Archives of Virology

, 153:1263 | Cite as

Molecular characterization of Lolium latent virus, proposed type member of a new genus in the family Flexiviridae

  • Anna Maria Vaira
  • Clarissa J. Maroon-Lango
  • John Hammond
Original Article

Abstract

Lolium latent virus (LoLV) was recently detected in the USA for the first time in ryegrass hybrids (Lolium perenne × Lolium multiflorum). The genome of one USA isolate, LoLV-US1, has now been fully sequenced. The positive strand genomic RNA is 7674 nucleotides (nt) long and is organized in five open reading frames (ORFs) encoding the replication-associated protein, the movement-associated triple gene block proteins and the coat protein (CP). The genome organization is similar to that of viruses in the genera Potexvirus and Foveavirus; however, analysis of the complete LoLV genomic sequence, phylogenetic analyses of the deduced amino acid (aa) sequences of the polymerase and the CP, presence of a putative ORF 6, and the in vivo detection of two CPs in equimolar amounts, highlight features peculiar to LoLV. These characteristics indicate that LoLV forms a monotypic group separate from existing genera and unassigned species within the family Flexiviridae, for which we propose the genus name Lolavirus. One-step RT-PCR was developed for quick and reliable LoLV detection.

Notes

Acknowledgments

We would like to thank Scott Warnke, Ruhui Li and Hyoun-Sub Lim for helpful discussions and Mike Reinsel for invaluable technical assistance.

