Skip to content
1887

Journal of General Virology header logo Journal of General Virology

Volume 90, Issue 9

A novel putative virus of type B (Ascomycota: Helotiaceae) has a composite genome with endornavirus affinities No Access

Abstract

Ascospore and mycelial isolates of type B were found to contain three different dsRNA molecules with approximate lengths of 11, 5 and 3 kb. The 11 kb dsRNA encoded the genome of a putative virus and is named type B RNA virus XL (GaBRV-XL). GaBRV-XL probably exists in an unencapsulated state. We identified two distinct dsRNAs (10 374 and 10 375 bp) of GaBRV-XL, both of which coded for the same putative polyprotein (3249 amino acids) and contained four regions similar to putative viral methyltransferases, DExH box helicases, viral RNA helicase 1 and RNA-dependent RNA polymerases. While a cysteine-rich region with several CxCC motifs in GaBRV-XL was similar to that of putative endornaviruses, cluster analyses of conserved regions revealed GaBRV-XL to be distinct from a broad range of viral taxa but most closely related to virus 3. Collectively, these findings suggest that GaBRV-XL represents a novel virus group related to endornaviruses.

  • Received:
  • Accepted:
  • Published Online:
© SGM
Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.011973-0
2009-09-01
2025-04-20
Loading full text...

Full text loading...

