The major role of viruses in cellular evolution: Facts and hypotheses

Current Opinion in Virology

Volumn 3, Issue 5, 2013, Pages 558-565

  Forterre, Patrick ^a,b   Prangishvili, David ^a  

^a INSTITUT PASTEUR   (France)

^b UNIVERSITÉ PARIS SACLAY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

HELICASE; MITOCHONDRIAL RNA; SMALL INTERFERING RNA; VIRUS DNA; VIRUS PROTEIN; VIRUS RNA;

ARCHAEON; ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BIOSPHERE; EVOLUTION; HALOBACTERIALES; HORIZONTAL GENE TRANSFER; METHANOCOCCALES; METHANOMICROBIALES; METHANOPYRUS KANDLERI; METHANOSARCINA; MITOCHONDRIAL GENOME; NONHUMAN; PRIORITY JOURNAL; RNA VIRUS; SULFOLOBALES; THAUMARCHAEOTA; THERMOCOCCALES; THERMOPLASMATALES; VIRUS; VIRUS GENE; VIRUS GENOME; VIRUS PARTICLE;

ANIMALS; EVOLUTION, MOLECULAR; GENOME, VIRAL; HOST-PATHOGEN INTERACTIONS; HUMANS; VIRUS DISEASES; VIRUS INTEGRATION; VIRUSES;

EID: 84884223995     PISSN: 18796257     EISSN: 18796265     Source Type: Journal    
DOI: 10.1016/j.coviro.2013.06.013     Document Type: Review

References (58)

