1887

Abstract

The complete nucleotide sequence of RNA 1 of the tentative furovirus peanut clump virus (PCV) has been determined by characterization of cloned cDNA and by direct RNA sequencing. The sequence is 5897 nucleotides in length and contains three long open reading frames (ORFs). The 5′ -terminal proximal ORF has the potential to encode a polypeptide of 130942 (P131) containing methyltransferase and RNA helicase homologous domains and displaying homology with large nonstructural proteins of alpha-like viruses, which are known or thought to be involved in virus replication. The PI31 ORF is followed in-frame by a second ORF which is probably expressed by partial readthrough of the UGA termination codon of the P131 ORF to produce a polypeptide of 191044 (P191). The readthrough region of PI91 contains the characteristic ‘core’ RNA polymerase motif, indicating that the PCV replicase proteins are expressed as a pair of overlapping proteins as in the tobamoviruses, tobraviruses and the furovirus soil-borne wheat mosaic virus (SBWMV). Sequence comparisons indicate that PI31 and P191 are most closely related to the replicase proteins of SBWMV and the hordeivirus barley stripe mosaic virus (BSMV) but are only distantly related to the replicase of the furovirus beet necrotic yellow vein virus (BNYW). The 3′ -terminal proximal ORF can encode a putative polypeptide of 14556 (PI5) which displays homology to small cysteine-rich proteins of hordeiviruses and SBWMV. We have corrected four errors in the sequence of PCV RNA 2 published previously by Manohar . ( 195, 33–41, 1993). One of these changes causes two small ORFs near the 3′ terminus of RNA 2 to be fused together to create an ORF for a putative polypeptide of 16833 (PI7) which displays extensive homology with the third protein of the triple gene block of BSMV RNA .

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1994-11-01
2022-05-28
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References

