The archaeal legacy of eukaryotes: A phylogenomic perspective

Cold Spring Harbor Perspectives in Biology

Volumn 6, Issue 10, 2014, Pages

  Guy, Lionel ^a   Saw, Jimmy H ^a   Ettema, Thijs J G ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEA; EUKARYOTA;

ARCHAEAL GENOME; ARCHAEON; EUKARYOTE; GENETICS; GENOMICS; PHYLOGENY;

ARCHAEA; EUKARYOTA; GENOME, ARCHAEAL; GENOMICS; PHYLOGENY;

EID: 84903388029     PISSN: None     EISSN: 19430264     Source Type: Journal    
DOI: 10.1101/cshperspect.a016022     Document Type: Article

References (68)

1. Bell PJ. 2001. Viral eukaryogenesis: Was the ancestor of the nucleus a complex DNAvirus? J Mol Evol 53: 251–256.
2. Bernander R, Lind AE, Ettema TJ. 2011. An archaeal origin for the actin cytoskeleton: Implications for eukaryogen-esis. Commun Integr Biol 4: 664–667.
3. Brown JR, Doolittle WF. 1997. Archaea and the prokaryote-to-eukaryote transition. Microbiol Mol Biol Rev 61: 456–502.
4. Bult CJ, White O, Olsen GJ, Zhou L, Fleischmann RD, Sut-ton GG, Blake JA, FitzGerald LM, Clayton RA, Gocayne JD, et al. 1996. Complete genome sequence of the meth-anogenic archaeon, Methanococcus jannaschii. Science 273: 1058–1073.
5. Cavalier-Smith T. 1989. Molecular phylogeny. Archaebacte-ria and Archezoa. Nature 339: l00–101.
6. Cavalier-Smith T. 2002a. The neomuran originofarchaebac-teria, the negibacterial root of the universal tree and bac-terialmegaclassification. IntJSyst EvolMicrobiol 52:7–76.
7. Cavalier-Smith T. 2002b. The phagotrophic origin of eu-karyotes and phylogenetic classification of Protozoa. Int J Syst Evol Microbiol 52: 297–354.
8. Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P. 2006. Toward automatic reconstruction of a highly resolved tree of life. Science 311: 1283–1287.
9. Cox CJ, Foster PG, Hirt RP, Harris SR, Embley TM. 2008. The archaebacterial origin of eukaryotes. Proc Natl Acad Sci 105: 20356–20361.
10. Delsuc F, Brinkmann H, Philippe H. 2005. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 6: 361–375.
11. Devos DP, Reynaud EG. 2010. Evolution. Intermediate steps. Science 330: 1187–1188.
12. Elkins JG, Podar M, Graham DE, Makarova KS, Wolf Y, Randau L, Hedlund BP, Brochier-Armanet C, Kunin V, Anderson I, et al. 2008. A korarchaeal genome reveals insights into the evolution of the Archaea. Proc Natl Acad Sci 105: 8102–8107.
13. Embley TM. 2006. Multiple secondary origins of the anaerobic lifestyle in eukaryotes. Philos Trans R Soc Lond B Biol Sci 361: 1055–1067.
14. Embley TM, Martin W. 2006. Eukaryotic evolution, changes and challenges. Nature 440: 623–630.
15. Ettema TJ, Bernander R. 2009. Cell division and the ESCRT complex: A surprise from the Archaea. Commun Integr Biol 2: 86–88.
16. Ettema TJ, de Vos WM, van der Oost J. 2005. Discovering novel biology by in silico archaeology. Nat Rev Microbiol 3: 859–869.
17. Ettema TJ, Linda˚s AC, Bernander R. 2011. An actin-based cytoskeleton in Archaea. Mol Microbiol 80: 1052–1061.
18. Forterre P. 2005. The two ages of the RNA world, and the transition to the DNAworld: A story of viruses and cells. Biochimie 87: 793–803.
19. Forterre P. 2006. Three RNA cells for ribosomal lineages and three DNAviruses to replicate their genomes: A hypothesis for the origin of cellular domain. Proc Natl Acad Sci 103: 3669–3674.
20. Forterre P. 2011. A new fusion hypothesis for the origin of Eukarya: Better than previous ones, but probably also wrong. Res Microbiol 162: 77–91.
