1887

Abstract

The 8890 nucleotide RNA sequence of shallot virus X (ShVX), a new virus isolated from shallot, has been determined. The sequence contains six open reading frames (ORFs) which encode putative proteins (in the 5′ to 3′ direction) of 194528 (ORF1), 26333 (ORF2), 11245 (ORF3), 42209 (ORF4), 28486 (ORF5) and 14741 (ORF6). The ORF1 protein was found to be highly homologous to the putative potexvirus RNA replicases; ORF2, -3, -5 and -6 proteins also have analogues among the potex- and/or carlavirus-encoded proteins. ORF3 is followed by an AUG-lacking frame coding for an amino acid sequence homologous to that of the 7K to 8K proteins of the triple gene block of the above-mentioned viruses. The putative ORF4 protein has no reliable homology with proteins in the database. The results obtained testify that, except for the unique 42K protein gene, the ShVX genome combines a number of elements typical of both carla- and potexviruses.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/0022-1317-73-10-2553
1992-10-01
2024-12-06
Loading full text...

Full text loading...

/deliver/fulltext/jgv/73/10/JV0730102553.html?itemId=/content/journal/jgv/10.1099/0022-1317-73-10-2553&mimeType=html&fmt=ahah

References

  1. Beck D. L., Guilford P. J., Voot D. M., Andersen M. T., Forster R. L. S. 1991; Triple gene block proteins of white clover mosaic potexvirus are required for transport. Virology 183:695–702
    [Google Scholar]
  2. Bundin V. S., Vishnyakova O. A., Zakhariev V. M., Morozov S. Yu., Atabekov J. G., Skryabin K. G. 1986; Comparative studies of potexvirus genomes: homology between the primary structure of coat protein genes. Doklady Akademii Nauk SSSR 290:728–733 (in Russian)
    [Google Scholar]
  3. Corpet F. 1988; Multiple sequence alignment with hierarchical clustering. Nucleic Acids Research 16:10881–10890
    [Google Scholar]
  4. Dolja V. V., Grama D. P., Morozov S. Yu., Atabekov J. G. 1987; Potato virus X-related single- and double-stranded RNA. Characterization of terminal structures. FEBS Letters 214:308–312
    [Google Scholar]
  5. Forster R. L. S., Bevan M. W., Harbison S. A., Gardner R. C. 1988; The complete nucleotide sequence of the potexvirus white clover mosaic virus. Nucleic Acids Research 16:291–303
    [Google Scholar]
  6. Foster G. D., Millar A. W., Meehan B. M., Mills P. R. 1990; Nucleotide sequence of 3′-terminal region of Helenium virus S RNA. Journal of General Virology 71:1877–1880
    [Google Scholar]
  7. German S., Candresse T., Lanneau M., Huet J. C., Pernollet J. C., Dunez J. 1990; Nucleotide sequence and genomic organization of apple chlorotic leaf spot virus. Virology 179:104–112
    [Google Scholar]
  8. Gorbalenya A. E., Koonin E. V., Donchenko A. P., Blinov V. M. 1988; A novel superfamily of nucleoside triphosphate-binding motif-containing proteins which are probably involved in duplex unwinding in DNA and RNA replication and recombination. FEBS Letters 235:16–24
    [Google Scholar]
  9. Gramstat A., Courtpozanis A., Rohde W. 1990; The 12 kDa protein of potato virus M displays properties of a nucleic acid-binding regulatory protein. FEBS Letters 276:34–38
    [Google Scholar]
  10. Guilford P. G., Forster R. L. S. 1986; Detection of polyadenylated subgenomic RNAs in leaves infected with the potexvirus daphne virus X. Journal of General Virology 67:83–90
    [Google Scholar]
  11. Habili N., Symons H. 1989; Evolutionary relationship between luteoviruses and other RNA plant viruses based on sequence motifs in their putative RNA polymerases and nucleic acid helicases. Nucleic Acids Research 17:9543–9555
    [Google Scholar]
  12. Haylor M. T. M., Brunt A. A., Coutts R. H. A. 1990; Conservation of the 3′ terminal nucleotide sequence in five carlaviruses. Nucleic Acids Research 18:6127
    [Google Scholar]
  13. Hollings M., Brunt A. A. 1981; Potyviruses. In Handbook of Plant Virus Infections and Comparative Diagnosis pp. 731–807 Edited by Kurstak E. Amsterdam: Elsevier;
    [Google Scholar]
  14. Huisman M. J., Linthorst H. J. M., Bol J. F., Cornelissen B. J. C. 1988; The complete nucleotide sequence of potato virus X and its homologies at the amino acid level with various plus-stranded RNA viruses. Journal of General Virology 69:1789–1798
    [Google Scholar]
  15. Jelkmann W., Martin R. R., Lesemann D. -E., Vetten H. J., Skelton F. 1990; A new potexvirus associated with strawberry mild yellow edge disease. Journal of General Virology 71:1251–1258
    [Google Scholar]
  16. Klug A., Rhodes D. 1987; ‘Zinc fingers’: a novel protein motif for nucleic acid recognition. Trends in Biochemical Sciences 12:464–469
    [Google Scholar]
  17. Kroczek R. A., Siebert E. 1990; Optimization of Northern analysis by vacuum-blotting, RNA-transfer visualization, and ultraviolet fixation. Analytical Biochemistry 184:90–95
    [Google Scholar]
  18. Kyte J., Doolittle R. F. 1982; A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology 157:105–132
    [Google Scholar]
  19. Laemmli U. K. 1970; Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature, London 111:680–685
    [Google Scholar]
