A new virus from the plant pathogenic oomycete Phytophthora infestans with an 8 kb dsRNA genome: The sixth member of a proposed new virus genus

Virology

Volumn 435, Issue 2, 2013, Pages 341-349

  Cai, Guohong ^a   Krychiw, Jason F ^a   Myers, Kevin ^b   Fry, William E ^b   Hillman, Bradley I ^a  

^a RUTGERS UNIVERSITY   (United States)

^b Cornell University ^*  (United States)

Author keywords

Fungal virus; New virus genus; Oomycete; Phytophthora infestans; Potato late blight; RNA virus

Indexed keywords

DOUBLE STRANDED RNA; RNA DIRECTED RNA POLYMERASE;

ARTICLE; GENETIC LINKAGE; GENOME ANALYSIS; MIXED INFECTION; NEW GENUS; NEW SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; OOMYCETES; OPEN READING FRAME; PHYTOPHTHORA INFESTANS; PHYTOPHTHORA INFESTANS RNA VIRUS 3; PHYTOPHTHORA INFESTANS RNA VIRUS 4; PRIORITY JOURNAL; PROTEIN FUNCTION; RNA VIRUS; VIRUS CHARACTERIZATION; VIRUS FORMS; VIRUS GENOME; VIRUS ISOLATION;

COMPUTATIONAL BIOLOGY; GENOME, VIRAL; MOLECULAR SEQUENCE DATA; OOMYCETES; OPEN READING FRAMES; PHENOTYPE; PHYTOPHTHORA INFESTANS; PLANT DISEASES; RNA VIRUSES; SEQUENCE ANALYSIS, DNA; SOLANUM TUBEROSUM; SPECIES SPECIFICITY;

FUNGI; NARNAVIRIDAE; PHYTOPHTHORA INFESTANS; RNA VIRUSES; UNCLASSIFIED DSRNA VIRUSES;

EID: 84871687046     PISSN: 00426822     EISSN: 10960341     Source Type: Journal    
DOI: 10.1016/j.virol.2012.10.012     Document Type: Article

References (46)