1. D.M. Kristensen, A.R. Mushegian, V.V. Dolja, and E.V. Koonin New dimensions of the virus world discovered through metagenomics Trends Microbiol 18 2010 11 19
2. R. Danovaro, C. Corinaldesi, A. Dell'anno, J.A. Fuhrman, J.J. Middelburg, R.T. Noble, and C.A. Suttle Marine viruses and global climate change FEMS Microbiol Rev 35 2011 993 1034
3. E.V. Koonin, and Y.I. Wolf Evolution of microbes and viruses: a paradigm shift in evolutionary biology? Front Cell Infect Microbiol 2 2012 119
4. J.L. Mokili, F. Rohwer, and B.E. Dutilh Metagenomics and future perspectives in virus discovery Curr Opin Virol 2 2012 63 77
5. C. Canchaya, G. Fournous, and H. Brüssow The impact of prophages on bacterial chromosomes Mol Microbiol 53 2004 9 18 (Pubitemid 38901375)
6. V. Daubin, E. Lerat, and G. Perrière The source of laterally transferred genes in bacterial genomes Genome Biol 4 2003 R57
7. M. Horie, T. Honda, Y. Suzuki, Y. Kobayashi, T. Daito, T. Oshida, K. Ikuta, P. Jern, T. Gojobori, J.M. Coffin, and K. Tomonaga Endogenous non-retroviral RNA virus elements in mammalian genomes Nature 463 2010 84 87
8. N. De Parseval, and T. Heidmann Human endogenous retroviruses: from infectious elements to human genes Cytogenet Genome Res 110 2005 318 332 (Pubitemid 41159909)
9. D. Cortez, P. Forterre, and S. Gribaldo A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes Genome Biol 10 2009 R65
10. Witzany G Viruses: Essential Agents of Life 2012 Springer
11. D. Prangishvili, P. Forterre, and R.A. Garrett Viruses of the Archaea: a unifying view Nat Rev Microbiol 4 2006 837 848 (Pubitemid 44593950)
12. P. Forterre The origin of viruses and their possible roles in major evolutionary transitions Virus Res 117 2006 5 16
13. E.V. Koonin, T.G. Senkevich, and V.V. Dolja The ancient Virus World and evolution of cells Biol Direct 1 2006 29
14. M. Jalasvuori, and J.K. Bamford Structural co-evolution of viruses and cells in the primordial world Orig Life Evol Biosph 38 2008 165 181
15. P. Forterre, and M. Krupovic The origin of virions and virocells: the escape hypothesis revisited G. Witzany, Viruses: Essential Agents of Life 2012 Springer
16. H. Brüssow The not so universal tree of life or the place of viruses in the living world Philos Trans R Soc Lond B Biol Sci 364 2009 2263 2274
17. L.P. Villarreal, and G. Witzany Viruses are essential agents within the roots and stem of the tree of life J Theor Biol 262 2010 698 710
18. P. Forterre Darwin's goldmine is still open: variation and selection run the world Front Cell Infect Microbiol 2 2012 106 10.3389/fcimb.2012.00106
19. 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 Ann N Y Acad Sci 1178 2009 65 77
20. D. Moreira, and P. López-García Ten reasons to exclude viruses from the tree of life Nat Rev Microbiol 7 2009 306 311
21. D. Prangishvili, R.A. Garrett, and E.V. Koonin Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life Virus Res 117 2006 52 67
22. J. Filée, and M. Chandler Convergent mechanisms of genome evolution of large and giant DNA viruses Res Microbiol 159 2008 325 331
23. P. Forterre Giant viruses: conflicts in revisiting the virus concept Intervirology 53 2010 362 378
24. M. Häring, X. Peng, K. Brügger, R. Rachel, K.O. Stetter, R.A. Garrett, and D. Prangishvili Morphology and genome organisation of the virus PSV of the hyperthermophilic archaeal genera Pyrobaculum and Thermoproteus: a novel virus family, the Globuloviridae Virology 323 2004 232 242
25. T. Mochizuki, T. Yoshida, R. Tanaka, P. Forterre, Y. Sako, and P. Prangishvili Diversity of viruses of the hyperthermophilic archaeal genus Aeropyrum, and isolation of the Aeropyrum pernix bacilliform virus 1, APBV1, the first representative of the family "Clavaviridae" Virology 402 2010 347 354
26. D. Moreira, and C. Brochier-Armanet Giant viruses, giant chimeras: the multiple evolutionary histories of Mimivirus genes BMC Evol Biol 8 2008 12 10.1186/1471-2148-8-12 (Pubitemid 351342674)
27. K. Hamacher, T. Greiner, H. Ogata, J.L. Van Etten, M. Gebhardt, L.P. Villarreal, C. Cosentino, A. Moroni, and G. Thiel Phycodnavirus potassium ion channel proteins question the virus molecular piracy hypothesis PLoS ONE 7 2012 e38826 10.1371/journal.pone.0038826
28. M. Krupovic, 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 Mol Biol Evol 27 2010 2716 2732
29. A.S. Lang, O. Zhaxybayeva, and J.T. Beatty Gene transfer agents: phage-like elements of genetic exchange Nat Rev Microbiol 10 2012 472 482 10.1038/nrmicro2802