21. Forterre P, Gribaldo S. 2010. Bacteria with a eukaryotic touch: A glimpse of ancient evolution? Proc Natl Acad Sci 107: 12739–12740.
22. Foster PG, Cox CJ, Embley TM. 2009. The primary divisions of life: A phylogenomic approach employing composition-heterogeneous methods. Philos Trans R Soc Lond B Biol Sci 364: 2197–2207.
23. Gribaldo S, Poole AM, Daubin V, Forterre P, Brochier-Ar-manet C. 2010. The origin of eukaryotes and their relationship with the Archaea: Are we at a phylogenomic impasse? Nat Rev Microbiol 8: 743–752.
24. Guy L, Ettema TJ. 2011. The archaeal “TACK” superphylum and the origin of eukaryotes. Trends Microbiol 19: 580–587.
25. Henderson E, Oakes M, Clark MW, Lake JA, Matheson AT, Zillig W. 1984. A new ribosome structure. Science 225: 510–512.
26. Horiike T, Hamada K, Miyata D, Shinozawa T. 2004. The origin of eukaryotes is suggested as the symbiosis of py-rococcus into g-proteobacteria by phylogenetic tree based on gene content. J Mol Evol 59: 606–619.
27. Kelly S, Wickstead B, Gull K. 2011. Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukary-otes. Proc Biol Sci 278: 1009–1018.
28. Koonin EV. 2010. The origin and early evolution of eukary-otes in the light of phylogenomics. Genome Biol 11: 209.
29. Kozubal MA, Romine M, Jennings R, Jay ZJ, Tringe SG, Rusch DB, Beam JP, McCue LA, Inskeep WP. 2013. Geo-archaeota: A new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park. ISME J 7: 622–634.
30. Kurland CG, Collins LJ, Penny D. 2006. Genomics and the irreducible nature of eukaryote cells. Science 312: 1011–1014.
31. Lake JA. 1988. Origin of the eukaryotic nucleus determined by rate-invariant analysis ofrRNA sequences. Nature 331: 184–186.
32. Lake JA, Henderson E, Oakes M, Clark MW. 1984. Eocytes: A new ribosome structure indicates a kingdom with a close relationship to eukaryotes. Proc Natl Acad Sci 81: 3786–3790.
33. Lartillot N, Lepage T, Blanquart S. 2009. PhyloBayes 3: A Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25: 2286–2288.
34. Linda˚s AC, Karlsson EA, Lindgren MT, Ettema TJ, Bernander R. 2008. A unique cell division machinery in the Archaea. Proc Natl Acad Sci 105: 18942–18946.
35. Lopez-Garcia P, Moreira D. 1999. Metabolic symbiosisat the origin of eukaryotes. Trends Biochem Sci 24: 88–93.
36. Makarova KS, Aravind L, Galperin MY, Grishin NV, Tatusov RL, Wolf YI, Koonin EV. 1999. Comparative genomics of the Archaea (Euryarchaeota): Evolution of conserved protein families, the stable core, and the variable shell. Genome Res 9: 608–628.
37. Makarova KS, Yutin N, Bell SD, Koonin EV. 2010. Evolution of diverse cell division and vesicle formation systems in Archaea. Nat Rev Microbiol 8: 731–741.
38. Margulis L, Chapman M, Guerrero R, Hall J. 2006. The last eukaryotic common ancestor (LECA): Acquisition of cy-toskeletal motility from aerotolerant spirochetes in the Proterozoic Eon. Proc Natl Acad Sci 103: 13080–13085.
39. Martijn J, Ettema TJ. 2013. From archaeon to eukaryote: The evolutionary dark ages of the eukaryotic cell. Bio-chem Soc Trans 41: 451–457.
40. Martin W. 2005. Archaebacteria (Archaea) and the origin of the eukaryotic nucleus. Curr Opin Microbiol 8: 630–637.
41. Martin W, Muller M. 1998. The hydrogen hypothesis for the first eukaryote. Nature 392: 37–41.
42. McInerney JO, Martin W., Koonin EV, Allen JF, Galperin MY, Lane N, Archibald JM, Embley TM. 2011. Plancto-mycetes and eukaryotes: Acase of analogy not homology. BioEssays 33: 810–817.
