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Archaea
Volume 2013, Article ID 372396, 18 pages
http://dx.doi.org/10.1155/2013/372396
Review Article

The Common Ancestor of Archaea and Eukarya Was Not an Archaeon

1Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France
2Université Paris-Sud, Institut de Génétique et Microbiologie, CNRS UMR 8621, 91405 Orsay Cedex, France

Received 22 July 2013; Accepted 24 September 2013

Academic Editor: Gustavo Caetano-Anollés

Copyright © 2013 Patrick Forterre. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked 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. View at Google Scholar · View at Scopus
  2. W. Zillig, “Comparative biochemistry of Archaea and Bacteria,” Current Opinion in Genetics & Development, vol. 1, no. 4, pp. 544–551, 1991. View at Publisher · View at Google Scholar
  3. G. Olsen and C. R. Woese, “Archaeal genomics: an overview,” Cell, vol. 89, no. 7, pp. 991–994, 1997. View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  13. N. Yutin and E. V. Koonin, “Archaeal origin of tubulin,” Biology Direct, vol. 7, p. 10, 2012. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  17. T. Sato and H. Atomi, “Novel metabolic pathways in Archaea,” Current Opinion in Microbiology, vol. 14, no. 3, pp. 307–314, 2011. View at Publisher · View at Google Scholar
  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. View at Publisher · View at Google Scholar
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar
  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. View at Google Scholar
  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. View at Google Scholar
  24. M. Pina, A. Bize, P. Forterre, and D. Prangishvili, “The archeoviruses,” FEMS Microbiology Reviews, vol. 35, no. 6, pp. 1035–1054, 2011. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar
  27. M. Krupovič, 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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  30. M. K. Pietilä, 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. View at Google Scholar
  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. View at Publisher · View at Google Scholar
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar
  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. View at Google Scholar · View at Scopus
  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. View at Google Scholar · View at Scopus
  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. View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  38. P. Forterre, “Evolution, viral,” in Encyclopedia of Microbiology, M. Schaechter, Ed., pp. 370–389, Elsevier, New York, NY, USA, 3rd edition, 2009. View at Google Scholar
  39. A. K. Kalliomaa-Sanford, F. A. Rodriguez-Castañeda, 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. View at Publisher · View at Google Scholar
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar
  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. View at Publisher · View at Google Scholar
  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. View at Publisher · View at Google Scholar · View at Scopus
  44. A. M. Poole and D. Penny, “Evaluating hypotheses for the origin of eukaryotes,” BioEssays, vol. 29, no. 1, pp. 74–84, 2007. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  48. P. López-Garćia and D. Moreira, “Metabolic symbiosis at the origin of eukaryotes,” Trends in Biochemical Sciences, vol. 24, no. 3, pp. 88–93, 1999. View at Publisher · View at Google Scholar
  49. W. Martin and M. Müller, “The hydrogen hypothesis for the first eukaryote,” Nature, vol. 392, no. 6671, pp. 37–41, 1998. View at Google Scholar
  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. View at Publisher · View at Google Scholar · View at Scopus
  51. C. De Duve, “The origin of eukaryotes: a reappraisal,” Nature Reviews Genetics, vol. 8, no. 5, pp. 395–403, 2007. View at Publisher · View at Google Scholar
  52. T. Cavalier-Smith, “Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution,” Biology Direct, vol. 5, p. 7, 2010. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar
  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. View at Publisher · View at Google Scholar
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar
  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. View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar
  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. View at Google Scholar
  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. View at Publisher · View at Google Scholar · View at Scopus
  65. P. Forterre, “The virocell concept and environmental microbiology,” The ISME Journal, vol. 7, no. 2, pp. 233–236, 2013. View at Publisher · View at Google Scholar
  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. View at Publisher · View at Google Scholar
  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. View at Publisher · View at Google Scholar · View at Scopus
  68. W. Martin and E. V. Koonin, “Introns and the origin of nucleus-cytosol compartmentalization,” Nature, vol. 440, no. 7080, pp. 41–45, 2006. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar
  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. View at Publisher · View at Google Scholar · View at Scopus
  74. P. Forterre, “Giant viruses: conflicts in revisiting the virus concept,” Intervirology, vol. 53, no. 5, pp. 362–378, 2010. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar
  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. View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  83. C. O. Lovejoy, “Reexamining human origins in light of Ardipithecus ramidus,” Science, vol. 326, no. 5949, pp. 74e2–74e8, 2009. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar
  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. View at Publisher · View at Google Scholar
  86. M. Csurös 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. View at Publisher · View at Google Scholar
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Google Scholar
  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. View at Publisher · View at Google Scholar
  91. A. Harish, A. Tunlid, and G. C. Kurland, “Rooted phylogeny of the three superkingdoms,” Biochimie, vol. 95, no. 8, pp. 1593–1604, 2013. View at Publisher · View at Google Scholar
  92. M. Carlile, “Prokaryotes and eukaryotes: strategies and successes,” Trends in Biochemical Sciences, vol. 7, no. 4, pp. 128–130, 1982. View at Google Scholar · View at Scopus
  93. E. R. Angert, “DNA replication and genomic architecture of very large bacteria,” Annual Review of Microbiology, vol. 66, pp. 197–212, 2012. View at Google Scholar
  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. View at Publisher · View at Google Scholar · View at Scopus
  95. B. Dujon, “Yeast evolutionary genomics,” Nature Reviews Genetics, vol. 1, no. 7, pp. 512–524, 2010. View at Google Scholar
  96. K. O. Stetter, “A brief history of the discovery of hyperthermophilic life,” Biochemical Society Transactions, vol. 41, no. 1, pp. 416–420, 2013. View at Publisher · View at Google Scholar
  97. P. Forterre, “A hot topic: the origin of hyperthermophiles,” Cell, vol. 85, no. 6, pp. 789–792, 1996. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  100. Y. Koga, “Thermal adaptation of the archaeal and bacterial lipid membranes,” Archaea, vol. 2012, Article ID 789652, 6 pages, 2012. View at Publisher · View at Google Scholar
  101. T. D. Brock, “Life at high températures,” Science, vol. 158, no. 3804, pp. 1012–1019, 1967. View at Google Scholar
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Google Scholar
  104. E. V. Koonin, “The incredible expanding ancestor of eukaryotes,” Cell, vol. 140, no. 5, pp. 606–608, 2010. View at Publisher · View at Google Scholar · View at Scopus
  105. N. Lane and W. Martin, “The energetics of genome complexity,” Nature, vol. 467, no. 7318, pp. 929–934, 2010. View at Publisher · View at Google Scholar
  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. View at Publisher · View at Google Scholar · View at Scopus
  107. M. Krupovič, 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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar
  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. View at Google Scholar
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar
  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. View at Publisher · View at Google Scholar
  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. View at Publisher · View at Google Scholar · View at Scopus
  124. I. R. Arkhipova, “Distribution and phylogeny of penelope-like elements in eukaryotes,” Systematic Biology, vol. 55, no. 6, pp. 875–885, 2006. View at Publisher · View at Google Scholar · View at Scopus
  125. M. F. Singer, “Unusual reverse transcriptases,” Journal of Biological Chemistry, vol. 270, no. 42, pp. 24623–24626, 1995. View at Google Scholar
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  130. T. Cavalier-Smith, “Intron phylogeny: a new hypothesis,” Trends in Genetics, vol. 7, no. 5, pp. 145–148, 1991. View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  132. D. H. Bamford, “Do viruses form lineages across different domains of life?” Research in Microbiology, vol. 154, no. 4, pp. 231–236, 2003. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Google Scholar
  134. P. Forterre and H. Philippe, “Where is the root of the tree of life,” Bioessays, vol. 21, no. 10, pp. 871–879, 1999. View at Google Scholar
  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. View at Google Scholar
  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. View at Publisher · View at Google Scholar
  137. P. Forterre, “The origin of DNA genomes and DNA replication proteins,” Current Opinion in Microbiology, vol. 5, no. 5, pp. 525–532, 2002. View at Publisher · View at Google Scholar
  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. View at Publisher · View at Google Scholar · View at Scopus
  139. C. Cayrou, B. Henrissat, P. Gouret, P. Pontarotti, and M. Drancourt, “Peptidoglycan: a post-genomic analysis,” BMC Microbiology, vol. 12, p. 294, 2012. View at Publisher · View at Google Scholar
  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. View at Publisher · View at Google Scholar · View at Scopus
  141. D. Prangishvili, “The wonderful world of archaeal viruses,” Annual Review of Microbiology, vol. 67, pp. 565–585, 2013. View at Google Scholar
  142. P. Forterre and D. Prangishvili, “The major role of viruses in cellular evolution: facts and hypotheses,” Current Opinion in Virology, 2013. View at Google Scholar
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Google Scholar · View at Scopus
  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. View at Publisher · View at Google Scholar · View at Scopus
  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. View at Google Scholar
  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. View at Publisher · View at Google Scholar · View at Scopus
  149. N. R. Pace, “Time for a change,” Nature, vol. 441, no. 7091, p. 289, 2006. View at Publisher · View at Google Scholar
  150. P. Forterre, “Neutral terms,” Nature, vol. 335, p. 305, 1992. View at Google Scholar