Common origins and host-dependent diversity of plant and animal viromes

Current Opinion in Virology

Volumn 1, Issue 5, 2011, Pages 322-331

  Dolja, Valerian V ^a   Koonin, Eugene V ^b  

^a OREGON STATE UNIVERSITY   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CAPSID PROTEIN;

ANIMAL VIRUS; ARTICLE; GENETIC VARIABILITY; MOLECULAR EVOLUTION; NONHUMAN; PLANT VIRUS; PRIORITY JOURNAL; VIRAL GENETICS; VIRUS CARRIER; VIRUS CELL INTERACTION; VIRUS GENE; VIRUS TRANSMISSION;

EID: 81755166283     PISSN: 18796257     EISSN: 18796265     Source Type: Journal    
DOI: 10.1016/j.coviro.2011.09.007     Document Type: Review

References (57)

1. J. Keeling Genomics. Deep questions in the tree of life Science 317 2007 1875 1876
2. E.V. Koonin The origin and early evolution of eukaryotes in the light of phylogenomics Genome Biol 11 2010 209
3. C.A. Suttle Marine viruses - major players in the global ecosystem Nat Rev Microbiol 5 2007 801 812
4. F. Rohwer, and R.V. Thurber Viruses manipulate the marine environment Nature 459 2009 207 212
5. D.M. Kristensen, A. Mushegian, V.V. Dolja, and E.V. Koonin New dimensions of the virus world discovered through metagenomics Trends Microbiol 18 2010 11 19
6. G.F. Hatful Bacteriophage genomics Curr Opin Microbiol 11 2008 447 453
7. M. Pina, A. Bize, P. Forterre, and D. Prangishvili The archeoviruses FEMS Microbiol Rev 35 2011 1035 1054
8. A.I. Culley, A.S. Lang, and C.A. Suttle Metagenomic analysis of coastal RNA virus communities Science 312 2006 1795 1798
9. A.S. Lang, M.L. Rise, A.I. Culley, and G.F. Steward RNA viruses in the sea FEMS Microbiol Rev 33 2009 295 323
10. E.V. Koonin, T.G. Senkevich, and V.V. Dolja The ancient virus world and evolution of cells Biol Direct 1 2006 29
11. E.V. Koonin, Y.I. Wolf, K. Nagasaki, and V.V. Dolja The big bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups Nat Rev Microbiol 6 2008 925 939
12. E.V. Koonin Comparative genomics, minimal gene-sets and the last universal common ancestor Nat Rev Microbiol 1 2003 127 136
13. W.F. Doolittle, and E. Bapteste Pattern pluralism and the Tree of Life hypothesis Proc Natl Acad Sci U S A 104 2007 2043 2049
14. M.A. O'Malley, and E.V. Koonin How stands the Tree of Life a century and a half after The Origin? Biol Direct 6 2011 32
15. E.V. Koonin The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses J Gen Virol 72 Pt 9 1991 2197 2206
16. K.K.S. Ng, J.J. Arnold, and C.E. Cameron Structure-function relationships among RNA-dependent RNA polymerases Curr Top Microbiol Immunol 320 2008 137 156
17. J. Haseloff, P. Goelet, D. Zimmern, P. Ahlquist, R. Dasgupta, and P. Kaesberg Striking similarities in amino acid sequence among nonstructural proteins encoded by RNA viruses that have dissimilar genomic organization Proc Natl Acad Sci U S A 81 1984 4358 4362
18. H. Franssen, J. Leunissen, R. Goldbach, G. Lomonossoff, and D. Zimmern Homologous sequences in nonstructural proteins from cowpea mosaic virus and picornaviruses EMBO J 3 1984 855 861
19. E.V. Koonin, and V.V. Dolja Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences Crit Rev Biochem Mol Biol 28 1993 375 430
20. E.V. Koonin Evolution of double-stranded RNA viruses: a case for polyphyletic origin from different groups of positive-stranded RNA viruses Semin Virol 3 1992 327 339
21. A.E. Gorbalenya, F.M. Pringle, J.L. Zeddam, B.T. Luke, C.E. Cameron, J. Kalmakoff, T.N. Hanzlik, K.H. Gordon, and V.K. Ward The palm subdomain-based active site is internally permuted in viral RNA-dependent RNA polymerases of an ancient lineage J Mol Biol 324 2002 47 62
22. D.H. Bamford, J.M. Grimes, and D.I. Stuart What does structure tell us about virus evolution? Curr Opin Struct Biol 15 2005 655 663
23. O. Poch, I. Sauvaget, M. Delarue, and N. Tordo Identification of four conserved motifs among the RNA-dependent polymerase encoding elements EMBO J 8 1989 3867 3874
24. A.M. Lambowitz, and S. Zimmerly Mobile group II introns Annu Rev Genet 38 2004 1 35
25. J.L. Goodier, and H.H. Kazazian Retrotransposons revisited:the restraint and rehabilitation of parasites Cell 135 2008 23 35
26. T.H. Eickbush, and V.K. Jamburuthugoda The diversity of retrotransposons and the properties of their reverse transcriptases Virus Res 134 2008 221 234
27. T.V. Ilyina, and E.V. Koonin Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria Nucleic Acids Res 20 1992 3279 3285
