Archives of Virology

, 154:209 | Cite as

Complete genome analysis and immunodetection of a member of a novel virus species belonging to the genus Ampelovirus

  • Varvara I. Maliogka
  • C. I. Dovas
  • L. Lotos
  • K. Efthimiou
  • N. I. Katis
Original Article
First Online:
Received:
Accepted:

Abstract

A new grapevine leafroll-associated virus isolate (GLRaV-Pr) from Greek grapevines was recently reported. This virus, along with the genetically related GLRaV-4, -5, -6 and -9, form a separate diverse lineage within the genus Ampelovirus. In this paper, the complete nucleotide sequence of GLRaV-Pr was determined, making it the first fully sequenced virus of this lineage. Its genome is 13,696 nt long and contains seven open reading frames, which potentially encode a 253-kDa polyprotein containing papain-like protease, methyltransferase, AlkB and helicase domains, a 58.2-kDa RNA-dependent RNA polymerase, a 5.2-kDa hydrophobic protein, a 58.5-kDa heat shock 70 protein homologue, a 60-kDa protein, a 30-kDa coat protein (CP) and a 23-kDa protein. A virus-specific antibody was raised against the recombinant CP of GLRaV-Pr and was applied in western blot analysis. The genomic, serological and phylogenetic data reported here confirm that GLRaV-Pr is a member of a distinct Ampelovirus species. Comparisons of GLRaV-Pr with the only available genetically related, fully sequenced virus, PMWaV-1, PBNSPaV and the partially sequenced GLRaV-9 revealed that this lineage, including GLRaV-4, -5, -6, -9 and -De, exhibits a high uniformity of genome organization and includes the smallest and simplest viruses within the family Closteroviridae.

Keywords

Coat Protein Coat Protein Gene Grapevine Virus Grapevine Leafroll Disease Small Hydrophobic Protein 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
This is a preview of subscription content, log in to check access.

Notes

Acknowledgments

This work was financed by a research project for the reinforcement of new scientists [PENED 2003, funded by 75% of the public cost from the European Union, 25% from the Greek state (Ministry of Development-General Secretariat of Research and Technology, GSRT) and from the private sector (E.P.A.N.-Third European Community Framework)]. The authors wish to thank Dr. P. Gugerli (Agroscope Changins-Wadenswil Research Station ACW, Switzerland) for providing the GLRaV-9 isolate and also H. Bouzalas and E. Chatzinasiou (Laboratory of Microbiology and Infectious Diseases, School of Veterinary Medicine) for their help with rabbit immunization.

