3D Structures of Fungal Partitiviruses

Advances in Virus Research

Volumn 86, Issue , 2013, Pages 59-85

  Nibert, Max L ^a   Tang, Jinghua ^b   Xie, Jiatao ^c   Collier, Aaron M ^d   Ghabrial, Said A ^c   Baker, Timothy S ^b   Tao, Yizhi J ^d  

^a HARVARD MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF KENTUCKY   (United States)

^d RICE UNIVERSITY   (United States)

Author keywords

Capsid; DsRNA; Fungal virus; Mycovirus; Partitivirus; Picobirnavirus; T=1; Virus evolution; Virus structure

Indexed keywords

EID: 84874973511     PISSN: 00653527     EISSN: 15578399     Source Type: Book Series    
DOI: 10.1016/B978-0-12-394315-6.00003-9     Document Type: Chapter

References (59)

1. Boccardo G., Candresse T. Complete sequence of the RNA1 of an isolate of White clover cryptic virus 1, type species of the genus Alphacryptovirus. Archives of Virology 2005, 150:399-402.
2. Bozarth R.F., Wood H.A., Mandelbrot A. The Penicillium stoloniferum virus complex: Two similar double-stranded RNA virus-like particles in a single cell. Virology 1971, 45:516-523.
3. Bruenn J.A. A closely related group of RNA-dependent RNA polymerases from double-stranded RNA viruses. Nucleic Acids Research 1993, 21:5667-5669.
4. Buck K.W. Semi-conservative replication of double-stranded RNA by a virion-associated RNA polymerase. Biochemical and Biophysical Research Communications 1978, 84:639-645.
5. Buck K.W., Kempson-Jones G.F. Biophysical properties of Penicillium stoloniferum virus S. Journal of General Virology 1973, 18:223-235.
6. Buck K.W., Kempson-Jones G.F. Capsid polypeptides of two viruses isolated from Penicillium stoloniferum. Journal of General Virology 1974, 22:441-445.
7. Butcher S.J., Grimes J.M., Makeyev E.V., Bamford D.H., Stuart D.I. A mechanism for initiating RNA-dependent RNA polymerization. Nature 2001, 410:235-240.
8. Castón R.J., Luque D., Trus B.L., Rivas G., Alfonso C., González J.M., et al. Three-dimensional structure and stoichiometry of Helminthosporium victoriae 190S totivirus. Virology 2006, 347:323-332.
9. Castón J.R., Trus B.L., Booy F.P., Wickner R.B., Wall J.S., Steven A.C. Structure of L-A virus: A specialized compartment for the transcription and replication of double-stranded RNA. The Journal of Cell Biology 1997, 138:975-985.
10. Cheng R.H., Caston J.R., Wang G.-J., Gu F., Smith T.J., Baker T.S., et al. Fungal virus capsids, cytoplasmic compartments for the replication of double-stranded RNA, formed as icosahedral shells of asymmetric gag dimers. Journal of Molecular Biology 1994, 244:255-258.
11. Chiba S., Kondo H., Tani A., Saisho D., Sakamoto W., Kanematsu S., et al. Widespread endogenization of genome sequences of non-retroviral RNA viruses into plant genomes. PLoS Pathogens 2011, 7:e1002146.
12. Chiba S., Salaipeth L., Lin Y.H., Sasaki A., Kanematsu S., Suzuki N. A novel bipartite double-stranded RNA mycovirus from the white root rot fungus Rosellinia necatrix: Molecular and biological characterization, taxonomic considerations, and potential for biological control. Journal of Virology 2009, 83:12801-12812.
13. Compel P., Papp I., Bibo M., Fekete C., Hornok L. Genetic relationships and genome organization of double-stranded RNA elements of Fusarium poae. Virus Genes 1999, 18:49-56.
14. Coulibaly F., Chevalier C., Gutsche I., Pous J., Navaza J., Bressanelli S., et al. The birnavirus crystal structure reveals structural relationships among icosahedral viruses. Cell 2005, 120:761-772.
15. Crawford L.J., Osman T.A., Booy F.P., Coutts R.H., Brasier C.M., Buck K.W. Molecular characterization of a partitivirus from Ophiostoma himal-ulmi. Virus Genes 2006, 33:33-39.
16. Delmas B. Picobirnaviridae. Virus taxonomy: Ninth report of the international committee on taxonomy of viruses 2011, 535-539. Elsevier, Oxford, UK. A.M.Q. King, M.J. Adams, E.B. Carstens, E.J. Lefkowitz (Eds.).
17. Delmas B., Mundt E., Vakharia V.N., Wu J.L. Birnaviridae. Virus taxonomy: Ninth report of the international committee on taxonomy of viruses 2011, 499-507. Elsevier, Oxford, UK. A.M.Q. King, M.J. Adams, E.B. Carstens, E.J. Lefkowitz (Eds.).
