1887

Abstract

This study reports the first sequence of a flexuous rod-shaped mycovirus and also the first molecular characterization of a virus that infects the plant-pathogenic fungus . The mycovirus virus F (BVF) contains an ssRNA genome of 6827 nucleotides and a poly(A) tract at or very near the 3′ terminus. Computer analysis of the genomic cDNA sequence of BVF revealed two potential open reading frames (ORFs) encoding proteins of 212 kDa (ORF1) and 32 kDa (ORF2). ORF1 showed significant sequence identity to the RNA-dependent RNA polymerase (RdRp)-containing proteins of plant ‘tymo-’ and ‘potex-like’ viruses. However, the ORF1 protein contained an opal putative readthrough codon between the helicase and RdRp regions, a feature not seen in this position in ‘tymo-’ and ‘potex-like’ replicases sequenced to date. ORF2 shared amino acid similarity with coat proteins of plant ‘potex-like’ viruses. Three untranslated regions were present in the genome, comprising a region of 63 nucleotides preceding the initiation codon of ORF1, a 93 nucleotide stretch between ORFs 1 and 2 and a 3′-terminal region of 70 nucleotides preceding the poly(A) tract. The nucleotide sequence of a putative defective RNA (D-RNA) of 829 nucleotides was also determined. The D-RNA contained one potential ORF comprising the N-terminal region of the replicase fused in-frame to the C-terminal region of the coat protein. It is proposed that the mycovirus BVF belongs to a new, as yet unassigned genus in the plant ‘potex-like’ virus group.

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2001-01-01
2019-09-16
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References

  1. Abou-Ghanem, N., Saldarelli, P., Minafra, A., Buzkan, N., Castellano, M. A. & Martelli, G. P. ( 1997; ). Properties of grapevine virus D, a novel putative trichovirus. Journal of Plant Pathology 78, 15-25.
    [Google Scholar]
  2. Ballance, D. J. ( 1990; ). Transformation systems for filamentous fungi and an overview of fungal gene structure. In Molecular Industrial Mycology: Systems and Applications for Filamentous Fungi, vol. 8 , pp. 1-29. Edited by S. A. Long& R. M. Berka. New York:Dekker.
  3. Bransom, K. L., Weiland, J. J., Tsai, C.-H. & Dreher, T. W. ( 1995; ). Coding density of the turnip yellow mosaic virus genome: roles of the overlapping coat protein and p206-readthrough coding regions. Virology 206, 403-412.[CrossRef]
    [Google Scholar]
  4. Buck, K. W. ( 1986; ). Fungal virology – an overview. In Fungal Virology , pp. 1-84. Edited by K. W. Buck. Boca Raton, FL:CRC Press.
  5. Buck, K. W. ( 1996; ). Comparison of the replication of positive-stranded RNA viruses of plants and animals. Advances in Virus Research 47, 159-251.
    [Google Scholar]
  6. Buck, K. W. ( 1998; ). Molecular variability of viruses of fungi. In Molecular Variability of Fungal Pathogens , pp. 53-72. Edited by P. D. Bridge, Y. Couteaudier& J. M. Clarkson. Wallingford, UK:CAB International.
  7. Calvert, L. A., Cuervo, M. I., Ospina, M. D., Fauquet, C. M. & Ramirez, B.-C. ( 1996; ). Characterization of cassava common mosaic virus and a defective RNA species. Journal of General Virology 77, 525-530.[CrossRef]
    [Google Scholar]
  8. Castro, M., Kramer, K., Valdivia, L., Ortiz, S., Benavente, J. & Castillo, A. ( 1999; ). A new double-stranded RNA mycovirus from Botrytis cinerea. FEMS Microbiology Letters 175, 95-99.[CrossRef]
    [Google Scholar]
