1887

Abstract

Double-stranded RNA preparations produced from potato plants graft-inoculated with a Peruvian isolate of (PYVV; genus , family ) contain five RNA species denoted RNA 1, RNA 2, RNA 3, x and y of approximately 8, 5·3, 3·8, 2·0 and 1·8 kbp, respectively. The complete nucleotide sequences of PYVV RNAs 1, 2 and 3 and Northern hybridization analysis showed that PYVV RNA 1 contained the replication module and an additional open reading frame (p7), while two distinct species, RNAs 2 and 3, contain the hallmark gene array. Pairwise comparisons and phylogeny of genome-encoded proteins showed that PYVV shares significant homology with other criniviruses but is most closely related to the -vectored . Secondary structure prediction of the 3′-untranslated regions of all three PYVV RNAs revealed four conserved stem–loop structures and a 3′-terminal pseudoknot structure, also predicted for all fully characterized members of the genus and some members of the genera and .

Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.79910-0
2004-07-01
2019-11-22
Loading full text...

Full text loading...

/deliver/fulltext/jgv/85/7/vir852065.html?itemId=/content/journal/jgv/10.1099/vir.0.79910-0&mimeType=html&fmt=ahah

References

  1. Agranovsky, A. A., Koonin, E. V., Boyko, V. P., Maiss, E., Frötschul, R., Lunina, N. & Atabekov, J. G. ( 1994; ). Beet yellows closterovirus: complete genome structure and identification of a leader papain-like thiol protease. Virology 198, 311–324.[CrossRef]
    [Google Scholar]
  2. Agranovsky, A. A., Lesemann, D. E., Maiss, E. M., Hull, R. & Atabekov, J. G. ( 1995; ). “Rattlesnake” structure of a filamentous plant RNA virus built of two capsid proteins. Proc Natl Acad Sci U S A 92, 2470–2473.[CrossRef]
    [Google Scholar]
  3. Aguilar, J. M., Franco, M., Marco, C. F., Berdiales, B., Rodriguez-Cerezo, E., Truniger, V. & Aranda, M. A. ( 2003; ). Further variability within the genus Crinivirus, as revealed by determination of the complete RNA genome sequence of Cucurbit yellow stunting disorder virus. J Gen Virol 84, 2555–2564.[CrossRef]
    [Google Scholar]
  4. Altschul, S. F., Madden, T. L., Schaffer, 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]
  5. Alzhanova, D. V., Hagiwara, Y., Peremyslov, V. V. & Dolja, V. V. ( 2000; ). Genetic analysis of the cell-to-cell movement of beet yellows closterovirus. Virology 268, 192–200.[CrossRef]
    [Google Scholar]
  6. Alzhanova, D. V., Napuli, A. J., Creamer, R. & Dolja, V. V. ( 2001; ). Cell-to-cell movement and assembly of a plant closterovirus: roles for the capsid proteins and Hsp homolog. EMBO J 20, 6997–7007.[CrossRef]
    [Google Scholar]
  7. Bringloe, D. H., Gultyaev, A. P., Pelpel, M., Pleij, C. W. A. & Coutts, R. H. A. ( 1998; ). The nucleotide sequence of satellite tobacco necrosis virus strain C and helper-assisted replication of wild-type and mutant clones of the virus. J Gen Virol 79, 1539–1546.
    [Google Scholar]
  8. Buck, K. W. ( 1996; ). Comparison of the replication of positive-stranded RNA viruses of plants and animals. Adv Virus Res 47, 159–251.
    [Google Scholar]
  9. Che, X., Dawson, W. O. & Bar-Joseph, M. ( 2003; ). Defective RNAs of Citrus tristeza virus analogous to Crinivirus genomic RNAs. Virology 310, 298–309.[CrossRef]
    [Google Scholar]
  10. Coutts, R. H. A. & Livieratos, I. C. ( 2003a; ). Nucleotide sequence and genome organization of Cucurbit yellow stunting disorder virus RNA1. Arch Virol 148, 2055–2062.[CrossRef]
    [Google Scholar]
  11. Coutts, R. H. A. & Livieratos, I. C. ( 2003b; ). A rapid method for sequencing the 5′- and 3′-termini of dsRNA viral templates using RLM-RACE. J Phytopathol 151, 525–527.[CrossRef]
