Complete nucleotide sequence and genome organization of Pelargonium line pattern virus and its relationship with the family Tombusviridae

Archives of Virology

Volumn 150, Issue 5, 2005, Pages 949-965

  Castano A ^a   Hernandez C ^a  

^a Universitat Politècnica de València   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; VIRUS RNA;

ARTICLE; CLASSIFICATION; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PELARGONIUM; PHYLOGENY; PLANT VIRUS; TOMBUSVIRUS; VIROLOGY; VIRUS GENOME;

BASE SEQUENCE; DNA, COMPLEMENTARY; GENOME, VIRAL; MOLECULAR SEQUENCE DATA; PELARGONIUM; PHYLOGENY; PLANT VIRUSES; RNA, VIRAL; SEQUENCE ANALYSIS, DNA; TOMBUSVIRIDAE;

CARMOVIRUS; PANICOVIRUS; PELARGONIUM; PELARGONIUM LINE PATTERN VIRUS; TOMBUSVIRIDAE; TOMBUSVIRUS;

EID: 17644361996     PISSN: 03048608     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00705-004-0464-y     Document Type: Article

References (56)

1. Andriessen M, Meulewaeter F, Cornelissen M (1995) Expression of Tobacco necrosis virus open reading frames 1 and 2 is sufficient for the replication of satellite Tobacco necrosis virus. Virology 212: 222-224
2. Ahlquist P, Janda M (1984) cDNA cloning and in vitro transcription of the complete Brome mosaic virus genome. Mol Cell Biol 4: 2876-2882
3. Ahlquist P, Luckow V, Kaesberg P (1981) Complete nucleotide sequence of Brome mosaic virus RNA 3. J Mol Biol 153: 23-38
4. Bouwen I, Maat DZ (1992) Pelargonium flower-break and Pelargonium line pattern viruses in the Netherlands; purification, antiserum preparation, serological identification, and detection in pelargonium by ELISA. Neth Plant Pathol 98: 141-156
5. Brierley I (1995) Ribosomal frameshifting on viral RNAs. J Gen Virol 76: 1885-1892
6. Brierley I, Jenner AJ, Inglis SC (1992) Mutational analysis of the "slippery sequence" component of a coronavirus ribosomal frameshifting signal. J Mol Biol 227: 463-479
7. Bringloe DH, Pleij CW, Coutts RH (1999) Mutation analysis of cis-elements in the 3′- and 5′-untranslated regions of satellite Tobacco necrosis virus strain C RNA. Virology 264: 76-84
8. Cañizares MC, Marcos JF, Pallás V (2001) Molecular variability of twenty-one geographically distinct isolates of Carnation mottle virus (CarMV) and phylogenetic relationships within the Tombusviridae family. Arch Virol 146: 2039-2051
9. Carpenter CD, Simon AE (1998) Analysis of sequences and predicted structures required for viral satellite RNA accumulation by in vivo genetic selection. Nucleic Acids Res 26: 2426-2432
10. Fabian MR, Na H, Ray D, White KA (2003) 3′-Terminal RNA secondary structures are important for accumulation of Tomato bushy stunt DI RNAs. Virology 313: 567-580
11. Franck A, Loebenstein G (1994) Virus and virus-like diseases of pelargonium in Israel. Acta Hortic 377: 31-39
12. Futterer J, Hohn T (1996) Translation in plants-rules and exceptions. Plant Mol Biol 32: 159-189
13. Goldberg K-B, Modrell B, Hillman BI, Heaton LA, Choi TJ, Jackson AO (1991) Structure of the glycoprotein gene of Sonchus yellow net virus, a plant rhabdovirus. Virology 185: 32-38
14. Hacker DL, Petty ITD, Wei N, Morris TJ (1992) Turnip crinkle virus genes required for RNA replication and virus movement. Virology 186: 1-8
15. Heinze C, Wobbe V, Lesemann DE, Zhang DY, Willingmann P, Adam G (2004) Pelargonium necrotic spot virus: a new member of the genus Tombusvirus. Arch Virol 149: 1527-1539
16. Huang M, Koh D, Weng L, Chang M, Yap Y, Zhang L, Wong S (2000) Complete nucleotide sequence and genome organization of Hibiscus chlorotic ringspot virus, a new member of the genus Carmovirus: evidence for the presence and expression of two novel open reading frames. J Virol 74: 3149-3155
17. Isogai M, Uyeda I, Hataya T (1998) An efficient cloning strategy for viral double-stranded RNAs with unknown sequences. Ann Phytopathol Soc Jpn 64: 244-248
18. Jones AT, McGavin WJ, Brunt AA, Phillips S (2000) Elderberry latent virus: its relationship to Pelargonium ringspot virus and its identification as a distinct member of the genus Carmovirus, family Tombusviridae. Ann Appl Biol 136: 147-152
19. Kinard GR, Jordan RL, Hurtt SS (1996) Partial characterization of Pelargonium line pattern and Pelargonium ringspot viruses. Acta Hortic 432: 148-155
20. Kinard GR, Jordan RL (1998) Genome organization of Pelargonium ringspot and Elderberry latent viruses. Phytopathology 88: S48
21. Kinard GR, Jordan R (2002) Genome organization of Pelargonium chlorotic ring pattern virus: further implications for Tombusviridae taxonomy. Acta Hortic 568: 17-27
22. 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: 375-430
23. Kozak M (1986) Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell 44: 283-292
24. Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA 2: molecular evolutionary genetics analysis software. Bioinformatics 17: 1244-1245