  9. Coley-Smith, J. R., Verhoeff, K. & Jarvis, W. R. (1980). The Biology of Botrytis. London: Academic Press.
  10. Devereux, J., Haeberli, P. & Smithies, O. ( 1984; ). A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Research 12, 387-395.[CrossRef]
    [Google Scholar]
  11. Ding, S., Keese, P. & Gibbs, A. ( 1990a; ). The nucleotide sequence of the genomic RNA of kennedya yellow mosaic tymovirus-Jervis Bay isolate: relationships with potex- and carlaviruses. Journal of General Virology 71, 925-931.[CrossRef]
    [Google Scholar]
  12. Ding, S. W., Howe, J., Keese, P., Mackenzie, A., Meek, D., Osorio-Keese, M., Skotnicki, M., Srifah, P., Torronen, M. & Gibbs, A. ( 1990b; ). The tymobox, a sequence shared by most tymoviruses: its use in molecular studies of tymoviruses. Nucleic Acids Research 18, 1181-1187.[CrossRef]
    [Google Scholar]
  13. Dolja, V. V., Boyko, V. P., Agranovsky, A. A. & Koonin, E. V. ( 1991; ). Phylogeny of capsid proteins of rod-shaped and filamentous RNA plant viruses: two families with distinct patterns of sequence and probably structure conservation. Virology 184, 79-86.[CrossRef]
    [Google Scholar]
  14. Domier, L. L., Franklin, K. M., Shahabuddin, M., Hellmann, G. M., Overmeyer, J. H., Hiremath, S. T., Siaw, M. F., Lomonossoff, G. P., Shaw, J. G. & Rhoads, R. E. ( 1986; ). The nucleotide sequence of tobacco vein mottling virus RNA. Nucleic Acids Research 14, 5417-5430.[CrossRef]
    [Google Scholar]
  15. Dreher, T. W. & Bransom, K. L. ( 1992; ). Genomic RNA sequence of turnip yellow mosaic virus isolate TYMC, a cDNA-based clone with verified infectivity. Plant Molecular Biology 18, 403-406.[CrossRef]
    [Google Scholar]
  16. Edwards, M. C., Zhang, Z. & Weiland, J. J. ( 1997; ). Oat blue dwarf marafivirus resembles the tymoviruses in sequence, genome organization, and expression strategy. Virology 232, 217-229.[CrossRef]
    [Google Scholar]
  17. Felsenstein, J. ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.[CrossRef]
    [Google Scholar]
  18. Felsenstein, J. (1995). PHYLIP version 3.5. Department of Genetics, University of Washington, Seattle, WA, USA.
  19. Fisher, D. B. ( 1999; ). The estimated pore diameter for plasmodesmal channels in the Abutilon nectary trichome should be about 4 nm, rather than 3 nm. Planta 208, 299-300.[CrossRef]
    [Google Scholar]
  20. German, S., Candresse, T., Lanneau, M., Huet, J. C., Pernollet, J. C. & Dunez, T. ( 1990; ). Nucleotide sequence and genomic organization of apple chlorotic leaf spot closterovirus. Virology 179, 104-112.[CrossRef]
    [Google Scholar]
  21. Gibbs, A. & Keese, P. K. ( 1994; ). In search of the origins of viral genes. In Molecular Basis of Viral Evolution , pp. 76-90. Edited by A. J. Gibbs, C. H. Calisher& F. Garcia-Arenal. Cambridge:Cambridge University Press.
  22. Gorbalenya, A. E. & Koonin, E. V. ( 1989; ). Viral proteins containing the purine NTP-binding sequence pattern. Nucleic Acids Research 17, 8413-8440.[CrossRef]
    [Google Scholar]
  23. Gordon, K., Futterer, J. & Hohn, T. ( 1992; ). Efficient initiation of translation at non-AUG triplets in plant cells. Plant Journal 2, 809-813.
    [Google Scholar]
  24. Gull, K. ( 1978; ). Form and function of septa in filamentous fungi. In The Filamentous Fungi, vol. 3 , pp. 78-93. Edited by J. E. Smith& D. R. Berry. New York:John Wiley.
