Skip to main content
SpringerLink
Log in

The complete nucleotide sequence of yam mosaic virus (Ivory Coast isolate) genomic RNA

  • Original Papers
  • Published:
Archives of Virology Aims and scope Submit manuscript

Summary

The complete nucleotidic sequence of the yam mosaic virus (YMV) RNA was determined following the cloning of partial segments of the genome by reverse transcription and polymerase chain reactions (RT-PCR) using degenerate and/or specific oligonucleotide primers. YMV genomic RNA is 9,608 nucleotides in length and contains one open reading frame (ORF) encoding a polyprotein of 3,103 amino acids (aa) with a calculated Mr of 350,915. The 5′ leader sequence of YMV RNA preceding the ORF is 134 nucleotides (nt) long while the 3′ untranslated region (UTR) is 165 nt excluding the poly(A) tail. A computer algorithm predicted that the 3′UTR forms four stem loop structures which form a cloverleaf-like secondary structure. These structures apparently share some homologies with those observed in the 3′UTR of the potato virus Y-NL1 strain. Seven potential recognition sites for the NIa protease were found: one putative cleavage site for the P1 proteinase and one for the HC proteinase. The organization of the YMV genome is therefore similar to the other members of the genusPotyvirus based upon conserved sequence motifs common amongst members of this group. Despite its similarity with the other potyviruses in these conserved regions, YMV appears to be a distinct potyvirus species based upon a comparison of its sequence with those of other potyviruses.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Allison R, Johnston RE, Dougherty WG (1986) The nucleotide sequence of the coding region of tobacco etch virus genomic RNA: evidence for the synthesis of a single polyprotein. Virology 154: 9–20

    Google Scholar 

  2. Atreya PL, Atreya CD, Pirone TP (1991) Amino acid substitutions in the coat protein result in loss of insect transmissibility of a plant virus. Proc Natl Acad Sci USA 88: 7887–7891

    Google Scholar 

  3. Atreya CD, Atreya PL, Thornbury DW, Pirone TP (1992) Site-directed mutations in the potyvirus HC-PRO gene affect helper component activity, virus accumulation, and symptom expression in infected tobacco plants. Virology 191: 106–111

    Google Scholar 

  4. Balint R, Plooy I, Steele (1990) The nucleotide sequence of zucchini yellow mosaic potyvirus. Abstr.-VIII Int. Cong. Virol. 8: 84–107

    Google Scholar 

  5. Boeglin M, Labonne G, Degras L, Quiot-Douine L, Quiot JB (1993) Mise en évidence de la présence du virus de la mosaïque de l'igname sur igname (Dioscorea trifida) en Guyane. Communication to the Carribbean Food Crop Society at Martinique in July 1993

  6. Carrington JC, Cary SM, Parks TD, Dougherty WG (1989a) A second proteinase encoded by a plant potyvirus genome. EMBO J 8: 365–370

    Google Scholar 

  7. Carrington JC, Herndon KL (1992) Characterization of the potyviral HC-Pro autoproteolytic cleavage site. Virology 187: 308–315

    Google Scholar 

  8. Cattaneo R (1994) Biased (A-I) hypermutation of animal RNA virus genomes. Curr Opin Genet Dev 4: 895–900

    Google Scholar 

  9. Cronin S, Verchot J, Haldeman-Cahill R, Schaad MC, Carrington JC (1995) Long distance movement factor: a novel transport function of the potyvirus helper component-proteinase. Plant Cell 7: 549–559

    Google Scholar 

  10. DeBorde DC, Naeve CW, Herlocher ML, Maassab HF (1986) Resolution of a common RNA sequencing ambiguity by terminal deoxynucleotidyl transferase. Anal Biochem 157: 275–282

    Google Scholar 

  11. Dolja VV, Boyko VP, Agravnosky AA, Koonin EV (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

    Google Scholar 

  12. Dolja VV, Haldeman R, Robertson NL, Dougherty WG, Carrington JC (1994) Distinct functions of capsid protein in assembly and movement of tobacco etch potyvirus in plants. EMBO J 13: 1482–1491

    Google Scholar 

  13. Dolja VV, Haldeman-Cahill R, Montgomery AE, Vandenbosh KA, Carrington JC (1995) Capsid protein determinants involved in cell-to-cell and long distance movement of tobacco etch potyvirus. Virology 206: 1007–1016

    Google Scholar 

  14. Domier LL, Franklin KM, Shahabuddin M, Hellmann GM, Overmeyer JH, Hiremath ST, Siaw MFE, Lomonossoff GP, Shaw JG, Rhoads RE (1986) The nucleotide sequence of tobacco vein mottling virus RNA. Nucleic Acids Res 13: 5417–5430

