Archives of Virology

, 154:1729 | Cite as

Identification and molecular characterization of a marafivirus in Rubus spp.

  • Sead Sabanadzovic
  • Nina Abou Ghanem-Sabanadzovic
Original Article

Abstract

An undescribed virus with isometric particles and a diameter of ca. 30 nm was identified in diseased samples of wild and cultivated Rubus species and molecularly characterized. Its genome was 6,463 nt, excluding the 3′-terminal poly(A) tail, and contained a single open reading frame coding for a 2,035-amino-acid-long precursor polypeptide (p223). The amino terminal portion of p223, identified as a replication-associated polyprotein, contained conserved motifs of methyltransferase, endopeptidase/protease, helicase and RNA-dependent RNA polymerase. The carboxy terminus of the large polypeptide is involved in the formation of two viral coat protein subunits with deduced molecular masses of 23 and 21 kDa. Pairwise comparisons and phylogenetic analyses showed closest relationships of this virus with oat blue dwarf virus and citrus sudden death-associated virus, sharing levels of genome sequence conservation far below the species demarcation level established for tymovirids. Our data indicate that this virus, for which the name blackberry virus S (BlVS) is proposed, is a hitherto undescribed species of the genus Marafivirus, family Tymoviridae. A survey conducted in Mississippi, USA, has shown that BlVS is also present in cultivated Rubus germplasm. This work represents the first report of a marafivirus infecting small fruits.