References

  1. 1.
    Adams MJ, Accotto GP, Agranovsky AA, Bar-Joseph M, Boscia D, Brunt AA, Candresse T, Coutts RHA, Dolja VV, Falk BW, Foster GD, Gonsalves D, Jelkmann W, Karasev A, Martelli GP, Mawassi M, Milne RG, Minafra A, Namba S, Rowhani A, Vetten HJ, Vishnichencho VK, Wisler GC, Yoshikawa N, Zavriev SK (2005) Family Flexiviridae. In: Fauquet CM (ed) Virus taxonomy—Eighth report of the International Committee on Taxonomy of Viruses. Elsevier Academic Press, San Diego, London, pp 1089–1124Google Scholar
  2. 2.
    Adams MJ, Antoniw JF, Bar-Joseph M, Brunt AA, Candresse T, Foster GD, Martelli GP, Milne RG, Zavriev SK, Fauquet CM (2004) The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation. Arch Virol 149:1045–1060PubMedGoogle Scholar
  3. 3.
    Aravind L, Koonin EV (2001) The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases. Genome Biol 2(3):research0007.1–0007.8Google Scholar
  4. 4.
    Beck DL, Guilford PJ, Voot DM, Andersen MT, Forster RL (1991) Triple gene block proteins of white clover mosaic potexvirus are required for transport. Virology 183:695–702PubMedCrossRefGoogle Scholar
  5. 5.
    Bratlie MS, Drabløs F (2005) Bioinformatic mapping of AlkB homology domains in viruses. BMC Genomics 6:1—http://www.biomedcentral.com/1471-2164/6/1
  6. 6.
    Chen J, Chen J, Adams MJ (2001) A universal PCR primer to detect members of the Potyviridae and its use to examine the taxonomic status of several members of the family. Arch Virol 146(4):757–766PubMedCrossRefGoogle Scholar
  7. 7.
    Chiba M, Reed JC, Prokhnevsky AI, Chapman EJ, Mawassi M, Koonin EV, Carrington JC, Dolja VV (2006) Diverse suppressors of RNA silencing enhance Agroinfection by a viral replicon. Virology 346:7–14PubMedCrossRefGoogle Scholar
  8. 8.
    Cserzo M, Eisenhaber F, Eisenhaber B, Simon I (2002) On filtering false positive transmembrane protein predictions. Protein Eng 15:745–752PubMedCrossRefGoogle Scholar
  9. 9.
    Deng M, Bragg JN, Ruzin S, Schichnes D, King D, Goodin MM, Jackson AO (2007) Role of the Sonchus yellow net virus N protein in formation of nuclear viroplasm. J Virol 81:5362–5374PubMedCrossRefGoogle Scholar
  10. 10.
    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 Lett 276:34–38PubMedCrossRefGoogle Scholar
  11. 11.
    Hammond J, Reinsel MD, Maroon-Lango CJ (2006) Identification and full sequence of an isolate of Alternanthera mosaic potexvirus infecting Phlox stolonifera. Arch Virol 151:477–493PubMedCrossRefGoogle Scholar
  12. 12.
    Howitt RLJ, Beever RE, Pearson MN, Forster RLS (2006) Genome characterization of a flexuous rod-shaped mycovirus, Botrytis virus X, reveals high amino acid identity to genes from plant “potex-like” viruses. Arch Virol 151:563–579PubMedCrossRefGoogle Scholar
  13. 13.
    Huth W, Lesemann DE, Götz R, Vetten HJ (1995) Some properties of Lolium latent virus. Agronomie 15:508CrossRefGoogle Scholar
  14. 14.
    James D, Varga A, Croft H (2007) Analysis of the complete genome of peach chlorotic mottle virus: identification of non-AUG start codons, in vitro coat protein expression, and elucidation of serological cross-reactions. Arch Virol 152:2207–2215PubMedCrossRefGoogle Scholar
  15. 15.
    Jordan R, Hammond J (1991) Comparison and differentiation of potyvirus isolates and identification of strain-, virus-, subgroup-specific, and potyvirus group-common epitopes using monoclonal antibodies. J Gen Virol 72:25–36PubMedCrossRefGoogle Scholar
  16. 16.
    Joshi CP, Zhou H, Huang X, Chiang VL (1997) Context sequences of translation initiation codon in plants. Plant Mol Biol 35:993–1001PubMedCrossRefGoogle Scholar
  17. 17.
    Komatsu K, Yamaji Y, Ozeki J, Hashimoto M, Kagiwada S, Takahashi S, Namba S (2007) Nucleotide sequence analysis of seven Japanese isolates of Plantago asiatica mosaic virus (PlAMV): a unique potexvirus with significantly high genomic and biological variability within the species. Arch Virol 153:193–198PubMedCrossRefGoogle Scholar
  18. 18.
    Li R, Maroon-Lango C, Mock R, Hammond J (2008) Lolium latent virus. Chap 15 In: Rao GP, Bragard C and Lebas BSM (eds) Characterization, diagnosis and management of plant viruses, vol 4. Grain crops and ornamentals, Studium Press, Texas, USA, pp 215–220Google Scholar
  19. 19.
    Maroon-Lango C, Hammond J, Warnke S, Li R, Mock R (2006) First report of Lolium latent virus in ryegrass in the USA. Plant Dis 90:528CrossRefGoogle Scholar
  20. 20.
    Martelli GP, Adams MJ, Kreuze JF, Dolja VV (2007) Family Flexiviridae: a case study in virion and genome plasticity. Ann Rev of Phytopathol 45:73–100CrossRefGoogle Scholar
  21. 21.
    Morozov SYu, Solovyev AG (2003) Triple gene block: modular design of a multifunctional machine for plant virus movement. J Gen Virol 84:1351–1366Google Scholar
  22. 22.
    Robertson NL, French R, Morris TJ (2000) The open reading frame 5A of foxtail mosaic virus is expressed in vivo and is dispensable for systemic infection. Arch Virol 145:1685–1698PubMedCrossRefGoogle Scholar
  23. 23.
    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
  24. 24.
    Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599PubMedCrossRefGoogle Scholar
  25. 25.
    Verchot-Lubicz J, Ye C-M, Bamunusinghe D (2007) Molecular biology of potexviruses: recent advances. J Gen Virol 88:1643–1655PubMedCrossRefGoogle Scholar
  26. 26.
    Wong SM, Mahtani PH, Lee KC, Yu HH, Tan Y, Neo KK, Chan Y, Wu M, Chng CC (1997) Cymbidium mosaic potexvirus RNA: complete nucleotide sequence and phylogenetic analysis. Arch Virol 142:383–391PubMedCrossRefGoogle Scholar
  27. 27.
    Wu F-S, Wang M-Y (1984) Extraction of proteins for sodium dodecyl sulfate-polyacrylamide gel electrophoresis from protease-rich plant tissues. Anal Biochem 139:100–103PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Anna Maria Vaira
    • 1
    • 3
  • Clarissa J. Maroon-Lango
    • 2
  • John Hammond
    • 3
  1. 1.Istituto di Virologia Vegetale, CNRTorinoItaly
  2. 2.Plant Germplasm Quarantine Program, PPQ-PHP, USDA-APHISBeltsvilleUSA
  3. 3.Floral and Nursery Plants Research Unit, USDA-ARS, US National Arboretum, B-010ABeltsvilleUSA

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