References

  1. Abascal, F., Zardoya, R. & Posada, D.(2005). ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21, 2104–2105.[CrossRef] [Google Scholar]
  2. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J.(1997). Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25, 3389–3402.[CrossRef] [Google Scholar]
  3. Chen, J., Wei, C. B., Zheng, H. Y., Shi, Y. H., Adams, M. J., Lin, L., Zhang, Q. Y., Wang, S. J. & Chen, J. P.(2005). Characterisation of the welsh onion isolate of Shallot yellow stripe virus from China. Arch Virol 150, 2091–2099.[CrossRef] [Google Scholar]
  4. Coutts, R. H.(2005). First report of an endornavirus in the Cucurbitaceae. Virus Genes 31, 361–362.[CrossRef] [Google Scholar]
  5. De Tomassi, A., Pizzuti, M., Graziani, R., Sbardellati, A., Altamura, S., Paonessa, G. & Traboni, C.(2002). Cell clones selected from the Huh7 human hepatoma cell line support efficient replication of a subgenomic GB virus B replicon. J Virol 76, 7736–7746.[CrossRef] [Google Scholar]
  6. Diao, A., Chen, J., Gitton, F., Antoniw, J. F., Mullins, J., Hall, A. M. & Adams, M. J.(1999a). Sequences of European wheat mosaic virus and Oat golden stripe virus and genome analysis of the genus Furovirus. Virology 261, 331–339.[CrossRef] [Google Scholar]
  7. Diao, A., Chen, J., Ye, R., Zheng, T., Yu, S., Antoniw, J. F. & Adams, M. J.(1999b). Complete sequence and genome properties of Chinese wheat mosaic virus, a new furovirus from China. J Gen Virol 80, 1141–1145. [Google Scholar]
  8. Fukuhara, T., Moriyama, H. & Nitta, T.(1995). The unusual structure of a novel RNA replicon in rice. J Biol Chem 270, 18147–18149.[CrossRef] [Google Scholar]
  9. Fukuhara, T., Koga, R., Aoki, N., Yuki, C., Yamamoto, N., Oyama, N., Udagawa, T., Horiuchi, H., Miyazaki, S. & other authors(2005). The wide distribution of endornaviruses, large double-stranded RNA replicons with plasmid-like properties. Arch Virol 151, 995–1002. [Google Scholar]
  10. Gentit, P., Foissac, X., Svanella-Dumas, L., Peypelut, M., Macquaire, G. & Candresse, T.(2001). Biological properties and partial molecular characterisation of two foveaviruses associated with similar disorders of cherry trees. Acta Hortic 550, 161–168. [Google Scholar]
  11. Gibbs, M. J., Koga, R., Moriyama, H., Pfeiffer, P. & Fukuhara, T.(2000). Phylogenetic analysis of some large double-stranded RNA replicons from plants suggests they evolved from a defective single-stranded RNA virus. J Gen Virol 81, 227–233. [Google Scholar]
  12. Giritch, A., Ganal, M., Stephan, U. W. & Bäumlein, H.(1998). Structure, expression and chromosomal localisation of the metallothionein-like gene family of tomato. Plant Mol Biol 37, 701–714.[CrossRef] [Google Scholar]
  13. Gomez de Cedrón, M., Ehsani, N., Mikkola, M. L., García, J. A. & Kääriäinen, L.(1999). RNA helicase activity of Semliki Forest virus replicase protein NSP2. FEBS Lett 448, 19–22.[CrossRef] [Google Scholar]
  14. Grebennikova, T. V., Zaberezhnyi, A. D., Sergeev, V. A., Biketov, S. F., Aliper, T. I. & Nepoklonov, E. A.(1999). Genetic characteristics of the KC vaccine strain of hog cholera virus: comparative analysis of the primary sequence of surface glycoprotein Erns, E1, and E2 genes. Mol Gen Mikrobiol Virusol 2, 34–40 (in Russian). [Google Scholar]
  15. Guindon, S., Lethiec, F., Duroux, P. & Gascuel, O.(2005).phyml Online – a web server for fast maximum likelihood-based phylogenetic interference. Nucleic Acids Res 33, W557–W559.[CrossRef] [Google Scholar]
  16. Hacker, C. V., Brasier, C. M. & Buck, K. W.(2005). A double-stranded RNA from a Phytophthora species is related to the plant endornaviruses and contains a putative UDP glycosyltransferase gene. J Gen Virol 86, 1561–1570.[CrossRef] [Google Scholar]
  17. Hantula, J. & Müller, M. M.(1997). Variation within Gremmeniella abietina in Finland and other countries as determined by random amplified microsatellites (RAMS). Mycol Res 101, 169–175.[CrossRef] [Google Scholar]
  18. Hillman, B. I., Supyani, S., Kondo, H. & Suzuki, N.(2004). A reovirus of the fungus Cryphonectria parasitica that is infectious as particles and related to the Coltivirus genus of animal pathogens. J Virol 78, 892–898.[CrossRef] [Google Scholar]
  19. Huelsenbeck, J. P., Ronquist, F., Nielsen, R. & Bollback, J. P.(2001). Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294, 2310–2314.[CrossRef] [Google Scholar]