    Google Scholar 

  15. Dougherty WG, Hiebert E (1980) Translation of potyvirus RNA in a rabbit reticulocyte lysate: cell-free translation strategy and a genetic map of the potyviral genome. Virology 104: 183–194

    Google Scholar 

  16. Dougherty WG, Carrington JC (1988) Expression and function of potyviral gene products. Annu Rev Phytopathol 26: 123–143

    Google Scholar 

  17. Dougherty WG, Carrington JC, Cary SM, Parks TD (1988) Biochemical and mutational analysis of a plant virus polyprotein cleavage site. EMBO J 7: 1281–1287

    Google Scholar 

  18. Dougherty WG, Parks TD (1989) Molecular genetic and biochemical evidence for the involvement of the heptapeptide cleavage sequence in determining the reaction profile at two tobacco etch virus cleavage sites in cell-free assays. Virology 172: 144–155

    Google Scholar 

  19. Dougherty WG, Parks TD, Cary SM, Bazan JF, Fletterick RJ (1989) Characterization of the catalytic residues of the tobacco etch virus 49-kDa proteinase. Virology 172: 302–310

    Google Scholar 

  20. FAO (1993) Production yearbook 47

  21. Fichot O, Girard M (1990) An improved method for sequencing of RNA templates. Nucleic Acids Res 18: 6162

    Google Scholar 

  22. Frenkel MJ, Ward CW, Shukla DD (1989) The use of 3′ non-codingnucleotide sequences in the taxonomy of potyviruses: application to watermelon mosaic virus 2 and soybean mosaic virus-N. J Gen Virol 70: 2775–2783

    Google Scholar 

  23. Gallie DR, Sleat DE, Watts JW, Turner PC, Wilson TMA (1987) A comparison of eukaryotic viral 5′-leader sequences as enhancers of mRNA expressionin vivo. Nucleic Acids Res 15: 8693–8711

    Google Scholar 

  24. Garcia JA, Martin MT, Cervera MT, Riechmann JL (1992) Proteolytic processing of the plum pox potyvirus polyprotein by the NIa protease at a novel cleavage site. Virology 188: 697–703

    Google Scholar 

  25. Gorbalenya AE, Donchenko AP, Blinov VM, Koonin EV (1989) Cysteine proteases of positive strand RNA viruses and chymotrypsin-like serine proteases: a distinct protein superfamily with a common structural fold. FEBS Lett 243: 103–114

    Google Scholar 

  26. Goudou-Urbino C, Konate G, Quiot JB, Dubern J (1996) Etiology and ecology of a yam mosaic disease in Burkina Faso. Trop Sci (in press)

  27. Gough KH, Shukla DD (1993) Nucleotide sequence of Johnsongrass mosaic potyvirus. Intervirology 36: 181–192

    Google Scholar 

  28. Gunasinghe UB, Flasinski S, Nelson RS, Cassidy BG (1994) Nucleotide sequence and genome organization of peanut stripe potyvirus. J Gen Virol 75: 2519–2526

    Google Scholar 

  29. Huet H, Gal-On A, Meir E, Lecoq H, Raccah B (1994) Mutations in the helper component protease gene of zucchini yellow mosaic virus affect its ability to mediate aphid transmissibility. J Gen Virol 75: 1407–1414

    Google Scholar 

  30. Jayaram C, Hill JH, Miller WA (1992) Complete nucleotide sequences of two soybean mosaic virus strains differentiated by response of soybean containing the Rsv resistance gene. J Gen Virol 73: 2067–2077

    Google Scholar 

  31. Johansen E, Rasmussen OF, Heide M, Borkhardt B (1991) The complete nucleotide sequence of pea seed-borne mosaic virus RNA. J Gen Virol 72: 2625–2632

    Google Scholar 

  32. Kasschau KD, Carrington JC (1995) Requirement of HC-Pro processing during genome amplification of tobacco etch potyvirus. Virology 209: 268–273

    Google Scholar 

  33. Kobe B, Deisenhofer J (1994) Proteins with leucine-rich repeats. Curr Opin Struct Biol 5: 409–416

    Google Scholar 

  34. Koonin EV (1991) The phylogeny of RNA-dependent RNA polymerases of positive strand RNA viruses. J Gen Virol 72: 2197–2206

    Google Scholar 

  35. Laín S, Riechmann JL, Garcia JA (1989) The complete nucleotide sequence of plum pox potyvirus RNA. Virus Res 13: 157–172

    Google Scholar 

  36. Laín S, Riechmann JL, Garcia JA (1990) RNA helicase: novel activity associated with a protein encoded by a positive strand RNA virus. Nucleic Acids Res 18: 7003–7006