    [Google Scholar]
  12. Deveraux, J., Haeberli, P. & Smithies, O. ( 1984; ). A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res 12, 387–395.[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. Dreher, T. W. ( 1999; ). Functions of the 3′-untranslated regions of positive strand RNA viral genomes. Annu Rev Phytopathol 37, 151–174.[CrossRef]
    [Google Scholar]
  15. Gultyaev, A. P., van Batenburg, F. H. D. & Pleij, C. W. A. ( 1995; ). The computer simulation of RNA folding pathways using a genetic algorithm. J Mol Biol 250, 37–51.[CrossRef]
    [Google Scholar]
  16. Hartono, S., Natsuaki, T., Genda, Y. & Okuda, S. ( 2003; ). Nucleotide sequence and genome organization of Cucumber yellows virus, a member of the genus Crinivirus. J Gen Virol 84, 1007–1012.[CrossRef]
    [Google Scholar]
  17. Karasev, A. V. ( 2000; ). Genetic diversity and evolution of closteroviruses. Annu Rev Phytopathol 38, 293–324.[CrossRef]
    [Google Scholar]
  18. Klaassen, V. A., Boeshore, M. L., Koonin, E. V., Tian, T. & Falk, B. W. ( 1995; ). Genome structure and phylogenetic analysis of lettuce infectious yellows virus, a whitefly-transmitted, bipartite closterovirus. Virology 208, 99–110.[CrossRef]
    [Google Scholar]
  19. Klaassen, V. A., Mayhew, D., Fisher, D. & Falk, B. W. ( 1996; ). In vitro transcripts from cloned cDNAs of the lettuce infectious yellows closterovirus bipartite genomic RNAs are competent for replication in Nicotiana benthamiana protoplasts. Virology 222, 169–175.[CrossRef]
    [Google Scholar]
  20. Kreuze, J. F., Savenkov, E. I. & Valkonen, J. P. T. ( 2002; ). Complete genome sequence and analysis of the subgenomic RNAs of Sweet potato chlorotic stunt virus reveal several new features for the genus Crinivirus. J Virol 76, 9260–9270.[CrossRef]
    [Google Scholar]
  21. Liu, X. & Gorovsky, M. A. ( 1993; ). Mapping the 5′ and 3′ ends of Tetrahymena thermophila mRNAs using RNA ligase-mediated amplification of cDNA ends. Nucleic Acids Res 21, 4954–4960.[CrossRef]
    [Google Scholar]
  22. Livieratos, I. C. & Coutts, R. H. A. ( 2002; ). Nucleotide sequence and phylogenetic analysis of Cucurbit yellow stunting disorder virus RNA2. Virus Genes 24, 225–230.[CrossRef]
    [Google Scholar]
  23. Livieratos, I. C., Katis, N. & Coutts, R. H. A. ( 1998; ). Differentiation between cucurbit yellow stunting disorder virus and beet pseudo-yellows virus by a reverse transcription-polymerase chain reaction assay. Plant Pathol 47, 362–369.[CrossRef]
    [Google Scholar]
  24. Livieratos, I. C., Avgelis, A. D. & Coutts, R. H. A. ( 1999; ). Molecular characterization of the cucurbit yellow stunting disorder virus coat protein gene. Phytopathology 89, 1030–1035.
    [Google Scholar]
  25. Livieratos, I. C., Müller, G., Salazar, L. F., Eliasco, E. & Coutts, R. H. A. ( 2002; ). Identification and sequence analysis of Potato yellow mosaic virus capsid protein minor gene. Virus Genes 25, 317–322.[CrossRef]
    [Google Scholar]
  26. Martelli, G. P., Agranovsky, A. A., Bar-Joseph, M. & 13 other authors ( 2002; ). The family Closteroviridae revised. Arch Virol 147, 2039–2044.[CrossRef]
    [Google Scholar]
  27. Napuli, A. J., Falk, B. W. & Dolja, V. V. ( 2000; ). Interaction between HSP70-homolog and filamentous virions of beet yellows virus. Virology 274, 232–239.[CrossRef]
    [Google Scholar]
  28. Napuli, A. J., Alzhanova, D. V., Doneanu, C. E., Barofsy, D. F., Koonin, E. V. & Dolja, V. V. ( 2003; ). The 64-kilodalton capsid protein homolog of Beet yellows virus is required for assembly of virion tails. J Virol 77, 2377–2384.[CrossRef]
    [Google Scholar]