  25. Gull, K. & Trinci, A. P. J. ( 1971; ). Fine structure of spore germination in Botrytis cinerea. Journal of General Microbiology 68, 207-220.[CrossRef]
    [Google Scholar]
  26. Hamilton, W. D. O., Boccara, M., Robinson, D. J. & Baulcombe, D. C. ( 1987; ). The complete nucleotide sequence of tobacco rattle virus RNA-1. Journal of General Virology 68, 2563-2575.[CrossRef]
    [Google Scholar]
  27. Hansen, D. R., Van Alfen, N. K., Gillies, K. & Powell, W. A. ( 1985; ). Naked dsRNA associated with hypovirulence of Endothia parasitica is packaged in fungal vesicles. Journal of General Virology 66, 2605-2614.[CrossRef]
    [Google Scholar]
  28. Hong, Y., Cole, T. E., Brasier, C. M. & Buck, K. W. ( 1998; ). Novel structures of two virus-like RNA elements from a diseased isolate of the Dutch elm disease fungus, Ophiostoma novo-ulmi. Virology 242, 80-89.[CrossRef]
    [Google Scholar]
  29. Howitt, R. L. J., Beever, R. E., Pearson, M. N. & Forster, R. L. S. ( 1995; ). Presence of double-stranded RNA and virus-like particles in Botrytis cinerea. Mycological Research 99, 1472-1478.[CrossRef]
    [Google Scholar]
  30. Jelkmann, W. ( 1994; ). Nucleotide sequences of apple stem pitting virus and of the coat protein gene of a similar virus from pear associated with vein yellows disease and their relationship with potex- and carlaviruses. Journal of General Virology 75, 1535-1542.[CrossRef]
    [Google Scholar]
  31. Jelkmann, W. ( 1995; ). Cherry virus A: cDNA cloning of dsRNA, nucleotide sequence analysis and serology reveal a new plant capillovirus in sweet cherry. Journal of General Virology 76, 2015-2024.[CrossRef]
    [Google Scholar]
  32. Jelkmann, W., Maiss, E. & Martin, R. R. ( 1992; ). The nucleotide sequence and genome organization of strawberry mild yellow edge-associated potexvirus. Journal of General Virology 73, 475-479.[CrossRef]
    [Google Scholar]
  33. Kanyuka, K. V., Vishnichenko, V. K., Levay, K. E., Kondrikov, D. Yu., Ryabov, E. V. & Zavriev, S. K. ( 1992; ). Nucleotide sequence of shallot virus X RNA reveals a 5′-proximal cistron closely related to those of potexviruses and a unique arrangement of the 3′-proximal cistrons. Journal of General Virology 73, 2553-2560.[CrossRef]
    [Google Scholar]
  34. Koonin, E. V. ( 1991; ). The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses. Journal of General Virology 72, 2197-2206.[CrossRef]
    [Google Scholar]
  35. Koonin, E. V. & Dolja, V. V. ( 1993; ). Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. Critical Reviews in Biochemistry and Molecular Biology 28, 375-430.[CrossRef]
    [Google Scholar]
  36. Lakshman, D. K., Jian, J. & Tavantzis, S. M. ( 1998; ). A double-stranded RNA element from a hypovirulent strain of Rhizoctonia solani occurs in DNA form and is genetically related to the pentafunctional AROM protein of the shikimate pathway. Proceedings of the National Academy of Sciences, USA 95, 6425-6429.[CrossRef]
    [Google Scholar]
  37. Li, G. & Rice, C. M. ( 1993; ). The signal for translational readthrough of a UGA codon in Sindbis virus RNA involves a single cytidine residue immediately downstream of the termination codon. Journal of Virology 67, 5062-5067.
    [Google Scholar]
  38. Lucas, W. J. & Gilbertson, R. L. ( 1994; ). Plasmodesmata in relation to viral movement within leaf tissues. Annual Review of Phytopathology 32, 387-411.[CrossRef]
    [Google Scholar]
  39. MacFarlane, S. A., Taylor, S. C., King, D. I., Hughes, G. & Davies, J. W. ( 1989; ). Pea early browning virus RNA1 encodes four polypeptides including a putative zinc-finger protein. Nucleic Acids Research 17, 2245-2260.[CrossRef]
    [Google Scholar]
  40. Minafra, A., Saldarelli, P. & Martelli, G. P. ( 1997; ). Grapevine virus A: nucleotide sequence, genome organization, and relationship in the Trichovirus genus. Archives of Virology 142, 417-423.[CrossRef]
    [Google Scholar]
  41. Morozov, S. Yu., Kanyuka, K. V., Levay, K. E. & Zavriev, S. K. ( 1990; ). The putative RNA replicase of potato virus M: obvious sequence similarity with potex- and tymoviruses. Virology 179, 911-914.[CrossRef]
    [Google Scholar]
  42. Nuss, D. L. ( 1988; ). Deletion mutants of double-stranded RNA genetic elements found in plants and fungi. In RNA Genetics, vol. 2 , pp. 187-210. Edited by E. Domingo, J. J. Holland& P. Ahlquist. Boca Raton, FL:CRC Press.
  43. Ochi, M., Kashiwazaki, S., Hiratsuka, K., Namba, S. & Tsuchizaki, T. ( 1992; ). Nucleotide sequence of the 3′-terminal region of potato virus T RNA. Annals of the Phytopathological Society of Japan 58, 416-425.[CrossRef]
    [Google Scholar]
  44. Ohshima, K., Nakaya, T., Matsumura, T., Shikata, E. & Kimura, I. ( 1993; ). Nucleotide sequences of coat protein and 17K protein genes for a potato leafroll virus Japanese isolate. Annals of the Phytopathological Society of Japan 59, 204-208.[CrossRef]
    [Google Scholar]
  45. Revill, P. A., Davidson, A. D. & Wright, P. J. ( 1994; ). The nucleotide sequence and genome organization of mushroom bacilliform virus: a single-stranded RNA virus of Agaricus bisporus (Lange) Imbach. Virology 202, 904-911.[CrossRef]
    [Google Scholar]
  46. Roux, L. ( 1994; ). Defective-interfering viruses. In Encyclopedia of Virology, vol. 1 , pp. 320-323. Edited by R. G. Webster& A. Granoff. New York:Academic Press.