  20. ICTVdB Management(2006). 00.108.0.01. Endornavirus. In ICTVdB – The Universal Virus Database, version 4. Edited by C. Büchen-Osmond. New York: Columbia University.
  21. Kadaré, G. & Haenni, A. L.(1997). Virus-encoded RNA helicases. J Virol 71, 2583–2590. [Google Scholar]
  22. Koenig, R., Pleij, C. W. & Huth, W.(1999). Molecular characterization of a new furovirus mainly infecting rye. Arch Virol 144, 2125–2140.[CrossRef] [Google Scholar]
  23. Koonin, E. V. & Dolja, V. V.(1993). Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. Crit Rev Biochem Mol Biol 28, 375–430.[CrossRef] [Google Scholar]
  24. Kumar, S., Tamura, K. & Nei, M.(2004).mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150–163.[CrossRef] [Google Scholar]
  25. Lu, J., Zheng, Y., Yamagishi, H., Odaka, M., Tsujimura, M., Maeda, M. & Endo, I.(2003). Motif CXCC in nitrile hydratase activator is critical for NHase biogenesis in vivo. FEBS Lett 553, 391–396.[CrossRef] [Google Scholar]
  26. Marchler-Bauer, A. & Bryant, S. H.(2004). CD-Search: protein domain annotations on the fly. Nucleic Acids Res 32, W327–W331.[CrossRef] [Google Scholar]
  27. Mayer, D., Thayer, T. M., Hofmann, M. A. & Tratschin, J. D.(2003). Establishment and characterisation of two cDNA-derived strains of classical swine fever virus, one highly virulent and one avirulent. Virus Res 98, 105–116.[CrossRef] [Google Scholar]
  28. Moriyama, H., Horiuchi, H., Nitta, T. & Fukuhara, T.(1999). Unusual inheritance of evolutionarily-related double-stranded RNAs in interspecific hybrid between rice plants Oryza sativa and Oryza rufipogon. Plant Mol Biol 39, 1127–1136.[CrossRef] [Google Scholar]
  29. Morris, T. J. & Dodds, J. A.(1979). Isolation and analysis of double-stranded RNA from virus-infected plant and fungal tissue. Phytopathology 69, 854–858.[CrossRef] [Google Scholar]
  30. Müller, M. M. & Uotila, A.(1997). The diversity of Gremmeniella abietina var. abietina FAST-profiles. Mycol Res 101, 557–564.[CrossRef] [Google Scholar]
  31. Müller, M. M., Kantola, R. & Kitunen, V.(1994). Combining sterol and fatty acid profiles for the characterization of fungi. Mycol Res 98, 593–603.[CrossRef] [Google Scholar]
  32. Nakao, H., Okamoto, H., Tokita, H., Inoue, T., Iizuka, H., Pozzato, G. & Mishiro, S.(1996). Full-length genomic sequence of a hepatitis C virus genotype 2c isolate (BEBE1) and the 2c-specific PCR primers. Arch Virol 141, 701–704.[CrossRef] [Google Scholar]
  33. Osaki, H., Nakamura, H., Sasaki, A., Matsumoto, N. & Yoshida, K.(2006). An endornavirus from a hypovirulent strain of the violet root rot fungus, Helicobasidium mompa. Virus Res 118, 143–149.[CrossRef] [Google Scholar]
  34. Page, R. D. M.(1996). TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12, 357–358. [Google Scholar]
  35. Pfeiffer, P.(1998). Nucleotide sequence, genetic organization and expression strategy of the double-stranded RNA associated with the ‘447’ cytoplasmic male sterility trait in Vicia faba. J Gen Virol 79, 2349–2358. [Google Scholar]
  36. Pfeiffer, P., Jung, J. L., Heitzler, J. & Keith, G.(1993). Unusual structure of the double-stranded RNA associated with the ‘447’ cytoplasmic male sterility in Vicia faba. J Gen Virol 74, 1167–1173.[CrossRef] [Google Scholar]
  37. Phillips, A. J. L.(1993). The use of protoplasts for the preparation of homokaryons from heterokaryotic isolates of Rhizoctonia solani. Mycol Res 97, 456–460.[CrossRef] [Google Scholar]
  38. Ratti, C., Budge, G., Ward, L., Clover, G., Rubies-Autonell, C. & Henry, C.(2004). Detection and relative quantitation of Soil-borne cereal mosaic virus (SBCMV) and Polymyxa graminis in winter wheat using real-time PCR (TaqMan). J Virol Methods 122, 95–103.[CrossRef] [Google Scholar]
  39. Rong, R., Rao, S., Scott, S. W., Carner, G. R. & Tainter, F. H.(2002). Complete sequence of the genome of two dsRNA viruses from Discula destructiva. Virus Res 90, 217–224.[CrossRef] [Google Scholar]
  40. Ronquist, F. & Huelsenbeck, J. P.(2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572–1574.[CrossRef] [Google Scholar]
  41. Rott, M. E. & Jelkmann, W.(2005). Little cherry virus-2: sequence and genomic organization of an unusual member of the Closteroviridae. Arch Virol 150, 107–123.[CrossRef] [Google Scholar]