    Google Scholar 

  37. Laín S, Martin MT, Riechmann JL, Garcia JA (1991) Novel catalytic activity associated with positive-strand RNA virus infection: Nucleic acid-stimulated ATPase activity of the plum pox potyvirus helicase-like protein. J Virol 65: 1–6

    Google Scholar 

  38. Langeveld SA, Dore JM, Memelink J, Derks AFLM, van der Vlugt CIM, Asje CJ, Bol JF (1991) Identification of potyviruses using the polymerase chain reaction with degenerate primers. J Gen Virol 72: 1531–1541

    Google Scholar 

  39. Lütcke HA, Chow KC, Michel FS, Moss KA, Kern HF, Scheele GA (1987) Selection of AUG initiation codons in plants and animals. EMBO J 6: 43–48

    Google Scholar 

  40. Marchoux G (1980) Pathologie des ignames en Guadeloupe; maladies virales. Les Colloques de l'INRA, l'Igname Séminaire International de Pointe-à-Pitre, 28 July–2 August 1980, 93–105

  41. Matthews REF (1991) Plant virology, 3rd ed. Academic Press, San Diego

    Google Scholar 

  42. Mavankal J, Rhoads RE (1991)In vitro cleavage at or near the N-terminus of the helper component protein in the tobacco vein mottling virus polyprotein. Virology 185: 721–731

    Google Scholar 

  43. Migliori A, Cadhilac B (1976) Contribution à l'étude de la maladie du virus de l'ignameDioscorea trifida en Guadeloupe. Ann Phytopatol 8: 73–78

    Google Scholar 

  44. Nicolas O, Laliberté JF (1991) The use of PCR for the cloning of large cDNAs fragments of turnip mosaic potyvirus. J Virol Methods 32: 57–66

    Google Scholar 

  45. Nicolas O, Laliberté JF (1992) The complete sequence of turnip mosaic potyvirus RNA. J Gen Virol 73: 2785–2793

    Google Scholar 

  46. Oh CS, Carrington JC (1989) Identification of essential residues in potyvirus proteinase HC-Pro by site-directed mutagenesis. Virology 173: 692–699

    Google Scholar 

  47. Padgett HS, Beachy RN (1993) Analysis of a tobacco mosaic virus strain capable of overcoming N gene-mediated resistance. Plant Cell 5: 577–586

    Google Scholar 

  48. Puurand U, Makinen K, Paulin L, Saarma M (1994) The nucleotide sequence of potato virus A genomic RNA and its sequence similarities with other potyviruses. J Gen Virol 75: 457–461

    Google Scholar 

  49. Reckhaus P, Nienhaus F (1981) Etiology of a virus disease of white yamDioscorea rotundata in Togo. J Plant Dis Protect 88: 492–509

    Google Scholar 

  50. Riechmann JL, Lain S, Garcia JA (1992) Highlights and prospects of potyvirus molecular biology. J Gen Virol 73: 1–16

    Google Scholar 

  51. Robaglia C, Durand-Tardiff M, Tronchet M, Boudazin G, Astier-Manifacier S, Casse-Delbart F, (1989) Nucleotide sequence of potato virus Y (strain N) genomic RNA. J Gen Virol 70: 935–947

    Google Scholar 

  52. Rodriguez-Cerezo E, Gamble-Klein P, Shaw JG (1991) A determinant of disease symptom severity is located in the 3′-terminal noncoding region of the RNA of a plant virus. Proc Natl Acad Sci USA 88: 9863–9867

    Google Scholar 

  53. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74: 5463–5467

    Google Scholar 

  54. Shahabuddin M, Shaw JG, Rhoads RE (1988) Mapping of the tobacco vein mottling virus VPg cistron. Virology 163: 635–637

    Google Scholar 

  55. Shukla DD, Ward CW (1988) Amino acid sequence homology of coat proteins as a basis for identification and classification of the potyvirus group. J Gen Virol 69: 2703–2710

    Google Scholar 

  56. Shukla DD, Ward CW, Brunt AA (1994) The potyviridae. CAB International, Cambridge

    Google Scholar 

  57. Sleat DE, Hull R, Turner PC, Wilson TMA (1988) Studies on the mechanism of translation enhancement by the 5′ leader of tobacco mosaic virus RNA. Eur J Biochem 175: 75–86

    Google Scholar 

  58. Terauchi R, Chikaleke VA, Thottappilly G, Hahn SK (1992) Origin and phylogeny of Guinea yams as revealed by RFLP analysis of chloroplast DNA and nuclear ribosomal DNA. Theor Appl Genetics 83: 743–751