  47. 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. Journal of General Virology 73, 2129-2134.[CrossRef]
    [Google Scholar]
  48. Saldarelli, P., Minafra, A. & Martelli, G. P. ( 1996; ). The nucleotide sequence and genomic organization of grapevine virus B. Journal of General Virology 77, 2645-2652.[CrossRef]
    [Google Scholar]
  49. Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989). Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
  50. Sato, K., Yoshikawa, N. & Takahashi, T. ( 1993; ). Complete nucleotide sequence of the genome of an apple isolate of apple chlorotic leaf spot virus. Journal of General Virology 74, 1927-1931.[CrossRef]
    [Google Scholar]
  51. Shapira, R., Choi, G. H. & Nuss, D. L. ( 1991; ). Virus-like genetic organization and expression strategy for a double-stranded RNA genetic element associated with biological control of chestnut blight. EMBO Journal 10, 731-739.
    [Google Scholar]
  52. 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]
  53. Solovyev, A. G., Novikov, V. K., Merits, A., Savenkov, E. I., Zelenina, D. A., Tyulkina, L. G. & Morozov, S. Yu. ( 1994; ). Genome characterization and taxonomy of Plantago asiatica mosaic potexvirus. Journal of General Virology 75, 259-267.[CrossRef]
    [Google Scholar]
  54. Song, S. I., Song, J. T., Kim, C. H., Lee, J. S. & Choi, Y. D. ( 1998; ). Molecular characterization of the garlic virus X genome. Journal of General Virology 79, 155-159.
    [Google Scholar]
  55. Sumi, S., Tsuneyoshi, T. & Furutani, H. ( 1993; ). Novel rod-shaped viruses isolated from garlic, Allium sativum, possessing a unique genome organization. Journal of General Virology 74, 1879-1885.[CrossRef]
    [Google Scholar]
  56. Thompson, J. D., Higgins, D. G. & Gibson, T. J. ( 1994; ). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22, 4673-4680.[CrossRef]
    [Google Scholar]
  57. Vilches, S. & Castillo, A. ( 1997; ). A double-stranded RNA mycovirus in Botrytis cinerea. FEMS Microbiology Letters 155, 125-130.[CrossRef]
    [Google Scholar]
  58. Vogel, H. J. ( 1964; ). Distribution of lysine pathways among fungi: evolutionary implications. American Naturalist 98, 435-446.[CrossRef]
    [Google Scholar]
  59. Weiller, G. F. & Gibbs, A. ( 1995; ). DIPLOMO: the tool for a new type of evolutionary analysis. Computer Applications in the Biosciences 11, 535-540.
    [Google Scholar]
  60. White, K. A., Bancroft, J. B. & Mackie, G. A. ( 1992; ). Coding capacity determines in vivo accumulation of a defective RNA of clover yellow mosaic virus. Journal of Virology 66, 3069-3076.
    [Google Scholar]
  61. Wu, S. X., Rinehart, C. A. & Kaesberg, P. ( 1987; ). Sequence and organization of southern bean mosaic virus genomic RNA. Virology 161, 73-80.[CrossRef]
    [Google Scholar]
  62. Yokoi, T., Takemoto, Y., Suzuki, M., Yamashita, S. & Hibi, T. ( 1999; ). The nucleotide sequence and genome organization of Sclerophthora macrospora virus B. Virology 264, 344-349.[CrossRef]
    [Google Scholar]
  63. Yoshikawa, N., Sasaki, E., Kato, M. & Takahashi, T. ( 1992; ). The nucleotide sequence of apple stem grooving capillovirus genome. Virology 191, 98-105.[CrossRef]
    [Google Scholar]
  64. Yoshikawa, N., Iida, H., Goto, S., Magome, H., Takahashi, T. & Terai, Y. ( 1997; ). Grapevine berry inner necrosis, a new trichovirus: comparative studies with several known trichoviruses. Archives of Virology 142, 1351-1363.[CrossRef]
    [Google Scholar]
  65. Zavriev, S. K., Kanyuka, K. V. & Levay, K. E. ( 1991; ). The genome organization of potato virus M RNA. Journal of General Virology 72, 9-14.[CrossRef]
    [Google Scholar]
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