  20. Levay K., Zavriev S. 1991; Nucleotide sequence and gene organization of the 3′-terminal region of chrysanthemum virus B genomic RNA. Journal of General Virology 72:2333–2337
    [Google Scholar]
  21. Mackenzie D. J., Tremaine J. H., Stace-Smith R. 1989; Organization and interviral homologies of the 3′-terminal portion of potato virus S RNA. Journal of General Virology 70:1053–1063
    [Google Scholar]
  22. Mackie G. A., Johnson R., Bancroft J. B. 1988; Single- and double-stranded viral RNAs in plants infected with the potexvirus papaya mosaic virus and foxtail mosaic virus. Intervirology 29:170–177
    [Google Scholar]
  23. Memelink J., van der Vlugt C. I. M., Linthorst H. J. M., Derks A. F. L. M., Asjes C. J., Bol J. F. 1990; Homologies between the genomes of a carlavirus (lily symptomless virus) and potexvirus (lily virus X) from lily plants. Journal of General Virology 71:917–924
    [Google Scholar]
  24. Monis J., de Zoeten G. A. 1990; Molecular cloning and physical mapping of potato virus S complementary DNA. Phytopathology 80:446–450
    [Google Scholar]
  25. Morch M.-D., Boyer J.-C., Haenni A.-L. 1988; Overlapping open reading frames revealed by complete nucleotide sequencing of turnip yellow mosaic virus genomic RNA. Nucleic Acids Research 16:6157–6173
    [Google Scholar]
  26. Morozov S. Yu., Gorbulev V. G., Novikov V. K., Agranovski A. A., Kozlov Yu. V., Atabekov J. G., Bayev A. A. 1983; The primary structure of the 5′ and 3′ terminal regions of the genomic RNA of potato virus X. Doklady Akademii Nauk, SSSR 259:723–725 (in Russian)
    [Google Scholar]
  27. Morozov S. Yu., Dolja V. V., Atabekov J. G. 1989; Probable reassortment of genomic elements among elongated RNA-containing plant viruses. Journal of Molecular Evolution 29:52–62
    [Google Scholar]
  28. Morozov S. Yu., Kanyuka K. V., Levay K. E., Zavriev S. K. 1990a; The putative RNA replicase of potato virus M: obvious sequence similarity with potex- and tymoviruses. Virology 179:911–914
    [Google Scholar]
  29. Morozov S. Yu., Miroshnichenko N. A., Zelenina D. A., Fedorkin O. N., Solovijev A. G., Lukasheva L. I., Atabekov J. G. 1990b; Expression of RNA transcripts of potato virus X full-length and subgenomic cDNAs. Biochimie 72:677–684
    [Google Scholar]
  30. Morozov S. Yu., Miroshnichenko N. A., Solovijev A. G., Zelenina D. A., Fedorkin O. N., Lukasheva L. I., Grachev S. A., Chernov B. K. 1991; In vitro membrane binding of the translation products of the carlavirus 7-kDa protein genes. Virology 183:782–785
    [Google Scholar]
  31. Palmiter R. D. 1974; Magnesium precipitation of ribonucleoprotein complexes: expedient techniques for the isolation of undegraded polysomes and messenger ribonucleic acid. Biochemistry 13:3606–3612
    [Google Scholar]
  32. Poch O., Sauvaget I., Delahub M., Tordo N. 1989; Identification of four conserved motifs among the RNA-dependent polymerase encoding elements. EMBO Journal 8:3867–3874
    [Google Scholar]
  33. Randles J. M., Rohde W. 1990; Nicotiana velutina mosaic virus: evidence for a bipartite genome comprising 3 kb and 8 kb RNAs. Journal of General Virology 71:1019–1027
    [Google Scholar]
  34. Rozanov M. N., Morozov S. Yu., Skryabin K. G. 1990; Unexpected close relationship between the large nonvirion proteins of filamentous potexviruses and spherical tymoviruses. Virus Genes 3:370–379
    [Google Scholar]
  35. Rupasov V. V., Morozov S. Yu., 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]
  36. Sehnke P. C., Mason A. M., Hood S. J., Lister R. M., Johnson J. E. 1989; A ‘zinc finger’-type binding domain in tobacco streak virus coat protein. Virology 168:48–56
    [Google Scholar]
  37. Sit T. L., AbouHaidar M. G., Holy S. 1989; Nucleotide sequence of papaya mosaic virus RNA. Journal of General Virology 70:2325–2331
    [Google Scholar]
  38. Sit T. L., White K. A., Holy S., Padmanabhan U., Eweida M., Hiebert M., Mackie G. A., AbouHaidar M. G. 1990; Complete nucleotide sequence of clover yellow mosaic virus RNA. Journal of General Virology 71:1913–1920
    [Google Scholar]
  39. Skryabin K. G., Morozov S. Yu., Kraev A. S., Rozanov M. N., Chernov B. K., Lukasheva L. I., Atabekov J. G. 1988; Conserved and variable elements in RNA genomes of potexviruses. FEBS Letters 240:33–40
    [Google Scholar]
  40. Trifonov E. N. 1987; Translation framing code and frame-monitoring mechanism as suggested by the analysis of mRNA and 16S rRNA nucleotide sequences. Journal of Molecular Biology 194:643–652
    [Google Scholar]
  41. Vishnichenko V. K., Konareva T. N., Zavriev S. K. 1992; A new filamentous virus in shallot. Plant Pathology (in press)
    [Google Scholar]
  42. 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
    [Google Scholar]
  43. Zuidema D., Linthorst H. J. M., Huisman M. J., Asjes C. J., Bol J. F. 1989; Nucleotide sequence of narcissus mosaic virus RNA. Journal of General Virology 70:267–276
    [Google Scholar]
/content/journal/jgv/10.1099/0022-1317-73-10-2553
Loading
/content/journal/jgv/10.1099/0022-1317-73-10-2553
Loading

Data & Media loading...

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