Advertisement

Archives of Virology

, Volume 150, Issue 9, pp 1845–1855 | Cite as

The complete genome sequence, organization and affinities of carrot red leaf virus

  • L. F. Huang
  • M. Naylor
  • D. W. Pallett
  • J. Reeves
  • J. I. Cooper
  • H. Wang
Article

Summary.

A sequence of 5723 nucleotides (GenBank accession number: AY695933) is reported for the RNA genome of an isolate of Carrot red leaf virus (CtRLV). The sequence is predicted to contain six large open reading frames and non coding sequences of 28 nucleotides at the 5′ end, 110 nucleotides at the 3′ end, and 215 nucleotides between the two main blocks of coding sequences. The 5′ coding region encodes two polypeptides with calculated molecular masses (Mr) of 28.6 kDa (P0) and 68.2 kDa (P1) that overlap in different reading frames. Circumstantially, the third ORF in the 5′ block is putatively translated by frameshift read-through to yield a polypeptide (P1 + P2) with a calculated Mr of 116.9 kDa. Frameshifting is predicted at a “shifty” sequence (GGGAAAC; nt 1523–1529) also found in most members of the genus Polerovirus. The C-terminal region of the 116.9 kDa polypeptide includes the consensus sequence for the viral RNA-directed RNA polymerase. The 3′ block of coding sequence defines three putative polypeptides of: 23.0 kDa (P3), 21.3 kDa (P4, in a different reading frame) and 77.2 kDa (P3 + P5, by read-through of P3) respectively. From the genome structure of CtRLV, it is suggested that this virus belongs to the genus Polerovirus, rather than either the genus Luteovirus or the genus Enamovirus.

