Sequence analysis of rice hoja blanca virus RNA 3 Free

Abstract

RNA 3 of rice hoja blanca tenuivirus (RHBV) has 2299 nucleotides and resembles RNA 3 of other tenuiviruses such as maize stripe (MStV) and rice stripe (RStV) viruses in potentially coding with an ambisense strategy for two proteins. Both the viral-sense protein of 23K and the complementary-sense protein of 35K have about 46% amino acid identity with the analogous proteins encoded by RNA 3 of MStV and RStV. As the proteins of MStV and RStV have about 65 % identity between themselves, RHBV cannot be a South and Central American strain of the Asian RStV. The intergenic region resembles those of other tenuiviruses, being rich in A and U residues, but its predicted folding pattern is unlike those of other tenuiviruses. Instead, the predicted folding of the intergenic region was indistinguishable from that of the coding regions and there was no evidence for a distinct hairpin-loop structure. The significance to the evolution of tenuiviruses of the similarities that the two proteins have with their analogues in other tenuiviruses is discussed.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/0022-1317-75-8-2127
1994-08-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/jgv/75/8/JV0750082127.html?itemId=/content/journal/jgv/10.1099/0022-1317-75-8-2127&mimeType=html&fmt=ahah

References

  1. 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]
  2. Eckert K. A., Kunkel T. A. 1991; The fidelity of DNA polymerases used in the polymerase chain reaction. In PCR: A Practical Approach pp. 225–243 McPherson M. J., Quirke P., Taylor G. R. Edited by Oxford: IRL Press;
    [Google Scholar]
  3. Elliott R. M. 1990; Molecular biology of the Bunyaviridae. Journal of General Virology 71:501–522
    [Google Scholar]
  4. Emery V. C., Bishop D. H. L. 1987; Characterization of Punta Toro S mRNA species and identification of an inverted complementary sequence in the intergenic region of Punta Toro phlebovirus ambisense S RNA that is involved in mRNA transcription termination. Virology 156:1–11
    [Google Scholar]
  5. Fichot O., Girard M. 1990; An improved method for sequencing of RNA templates. Nucleic Acids Research 18:6162
    [Google Scholar]
  6. Gelfand D. H., White T. J. 1990; Thermostable DNA polymerases. In PCR Protocols: A Guide to Methods and Applications pp. 129–141 Innes M. A., Gelfand D. H., Sninsky J. J., White T. J. Edited by New York & London: Academic Press;
    [Google Scholar]
  7. German T. L., Ullman D. E., Moyer J. W. 1992; Tospoviruses: diagnosis, molecular biology, phylogeny, and vector relationships. Annual Review of Phytopathology 30:315–348
    [Google Scholar]
  8. Huiet L., Klaassen V., Tsai J. H., Falk B. W. 1991; Nucleotide sequence and RNA hybridization analyses reveal an ambisense coding strategy for maize stripe virus RNA 3. Virology 182:47–54
    [Google Scholar]
  9. Huiet L., Tsai J. H., Falk B. W. 1992; Complete sequence of maize stripe virus RNA4 and mapping of its subgenomic RNAs. Journal of General Virology 73:1603–1607 corrigendum 3049
    [Google Scholar]
  10. Kakutani T., Hayano Y., Hayashi T., Minobe Y. 1990; Ambisense segment 4 of rice stripe virus: possible evolutionary relationship with phleboviruses and uukuviruses (Bunyaviridae). Journal of General Virology 71:1427–1432
    [Google Scholar]
  11. Kakutani T., Hayano Y., Hayashi T., Minobe Y. 1991; Ambisense segment 3 of rice stripe virus: the first instance of a virus containing two ambisense segments. Journal of General Virology 72:465–468
    [Google Scholar]
  12. Koonin E. V. 1991; The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses. Journal of General Virology 72:2197–2206
    [Google Scholar]
  13. Kotewicz M. L., Sampson C. M., D’Alessio J. M., Gerard G. F. 1988; Isolation of cloned Moloney murine leukemia virus reverse transcriptase lacking ribonuclease H activity. Nucleic Acids Research 16:265
    [Google Scholar]
  14. Kwiatowski J., Skarechy D., Hernandez S., Pham D., Quijas F., Ayala F. J. 1991; High fidelity of the polymerase chain reaction. Molecular Biology and Evolution 8:884–887
    [Google Scholar]
  15. Morales F. J., Niessen A. I. 1983; Association of spiral filamentous viruslike particles with rice hoja blanca virus. Phytopathology 73:971–974
    [Google Scholar]
  16. Ramírez B. -C., Haenni A. -L. 1994; Molecular biology of tenuiviruses, a remarkable group of plant viruses. Journal of General Virology 75:467–475
    [Google Scholar]
  17. Ramírez B. -C., Macaya G., Calvert L. A., Haenni A. -L. 1992; Rice hoja blanca virus genome characterization and expression in vitro. Journal of General Virology 73:1457–1464
    [Google Scholar]
  18. Ramírez B. -C., Lozano I., Constantino L. -M., Haenni A. -L., Calvert L. A. 1993; Complete nucleotide sequence and coding strategy of rice hoja blanca virus RNA4. Journal of General Virology 74:2463–2468
    [Google Scholar]
  19. Reiss J., Krawczak M., Schloesser M., Wagner M., Cooper D. N. 1990; The effect of replication errors on the mismatch analysis of PCR amplified DNA. Nucleic Acids Research 18:973–978
    [Google Scholar]
  20. Schmaljohn C. S., Patterson J. L. 1990; Bunyaviridae and their replication. In Virology, 2nd edn. pp. 1175–1193 Fields B. N., Knipe D. M. Edited by New York: Raven Press;
    [Google Scholar]
  21. Strauss J. H., Strauss E. G. 1988; Evolution of RNA viruses. Annual Review of Microbiology 42:657–683
    [Google Scholar]
  22. Takahashi M., Toriyama S., Kikushi Y., Hayakawa T., Ishihama A. 1990; Complementarity between the 5′- and 3′- terminal sequences of rice stripe virus RNAs. Journal of General Virology 71:2817–2821
    [Google Scholar]
  23. Takahashi M., Toriyama S., Hamamatsu C., Ishihama A. 1993; Nucleotide sequence and possible ambisense coding strategy of rice stripe virus RNA segment 2. Journal of General Virology 74:769–773
    [Google Scholar]
  24. Tordo N., De Haan P., Goldbach R., Poch O. 1992; Evolution of negative strand RNA genomes. Seminars in Virology 3:341–357
    [Google Scholar]
  25. Zhu Y., Hayakawa T., Toriyama S., Takahashi M. 1991; Complete nucleotide sequence of RNA 3 of rice stripe virus: an ambisense coding strategy. Journal of General Virology 72:763–767
    [Google Scholar]
  26. Zhu Y., Hayakawa T., Toriyama S. 1992; Complete nucleotide sequence of RNA 4 of rice stripe virus isolate T, and comparison with another isolate and with maize stripe virus. Journal of General Virology 73:1309–1312
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/0022-1317-75-8-2127
Loading
/content/journal/jgv/10.1099/0022-1317-75-8-2127
Loading

Data & Media loading...

Most cited Most Cited RSS feed