References

  1. 1.
    Aas PA, Otterlei M, Falnes PO, Vagbo CB, Skorpen F, Akbari M, Sundheim O, Bjoras M, Slupphaug G, Seeberg E, Krokan HE (2003) Human and bacterial oxidative demethylases repair alkylation damage in both RNA and DNA. Nature 421:859–863PubMedCrossRefGoogle Scholar
  2. 2.
    Abascal F, Zardoya R, Posada D (2004) Prot Test: selection of best-fit models of protein evolution. Bioinformatics 21:2104–2105CrossRefGoogle Scholar
  3. 3.
    Agranovski AA, Koonin EV, Boyko VP, Maiss E, Frotschl R, Lunina NA, Atabekov JG (1994) Beet yellows closterovirus: complete genome structure and identification of a leader papain-like thiol protease. Virology 198:311–324CrossRefGoogle Scholar
  4. 4.
    Agranovski AA, Lesemann DE, Maiss E, Hull R, Atabekov JG (1995) ”Rattlesnake” structure of a filamentous plant RNA virus built of two capsid proteins. Proc Natl Acad Sci USA 92:2470–2473CrossRefGoogle Scholar
  5. 5.
    Al Rwahnih M, Uyemoto JK, Falk BW, Rowhani A (2007) Molecular characterization and detection of plum bark necrosis stem pitting-associated virus. Arch Virol 152:2197–2206PubMedCrossRefGoogle Scholar
  6. 6.
    Alzhanova DV, Napuli A, Creamer R, Dolja VV (2001) Cell-to-cell movement and assembly of a plant closterovirus: roles for the capsid proteins and HSP70 homolog. EMBO J 20:6997–7007PubMedCrossRefGoogle Scholar
  7. 7.
    Do CB, Mahabhashyam MSP, Brudno M, Batzoglou S (2005) PROBCONS: probabilistic consistency-based multiple sequence alignment. Genome Res 15:330–340PubMedCrossRefGoogle Scholar
  8. 8.
    Dolja VV (2003) Beet yellows virus: the importance of being different. Mol Plant Pathol 4:91–98CrossRefGoogle Scholar
  9. 9.
    Dolja VV, Boyko VP, Agranovsky 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 184:79–86PubMedCrossRefGoogle Scholar
  10. 10.
    Dolja VV, Karasev AV, Koonin EV (1994) Molecular biology and evolution of closteroviruses: sophisticated build-up of large RNA genomes. Annu Rev Phytopathol 32:261–285CrossRefGoogle Scholar
  11. 11.
    Dolja VV, Kreuze JF, Valkonen JPT (2006) Comparative and functional genomics of closteroviruses. Virus Res 117:38–51PubMedCrossRefGoogle Scholar
  12. 12.
    Dovas CI, Katis NI (2003) Application of a spot multiplex nested RT-PCR for the simultaneous detection of viruses associated to rugose wood and leafroll grapevine diseases. In: Extended abstracts of the 14th meeting of the ICVG, September 12–17, Locorotondo (Bari), Italy, pp 192–193Google Scholar
  13. 13.
    Dovas CI, Maliogka VI, Katis NI (2006) Generic and specific detection of grapevine leafroll associated viruses using ramped annealing nested PCR. In: Extended abstracts of the 15th Meeting of the ICVG, April 2006. Stellenboch, South Africa, pp 115–116Google Scholar
  14. 14.
    Fazeli CF, Rezaian MA (2000) Nucleotide sequence and organization of ten open reading frames in the genome of Grapevine leafroll-associated virus 1 and identification of three subgenomic RNAs. J Gen Virol 81:605–615PubMedGoogle Scholar
  15. 15.
    Febres VJ, Ashoulin L, Mawassi M, Frank A, Bar-Joseph M, Manjunath KL, Lee RF, Niblett CL (1996) The p27 protein is present at one end of citrus tristeza virus particles. Phytopathology 86:1331–1335Google Scholar
  16. 16.
    Gugerli P (2003) Grapevine leafroll and related viruses. In: Extended abstracts of the 14th meeting of the ICVG. September 12–17, Locorotondo (Bari), Italy, pp 25–31Google Scholar
  17. 17.
    Good X, Monis J (2001) Partial genome organization, identification of the coat protein gene and detection of grapevine leafroll-associated virus–5. Phytopathology 91:274–281PubMedCrossRefGoogle Scholar
  18. 18.
    Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696–704PubMedCrossRefGoogle Scholar
  19. 19.
    Halgren A, Tzanetakis IE, Martin RR (2007) Identification, characterization and detection of Black raspberry necrosis virus. Phytopathology 97:44–50PubMedCrossRefGoogle Scholar
  20. 20.
    Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17:754–755PubMedCrossRefGoogle Scholar
  21. 21.
    Karasev AV (2000) Genetic diversity and evolution of closteroviruses. Annu Rev Phytopathol 38:293–324PubMedCrossRefGoogle Scholar
  22. 22.
    Karasev AV, Nikolaeva OV, Mushegian AR, Lee RF, Dawson WO (1996) Organization of the 3′ terminal half of beet yellow stunt virus genome and implications for the evolution of closteroviruses. Virology 221:199–207PubMedCrossRefGoogle Scholar
  23. 23.
    Koonin EV (1991) The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses. J Gen Virol 72:2197–2206PubMedCrossRefGoogle Scholar
  24. 24.
    Koonin EV, Dolja VV (1993) Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. Crit Rev Biochem Mol Biol 28:375–430PubMedCrossRefGoogle Scholar
  25. 25.
    Kozak M (1986) Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell 44:283–292PubMedCrossRefGoogle Scholar
  26. 26.
    Krogh A, Larsson B, von Heijne B, Sonnhammer ELL (2001) Predicting transmembrane protein topology with a hidden Markov model, application to complete genomes. J Mol Biol 305:567–580PubMedCrossRefGoogle Scholar
  27. 27.
    Ling KS, Zhu HY, Drong RF, Slightom JL, McFerson JR, Gonsalves D (1997) The coat protein of grapevine leafroll associated closterovirus-3, nucleotide sequencing and expression in transgenic plants. Arch Virol 142:1101–1116PubMedCrossRefGoogle Scholar