18. Diprose J.M., Burroughs J.N., Sutton G.C., Goldsmith A., Gouet P., Malby R., et al. Translocation portals for the substrates and products of a viral transcription complex: The bluetongue virus core. The EMBO Journal 2001, 20:7229-7239.
19. Dunn, S. E., Li, H., Cardone, G., Nibert, M. L., Ghabrial, S. A., and Baker, T. S. (2013). Three-dimensional structure of the genus Victorivirus prototype strain HvV190S suggests that the capsid proteins in all totiviruses may share a conserved core. PLOS Pathogens, in press.
20. Duquerroy S., Da Costa B., Henry C., Vigouroux A., Libersou S., Lepault J., et al. The picobirnavirus crystal structure provides functional insights into virion assembly and cell entry. The EMBO Journal 2009, 28:1655-1665.
21. Earnshaw W.C., Harrison S.C. DNA arrangement in isometric phage heads. Nature 1977, 268:598-602.
22. Ghabrial S.A., Nibert M.L., Maiss E., Lesker T., Baker T.S., Tao Y.J. Partitiviridae. Virus taxonomy: Ninth report of the international committee on taxonomy of viruses 2011, 523-534. Elsevier, Oxford, UK. A.M.Q. King, M.J. Adams, E.B. Carstens, E.J. Lefkowitz (Eds.).
23. Ghabrial S.A., Ochoa W.F., Baker T.S., Nibert M.L. Partitiviruses: General features. Encyclopedia of virology 2008, Vol. 4:68-75. Elsevier, Oxford, UK. 3rd ed. B.W.J. Mahy, M.H.V. van Regenmortel (Eds.).
24. Gómez-Blanco J., Luque D., González J.M., Carrascosa J.L., Alfonso C., Trus B., et al. Cryphonectria nitschkei virus 1 structure shows that the capsid protein of chrysoviruses is a duplicated helix-rich fold conserved in fungal double-stranded RNA viruses. Journal of Virology 2012, 86:8314-8318.
25. Grimes J.M., Burroughs J.N., Gouet P., Diprose J.M., Malby R., Ziéntara S., et al. The atomic structure of the bluetongue virus core. Nature 1998, 395:470-478.
26. Huiskonen J.T., de Haas F., Bubeck D., Bamford D.H., Fuller S.D., Butcher S.J. Structure of the bacteriophage φ6 nucleocapsid suggests a mechanism for sequential RNA packaging. Structure 2006, 14:1039-1048.
27. Kainov D.E., Butcher S.J., Bamford D.H., Tuma R. Conserved intermediates on the assembly pathway of double-stranded RNA bacteriophages. Journal of Molecular Biology 2003, 328:791-804.
28. Kanematsu S., Sasaki A., Onoue M., Oikawa Y., Ito T. Extending the fungal host range of a partitivirus and a mycoreovirus from Rosellinia necatrix by inoculation of protoplasts with virus particles. Phytopathology 2010, 100:922-930.
29. Kim J.W., Choi E.Y., Lee J.I. Genome organization and expression of the Penicillium stoloniferum virus F. Virus Genes 2005, 31:175-183.
30. Kim J.W., Kim S.Y., Kim K.M. Genome organization and expression of the Penicillium stoloniferum virus S. Virus Genes 2003, 27:249-256.
31. Lawton J.A., Estes M.K., Prasad B.V.V. Three-dimensional visualization of mRNA release from actively transcribing rotavirus particles. Nature Structural Biology 1997, 4:118-121.
32. Li L., Tian Q., Du Z., Duns G.J., Chen J. A novel double-stranded RNA virus detected in Primula malacoides is a plant-isolated partitivirus closely related to partitivirus infecting fungal species. Archives of Virology 2009, 154:565-572.
33. Lin Y.H., Chiba S., Tani A., Kondo H., Sasaki A., Kanematsu S., et al. A novel quadripartite dsRNA virus isolated from a phytopathogenic filamentous fungus, Rosellinia necatrix. Virology 2012, 426:42-50.
34. Liu H., Fu Y., Xie J., Cheng J., Ghabrial S.A., Li G., et al. Widespread horizontal gene transfer from double-stranded RNA viruses to eukaryotic nuclear genomes. Journal of Virology 2011, 84:11876-11887.
35. Lu X., McDonald S.M., Tortorici M.A., Tao Y.J., Vasquez-Del Carpio R., Nibert M.L., et al. Mechanism for coordinated RNA packaging and genome replication by rotavirus polymerase VP1. Structure 2008, 16:1678-1688.
36. Luque D., González J.M., Garriga D., Ghabrial S.A., Havens W.M., Trus B., et al. The T=1 capsid protein of Penicillium chrysogenum virus is formed by a repeated helix-rich core indicative of gene duplication. Journal of Virology 2010, 84:7256-7266.
37. Maniatis T., Venable J.H., Lerman L.S. The structure of psi DNA. Journal of Molecular Biology 1974, 84:37-64.
38. McClain B., Settembre E., Temple B.R., Bellamy A.R., Harrison S.C. X-ray crystal structure of the rotavirus inner capsid particle at 3.8 Å resolution. Journal of Molecular Biology 2010, 397:587-599.
