Analysis of the RNA of : evidence for a tripartite genome and conserved 3′-terminal structures among members of the genus Free

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 .

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2004-07-01
2024-03-29
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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]
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