  28. 28.
    Ling K-S, Zhu H-Y, Gonsalves D (2004) Complete nucleotide sequence and genome organization of Grapevine leafroll-associated virus 3, type member of the genus Ampelovirus. J Gen Virol 85:2099–2102PubMedCrossRefGoogle Scholar
  29. 29.
    Maliogka VI, Dovas CI, Katis NI (2008) Evolutionary relationships of virus species belonging to a distinct lineage within the Ampelovirus genus. Virus Res 135:125–135PubMedCrossRefGoogle Scholar
  30. 30.
    Marchler-Bauer A, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD et al (2003) CDD, a curated Entrez database of conserved domain alignments. Nucleic Acids Res 31:383–387PubMedCrossRefGoogle Scholar
  31. 31.
    Martelli GP, Agranovsky AA, Bar-Joseph M, Boscia D, Candresse T, Coutts RHA, Dolja VV, Falk BW, Gonsalves D, Jelkmann W, Karasev AV, Minafra A, Namba S, Vetten HJ, Wisler GC, Yoshikawa N (2002) The family Closteroviridae revised. Arch Virol 147:2039–2044PubMedCrossRefGoogle Scholar
  32. 32.
    Martelli GP, Adams MJ, Kreuze JF, Dolja VV (2007) Family Flexiviridae: a case study in virion and genome plasticity. Annu Rev Phytopathol 45:73–100PubMedCrossRefGoogle Scholar
  33. 33.
    Melzer MJ, Karasev AV, Sether DM, Hu JS (2001) Nucleotide sequence, genome organization and phylogenetic analysis of pineapple mealybug wilt-associated virus-2. J Gen Virol 82:1–7PubMedGoogle Scholar
  34. 34.
    Melzer MJ, Sether DM, Karasev AV, Borth W, Hu JS (2008) Complete nucleotide sequence and genome organization of pineapple mealybug wilt-associated virus-1. Arch Virol 153:707–714PubMedCrossRefGoogle Scholar
  35. 35.
    Minafra A, Casati P, Elicio V, Rowhani A, Saldarelli P, Savino V, Martelli GP (2000) Serological detection of Grapevine rupestris stem pitting-associated virus (GRSPaV) by a polyclonal antiserum to recombinant virus coat protein. Vitis 39:115–118Google Scholar
  36. 36.
    Napuli AJ, Alzhanova DV, Doneanu CE, Barofsky DF, Koonin EV, Dolja VV (2003) The 64-kDa capsid protein homolog of beet yellows virus is required for assembly of virion tails. J Virol 77:2377–2384PubMedCrossRefGoogle Scholar
  37. 37.
    Napuli AJ, Falk BW, Dolja VV (2000) Interaction between HSP70 homolog and filamentous virions of the Beet yellows virus. Virology 274:232–239PubMedCrossRefGoogle Scholar
  38. 38.
    Peremyslov VV, Andreev IA, Prokhnevsky AI, Duncan GH, Taliansky ME, Dolja VV (2004) Complex molecular architecture of beet yellows virus particles. Proc Natl Acad Sci USA 101:5030–5035PubMedCrossRefGoogle Scholar
  39. 39.
    Rott ME, Jelkmann W (2004) Little cherry virus 2: sequence and genomic organization of an unusual member of the Closteroviridae. Arch Virol 150:107–123PubMedCrossRefGoogle Scholar
  40. 40.
    Rozanov MN, Koonin EV, Gorbalenya AE (1992) Conservation of the putative methyltransferase domain: a hallmark of the “Sindbis-like” supergroup of positive strand RNA viruses. J Gen Virol 73:2129–2134PubMedCrossRefGoogle Scholar
  41. 41.
    Satyanarayana T, Gowda S, Ayllon MA, Dawson WO (2004) Closterovirus bipolar virion: evidence for initiation of assembly by minor coat protein and its restriction to the genomic RNA 5′ region. Proc Natl Acad Sci USA 101:799–804PubMedCrossRefGoogle Scholar
  42. 42.
    Satyanarayana T, Gowda S, Mawassi M, Albiach-Marti MR, Ayllon MA, Robertson C, Garnsey SM, Dawson WO (2000) Closterovirus encoded HSP70 homolog and p61 in addition to both coat proteins function in efficient virion assembly. Virology 278:253–265PubMedCrossRefGoogle Scholar
  43. 43.
    Susaimuthu J, Tzanetakis IE, Gergerich RC, Martin RR (2006) Blackberry virus Y: a potyvirus component of blackberry yellows disease. Phytopathology 96:S112Google Scholar
  44. 44.
    Tian T, Rubio L, Yeh HH, Crawford B, Falk BW (1999) Lettuce infectious yellows virus: in vitro acquisition analysis using partially purified virions and the whitefly, Bemisia tabaci. J Gen Virol 80:1111–1117PubMedGoogle Scholar
  45. 45.
    Ting J, Lee AS (1988) Human gene encoding the 78,000-dalton glucose-regulated protein and its pseudogene: structure, conservation, and regulation. DNA 7:275–286PubMedCrossRefGoogle Scholar
  46. 46.
    Valverde R, Nameth ST, Jordan RL (1990) Analysis of double-stranded RNA for plant virus diagnosis. Plant Dis 74:255–258CrossRefGoogle Scholar
  47. 47.
    Walter B, Martelli GP (1997) Clonal and sanitary selection of the grapevine. In: Walter B (ed) Sanitary selection of the grapevine: protocols for detection of viruses and virus-like diseases. Institut National de la Recherche Agronomique, Colmar, pp 43–95Google Scholar
  48. 48.
    Zhu H-Y, Ling K-S, Goszczynski DE, McFerson JR, Gonsalves D (1998) Nucleotide sequence and genome organization of grapevine leafroll-associated virus-2 are similar to beet yellows virus, the closterovirus type member. J Gen Virol 79:1289–1298PubMedGoogle Scholar

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Varvara I. Maliogka
    • 1
  • C. I. Dovas
    • 2
  • L. Lotos
    • 1
  • K. Efthimiou
    • 1
  • N. I. Katis
    • 1
  1. 1.Plant Pathology Laboratory, School of AgricultureAristotle University of ThessalonikiThessalonikiGreece
  2. 2.Laboratory of Microbiology and Infectious Diseases, School of Veterinary MedicineAristotle University of ThessalonikiThessalonikiGreece

Personalised recommendations