Complete nucleotide sequence of Cherry leaf roll virus (CLRV), a subgroup C nepovirus

Virus Research

Volumn 163, Issue 2, 2012, Pages 678-683

  von Bargen, Susanne ^a   Langer, Juliane ^a   Robel, Jenny ^a   Rumbou, Artemis ^a,b   Büttner, Carmen ^a  

^a HUMBOLDT UNIVERSITY   (Germany)

^b INSTITUTE OF TECHNOLOGY OF AGRICULTURAL PRODUCTS   (Greece)

Author keywords

CLRV rhubarb isolate; Genome organization; Protein domains; Terminal sequence duplication

Indexed keywords

COAT PROTEIN; HELICASE; PLANT VIRUS MOVEMENT PROTEIN; POLYPROTEIN; PROTEINASE;

5' UNTRANSLATED REGION; ARTICLE; CHERRY LEAF ROLL VIRUS; MOLECULAR WEIGHT; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PLANT VIRUS; PRIORITY JOURNAL;

CLUSTER ANALYSIS; GENOME, VIRAL; MOLECULAR WEIGHT; NEPOVIRUS; OPEN READING FRAMES; PHYLOGENY; PLANT DISEASES; PRUNUS; RNA, VIRAL; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY; VIRAL PROTEINS;

CHERRY LEAF ROLL VIRUS; NEPOVIRUS; RHEUM X HYBRIDUM; SUBGROUP C;

EID: 84856554240     PISSN: 01681702     EISSN: 18727492     Source Type: Journal    
DOI: 10.1016/j.virusres.2011.12.018     Document Type: Article

References (48)

1. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990, 215:403-410.
2. Blom N., Hansen J., Blaas D., Brunak S. Cleavage site analysis in picornaviral polyproteins: discovering cellular targets by neural networks. Protein Sci. 1996, 5:2203-2216.
3. Borja M., Sanchez F., Rowhani A., Bruening G., Ponz F. Long, nearly identical untranslated sequences at the 3' terminal regions of the genomic RNAs of cherry leafroll virus (walnut strain). Virus Genes 1995, 10:245-252.
4. Brooks M., Bruening G. A subgenomic RNA associated with Cherry leafroll virus infections. Virology 1995, 211:33-41.
5. Büttner C., von Bargen S., Bandte M., Myrta A. Cherry leaf roll virus. Virus and Virus-Like Diseases of Pome and Stone Fruits 2011, 119-125. APS Press, St. Paul, USA. A. Hadidi, M. Barba, T. Candresse, W. Jelkmann (Eds.).
6. Carrier K., Hans F., Sanfacon H. Mutagenesis of amino acids at two tomato ringspot nepovirus cleavage sites: effect on proteolytic processing in cis and in trans by the 3C-like protease. Virology 1999, 258:161-175.
7. Carrier K., Xiang Y., Sanfacon H. Genomic organization of RNA2 of Tomato ringspot virus: processing at a third cleavage site in the N-terminal region of the polyprotein in vitro. J. Gen. Virol. 2001, 82:1785-1790.
8. Chen J., Chen J., Adams M.J. 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. 2001, 146:757-766.
9. Chisholm J., Wieczorek A., Sanfacon H. Expression and partial purification of recombinant tomato ringspot nepovirus 3C-like proteinase: comparison of the activity of the mature proteinase and the VPg-proteinase precursor. Virus Res. 2001, 79:153-164.
10. Elbeaino T., Digiaro M., Fallanaj F., Kuzmanovic S., Martelli G.P. Complete nucleotide sequence and genome organisation of grapevine Bulgarian latent virus. Arch. Virol. 2011, 156:875-879.
11. Froussard P. A random-PCR method (rPCR) to construct whole cDNA library from low amounts of RNA. Nucleic Acids Res. 1992, 20:2900.
12. Fuchs M., Pinck M., Serghini M.A., Ravelonandro M., Walter B., Pinck L. The nucleotide sequence of satellite RNA in grapevine fanleaf virus, strain F13. J. Gen. Virol. 1989, 70:955-962.
13. Gorbalenya A.E., Blinov V.M., Donchenko A.P., Koonin E.V. A NTP-binding motif is the most conserved sequence in a highly diverged monophyletic group of proteins involved in positive strand RNA viral replication. J. Mol. Evol. 1989, 28:256-268.
14. Gorbalenya A.E., Donchenko A.P., Blinov V.M., Koonin E.V. Cysteine proteases of positive strand RNA viruses and chymotrypsin-like serine proteases. FEBS Lett. 1989, 243:103-114.
15. Gorbalenya A.E., Koonin E.V., Wolf Y.I. A new superfamily of putative NTP-binding domains encoded by genomes of small DNA and RNA viruses. FEBS Lett. 1990, 262:145-148.
16. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 1999, 41:95-98.
17. Hans F., Sanfacon H. Tomato ringspot nepovirus protease: characterization and cleavage site specificity. J. Gen. Virol. 1995, 76:917-927.
18. Hellen C.U.T., Cooper J.I. The genome-linked protein of cherry leaf roll virus. J. Gen. Virol. 1987, 68:2913-2917.
19. Jafarpour B., Sanfacon H. Insertion of large amino acid repeats and point mutations contribute to a high degree of sequence diversity in the X4 protein of tomato ringspot virus (genus Nepovirus). Arch. Virol. 2009, 154:1713-1717.
20. Koonin E.V., Dolja V.V. Evolution and taxonomy of positive strand RNA viruses: implications of comparative analysis of amino acid sequences. Crit. Rev. Biochem. Mol. Biol. 1993, 28:375-430.
21. Kozak M. Regulation of translation via mRNA structure in prokaryotes and eukaryotes. Gene 2005, 361:13-37.
22. Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J., Higgins D.G. Clustal W and Clustal X version 20. Bioinformatics 2007, 23:2947-2948.
23. Latvala-Kilby S., Lehto K. The complete nucleotide sequence of RNA2 of blackcurrant reversion nepovirus. Virus Res. 1999, 65:87-92.
24. Le Gall O., Christian P., Fauquet C.M., King A.M.Q., Knowles N.J., Nakashima N., Stanway G., Gorbalenya A.E. Picornavirales, a proposed order of positive-sense single-stranded RNA viruses with a pseudo-T=3 virion architecture. Arch. Virol. 2008, 153:715-727.
25. Marais A., Faure C., Candresse T., Hulle M. First report of nasturtium as a natural host of Cherry leaf roll virus on Amsterdam Island. Plant Dis. 2010, 94:477.
26. Marchler-Bauer A., Anderson J.B., Chitsaz F., et al. CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Res. 2009, 37:205-210.