30. M. Krupovic, and P. Forterre Microviridae goes temperate: microvirus-related proviruses reside in the genomes of Bacteroidetes PLoS ONE 6 2011 e19893 10.1371/journal.pone.0019893
31. N. Bannert, and R. Kurth The evolutionary dynamics of human endogenous retroviral families Annu Rev Genom Hum Genet 7 2006 149 173 (Pubitemid 44627926)
32. J.M. Claverie Viruses take center stage in cellular evolution Genome Biol 7 2006 110
33. P. Forterre The virocell concept eLS 2012 10.1002/9780470015902.a0023264
34. P. Forterre Manipulation of cellular syntheses and the nature of viruses: the virocell concept C R Chim 2010 10.1016/j.crci.2010.06.007
35. P. Forterre The virocell concept and environmental microbiology ISME J 7 2013 233 236
36. A. Abroi, and J. Gough Are viruses a source of new protein folds for organisms? Bioessays 33 2011 626 635
37. C. Peltier, L. Schmidlin, E. Klein, L. Taconnat, E. Prinsen, M. Erhardt, D. Heintz, G. Weyens, M. Lefevre, J.P. Renou, and D. Gilmer Expression of the beetnecrosis yellow vein virus p25 protein induces hormonal changes and a root branching phenotype in Arabidopsis thaliana Transgenic Res 20 2011 443 466
38. H. Brüssow, C. Canchaya, and W.D. Hardt Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion Microbiol Mol Biol Rev 68 2004 560 602 (Pubitemid 39238283)
39. B. Busby, D.M. Kristensen, and E.V. Koonin Contribution of phage-derived genomic islands to the virulence of facultative bacterial pathogens Environ Microbiol 15 2013 307 312
40. J. Thézé, A. Bézier, G. Periquet, J.M. Drezen, and E.A. Herniou Paleozoic origin of insect large dsDNA viruses Proc Natl Acad Sci U S A 108 2011 15931 15935
41. K.S. Makarova, Y.I. Wolf, and E.V. Koonin Comparative genomics of defense systems in archaea and bacteria Nucleic Acids Res 41 2013 4360 4377
42. A. Stern, and R. Sorek The phage-host arms race: shaping the evolution of microbes Bioessays 33 2011 43 51
43. A. Cibrián-Jaramillo, and R.A. Martienssen Darwin's "Abominable Mystery": the role of RNA interference in the evolution of flowering plants Cold Spring Harb Symp Quant Biol 74 2009 267 273
44. J. Filée, and P. Forterre Viral proteins functioning in organelles: a cryptic origin? Trends Microbiol 13 2005 510 513 (Pubitemid 41506891)
45. W. Wei, R.E. Davis, R. Jomantiene, and Y. Zhao Ancient, recurrent phage attacks and recombination shaped dynamic sequence-variable mosaics at the root of phytoplasma genome evolution Proc Natl Acad Sci U S A 105 2008 11827 11832
46. S.G. Gornik, K.L. Ford, T.D. Mulhern, A. Bacic, G.I. McFadden, and R.F. Waller Loss of nucleosomal DNA condensation coincides with appearance of a novel nuclear protein in dinoflagellates Curr Biol 22 2012 2303 2312
47. A. Dupressoir, C. Lavialle, and T. Heidmann From ancestral infectious retroviruses to bona fide cellular genes: role of the captured syncytins in placentation Placenta 33 2012 663 671
48. L.I. Larsson, B. Bjerregaard, and J.F. Talts Cell fusions in mammals Histochem Cell Biol 129 2008 551 561
49. T. Sasaki, H. Nishihara, M. Hirakawa, K. Fujimura, M. Tanaka, N. Kokubo, C. Kimura-Yoshida, I. Matsuo, K. Sumiyama, and N. Saitou Possible involvement of SINEs in mammalian-specific brain formation Proc Natl Acad Sci U S A 105 2008 4220 4225 (Pubitemid 351754361)
50. P. Forterre The origin of DNA genomes and DNA replication proteins Curr Opin Microbiol 5 2002 525 532
51. M. Takemura Poxviruses and the origin of the eukaryotic nucleus J Mol Evol 52 2001 419 425
52. P.J. Bell Viral eukaryogenesis: was the ancestor of the nucleus a complex DNA virus? J Mol Evol 53 2001 251 256 (Pubitemid 32783800)
53. D. Prangishvili The wonderful world of archaeal viruses Annu Rev Microbiol 67 2013 565 568 in press
54. P. Forterre Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: a hypothesis for the origin of cellular domain Proc Natl Acad Sci U S A 103 2006 3374 3669
55. T.E.F. Quax, S. Lucas, J. Reimann, G. Pehau-Arnaudet, M.C. Prevost, P. Forterre, S.V. Albers, and D. Prangishvili Simple and elegant design of a virion egress structure in Archaea Proc Natl Acad Sci U S A 108 2011 3354 3359
56. G. Piganeau, N. Grimsley, and H. Moreau Genome diversity in the smallest marine photosynthetic eukaryotes Res Microbiol 162 2011 570 577
57. C. Brochier-Armanet, B. Boussau, S. Gribaldo, and P. Forterre Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota Nat Rev Microbiol 6 2008 245 252 (Pubitemid 351256319)
58. A. Bize, E.A. Karlsson, K. Ekefjärd, T.E. Quax, M. Pina, M.C. Prevost, P. Forterre, O. Tenaillon, R. Bernander, and D. Prangishvili A unique virus release mechanism in the Archaea Proc Natl Acad Sci U S A 106 2009 11306 11311