28. R.P. Novick Contrasting lifestyles of rolling-circle phages and plasmids Trends Biochem Sci 23 1998 434 438
29. L.M. Iyer, E.V. Koonin, D.D. Leipe, and L. Aravind Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members Nucleic Acids Res 33 2005 3875 3896
30. L.M. Iyer, L. Aravind, and E.V. Koonin Common origin of four diverse families of large eukaryotic DNA viruses J Virol 75 2001 11720 11734
31. E.V. Koonin, and N. Yutin Origin and evolution of eukaryotic large nucleo-cytoplasmic DNA viruses Intervirology 53 2010 284 292
32. S.D. Benson, J.K. Bamford, D.H. Bamford, and R.M. Burnett Does common architecture reveal a viral lineage spanning all three domains of life? Mol Cell 16 2004 673 685
33. R. Khayat, L. Tang, E.T. Larson, C.M. Lawrence, M. Young, and J.E. Johnson Structure of an archaeal virus capsid protein reveals a common ancestry to eukaryotic and bacterial viruses Proc Natl Acad Sci U S A 102 2005 18944 18949
34. W.H. Wilson, J.L. Van Etten, and M.J. Allen The phycodnaviridae: the story of how tiny giants rule the world Curr Top Microbiol Immunol 328 2009 1 42
35. Y. Benitez-Alfonso, C. Faulkner, C. Ritzenthaler, and A.J. Maule Plasmodesmata: gateways to local and systemic virus infection Mol Plant Microbe Interact 23 2010 1403 1412
36. M.R. Rojas, C. Hagen, W.J. Lucas, and R.L. Gilbertson Exploiting clinks in the plant's armor: evolution and emergence of geminiviruses Annu Rev Phytopathol 43 2005 361 394
37. E.V. Koonin, A.R. Mushegian, E.V. Ryabov, and V.V. Dolja Diverse groups of plant RNA and DNA viruses share related movement proteins that may possess chaperone-like activity J Gen Virol 72 1991 2895 2903
38. U. Melcher The '30K' superfamily of viral movement proteins J Gen Virol 81 2000 257 266
39. S.W. Ding, and O. Vionnet Antiviral immunity directed by small RNAs Cell 130 2007 413 426
40. Q. Wu, X. Wang, and S.W. Ding Viral suppressors of RNA-based viral immunity: host targets Cell Host Microbe 8 2010 12 15
41. 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
42. O. Takeuchi, and S. Akira Innate immunity to viral infection Immunol Rev 227 2009 75 86
43. V.I. Agol, and A.P. Gmyl Viral security proteins: counteracting host defences Nat Rev Microbiol 8 2010 867 878
44. M. Krupovic, and D.H. Bamford Virus evolution: how far does the double beta-barrel viral lineage extend? Nat Rev Microbiol 6 2008 941 948
45. V.V. Dolja, V.P. Boyko, A.A. Agranovsky, and E.V. Koonin Phylogeny of capsid proteins of rod-shaped and filamentous plant viruses: two families with distinct patterns of sequence and probably structure conservation Virology 184 1991 79 86
46. A. Niehl, and M. Heinlein Cellular pathways for viral transport through plasmodesmata Protoplasma 248 2011 75 99
47. A. Monier, J.B. Larsen, R.A. Sandaa, G. Bratbak, J.M. Claverie, and H. Ogata Marine mimivirus relatives are probably large algal viruses Virol J 5 2008 12
48. S.A. Hogenhout, E.D. Ammar, A.E. Whitefield, and M.G. Redibaugh Insect vector interactions with persistently transmitted viruses Annu Rev Phytopathol 46 2008 327 359
49. S.C. Weaver Evolutionary influences in arboviral disease Curr Top Microbiol Immunol 299 2006 285 314
50. S. Bekal, L.L. Domier, T.L. Niblack, and K.N. Lambert Discovery and initial analysis of novel viral genomes in the soybean cyst nematode J Gen Virol 92 2011 1870 1879
51. T. Finsterbusch, and A. Mankertz Porcine circoviruses - small but powerful Virus Res 143 2009 177 183
52. H. Jeske Geminiviruses Curr Top Microbiol Immunol 331 2009 185 226
53. Y. Tomaru, Y. Takao, H. Suzuki, T. Nagumo, K. Koike, and K. Nagasaki Isolation and characterization of a single-stranded DNA virus infecting Chaetoceros lorenzianus Grunow Appl Environ Microbiol 77 2011 5285 5293
54. M. Krupovic, J.J. Ravantti, and D.H. Bamford Geminiviruses: a tale of a plasmid becoming a virus BMC Evol Biol 9 2009 112
55. L.A. Selth, J.W. Randles, and M.A. Rezaian Agrobacterium tumefaciens supports DNA replication of diverse geminivirus types FEBS Lett 516 2002 179 182
56. E.V. Koonin, and T.V. Ilyina Geminivirus replication proteins are related to prokaryotic plasmid rolling circle DNA replication initiator proteins J Gen Virol 73 Pt 10 1992 2763 2766
57. H.S. Yoon, D.C. Price, R. Stepanauskas, V.D. Rajah, M.E. Sieracki, W.H. Wilson, E.C. Yang, S. Duffy, and D. Bhattacharya Single-cell genomics reveals organismal interactions in uncultivated marine protists Science 332 2011 714 717