39. Mendez I.I., Weiner S.G., She Y.M., Yeager M., Coombs K.M. Conformational changes accompany activation of reovirus RNA-dependent RNA transcription. Journal of Structural Biology 2008, 162:277-289.
40. Naitow H., Tang J., Canady M., Wickner R.B., Johnson J.E. L-A virus at 3.4 Å resolution reveals particle architecture and mRNA decapping mechanism. Nature Structural Biology 2002, 9:725-728.
41. Nibert M.L., Woods K.M., Upton S.J., Ghabrial S.A. Cryspovirus: A new genus of protozoan viruses in the family Partitiviridae. Archives of Virology 2009, 154:1959-1965.
42. Ochoa W.F., Havens W.M., Sinkovits R.S., Nibert M.L., Ghabrial S.A., Baker T.S. Partitivirus structure reveals a 120-subunit, helix-rich capsid with distinctive surface arches formed by quasisymmetric coat-protein dimers. Structure 2008, 16:776-786.
43. Oh C.S., Hillman B.I. Genome organization of a partitivirus from the filamentous ascomycete Atkinsonella hypoxylon. Journal of General Virology 1995, 76:1461-1470.
44. Ortín J., Parra F. Structure and function of RNA replication. Annual Review of Microbiology 2006, 60:305-326.
45. Pan J., Dong L., Lin L., Ochoa W.F., Sinkovits R.S., Havens W.M., et al. Atomic structure reveals the unique capsid organization of a dsRNA virus. Proceedings of the National Academy of Sciences of the United States of America 2009, 106:4225-4230.
46. Pan J., Vakharia V.N., Tao Y.J. The structure of a birnavirus polymerase reveals a distinct active site topology. Proceedings of the National Academy of Sciences of the United States of America 2007, 104:7385-7390.
47. Reinisch K.M., Nibert M.L., Harrison S.C. Structure of the reovirus core at 3.6-Å resolution. Nature 2000, 404:960-967.
48. Sasaki A., Kanematsu S., Onoue M., Oyama Y., Yoshida K. Infection of Rosellinia necatrix with purified viral particles of a member of Partitiviridae (RnPV1-W8). Archives of Virology 2006, 151:697-707.
49. Sen A., Heymann J.B., Cheng N., Qiao J., Mindich L., Steven A.C. Initial location of the RNA-dependent RNA polymerase in the bacteriophage φ6 procapsid determined by cryo-electron microscopy. The Journal of Biological Chemistry 2008, 283:12227-12231.
50. Tang J., Ochoa W.F., Li H., Havens W.M., Nibert M.L., Ghabrial S.A., et al. Structure of Fusarium poae virus 1 shows conserved and variable elements of partitivirus capsids and evolutionary relationships to picobirnavirus. Journal of Structural Biology 2010, 172:363-371.
51. Tang J., Ochoa W.F., Sinkovits R.S., Poulos B.T., Ghabrial S.A., Lightner D.V., et al. Infectious myonecrosis virus has a totivirus-like, 120-subunit capsid, but with fiber complexes at the fivefold axes. Proceedings of the National Academy of Sciences of the United States of America 2008, 105:17526-17531.
52. Tang J., Pan J., Havens W.M., Ochoa W.F., Guu T.S., Ghabrial S.A., et al. Backbone trace of partitivirus capsid protein from electron cryomicroscopy and homology modeling. Biophysical Journal 2010, 99:685-694.
53. Tao Y., Farsetta D.L., Nibert M.L., Harrison S.C. RNA synthesis in a cage-Structural studies of reovirus polymerase λ3. Cell 2002, 111:733-745.
54. Willenborg J., Menzel W., Vetten H.J., Maiss E. Molecular characterization of two alphacryptovirus dsRNAs isolated from Daucus carota. Archives of Virology 2009, 154:541-543.
55. Yang C., Ji G., Liu H., Zhang K., Liu G., Sun F., et al. Cryo-EM structure of a transcribing cypovirus. Proceedings of the National Academy of Sciences of the United States of America 2012, 109:6118-6123.
56. Yu X., Jin L., Zhou Z.H. 3.88 Å structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy. Nature 2008, 453:415-419.
57. Zhang X., Walker S.B., Chipman P.R., Nibert M.L., Baker T.S. Reovirus polymerase λ3 localized by cryo-electron microscopy of virions at a resolution of 7.6 Å. Nature Structural Biology 2003, 10:1011-1018.
58. Zhou Z.H., Baker M.L., Jiang W., Dougherty M., Jakana J., Dong G., et al. Electron cryomicroscopy and bioinformatics suggest protein fold models for rice dwarf virus. Nature Structural Biology 2001, 8:868-873.
59. Ziegler A., Matoušek J., Steger G., Schubert J. Complete sequence of a cryptic virus from hemp (Cannabis sativa). Archives of Virology 2012, 157:383-385.