68]
W. Martin and E. V. Koonin, “Introns and the origin of nucleus-cytosol compartmentalization,” Nature, vol. 440, no. 7080, pp. 41–45, 2006.
[69]
G. Jékely, “Origin of the nucleus and Ran-dependent transport to safeguard ribosome biogenesis in a chimeric cell,” Biology Direct, vol. 3, p. 31, 2008.
[70]
C. R. Woese, “Interpreting the universal phylogenetic tree,” Proceedings of the National Academy of Sciences of the United States of America, vol. 97, no. 15, pp. 8392–8396, 2000.
[71]
O. Matte-Tailliez, C. Brochier, P. Forterre, and H. Philippe, “Archaeal phylogeny based on ribosomal proteins,” Molecular Biology and Evolution, vol. 19, no. 5, pp. 631–639, 2002.
[72]
H. Philippe and P. Forterre, “The rooting of the universal tree of life is not reliable,” Journal of Molecular Evolution, vol. 49, no. 4, pp. 509–523, 1999.
[73]
L. P. Villarreal and V. R. DeFilippis, “A hypothesis for DNA viruses as the origin of eukaryotic replication proteins,” Journal of Virology, vol. 74, no. 15, pp. 7079–7084, 2000.
[74]
P. Forterre, “Giant viruses: conflicts in revisiting the virus concept,” Intervirology, vol. 53, no. 5, pp. 362–378, 2010.
[75]
L. G. Pühler, H. Leffers, F. Gropp et al., “Archaebacterial DNA-dependent RNA polymerase testify to the evolution of the eukaryotic nuclear genome,” Proceedings of the National Academy of Sciences of the United States of America, vol. 86, no. 12, pp. 4569–4573, 1989.
[76]
E. Lasek-Nesselquist and J. P. Gogarten, “The effects of model choice and mitigating bias on the ribosomal tree of life,” Molecular Phylogenetics and Evolution, vol. 69, no. 1, pp. 17–38, 2013.
[77]
P. Forterre, “Thermoreduction, a hypothesis for the origin of prokaryotes,” Comptes Rendus de l'Academie des Sciences, vol. 318, no. 4, pp. 415–422, 1995.
[78]
D. Raoult, S. Audic, C. Robert et al., “The 1.2-megabase genome sequence of Mimivirus,” Science, vol. 306, no. 5700, pp. 1344–1350, 2004.
[79]
T. A. Williams, T. M. Embley, and E. Heinz, “Informational gene phylogenies do not support a fourth domain of life for nucleocytoplasmic large DNA viruses,” PLoS One, vol. 6, no. 6, Article ID e21080, 2011.
[80]
B. Boussau, S. Blanquart, A. Necsulea, N. Lartillot, and M. Gouy, “Parallel adaptations to high temperatures in the Archaean eon,” Nature, vol. 456, no. 7224, pp. 942–945, 2008.
[81]
M. Groussin and M. Gouy, “Adaptation to environmental temperature is a major determinant of molecular evolutionary rates in archaea,” Molecular Biology and Evolution, vol. 28, no. 9, pp. 2661–2674, 2011.
[82]
C. Brochier-Armanet, B. Boussau, S. Gribaldo, and P. Forterre, “Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota,” Nature Reviews Microbiology, vol. 6, no. 3, pp. 245–252, 2008.
[83]
C. O. Lovejoy, “Reexamining human origins in light of Ardipithecus ramidus,” Science, vol. 326, no. 5949, pp. 74e2–74e8, 2009.
[84]
Y. I. Wolf and E. V. Koonin, “Genome reduction as the dominant mode of evolution,” Bioessays, vol. 35, no. 9, pp. 829–837, 2013.
[85]
Y. I. Wolf, K. S. Makarova, N. Yutin, and E. V. Koonin, “Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer,” Biology Direct, vol. 7, p. 46, 2012.
[86]
M. Csur？s and I. Miklós, “Streamlining and large ancestral genomes in Archaea inferred with a phylogenetic birth-and-death model,” Molecular Biology and Evolution, vol. 26, no. 9, pp. 2087–2095, 2009.
[87]
O. Lecompte, R. Ripp, J. Thierry, D. Moras, and O. Poch, “Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale,” Nucleic Acids Research, vol. 30, no. 24, pp. 5382–5390, 2002.