  29. Offei, S. K., Arciniegas, N., Müller, G., Guzmán, M., Salazar, L. F. & Coutts, R. H. A. ( 2004; ). Molecular variation of Potato yellow vein virus isolates. Arch Virol 149, 821–827.[CrossRef]
    [Google Scholar]
  30. Page, R. D. M. ( 1996; ). treeview: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12, 357–358.
    [Google Scholar]
  31. Peng, C. W., Peremyslov, V. V., Mushegian, A. R., Dawson, W. O. & Dolja, V. V. ( 2001; ). Functional specialization and evolution of leader proteinases in the family Closteroviridae. J Virol 75, 12153–12160.[CrossRef]
    [Google Scholar]
  32. Peng, C. W., Napuli, A. J. & Dolja, V. V. ( 2003; ). Leader proteinase of Beet yellows virus functions in long-distance transport. J Virol 77, 2843–2849.[CrossRef]
    [Google Scholar]
  33. Peremyslov, V. V. & Dolja, V. V. ( 2002; ). Identification of the subgenomic mRNAs that encode the 6-kDa movement protein and Hsp70 homolog of Beet yellows virus. Virology 295, 299–306.[CrossRef]
    [Google Scholar]
  34. Pleij, C. W. A., Rietveld, K. & Bosch, L. ( 1985; ). A new principle of RNA folding based on pseudoknotting. Nucleic Acids Res 13, 1717–1731.[CrossRef]
    [Google Scholar]
  35. Rubio, L., Yeh, H.-H., Tian, T. & Falk, B. W. ( 2000; ). A heterogeneous population of defective RNAs is associated with Lettuce infectious yellows virus (LIYV). Virology 271, 205–212.[CrossRef]
    [Google Scholar]
  36. Salazar, L. F., Müller, G., Querci, M., Zapata, J. L. & Owens, R. A. ( 2000; ). Potato yellow vein virus: its host range, distribution in South America, and identification as a crinivirus transmitted by Trialeurodes vaporariorum. Ann Appl Biol 137, 7–19.[CrossRef]
    [Google Scholar]
  37. Satyanarayana, T., Gowda, S., Mawassi, M., Albiach-Marti, M. R., Aylion, M. A., Robertson, C., Garnsey, S. M. & Dawson, W. O. ( 2000; ). Closterovirus encoded HSP70 homolog and p61 in addition to both coat proteins function in efficient virion assembly. Virology 278, 253–265.[CrossRef]
    [Google Scholar]
  38. Satyanarayana, T., Gowda, S., Aylion, M. A., Albiach-Marti, M. R. & Dawson, W. O. ( 2002; ). Mutational analysis of the replication signals in the 3′-nontranslated region of Citrus tristeza virus. Virology 300, 140–152.[CrossRef]
    [Google Scholar]
  39. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. ( 1997; ). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876–4882.[CrossRef]
    [Google Scholar]
  40. Tian, T., Rubio, L., Yeh, H.-H., Crawford, B. & Falk, B. W. ( 1999; ). Lettuce infectious yellows virus: in vitro acquisition analysis using partially purified virions and the whitefly Bemisia tabaci. J Gen Virol 80, 1111–1117.
    [Google Scholar]
  41. Valverde, R., Nameth, S. T. & Jordan, R. L. ( 1990; ). Analysis of double-stranded RNA for plant virus diagnosis. Plant Dis 74, 255–258.
    [Google Scholar]
  42. Wisler, G. C., Duffus, J. E., Liu, H.-Y. & Li, R. H. ( 1998; ). Ecology and epidemiology of whitefly-transmitted closteroviruses. Plant Dis 82, 270–279.[CrossRef]
    [Google Scholar]
  43. Yeh, H.-H., Tian, T., Rubio, L., Crawford, B. & Falk, B. W. ( 2000; ). Asynchronous accumulation of Lettuce infectious yellows virus RNAs 1 and 2 and identification of an RNA 1 trans enhancer of RNA 2 accumulation. J Virol 74, 5762–5768.[CrossRef]
    [Google Scholar]
  44. Zinovkin, R. A., Jelkmann, W. & Agranovsky, A. A. ( 1999; ). The minor coat protein of beet yellows closterovirus encapsidates the 5′ terminus of RNA in virions. J Gen Virol 80, 269–272.
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/vir.0.79910-0
Loading
/content/journal/jgv/10.1099/vir.0.79910-0
Loading

Data & Media loading...

Most Cited This Month

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