25. Li WZ, Qu F, Morris TJ (1998) Cell-to-cell movement of Turnip crinkle virus is controlled by two small open reading frames that function in trans. Virology 244: 405-416
26. Liang XZ, Lucy AP, Ding SW, Wong SM (2002) The p23 protein of Hibiscus chlorotic ringspot virus is indispensable for host-specific replication. J Virol 76: 12312-12319
27. Lisa V, Vaira AM, Dellavalle G, Masenga V, Milne RG (1996) Viruses of pelargonium in Italy. Acta Hortic 432: 108-117
28. Lütke HA, Chow KC, Mickel FS, Moss KA, Kern HF, Scheele GA (1987) Selection of AUG initiation codons differs in plants and animals. EMBO J 6: 43-48
29. Marcos JF, Vilar M, Pérez-Payá E, Pallás V (1999) In vivo detection, RNA-binding properties and characterization of the RNA-binding domain of the p7 putative movement protein from Carnation mottle carmovirus (CarMV). Virology 255: 354-365
30. Mathews DH, Sabina J, Zuker M, Turner DH (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288: 911-940
31. Morozov S, Ry abov E, Leiser R, Zavriev S (1995) Use of highly conserved motifs in plant virus polymerases as the tags for specific detection of carmovirus-related RNA-dependent RNA-polymerase genes. Virology 207: 312-315
32. Morris T, Carrington J (1988) Carnation mottle virus and viruses with similar properties. In: Koenig R (ed). The plant viruses, vol 3: Polyhedral virions with monopartite RNA genomes. Plenum Press, New York, pp 73-112
33. Morris TJ, Dodds JA (1979) Isolation and analysis of double-stranded RNA from virus-infected plant and fungal tissue. Phytopathology 69: 854-858
34. Pearson WR, Wood T, Zhang Z, Miller W (1997) Comparison of DNA sequences with protein sequences. Genomics 46: 24-36
35. Plese N, Stefanac Z (1980). Some properties of a distinctive isometric virus from pelargonium. Acta Hortic 110: 183-190
36. Pogany J, Fabian MR, White KA, Nagy PD (2003) A replication silencer element in a plus-strand RNA virus. EMBO J 22: 5602-5611
37. Rico P, Hernández C (2004) Complete nucleotide sequence and genome organization of Pelargonium flower break virus. Arch Virol 149: 641-651
38. Riviere CJ, Rochon DM (1990) Nucleotide sequence and genomic organization of Melon necrotic spot virus. J Gen Virol 71: 1887-1896
39. Russo M, Burgyan J, Martelli GP (1994) Molecular Biology of Tombusviridae. Adv Virus Res 44: 381-428
40. Scholthof KB, Scholthof HB, Jackson AO (1995) The Tomato bushy stunt virus replicase proteins are coordinately expressed and membrane associated. Virology 208: 365-369
41. Stone OM (1980) Nine viruses isolated from pelargonium in the United Kingdom. Acta Hortic 110: 177-182
42. Stone OM, Hollings M (1971) Pelargonium. Rep Glasshouse Crops Res Inst 1970, pp 153-155
43. Stone OM, Hollings M (1976) Pelargonium. Rep Glasshouse Crops Res Inst 1975, pp 119-120
44. Stone OM, Hollings M (1977) Pelargonium. Rep Glasshouse Crops Res Inst 1976, pp 121-122
45. Stuart G, Moffett K, Bozarth RF (2004) A whole genome perspective on the phylogeny of the plant virus family Tombusviridae. Arch Virol 149: 1595-1610
46. Stupina V, Simon AE (1997) Analysis in vivo of Turnip crinkle virus satellite RNA C variants with mutations in the 3′-terminal minus-strand promoter. Virology 238: 470-477
47. Thompson JD, Gibson TJ, Plewniak F, Higgins DG (1997) The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882
48. Turina M, Maruoka M, Monis J, Jackson AO, Scholthof KB (1998) Nucleotide sequence and infectivity of a full-length cDNA clone of Panicum mosaic virus. Virology 241: 141-155
49. Turina M, Desvoyes B, Scholthof KB (2000) A gene cluster encoded by Panicum mosaic virus is associated with virus movement. Virology 266: 120-128
50. Turner RL, Buck KW (1999) Mutational analysis of cis-acting sequences in the 3′- and 5′-untranslated regions of RNA 2 of Red clover necrotic mosaic virus. Virology 253: 115-124
51. Van Regenmortel MHV, Fauquet CM, Bishop DHL, Carstens EB, Estes MK, Lemon SM, Maniloff J, Mayo MA, McGeoch DJ, Pringle CR, Wickner RB (2000) Virus Taxonomy. Seventh Report of the International Committee on Taxonomy of Viruses, Academic Press, San Diego
52. Verwoerd TC, Dekker BMM, Hoekema A (1989) A small-scale procedure for the rapid isolation of plant RNAs. Nucleic Acids Res 17: 2362
53. Vilar M, Sauri A, Monne M, Marcos JF, von Heijne G, Pérez- Payá E, Mingarro I (2002) Insertion and topology of a plant viral movement protein in the endoplasmic reticulum membrane. J Biol Chem 244: 23447-23452
54. Vreede FT, Cloete M, Napier GB, van Dijk AA, Viljoen GJ (1998) Sequence-independent amplification and cloning of large dsRNA virus genome segments by poly(dA)-oligonucleotide ligation. J Virol Methods 72: 243-247
55. White KA, Skuzeski JM, Li W, Wei N, Morris TJ (1995) Inmunodetection, expression strategy and complementation of Turnip crinkle virus p28 and p88 replication components. Virology 211: 525-534
56. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415