  1. Agranovsky A. A., Karasev A. V., Novikov V. K., Lunina N. A., Loginov S., Tyulkina L. G. 1992; Poa semilatent virus, a hordeivirus having no internal polydisperse poly(A) in the 3′ noncoding region of the RNA genome. Journal of General Virology 73:2085–2092
    [Google Scholar]
  2. Bouzoubaa S., Guilley H., Jonard G., Richards K., Putz C. 1985; Nucleotide sequence analysis of RNA-3 and RNA-4 of beet necrotic yellow vein virus isolates F2 and Gl. Journal of General Virology 66:1553–1564
    [Google Scholar]
  3. Bouzoubaa S., Ziegler V., Beck D., Guilley FI., Richards K., Jonard G. 1986; Nucleotide sequence of beet necrotic yellow vein virus RNA-2. Journal of General Virology 67:1689–1700
    [Google Scholar]
  4. Bouzoubaa S., Quillet L., Guilley H., Jonard G., Richards K. 1987; Nucleotide sequence of beet necrotic yellow vein virus RNA 1. Journal of General Virology 68:615–626
    [Google Scholar]
  5. Brunt A. A. 1991; Soil-borne wheat mosaic virus group. In Classification and Nomenclature of Viruses, Fifth Report of the International Committee on Taxonomy of Viruses pp. 377–379 Francki R. I. B., Fauquet C. M., Knudson D. L., Brown F. Edited by New York: Springer-Verlag;
    [Google Scholar]
  6. Deborde D. C., Naeve C. W., Herlocher M. L., Maassab H. F. 1986; Resolution of a common RNA sequence ambiguity by terminal deoxynucleotidyl transferase. Analytical Biochemistry 157:275–282
    [Google Scholar]
  7. Devereux J., Haeberli P., Smithies O. 1984; A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Research 12:387–395
    [Google Scholar]
  8. Fichot O., Girard M. 1990; An improved method of sequencing of RNA templates. Nucleic Acids Research 18:6162
    [Google Scholar]
  9. Gilmer D., Bouzoubaa S., Hehn A., Guilley H., Richards K., Jonard G. 1992; Efficient cell-to-cell movement of beet necrotic yellow vein virus requires 3′ proximal genes located on RNA 2. Virology 189:40–47
    [Google Scholar]
  10. Goelet P., Lomonossoff G. P., Butler P. J. G., Akam M. E., Gait M. J., Karn J. 1982; Nucleotide sequence of tobacco mosaic virus RNA. Proceedings of the National Academy of Sciences, U.S.A 79:5818–5822
    [Google Scholar]
  11. Gubler U., Hoffman B. J. 1983; A simple and very efficient method for generating cDNA libraries. Gene 25:263–269
    [Google Scholar]
  12. Gustafson G., Hunter B. G., Hanau R., Armour S. L., Jackson A. O. 1987; Nucleotide sequence and genetic organization of barley stripe mosaic virus RNA γ. Virology 158:394–406
    [Google Scholar]
  13. Gustafson G. D., Armour S. L., Gamboa G. C., Burgett S. G., Shepherd J. W. 1989; Nucleotide sequence of barley stripe mosaic virus RNA α: RNA α encodes a single polypeptide with homology to corresponding proteins from other viruses and to the BSMV β protein. Virology 170:370–377
    [Google Scholar]
  14. 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
    [Google Scholar]
  15. Heidecker G., Messing J. 1983; Sequence analysis of zein cDNAs obtained by an efficient mRNA cloning method. Nucleic Acids Research 11:4891–4906
    [Google Scholar]
  16. Henikoff S. 1987; Unidirectional digestion with exonuclease III in DNA sequence analysis. Methods in Enzymology 155:156–165
    [Google Scholar]
  17. Hsu Y. H., Brakke M. K. 1985; Cell-free translation of soil-borne wheat mosaic virus RNAs. Virology 143:272–279
    [Google Scholar]
  18. Koenig R., Burgermeister W., Weich H., Sebald W., Kothe C. 1986; Uniform RNA patterns of beet necrotic yellow vein virus in sugar beet roots, but not in leaves from several plant species. Journal of General Virology 67:2043–2046
    [Google Scholar]
  19. 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 28:375–130
    [Google Scholar]
  20. 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
    [Google Scholar]
  21. Manohar S. K., Guilley H., Dollet M., Richards K., Jonard G. 1993; Nucleotide sequence and genetic organization of peanut clump virus RNA 2 and partial characterization of deleted forms. Virology 195:33–41
    [Google Scholar]
  22. Mayo M. A. M., Reddy D. V. R. 1985; Translation products of RNA from Indian peanut clump virus. Journal of General Virology 66:1347–1351
    [Google Scholar]
  23. Morozov S. Y., Dolja V. V., Atabekov J. G. 1989; Probable reassortment of genomic elements among elongated RNA-con- taining plant viruses. Journal of Molecular Evolution 29:52–62
    [Google Scholar]
  24. Petty I. T. D., French R., Jones R. W., Jackson A. O. 1990; Identification of barley stripe mosaic virus genes involved in viral RNA replication and systemic movement. EMBO Journal 9:3453–3457
    [Google Scholar]
  25. Reddy D. V. R., Rajeshwari R., Iizuka N., Lesemann D. E., Nolt B. L., Goto T. 1983; The occurrence of Indian peanut clump, a soil-borne virus disease of groundnuts (Arachis hypogaea) in India. Annals of Applied Biology 102:305–310
    [Google Scholar]
  26. Rupasov V. V., Morozov S. Y., Kanyuka K. V., Zavriev S. K. 1989; Partial nucleotide sequence of potato virus M RNA shows similarities to potexviruses in gene arrangement and the encoded amino acid sequences. Journal of General Virology 70:1861–1869
    [Google Scholar]
  27. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular Cloning: A Laboratory Manual, 2nd end. New York: Cold Spring Harbor Laboratory;
    [Google Scholar]
  28. Sanger F., Nicklen S., Coulson A. R. 1977; DNA sequencing with chain terminating inhibitors. Proceedings of the National Academy of Sciences, U.S.A 74:5463–5467
    [Google Scholar]
  29. Shirako Y., Brakke M. K. 1984; Spontaneous deletion mutation of soil-borne wheat mosaic virus RNA II. Journal of General Virology 65:855–858
    [Google Scholar]
  30. Shirako Y., Ehara Y. 1986; Comparison of the in vitro translation products of wild-type and a deletion mutant of soil-borne wheat mosaic virus. Journal of General Virology 61:1237–1245
    [Google Scholar]
  31. Shirako Y., Wilson T. M. A. 1993; Complete nucleotide sequence and organization of the bipartite RNA genome of soil-borne wheat mosaic virus. Virology 195:16–32
    [Google Scholar]
  32. Skuzeski J. M., Nichols L. M., Gesteland R. F., Atkins J. F. 1991; The signal for a leaky UAG stop codon in several plant viruses includes two downstream codons. Journal of Molecular Biology 218:365–373
    [Google Scholar]
  33. Tamada T., Kusume T. 1991; Evidence that the 75K readthrough protein of beet necrotic yellow vein virus RNA-2 is essential for transmission by the fungus Polymyxa betae. Journal of General Virology 72:1497–1504
    [Google Scholar]
  34. Thouvenel J. C., Fauquet C. 1981; Peanut clump virus. CMI/AAB Description of Plant Viruses235
    [Google Scholar]
  35. Thouvenel J. C., Dollet M., Fauquet C. 1976; Some properties of peanut clump, a newly discovered virus. Annals of Applied Biology 84:311–320
    [Google Scholar]
  36. Wesley S. V., Mayo M. A., Jolly C. A., Naidu R. A., Reddy D. V. R., Jana M. K., Parnaik V. K. 1994; The coat protein of Indian peanut clump virus: relationships with other furoviruses and with barley stripe mosaic virus. Archives of Virology 134:271–278
    [Google Scholar]
  37. Zhang H., Scholl R., Browse J., Summerville C. 1988; Double stranded DNA sequencing as a choice for DNA sequencing. Nucleic Acids Research 126:1220
    [Google Scholar]
  38. Ziegler V., Richards K., Guilley H., Jonard G., Putz C. 1985; Cell-free translation of beet necrotic yellow vein virus: readthrough of the coat protein cistron. Journal of General Virology 66:2079–2087
    [Google Scholar]
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