  42. Rozanov, M. N., Koonin, E. V. & Gorbalenya, A. E.(1992). Conservation of the putative methyltransferase domain: a hallmark of the ‘Sindbis-like’ supergroup of positive-strand RNA viruses. J Gen Virol 73, 2129–2134.[CrossRef] [Google Scholar]
  43. Schwer, B.(2001). A new twist on RNA helicases: DExH/D box proteins as RNPases. Nat Struct Biol 8, 113–116.[CrossRef] [Google Scholar]
  44. Shirako, Y. & Wilson, T. M.(1993). Complete nucleotide sequence and organization of the bipartite RNA genome of soil-borne wheat mosaic virus. Virology 195, 16–32.[CrossRef] [Google Scholar]
  45. Tanner, N. K. & Linder, P.(2001). DexD/H box RNA helicases: from generic motors to specific dissociation functions. Mol Cell 8, 251–262.[CrossRef] [Google Scholar]
  46. Thompson, J. D., Higgins, D. G. & Gibson, T. J.(1994).clustalw: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673–4680.[CrossRef] [Google Scholar]
  47. Tuomivirta, T. T. & Hantula, J.(2003). Two unrelated double-stranded RNA patterns in Gremmeniella abietina var. abietina type A code for putative viruses of the families Totiviridae and Partitiviridae. Arch Virol 148, 2293–2305.[CrossRef] [Google Scholar]
  48. Tuomivirta, T. T. & Hantula, J.(2005). Three unrelated viruses occur in a single isolate of Gremmeniella abietina var. abietina type A. Virus Res 110, 31–39.[CrossRef] [Google Scholar]
  49. Tuomivirta, T. T., Uotila, A. & Hantula, J.(2002). Two independent double-stranded RNA patterns occur in the Finnish Gremmeniella abietina var. abietina type A. For Pathol 32, 197–205.[CrossRef] [Google Scholar]
  50. Tzanetakis, I. E. & Martin, R. R.(2005). New features in the genus Ilarvirus revealed by the nucleotide sequence of Fragaria chiloensis latent virus. Virus Res 112, 32–37.[CrossRef] [Google Scholar]
  51. Uotila, A., Hantula, J., Väätänen, A. K. & Hamelin, C.(2000). Hybridization between two biotypes of Gremmeniella abietina var. abietina in artificial pairing. For Pathol 30, 211–219.[CrossRef] [Google Scholar]
  52. Valverde, R. A. & Gutierrez, D. L.(2007). Transmission of a dsRNA in bell pepper and evidence that it consists of the genome of an endornavirus. Virus Genes 35, 399–403.[CrossRef] [Google Scholar]
  53. van der Heijden, M. W. & Bol, J. F.(2002). Composition of alphavirus-like replication complexes: involvement of virus and host encoded proteins. Arch Virol 147, 875–898.[CrossRef] [Google Scholar]
  54. Velasco, L., Janssen, D., Ruiz-Garcia, L., Segundo, E. & Cuadrado, I. M.(2002). The complete nucleotide sequence and development of a differential detection assay for a pepper mild mottle virus (PMMoV) isolate that overcomes L3 resistance in pepper. J Virol Methods 106, 135–140.[CrossRef] [Google Scholar]
  55. Wakarchuk, D. A. & Hamilton, R. I.(1990). Partial nucleotide sequence from enigmatic dsRNAs in Phaseolus vulgaris. Plant Mol Biol 14, 637–639.[CrossRef] [Google Scholar]
  56. Xie, J., Wei, D., Jiang, D., Fu, Y., Li, G., Ghabrial, S. & Peng, Y.(2006). Characterization of debilitation-associated mycovirus infecting the plant-pathogenic fungus Sclerotinia sclerotiorum. J Gen Virol 87, 241–249.[CrossRef] [Google Scholar]
  57. Yang, Z. N. & Mirkov, T. E.(1997). Sequence and relationships of sugarcane mosaic and sorghum mosaic virus strains and development of RT-PCR-based RFLPs for strain discrimination. Phytopathology 87, 932–939.[CrossRef] [Google Scholar]
  58. Yang, J., Chen, J., Chen, J., Jiang, H., Zhao, Q. & Adams, M. J.(2001). Sequence of a second isolate of Chinese wheat mosaic furovirus. J Phytopathol 149, 135–140.[CrossRef] [Google Scholar]
  59. Zdobnov, E. M. & Apweiler, R.(2001). InterProScan – an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17, 847–848.[CrossRef] [Google Scholar]
/content/journal/jgv/10.1099/vir.0.011973-0
Loading
A novel putative virus of Gremmeniella abietina type B (Ascomycota: Helotiaceae) has a composite genome with endornavirus affinities
J. Gen. Virol. 90, 2299 (2009); https://doi.org/10.1099/vir.0.011973-0
/content/journal/jgv/10.1099/vir.0.011973-0
/content/journal/jgv/10.1099/vir.0.011973-0
Loading

Data & Media loading...

Supplements

[PDF file of Supplementary Tables S1 and S2](56 KB)

PDF

[PDF file of Supplementary Figs S1-S4](77 KB)

PDF

[Text file of Supplementary Figs S1-S4](19 KB)

TEXT

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error