[88]
E. Desmond, C. Brochier-Armanet, P. Forterre, and S. Gribaldo, “On the last common ancestor and early evolution of eukaryotes: reconstructing the history of mitochondrial ribosomes,” Research in Microbiology, vol. 162, no. 1, pp. 53–70, 2011.
[89]
M. Wang, C. G. Kurland, and Caetano-Anollés, “Reductive evolution of proteomes and protein structures,” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 29, pp. 11954–11958, 2011.
[90]
A. Nasir, K. M. Kim, and G. Caetano-Anolles, “Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya,” BMC Evolutionary Biology, vol. 12, p. 156, 2012.
[91]
A. Harish, A. Tunlid, and G. C. Kurland, “Rooted phylogeny of the three superkingdoms,” Biochimie, vol. 95, no. 8, pp. 1593–1604, 2013.
[92]
M. Carlile, “Prokaryotes and eukaryotes: strategies and successes,” Trends in Biochemical Sciences, vol. 7, no. 4, pp. 128–130, 1982.
[93]
E. R. Angert, “DNA replication and genomic architecture of very large bacteria,” Annual Review of Microbiology, vol. 66, pp. 197–212, 2012.
[94]
I. B. Rogozin, L. Carmel, M. Csuros, and E. V. Koonin, “Origin and evolution of spliceosomal introns,” Biology Direct, vol. 7, p. 11, 2012.
[95]
B. Dujon, “Yeast evolutionary genomics,” Nature Reviews Genetics, vol. 1, no. 7, pp. 512–524, 2010.
[96]
K. O. Stetter, “A brief history of the discovery of hyperthermophilic life,” Biochemical Society Transactions, vol. 41, no. 1, pp. 416–420, 2013.
[97]
P. Forterre, “A hot topic: the origin of hyperthermophiles,” Cell, vol. 85, no. 6, pp. 789–792, 1996.
[98]
N. Glansdorff, Y. Xu, and B. Labedan, “The last universal common ancestor: emergence, constitution and genetic legacy of an elusive forerunner,” Biology Direct, vol. 3, p. 29, 2008.
[99]
N. Glansdorff, Y. Xu, and B. Labedan, “The origin of life and the last universal common ancestor: do we need a change of perspective?” Research in Microbiology, vol. 160, no. 7, pp. 522–528, 2009.
[100]
Y. Koga, “Thermal adaptation of the archaeal and bacterial lipid membranes,” Archaea, vol. 2012, Article ID 789652, 6 pages, 2012.
[101]
T. D. Brock, “Life at high températures,” Science, vol. 158, no. 3804, pp. 1012–1019, 1967.
[102]
J. F. De Jonckheere, M. Baumgartner, S. Eberhardt, F. R. Opperdoes, and K. O. Stetter, “Oramoeba fumarolia gen. nov., sp. nov., a new marine heterolobosean amoeboflagellate growing at 54°C,” European Journal of Protistology, vol. 47, no. 1, pp. 16–23, 2011.
[103]
B. Bolduc, D. P. Shaughnessy, Y. I. Wolf, E. V. Koonin, F. F. Roberto, and M. Young, “Identification of novel positive-strand RNA viruses by metagenomic analysis of archaea-dominated Yellowstone hot Springs,” Journal of Virology, vol. 86, no. 10, pp. 5562–5573, 2012.
[104]
E. V. Koonin, “The incredible expanding ancestor of eukaryotes,” Cell, vol. 140, no. 5, pp. 606–608, 2010.
[105]
N. Lane and W. Martin, “The energetics of genome complexity,” Nature, vol. 467, no. 7318, pp. 929–934, 2010.
[106]
P. Forterre and S. Gribaldo, “Bacteria with a eukaryotic touch: a glimpse of ancient evolution?” Proceedings of the National Academy of Sciences of the United States of America, vol. 107, no. 29, pp. 12739–12740, 2010.
[107]
M. Krupovi？, S. Gribaldo, D. H. Bamford, and P. Forterre, “The evolutionary history of archaeal MCM helicases: a case study of vertical evolution combined with Hitchhiking of mobile genetic elements,” Molecular Biology and Evolution, vol. 27, no. 12, pp. 2716–2732, 2010.
[108]
J. Filée, P. Forterre, T. Sen-Lin, and J. Laurent, “Evolution of DNA polymerase families: evidences for multiple gene exchange between cellular and viral proteins,” Journal of Molecular Evolution, vol. 54, no. 6, pp. 763–773, 2002.