27. Mayo M.A., Fritsch C. A possible consensus sequence for VPg of viruses in the family Comoviridae. FEBS Lett. 1994, 354:129-130.
28. Mushegian A.R. The putative movement domain encoded by nepovirus RNA-2 is conserved in all sequenced nepoviruses. Arch. Virol. 1994, 135:437-441.
29. Ochman H., Ajioka J.W., Garza D., Hartl D.L. Inverse polymerase chain reaction. Biotechnology 1990, 8:759-760.
30. Pacot-Hiriart C., Latvala-Kilby S., Lehto K. Nucleotide sequence of black currant reversion associated nepovirus RNA1. Virus Res. 2001, 79:145-152.
31. Pallas V., Rowhani A., Daubert S., Bruening G. Properties and translation studies of cherry leaf roll virus (CLRV). Acta Hortic. 1991, 309:45-53.
32. Pesole G., Gissi C., Grillo G., Licciulli F., Liuni S., Saccone C. Analysis of oligonucleotide AUG start codon context in eukaryotic mRNAs. Gene 2000, 261:85-91.
33. Rebenstorf, K., 2005. Untersuchungen zur Epidemiologie des Cherry leaf roll virus (CLRV) - genetische und serologische Diversität in Abhängigkeit von der Wirtspflanzenart und der geographischen Herkunft. PhD thesis, Humboldt-Universität zu Berlin, Landwirtschaftlich-Gärtnerische Fakultät, 127 pp.
34. Rott M.E., Tremaine J.H., Rochon D.M. Nucleotide sequence of tomato ringspot virus RNA-2. J. Gen. Virol. 1991, 72:1505-1514.
35. Rott M.E., Tremaine J.H., Rochon D.M. Comparison of the 5' and 3' termini of Tomato ringspot virus RNA1 and RNA2: evidence for RNA recombination. Virology 1991, 185:468-472.
36. Rott M.E., Gilchrist A., Lee L., Rochon D.M. Nucleotide sequence of tomato ringspot virus RNA1. J. Gen. Virol. 1995, 76:465-473.
37. Sambrook J., Fritsch E.F., Maniatis T. Molecular Cloning - A Laboratory Manual 1989, Cold Spring Harbour Laboratory, Cold Spring Harbour, New York.
38. Sanfacon H., Wellink J., Le Gall O., Karasev A., van der Vlugt R., Wetzel T. Secoviridae: a proposed family of plant viruses within the order Picornavirales that combines the families Sequiviridae and Comoviridae, the unassigned genera Cheravirus and Sadwavirus, and the proposed genus Torradovirus. Arch. Virol. 2009, 154:899-907.
39. Scott N.W., Cooper J.I., Liu Y.Y., Hellen C.U.T. A 1.5kb sequence homology in 3'-terminal regions of RNA-1 and RNA-2 of a birch isolate of cherry leaf roll nepovirus is also present, in part, in a rhubarb isolate. J. Gen. Virol. 1992, 73:481-485.
40. Scott N.W., Cooper J.I., Edwards J.L. The identification, cloning and sequence analysis of the coat protein coding region of a birch isolate (I2) of cherry leaf roll nepovirus. Arch. Virol. 1993, 131:209-215.
41. Thompson J.R., Leone G., Lindner J.L., Jelkmann W., Schoen C.D. Characterization and complete nucleotide sequence of Strawberry mottle virus: a tentative member of a new family of bipartite plant picorna-like viruses. J. Gen. Virol. 2002, 83:229-239.
42. Tomlinson J.A., Walkey D.G.A. The isolation and identification of rhubarb viruses occurring in Britain. Ann. Appl. Biol. 1967, 59:415-427.
43. Wang A., Sanfacon H. Proteolytic processing at a novel cleavage site in the N-terminal region of the tomato ringspot nepovirus RNA-1-encoded polyprotein in vitro. J. Gen. Virol. 2000, 81:2771-2781.
44. Wang A., Carrier K., Chisholm J., Wieczorek A., Huguenot C., Sanfacon H. Proteolytic processing of tomato ringspot nepovirus 3C-like protease precursors: definition of the domains for the VPg, protease and putative RNA-dependent RNA polymerase. J. Gen. Virol. 1999, 80:799-809.
45. Werner R., Muehlbach H.P., Büttner C. Detection of cherry leaf roll nepovirus (CLRV) in birch, beech and petunia by immuno-capture RT-PCR using a conserved primer pair. Eur. J. Forest Pathol. 1997, 27:309-318.
46. Wood K.R. Nepovirus isolation and RNA extraction. Methods in Molecular Biology, Vol. 81: Pant Virology Protocols: from Virus Isolation to Transgenic Resistance 1998, 197-204. Humana Press Inc., Totowa, NJ, USA. G.D. Foster, S.C. Taylor (Eds.).
47. Zhang G., Sanfacon H. Characterization of membrane association domains within the tomato ringspot nepovirus X2 protein, an endoplasmic reticulum-targeted polytopic membrane protein. J. Virol. 2006, 80:10847-10857.
48. Zhou Y., Civerolo E.L., Melvin J.A. Comparative nucleotide sequences of the coat protein-encoding region of the genomes of cherry leafroll virus strains infecting walnut. Acta Hortic. 1998, 472:321-324.