43. Moreira D, Lopez-Garcia P. 1998. Symbiosis between meth-anogenic Archaea and d-proteobacteria as the origin of eukaryotes: The syntrophic hypothesis. J Mol Evol 47: 517–530.
44. Nunoura T, Takaki Y, Kakuta J, Nishi S, Sugahara J, Kazama H, Chee GJ, Hattori M, Kanai A, Atomi H, et al. 2011. Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res 39: 3204–3223.
45. Olsen GJ, Woese CR. 1997. Archaeal genomics:An overview. Cell 89: 991–994.
46. Pisani D, Cotton JA, McInerney JO. 2007. Supertrees disentangle the chimerical origin of eukaryotic genomes. Mol Biol Evol 24: 1752–1760.
47. Reynaud EG, Devos DP. 2011. Transitional forms between the three domains of life and evolutionary implications. Proc Biol Sci 278: 3321–3328.
48. Rivera MC, Jain R, Moore JE, Lake JA. 1998. Genomic evidence for two functionally distinct gene classes. Proc Natl Acad Sci 95: 6239–6244.
49. Sagan L. 1967. On the origin of mitosing cells. J Theor Biol 14: 255–274.
50. Searcy DG, Hixon WG. 1991. Cytoskeletal origins in sulfur-metabolizing archaebacteria. Bio Systems 25: 1–11.
51. Snel B, Bork P, Huynen MA. 1999. Genome phylogeny based on gene content. Nat Genet 21: 108–110.
52. Takemura M. 2001. Poxviruses and the origin of the eukary-otic nucleus. J Mol Evol 52: 419–425.
53. Tekaia F, Lazcano A, Dujon B. 1999. The genomic tree as revealed from whole proteome comparisons. Genome Res 9: 550–557.
54. Townsend JP, Lopez-Giraldez F. 2010. Optimal selection of gene and ingroup taxon sampling for resolving phyloge-netic relationships. Syst Biol 59: 446–457.
55. Viklund J, Ettema TJ, Andersson SG. 2012. Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade. Mol Biol Evol 29: 599–615.
56. Williams KP, Gillespie JJ, Sobral BW, Nordberg EK, Snyder EE, Shallom JM, Dickerman AW. 2010. Phylogeny of gammaproteobacteria. J Bacteriol 192: 2305–2314.
57. Williams TA, Foster PG, Nye TM, Cox CJ, Embley TM. 2012. A congruent phylogenomic signal places eukaryotes within the Archaea. Proc Biol Sci 279: 4870–4879.
58. Woese CR. 1987. Bacterial evolution. Microbiol Rev 51: 221–271.
59. Woese CR, Fox GE. 1977. Phylogenetic structure of the pro-karyotic domain: The primary kingdoms. Proc Natl Acad Sci 74: 5088–5090.
60. Woese CR, Kandler O, Wheelis ML. 1990. Towards a natural system of organisms: Proposal for the domains Ar-chaea, Bacteria, and Eucarya. Proc Natl Acad Sci 87: 4576–4579.
61. Wolf YI, Makarova KS, Yutin N, Koonin EV. 2012. Updated clusters of orthologous genes for Archaea: A complex ancestor of the Archaea and the byways of horizontal gene transfer. Biol Direct 7: 46.
62. Yutin N, Koonin EV. 2012. Archaeal origin of tubulin. Biol Direct 7: 10.
63. Yutin N, Makarova KS, Mekhedov SL, Wolf YI, Koonin EV. 2008. The deep archaeal rootsof eukaryotes. Mol Biol Evol 25: 1619–1630.
64. Yutin N, Wolf MY, Wolf YI, Koonin EV. 2009. The origins of phagocytosis and eukaryogenesis. Biol Direct 4: 9.
65. Yutin N, Puigbo P, Koonin EV, Wolf YI. 2012. Phylogeno-mics of prokaryotic ribosomal proteins. PloS ONE 7: e36972.
66. Zillig W, Schnabel R, Stetter KO. 1985. Archaebacteria and the origin of the eukaryotic cytoplasm. Curr Topics Mi-crobiol Immunol 114: 1–18.
67. Zillig W, Klenk HP, Palm P, Leffers H, Pühler G, Gropp F, Garrett RA. 1989a. Did eukaryotes originate by a fusion event? Endocytobiosis Cell Res 6: 1–25.
68. Zillig W, Klenk HP, Palm P, Puhler G, Gropp F, Garrett RA, Leffers H. 1989b. The phylogenetic relations of DNA-dependent RNA polymerases of archaebacteria, eukary-otes, and eubacteria. Canadian J Microbiol 35: 73–80.