[109]
E. V. Koonin and N. Yutin, “Origin and evolution of eukaryotic large nucleo-cytoplasmic DNA viruses,” Intervirology, vol. 53, no. 5, pp. 284–292, 2010.
[110]
J. M. Cock, L. Sterck, P. Rouzé et al., “The Ectocarpus genome and the independent evolution of multicellularity in brown algae,” Nature, vol. 465, no. 7298, pp. 617–621, 2010.
[111]
H. Ogata and J. Claverie, “Unique genes in giant viruses: regular substitution pattern and anomalously short size,” Genome Research, vol. 17, no. 9, pp. 1353–1361, 2007.
[112]
A. Dupressoir, C. Lavialle, and T. Heidmann, “From ancestral infectious retroviruses to bona fide cellular genes: role of the captured syncytins in placentation,” Placenta, vol. 33, no. 9, pp. 663–671, 2012.
[113]
A. C. Esser, N. Ahmadinejad, C. Wiegand et al., “A genome phylogeny for mitochondria among α-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes,” Molecular Biology and Evolution, vol. 21, no. 9, pp. 1643–1660, 2004.
[114]
M. C. Rivera and J. A. Lake, “The ring of life provides evidence for a genome fusion origin of eukaryotes,” Nature, vol. 431, no. 7005, pp. 152–155, 2004.
[115]
D. Pisani, J. A. Cotton, and J. O. McInerney, “Supertrees disentangle the chimerical origin of eukaryotic genomes,” Molecular Biology and Evolution, vol. 24, no. 8, pp. 1752–1760, 2007.
[116]
T. Thiergart, G. Landan, M. Schenk, T. Dagan, and W. F. Martin, “An evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin,” Genome Biology and Evolution, vol. 4, no. 4, pp. 466–485, 2012.
[117]
D. Alvarez-Ponce, P. Lopez, E. Bapteste, and J. O. McInerney, “Gene similarity networks provide tools for understanding eukaryote origins and évolution,” Proceedings of the National Academy of Sciences of the United States of America, vol. 110, no. 7, pp. 1594–1603, 2013.
[118]
W. F. Doolittle, “You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes,” Trends in Genetics, vol. 14, no. 8, pp. 307–311, 1998.
[119]
J. Filée and M. Chandler, “Convergent mechanisms of genome evolution of large and giant DNA viruses,” Research in Microbiology, vol. 159, no. 5, pp. 325–331, 2008.
[120]
P. Forterre and D. Prangishvili, “The great billion-year war between ribosome- and capsid-encoding organisms (cells and viruses) as the major source of evolutionary novelties,” Annals of the New York Academy of Sciences, vol. 1178, pp. 65–77, 2009.
[121]
E. V. Koonin and B. Moss, “Viruses know more than one way to don a cap,” Proceedings of the National Academy of Sciences of the United States of America, vol. 107, no. 8, pp. 3283–3284, 2010.
[122]
I. R. Arkhipova, M. A. Batzer, J. Brosius et al., “Genomic impact of eukaryotic transposable elements,” Mobile DNA, vol. 3, no. 1, p. 19, 2012.
[123]
E. A. Gladyshev and I. R. Arkhipova, “Telomere-associated endonuclease-deficient Penelope-like retroelements in diverse eukaryotes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 22, pp. 9352–9357, 2007.
[124]
I. R. Arkhipova, “Distribution and phylogeny of penelope-like elements in eukaryotes,” Systematic Biology, vol. 55, no. 6, pp. 875–885, 2006.
[125]
M. F. Singer, “Unusual reverse transcriptases,” Journal of Biological Chemistry, vol. 270, no. 42, pp. 24623–24626, 1995.
[126]
A. C. Chueh, E. L. Northrop, K. H. Brettingham-Moore, K. H. A. Choo, and L. H. Wong, “LINE retrotransposon RNA is an essential structural and functional epigenetic component of a core neocentromeric chromatin,” PLoS Genetics, vol. 5, no. 1, Article ID e1000354, 2009.
[127]
C. I. Bandea, “A unifyed scenario on the origin and évolution of cellular and viral domains,” Nature Preceedings, 2009, http://precedings.nature.com/.
