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Sequence analysis of RNA 1 of lilac leaf chlorosis virus supports a close relationship to subgroup 3 ilarviruses

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Abstract

Analysis of the nucleotide sequence of the RNA 1 of lilac leaf chlorosis virus (LLCV) supports a close relationship with subgroup 3 ilarviruses. LLCV RNA 1 consists of 3404 nucleotides (nt) and encodes a single open reading frame consisting of 3111 nt. The deduced protein (Mr 117 kDa) contains the putative methyltransferase domain in the N-terminal region, and the NTPase/helicase domain in the C-terminal region. A conserved 41-nt region was identified at the distal end of the 3′UTR of all three genomic fragments of LLCV, with hairpin structures that may constitute putative coat protein binding sites.

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References

  1. Aparicio F, Vilar M, Perez-Payá E, Pallás V (2003) The coat protein of prunus necrotic ringspot virus specifically binds to and regulates the conformation of its genomic RNA. Virology 313:213–223

    Article  PubMed  CAS  Google Scholar 

  2. Bol JF (1999) Alfalfa mosaic virus and ilarviruses: involvement of coat protein in multiple steps of the replication cycle. J Gen Virol 80:1089–1102

    PubMed  CAS  Google Scholar 

  3. Galipienso L, Rubio L, Lopez C, Soler S, Aramburu J (2009) Complete nucleotide sequence of a Spanish isolate of Parietaria mottle virus infecting tomato. Virus Genes 39:256–260

    Article  PubMed  CAS  Google Scholar 

  4. Gasteiger E, Hoogland C, Gattiker A (2005) Protein identification and analysis tools on the ExPASy Server. In: Walker JM et al (eds) The proteomics protocols handbook. Humana Press, New Jersey

    Google Scholar 

  5. Houser-Scott F, Baer ML, Liem KF, Cai J-M, Gehrke L (1994) Nucleotide sequence and structural determinants of specific binding of coat protein or coat protein peptides to the 3′ untranslated region of alfalfa mosaic virus RNA 4. J Virol 68:2194–2205

    PubMed  CAS  Google Scholar 

  6. Huson DH, Bryant D (2005) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23:254–267

    Article  PubMed  Google Scholar 

  7. James D, Howell WE, Mink GI (2001) Molecular evidence of the relationship between a virus associated with flat apple disease and Cherry rasp leaf virus as determined by RT-PCR. Plant Dis 85:47–52

    Article  CAS  Google Scholar 

  8. James D, Varga A, Leippi L, Godkin S, Masters C (2010) Sequence analysis of RNA 2 and RNA 3 of lilac leaf chlorosis virus: a putative new member of the genus Ilarvirus. Arch Virol 155:993–998

    Article  PubMed  CAS  Google Scholar 

  9. Laforest SM, Gehrke L (2004) Spatial determinants of the alfalfa mosaic virus coat protein binding site. RNA 10:48–58

    Article  PubMed  CAS  Google Scholar 

  10. Perriere G, Gouy M (1996) WWW-Query: an on-line retrieval system for biological sequence banks. Biochimie 78:364–369

    Article  PubMed  CAS  Google Scholar 

  11. Rice P, Longden I, Bleasby A (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16:276–277

    Article  PubMed  CAS  Google Scholar 

  12. Roossinck MJ, Bujarski J, Ding SW, Hajimorard R, Hanada K, Scott S, Tousignant M (2005) Bromoviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy: eight report of the international committee on taxonomy of viruses. Elsevier Academic Press, San Diego, California

    Google Scholar 

  13. Rose TM (2005) CODEHOP-mediated PCR–a powerful technique for the identification and characterization of viral genomes. Virol J 2:20

    Article  PubMed  Google Scholar 

  14. 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 73:2129–2134

    Article  PubMed  CAS  Google Scholar 

  15. Saitou N, Nei M (1987) The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    PubMed  CAS  Google Scholar 

  16. Scott SW, Ge X (1995) The nucleotide sequence of citrus leaf rugose virus RNA 1. J Gen Virol 76:3233–3238

    Article  PubMed  CAS  Google Scholar 

  17. Scott SW, Zimmerman MT, Rankin D (2006) Complete sequence of the RNA 1 and RNA 2 of Parietaria mottle virus. Arch Virol 151:1895–1898

    Article  PubMed  CAS  Google Scholar 

  18. USDA (2009) Lilac (Syringa vulgaris L.). Plant guide. USDA Natural Resources Conservation Service. http://plants.usda.gov/java/profile?symbol=SYVU

  19. Wang X, Lee W-M, Watanabe T, Schwartz M, Janda M, Ahlquist P (2005) Brome mosaic virus 1a nucleoside triphosphate/helicase domain plays crucial roles in recruiting RNA replication templates. Virology 79:13747–13758

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Sidney Laboratory, Centre for Plant Health, Canadian Food Inspection Agency, 8801 East Saanich Road, Sidney, BC, V8L 1H3, Canada

    D. James & A. Varga

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  1. D. James
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  2. A. Varga
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Correspondence to D. James.

Additional information

The nucleotide sequence has been deposited in EMBL Nucleotide Sequence Database under accession number HE572565.

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James, D., Varga, A. Sequence analysis of RNA 1 of lilac leaf chlorosis virus supports a close relationship to subgroup 3 ilarviruses. Arch Virol 157, 203–206 (2012). https://doi.org/10.1007/s00705-011-1134-5

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  • DOI: https://doi.org/10.1007/s00705-011-1134-5

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