1. Adl S.M., Simpson A.G.B., Farmer M.A., Andersen R.A., Anderson O.R., Barta J.R., Bowser S.S., Brugerolle G., Fensome R.A., Fredericq S., James T.Y., Karpov S., Kugrens P., Krug J., Lane C.E., Lewis L.A., Lodge J., Lynn D.H., Mann D.G., McCourt R.M., Mendoza L., Moestrup O., Mozley-Standridge S.E., Nerad T.A., Shearer C.A., Smirnov A.V., Spiegel F.W., Taylor M. The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J. Eukaryot. Microbiol. 2005, 52:399-451.
2. Al Rwahnih M., Daubert S., Úrbez-Torres J., Cordero F., Rowhani A. Deep sequencing evidence from single grapevine plants reveals a virome dominated by mycoviruses. Arch. Virol. 2011, 156:397-403.
3. Attoui H., Billoir F., Cantaloube J.F., Biagini P., de Micco P., de Lamballerie X. Strategies for the sequence determination of viral dsRNA genomes. J.Virol. Methods 2000, 89:147-158.
4. Baird S.D., Turcotte M., Korneluk R.G., Holcik M. Searching for IRES. RNA 2006, 12:1755-1785.
5. Bateman A., Coin L., Durbin R., Finn R.D., Hollich V., Griffiths-Jones S., Khanna A., Marshall M., Moxon S., Sonnhammer E.L.L., Studholme D.J., Yeats C., Eddy S.R. The Pfam protein families database. Nucl. Acids Res. 2004, 32(suppl_1):D138-141.
6. Bogatyreva N.S., Finkelstein A.V., Galzitskaya O.V. Trend of amino acid composition of proteins of different taxa. Journal of Bioinformatics & Computational Biology 2006, 4:597-608.
7. Bohlander S.K., Espinosa R., Lebeau M.M., Rowley J.D., Diaz M.O. A method for the rapid sequence-independent amplification of microdissected chromosomal material. Genomics 1992, 13:1322-1324.
8. Bompfünewerer A., Backofen R., Bernhart S., Hertel J., Hofacker I., Stadler P., Will S. Variations on RNA folding and alignment: lessons from Benasque. J. Math. Biol. 2008, 56:129-144.
9. Brierley I., Pennell S., Gilbert R.J.C. Viral RNA pseudoknots: versatile motifs in gene expression and replication. Nat. Rev. Microbiol. 2007, 5:598-610.
10. Brooks D.J., Fresco J.R., Lesk A.M., Singh M. Evolution of amino acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code. Mol. Biol. Evol. 2002, 19:1645-1655.
11. Bruenn J.A. A closely related group of RNA-dependent RNA polymerases from double-stranded RNA viruses. Nucl. Acids Res. 1993, 21:5667-5669.
12. Cai, G., Myers, K., Fry, W. E., Hillman, B.I. unpublished results.
13. Cai G., Myers K., Fry W., Hillman B. A member of the virus family Narnaviridae, from the plant pathogenic oomycete Phytophthora infestans. Arch. Virol. 2012, 157:165-169.
14. Cai G., Myers K., Hillman B.I., Fry W.E. A novel virus of the late blight pathogen, Phytophthora infestans, with two RNA segments and a supergroup 1 RNA-dependent RNA polymerase. Virology 2009, 392:52-61.
15. Chen B.J., Lamb R.A. Mechanisms for enveloped virus budding: can some viruses do without an ESCRT?. Virology 2008, 372:221-232.
16. Condron B.G., Atkins J.F., Gesteland R.F. Frameshifting in gene 10 of bacteriophage T7. J. Bacteriol. 1991, 173:6998-7003.
17. Dam E.B., Pleij C.W.A., Bosch L. RNA pseudoknots: translational frameshifting and readthrough on viral RNAs. Virus Genes 1990, 4:121-136.
18. Darty K., Denise A., Ponty Y. VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics 2009, 25:1974-1975.
19. De Wet J., Bihon W., Preisig O., Wingfield B.D., Wingfield M.J. Characterization of a novel dsRNA element in the pine endophytic fungus Diplodia scobiculata. Arch. Virol. 2011, 156:1199-1208.
20. den Boon J.A., Snijder E.J., Chirnside E.D., de Vries A.A., Horzinek M.C., Spaan W.J. Equine arteritis virus is not a togavirus but belongs to the coronaviruslike superfamily. J. Virol. 1991, 65:2910-2920.
21. Doudna J.A., Sarnow P. Translation initiation by viral internal ribosome entry sites. Translational Control in Biology and Medicine 2007, 129-153. Cold Spring Harbor Laboratory Press. M.B. Mathews, N. Sonenberg, J.W.B. Hershey (Eds.).
22. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32:1792-1797.
23. Filbin M.E., Kieft J.S. Toward a structural understanding of IRES RNA function. Curr. Opin. Struct. Biol. 2009, 19:267-276.
24. Freed E.O. Viral late domains. J. Virol. 2002, 76:4679-4687.
25. Fry W. Phytophthora infestans: the plant (and R gene) destroyer. Mol. Plant Pathol. 2008, 9:385-402.
26. Giedroc D.P., Theimer C.A., Nixon P.L. Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting. J. Mol. Biol. 2000, 298:167-185.
27. Goodwin S.B. The population genetics of Phytophthora. Phytopathology 1997, 87:462-473.
28. Herrero N., Zabalgogeazcoa I. Mycoviruses infecting the endophytic and entomopathogenic fungus Tolypocladium cylindrosporum. Virus Res. 2011, 160:409-413.
29. Huang C.-H., Lu C.L., Chiu H.-T. A heuristic approach for detecting RNA H-type pseudoknots. Bioinformatics 2005, 21:3501-3508.
30. Hulo N., Bairoch A., Bulliard V., Cerutti L., De Castro E., Langendijk-Genevaux P.S., Pagni M., Sigrist C.J.A. The PROSITE database. Nucleic Acids Res. 2006, 34(suppl_1):D227-230.
31. Jacks T., Madhani H.D., Masiarz F.R., Varmus H.E. Signals for ribosomal frameshifting in the Rous sarcoma virus gag-pol region. Cell 1988, 55:447-458.
32. Jacks T., Townsley K., Varmus H.E., Majors J. Two efficient ribosomal frameshifting events are required for synthesis of mouse mammary tumor virus gag-related polyproteins. Proc. Natl. Acad. Sci. USA 1987, 84:4298-4302.
33. Kozak M. Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell 1986, 44:283-292.
34. Kozlakidis Z., Hacker C.V., Bradley D., Jamal A., Phoon X., Webber J., Brasier C.M., Buck K.W., Coutts R.H.A. Molecular characterisation of two novel double-stranded RNA elements from Phlebiopsis gigantea. Virus Genes 2009, 39:132-136.
35. Lütcke H.A., Chow K.C., Mickel F.S., Moss K.A., Kern H.F., Scheele G.A. Selection of AUG initiation codons differs in plants and animals. EMBO J. 1987, 6:43-48.
36. Lambden P.R., Cooke S.J., Caul E.O., Clarke I.N. Cloning of noncultivatable human rotavirus by single primer amplification. J. Virol. 1992, 66:1817-1822.
37. Marchler-Bauer A., Bryant S.H. CD-Search: protein domain annotations on the fly. Nucleic Acids Res. 2004, 32(suppl_2):W327-331.
38. Moore R., Dixon M., Smith R., Peters G., Dickson C. Complete nucleotide sequence of a milk-transmitted mouse mammary tumor virus: two frameshift suppression events are required for translation of gag and pol. J. Virol. 1987, 61(2):480-490.
39. Parkin N.T., Chamorro M., Varmus H.E. Human immunodeficiency virus type 1 gag-pol frameshifting is dependent on downstream mRNA secondary structure: demonstration by expression in vivo. J. Virol. 1992, 66:5147-5151.
40. Reeder J., Steffen P., Giegerich R. pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows. Nucleic Acids Res. 2007, 35(suppl 2):W320-W324.
41. Spear A., Sisterson M.S., Yokomi R., Stenger D.C. Plant-feeding insects harbor double-stranded RNA viruses encoding a novel proline-alanine rich protein and a polymerase distantly related to that of fungal viruses. Virology 2010, 404:304-311.
42. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Method. Mol. Biol. Evol. 2011, 28:2731-2739.
43. Wirblich C., Bhattacharya B., Roy P. Nonstructural protein 3 of bluetongue virus assists virus release by recruiting ESCRT-I protein Tsg101. J. Virol. 2006, 80:460-473.
44. Wu T.-Y., Hsieh C.-C., Hong J.-J., Chen C.-Y., Tsai Y.-S. IRSS: a web-based tool for automatic layout and analysis of IRES secondary structure prediction and searching system in silico. BMC Bioinformatics 2009, 10:160.
45. Yu J., Kwon S.-J., Lee K.-M., Son M., Kim K.-H. Complete nucleotide sequence of double-stranded RNA viruses from Fusarium graminearum strain DK3. Arch. Virol. 2009, 154:1855-1858.
46. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31:3406-3415.