    Google Scholar 

  59. Terry ER (1977) Incidence symptomatology and transmission of a yam virus in Nigeria. Proceedings of the Fourth Symposium of the International Society of Tropical Roots Crops 170–173

  60. Teycheney PY, Tavert G, Delbos R, Ravelonandro M, Dunez J (1989) The complete nucleotide sequence of plum pox virus (strain D). Nucleic Acids Res 17: 10115–10116

    Google Scholar 

  61. Thouvenel JC, Fauquet C (1977) Une mosaïque de l'igname (Dioscorea cayenensis) causée par un virus filamenteux en Côte d'Ivorie. Comptes rendus hebdomadaires de l'Acadèmie des Sciences de Paris 284: 1947–1949

    Google Scholar 

  62. Thouvenel JC, Fauquet C (1979) Yam Mosaic a new potyvirus infectingDioscorea cayenensis in the Ivory Coast. Ann App Biol 93: 279–283

    Google Scholar 

  63. Thouvenel JC, Fauquet F (1986) Yam mosaic virus. CMI/AAB Descriptions of Plant Viruses, No. 314

  64. Thouvenel JC, Dumont R (1990) Perte de rendement de l'igname infectée par le virus de la mosaïque en Côte d'Ivoire. L'Agronomie Tropicale 45: 125–129

    Google Scholar 

  65. Turpen T (1989) Molecular cloning of a potato virus Y genome: nucleotide sequence homology in non-coding region of potyviruses. J Gen Virol 70: 1951–1960

    Google Scholar 

  66. Van Der Vlugt RAA, Leunissen J, Goldbach R (1993) Taxonomic relationships between distinct potato virus Y isolates based on detailed comparisons of the viral coat proteins and 3′-non translated regions. Arch Virol 131: 361–375

    Google Scholar 

  67. Vance VB, Moore D, Turpen TH, Bracker A, Hollowell VC (1992) The complete nucleotide sequence of pepper mottle virus genomic RNA: comparison of the encoded polyprotein with those of other sequenced potyviruses. Virology 191: 19–30

    Google Scholar 

  68. Verchot J, Herndon KL, Carrington JC (1992) Mutational analysis of the tobacco etch potyviral 35-kDa proteinase: identification of essential residues and requirements for autoproteolysis. Virology 190: 298–306

    Google Scholar 

  69. Verchot J, Koonin EV, Carrington JC (1991) The 35-kDa protein from the N-terminus of the potyviral polyprotein functions as a third virus-encoded proteinase. Virology 185: 527–535

    Google Scholar 

  70. Verchot J, Carrington JC (1995) Evidence that the potyvirus P1 proteinase functionsin trans as an accessory factor for genome amplification. J Virol 69: 3668–3674

    Google Scholar 

  71. Verwoerd TC, Dekker BMM, Hoekema A (1989) A small procedure for the rapid isolation of plant RNAs. Nucleic Acids Res 17: 236

    Google Scholar 

  72. Ward CW, McKern NM, Frenkel MJ, Shukla DD (1992) Sequence data as the major criterion for potyvirus classification. In: Barnett OW (ed) Potyvirus taxonomy. Springer, Wien New York, pp 283–297 (Arch Virol [Suppl 5])

    Google Scholar 

  73. Yeh SD, Jan FJ, Chiang CH, Doong TJ, Chen MC, Chung PH, Bau HJ (1992) Complete nucleotide sequence and genetic organization of papaya ringspot virus RNA. J Gen Virol 73: 2531–2541

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. International Laboratory for Tropical Agricultural Biotechnology (ILTAB/ORSTOM-TSRI), La Jolla, California, U.S.A.

    M. -E. Aleman, C. Brugidou, R. N. Beachy & C. Fauquet

  2. Division of Plant Biology, The Scripps Research Institute, La Jolla, California, U.S.A.

    R. N. Beachy

  3. CSIC, Apartado de Correos, Murcia, Spain

    J. F. Marcos

Authors
  1. M. -E. Aleman
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. J. F. Marcos
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. C. Brugidou
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. R. N. Beachy
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. C. Fauquet
    View author publications

    You can also search for this author in PubMed Google Scholar

Additional information

GenBank Accession number: U42596

Rights and permissions

Reprints and permissions

About this article

Cite this article

Aleman, M.E., Marcos, J.F., Brugidou, C. et al. The complete nucleotide sequence of yam mosaic virus (Ivory Coast isolate) genomic RNA. Archives of Virology 141, 1259–1278 (1996). https://doi.org/10.1007/BF01718829

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF01718829

Keywords

Search

Navigation