References

  1. 1.
    Abou Ghanem-Sabanadzovic N, Sabanadzovic S, Martelli GP (2003) Sequence analysis of the 3′end of three Grapevine fleck virus-like viruses from grapevine. Virus Genes 27:11–16CrossRefGoogle Scholar
  2. 2.
    Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 25:3389–3402CrossRefPubMedGoogle Scholar
  3. 3.
    Banttari EE, Zeyen RJ (1973) Oat blue dwarf virus. CMI/AAB Description Plant Viruses 123Google Scholar
  4. 4.
    Ding SW, Howe J, Keese P, Mackenzie A, Meek D, Osorio-Keese M, Skotnicki M, Srifah P, Torronen M, Gibbs AJ (1990) The tymobox, a sequence shared by most tymoviruses: its use in molecular studies of tymoviruses. Nucl Acids Res 18:1181–1187CrossRefPubMedGoogle Scholar
  5. 5.
    Dreher TW, Edwards MC, Gibbs AJ, Haenni A-L, Hammond RW, Jupin I, Koenig R, Sabanadzovic S, Abou Ghanem-Sabanadzovic N, Martelli GP (2005) Family Tymoviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Eight report of the international committee on taxonomy of viruses. Elsevier, Amsterdam, pp 1061–1074Google Scholar
  6. 6.
    Edwards MC, Zhang Z, Weiland JJ (1997) Oat blue dwarf marafivirus resembles the tymoviruses in sequence, genome organization, and expression strategy. Virology 232:217–229CrossRefPubMedGoogle Scholar
  7. 7.
    Foissac X, Svanella-Dumas L, Gentit P, Dulucq M-J, Marais A, Candresse T (2005) Polyvalent degenerate oligonucleotides reverse transcription-polymerase chain reaction: a polyvalent detection and characterization tool for trichoviruses, capilloviruses, and foveaviruses. Phytopathology 95:617–625CrossRefPubMedGoogle Scholar
  8. 8.
    Halgren A, Tzanetakis IE, Martin RR (2007) Identification, characterization, and detection of Black raspberry necrosis virus. Phytopathology 97:44–50CrossRefPubMedGoogle Scholar
  9. 9.
    Hammond RW, Ramirez P (2001) Molecular characterization of the genome of Maize rayado fino virus, the type member of the genus Marafivirus. Virology 282:338–347CrossRefPubMedGoogle Scholar
  10. 10.
    Jones AT, McGavin WJ, Gepp V, Zimmerman MT, Scott SW (2006) Purification and properties of Blackberry chlorotic ringspot, a virus species in subgroup 1 of the genus Ilarvirus found naturally infecting blackberry in the UK. Ann Appl Biol 149:125–135CrossRefGoogle Scholar
  11. 11.
    Katsuma S, Tanaka S, Omuro N, Takabuchi L, Daimon T, Imanishi S, Yamashita S, Iwanaga M, Mita K, Maeda S, Kobayashi M, Shimada T (2005) Novel macula-like virus identified in Bombyx mori cultured cells. J Virol 79:5577–5584CrossRefPubMedGoogle Scholar
  12. 12.
    Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) ClustalW2 and ClustalX version 2. Bioinformatics 23:2947–2948CrossRefPubMedGoogle Scholar
  13. 13.
    Lesemann D-E, Koenig R, Huth W, Brunt AA, Phillips S, Barton RJ (1983) Poinsettia mosaic virus—a tymovirus? J Phytopath 107:250–262CrossRefGoogle Scholar
  14. 14.
    Maccheroni W, Alegria MC, Greggio CC, Piazza JP, Kamla RF, Zacharias PRA, Bar-Joseph M, Kitajima EW, Assumpção LC, Camarotte G, Cardozo J, Casagrande EC, Ferrari F, Franco SF, Giachetto PF, Girasol A, Jordão H Jr, Silva VHA, Souza LCA, Aguilar-Vildoso CI, Zanca AS, Arruda P, Kitajima JP, Reinach FC, Ferro JA, da Silva ACR (2005) Identification and genomic characterization of a new virus (Tymoviridae family) associated with citrus sudden death disease. J Virol 79:3028–3037CrossRefPubMedGoogle Scholar
  15. 15.
    Martelli GP, Sabanadzovic S, Abou-Ghanem Sabanadzovic N, Edwards MC, Dreher T (2002) The family Tymoviridae. Arch Virol 147:1837–1846CrossRefPubMedGoogle Scholar
  16. 16.
    McGavin WJ, MacFarlane SA (2009) Rubus chlorotic mottle virus, a new sobemovirus infecting raspberry and bramble. Virus Res 139:10–13CrossRefPubMedGoogle Scholar
  17. 17.
    Page RD (1996) TreeView: an application to display phylogenetic trees on personal computers. Comp App Biol Sci 12:357–358Google Scholar
  18. 18.
    Sabanadzovic S, Abou-Ghanem N, Castellano MA, Digiaro M, Martelli GP (2000) Grapevine fleck virus-like viruses in Vitis. Arch Virol 145:553–565CrossRefPubMedGoogle Scholar
  19. 19.
    Sabanadzovic S, Abou Ghanem-Sabanadzovic N, Saldarelli P, Martelli GP (2001) Complete nucleotide sequence and genomic organization of Grapevine fleck virus. J Gen Virol 82:2009–2015PubMedGoogle Scholar
  20. 20.
    Sabanadzovic S, Abou Ghanem-Sabanadzovic N (2008) First report on Black raspberry necrosis virus in Rubus canadensis in Tennessee. Plant Dis 92:1254CrossRefGoogle Scholar
  21. 21.
    Sabanadzovic S, Abou Ghanem-Sabanadzovic N (2008) Molecular characterization and detection of a tripartite cryptic virus from rose. J Plant Path 90:287–293Google Scholar
  22. 22.
    Sabanadzovic S, Abou Ghanem-Sabanadzovic N, Gorbalenya AE (2009) Permutation of the active site of putative RNA-dependent RNA polymerase in a newly identified species of plant Alpha-like virus. Virology. doi:10.1016/j.virol.2009.08.006
  23. 23.
    Susaimuthu J, Tzanetakis IE, Gergerich RC, Martin RR (2008) A member of a new genus in the Potyviridae infects Rubus. Virus Res 131:145–151CrossRefPubMedGoogle Scholar
  24. 24.
    Susaimuthu J, Tzanetakis IE, Gergerich RC, Kim KS, Martin RR (2008) Viral interactions lead to decline of blackberry plants. Plant Dis 92:1288–1292CrossRefGoogle Scholar
  25. 25.
    Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucl Acids Res 22:4673–4680CrossRefPubMedGoogle Scholar
  26. 26.
    Tzanetakis IE, Martin RR (2004) First report of Beet pseudo yellows virus in blackberry in the United States. Plant Dis 88:223CrossRefGoogle Scholar
  27. 27.
    Tzanetakis IE, Susaimuthu J, Gergerich RC, Martin RR (2006) Nucleotide sequence of blackberry yellow vein associated virus, a novel member of the Closteroviridae. Virus Res 116:196–200CrossRefPubMedGoogle Scholar
  28. 28.
    Tzanetakis IE, Halgren A, Mosier N, Martin RR (2007) Identification and characterization of Raspberry mottle virus, a novel member of the Closteroviridae. Virus Res 127:26–33CrossRefPubMedGoogle Scholar
  29. 29.
    Valverde RA, Nameth ST, Jordan RL (1990) Analysis of double-stranded RNA for plant virus diagnosis. Plant Dis 74:255–258CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Sead Sabanadzovic
    • 1
  • Nina Abou Ghanem-Sabanadzovic
    • 1
  1. 1.Department of Entomology and Plant PathologyMississippi State UniversityMississippi StateUSA

Personalised recommendations