Keywords

Nucleotide Polypeptide Consensus Sequence Code Sequence Code Region 
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.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Barker H, Smith HG (1999) The Luteoviridae. CABI, WallingfordGoogle Scholar
  2. Chalhoub, BA, Kelly, L, Robaglia, C, Lapierre, HD 1994Sequence variability in the genome-3′-terminal region of BYDV for 10 geographically distinct Pav-like isolates of barley yellow dwarf virus – analysis of the Orf6 variation.Arch Virol139403416CrossRefPubMedGoogle Scholar
  3. D’Arcy CJ, Domier LL (2000) Luteoviridae. In: Van Regenmortel MHV, Fauquet CM, Bishop DHL, Carstens E, Estes M, Lemon S, Maniloff J, Mayo MA, McGeoch D, Pringle CR, Wickner RB (ed) Virus taxonomy, VIIth Report of the International Committee on Taxonomy of Viruses. Academic Press, New York, pp 775–784Google Scholar
  4. Domier, LL, McCoppin, NK, Larsen, RC, D’Arcy, CJ 2002Nucleotide sequence shows that bean leafroll virus has a luteovirus-like genome organization.J Gen Virol8317911798PubMedGoogle Scholar
  5. Felsenstein, J 1989PHYLIP – phylogeny inference package (Version 3.2).Cladistics5164166Google Scholar
  6. Francki RIB, Fauquet CM, Knudson DL, Brown F (1991) Classification and nomenclature of viruses. Fifth Report of the International Committee on Taxonomy of Viruses. Arch Virol Suppl 2Google Scholar
  7. Garcia, A, Vanduin, J, Pleij, CWA 1993Differential response to frameshift signals in eukaryotic and prokaryotic translational systems.Nucleic Acids Res21401406PubMedGoogle Scholar
  8. Gibbs, MJ, Cooper, JI 1995A recombinational event in the history of luteoviruses probably induced by base-pairing between genomes of distinct viruses.Virology29611291132CrossRefGoogle Scholar
  9. Gibbs, MJ, Cooper, JI, Waterhouse, PM 1996The genome organization and affinities of an Australian isolate of carrot mottle umbravirus.Virology224310313CrossRefPubMedGoogle Scholar
  10. Giedroc, DP, Theimer, CA, Nixon, PL 2000Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting.J Mol Biol298167185PubMedGoogle Scholar
  11. Goldbach, R, Le Gall, O, Wellink, J 1991Alpha-like viruses in plants.Sem Virol21925Google Scholar
  12. Koonin, EV, Dolja, VV 1993Evolution and taxonomy of positive-strand RNA viruses-implications of comparative-analysis of amino-acid sequences.Crit Rev Biochem Mol Bio28375430PubMedGoogle Scholar
  13. Kujawa, AB, Drugeon, G, Hulanicka, D, Haenni, AL 1993Structural requirements for efficient translational frameshifting in the synthesis of the putative viral RNA-dependent RNA polymerase of potato leaf roll virus.Nucleic Acids Res2121652171PubMedGoogle Scholar
  14. Kumar, S, Tamura, K, Jakobsen, IB, Nei, M 2001MEGA2: molecular evolutionary genetics analysis software.Bioinformatics1712441245CrossRefPubMedGoogle Scholar
  15. Martin, RR, Keese, PK, Young, MJ, Waterhouse, PM, Gerlach, WL 1990Evolution and molecular biology of luteoviruses.Annu Rev Phytopathol28341363CrossRefGoogle Scholar
  16. Mathews, DH, Disney, MD, Childs, JL, Schroeder, SJ, Zuker, M, Turner, DH 2004Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure.Proc Natl Acad Sci USA10172877292CrossRefPubMedGoogle Scholar
  17. Mayo, MA, Ziegler-Graff, V 1996Molecular biology of luteoviruses.Adv Virus Res46413460PubMedGoogle Scholar
  18. Miller, WA, Waterhouse, PM, Gerlach, WL 1988Sequence and organisation of barley yellow dwarf virus genomic RNA.Nucleic Acids Res1660976111PubMedGoogle Scholar
  19. Miller, WA, Dineshkumar, SP, Paul, CP 1995Luteovirus gene expression.CRC Crit Rev Plant Sci14179211Google Scholar
  20. Moonan, F, Molina, J, Mirkov, TE 2000Sugarcane yellow leaf virus: an emerging virus that has evolved by recombination between luteoviral and poleroviral ancestors.Virology269156171CrossRefPubMedGoogle Scholar
  21. Murant AF, Robinson DJ, Taliansky ME, de Zoeten GA, Falk BW, Gibbs MJ, Pieterson G, Waterhouse PM (2000) Umbravirus. In: Van Regenmortel MHV, Fauquet CM, Bishop DHL, Carstens E, Estes M, Lemon S, Maniloff J, Mayo MA, McGeoch D, Pringle CR, Wickner RB (ed) Virus taxonomy, VIIth Report of the International Committee on Taxonomy of Viruses. Academic Press, New York, San Diago, pp 785–790Google Scholar
  22. Naylor M, Godfray HCJ, Pallet DW, Tristem M, Reeves JP, Cooper JI (2002) Mutualistic interactions amongst viruses. In: Hails RS, Beringer JE, Godfray HCJ (ed) Genes in the environment. Cambridge University Press, Cambridge, pp 205–225Google Scholar
  23. Page, RDM 1996TreeView: An application to display phylogenetic trees on personal computers.Comput Appl Biosci12357358PubMedGoogle Scholar
  24. Rathjen, JP, Karageorgos, LE, Habili, N, Waterhouse, PM, Symons, RH 1994Soybean dwarf luteovirus contains the 3rd variant genome type in the luteovirus group.Virology198671679CrossRefPubMedGoogle Scholar
  25. Robinson, DJ, Ryabov, EV, Raj, SK, Roberts, IM, Taliansky, ME 1999Satellite RNA is essential for encapsidation of groundnut rosette umbravirus RNA by groundnut rosette assistor luteovirus coat protein.Virology254105114CrossRefPubMedGoogle Scholar
  26. Rozas, J, Sanchez-DelBarrio, JC, Messeguer, X, Rozas, R 2003DnaSP, DNA polymorphism analyses by the coalescent and other methods.Bioinformatics1924962497CrossRefPubMedGoogle Scholar
  27. Scott, KP, Farmer, MJ, Robinson, DJ, Torrance, L, Murant, AF 1996Comparison of the coat protein of ground nut rosette assistor virus with those of other luteoviruses.Ann Appl Biol1287783Google Scholar
  28. Smith, GR, Borg, Z, Lockhart, BEL, Braithwaite, KS, Gibbs, MJ 2000Sugarcane yellow leaf virus: a novel member of the Luteoviridae that probably arose by inter-species recombination.J Gen Virol8118651869PubMedGoogle Scholar
  29. Thompson, JD, Gibson, TJ, Plewniak, F, Jeanmougin, F, Higgins, DG 1997The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.Nucleic Acids Res2548764882CrossRefPubMedGoogle Scholar
  30. Veidt, I, Lot, H, Leiser, M, Scheidecker, D, Guilley, H, Richards, K, Jonard, G 1988Nucleotide sequence of beet western yellows virus RNA.Nucleic Acids Res1699179932PubMedGoogle Scholar
  31. Vercruysse, P, Gibbs, M, Tirry, L, Höfte, M 2000RT-PCR using redundant primers to detect the three viruses associated with carrot motley dwarf disease.J Virol Methods88153161CrossRefPubMedGoogle Scholar
  32. Waterhouse, PM, Murant, AF 1981Purification of carrot red leaf virus and evidence from four serological tests for its relationship to luteovirus.Ann Appl Biol97191204Google Scholar
  33. Waterhouse, PM, Murant, AF 1983Further evidence on the nature of the dependence of carrot mottle virus on carrot red leaf virus for transmission by aphids.Ann Appl Biol103455464Google Scholar
  34. Waterhouse PM, Gildow FE, Johnstone GR (1988) Luteovirus group. AAB Descriptions of plant viruses No. 339Google Scholar
  35. Watson, M, Serjeant, EP, Lennon, EA 1964Carrot motley dwarf and parsnip mottle viruses.Ann Appl Biol54153166Google Scholar

Copyright information

© Springer-Verlag/Wien 2005

Authors and Affiliations

  • L. F. Huang
    • 1
  • M. Naylor
    • 1
  • D. W. Pallett
    • 1
  • J. Reeves
    • 1
  • J. I. Cooper
    • 1
  • H. Wang
    • 1
  1. 1.NERC/Centre for Ecology and Hydrology-Oxford (formerly Institute of Virology and Environmental Microbiology)OxfordU.K.

Personalised recommendations