[128]
S. Miller and J. Krijnse-Locker, “Modification of intracellular membrane structures for virus replication,” Nature Reviews Microbiology, vol. 6, no. 5, pp. 363–374, 2008.
[129]
M. Suzan-Monti, B. La Scola, L. Barrassi, L. Espinosa, and D. Raoult, “Ultrastructural characterization of the giant volcano-like virus factory of Acanthamoeba polyphaga Mimivirus,” PLoS One, vol. 2, no. 3, Article ID e328, 2007.
[130]
T. Cavalier-Smith, “Intron phylogeny: a new hypothesis,” Trends in Genetics, vol. 7, no. 5, pp. 145–148, 1991.
[131]
C. E. Lane, K. Van Den Heuvel, C. Kozera et al., “Nucleomorph genome of Hemiselmis andersenii reveals complete intron loss and compaction as a driver of protein structure and function,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 50, pp. 19908–19913, 2007.
[132]
D. H. Bamford, “Do viruses form lineages across different domains of life?” Research in Microbiology, vol. 154, no. 4, pp. 231–236, 2003.
[133]
P. Forterre and M. Krupovic, “The origin of virions and virocells: the escape hypothesis revisited,” in Viruses: Essential Agents of Life, G. Witzany, Ed., pp. 43–60, Springer Science+Business Media, Dordrecht, The Netherlands, 2012.
[134]
P. Forterre and H. Philippe, “Where is the root of the tree of life,” Bioessays, vol. 21, no. 10, pp. 871–879, 1999.
[135]
P. Forterre, “The universal tree of life and the Last Universal Cellular Ancestor (LUCA): revolution and counter-revolutions,” in Evolutionary Genomics and Systems Biology, Caetano-Anollés, Ed., pp. 43–62, 2010.
[136]
C. R. Woese and G. E. Fox, “The concept of cellular évolution,” Journal of Molecular Evolution, vol. 10, no. 1, pp. 1–6, 1977.
[137]
P. Forterre, “The origin of DNA genomes and DNA replication proteins,” Current Opinion in Microbiology, vol. 5, no. 5, pp. 525–532, 2002.
[138]
J. Berthon, R. Fujikane, and P. Forterre, “When DNA replication and protein synthesis come together,” Trends in Biochemical Sciences, vol. 34, no. 9, pp. 429–434, 2009.
[139]
C. Cayrou, B. Henrissat, P. Gouret, P. Pontarotti, and M. Drancourt, “Peptidoglycan: a post-genomic analysis,” BMC Microbiology, vol. 12, p. 294, 2012.
[140]
M. Jalasvuori and J. K. H. Bamford, “Structural co-evolution of viruses and cells in the primordial world,” Origins of Life and Evolution of Biospheres, vol. 38, no. 2, pp. 165–181, 2008.
[141]
D. Prangishvili, “The wonderful world of archaeal viruses,” Annual Review of Microbiology, vol. 67, pp. 565–585, 2013.
[142]
P. Forterre and D. Prangishvili, “The major role of viruses in cellular evolution: facts and hypotheses,” Current Opinion in Virology, 2013.
[143]
T. E. F. Quax, S. Lucas, J. Reimann et al., “Simple and elegant design of a virion egress structure in Archaea,” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 8, pp. 3354–3359, 2011.
[144]
P. Forterre, “A hot story from comparative genomics: reverse gyrase is the only hyperthermophile-specific protein,” Trends in Genetics, vol. 18, no. 5, pp. 236–238, 2002.
[145]
C. Brochier-Armanet and P. Forterre, “Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers,” Archaea, vol. 2, no. 2, pp. 83–93, 2007.
[146]
P. Forterre and D. Gadelle, “Phylogenomics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms,” Nucleic Acids Research, vol. 37, no. 3, pp. 679–692, 2009.
[147]
D. L. Valentine, “Adaptations to energy stress dictate the ecology and evolution of the Archaea,” Nature Reviews Microbiology, vol. 5, no. 4, pp. 316–323, 2007.
[148]
P. Forterre, S. Gribaldo, D. Gadelle, and M. Serre, “Origin and evolution of DNA topoisomerases,” Biochimie, vol. 89, no. 4, pp. 427–446, 2007.
[149]
N. R. Pace, “Time for a change,” Nature, vol. 441, no. 7091, p. 289, 2006.
[150]
P. Forterre, “Neutral terms,” Nature, vol. 335, p. 305, 1992.
