Nemesia ring necrosis virus: a new tymovirus with a genomic RNA having a histidylatable tobamovirus-like 3′ end

References

1. Barends S., Bink H. H. J., van den Worm S. H. E., Pleij C. W. A., Kraal B. 2003; Entrapping ribosomes for viral translation: tRNA mimicry as a molecular Trojan horse. Cell 112:123–129 [CrossRef]
   [Google Scholar]
2. Barends S., Rudinger-Thirion J., Florentz C., Giegé R., Pleij C. W. A., Kraal B. 2004; tRNA-like structure regulates translation of Brome mosaic virus RNA. J Virol 78:4003–4010 [CrossRef]
   [Google Scholar]
3. Bink H. H. J., Hellendoorn K., van der Meulen J., Pleij C. W. A. 2002; Protonation of non-Watson–Crick base pairs and encapsidation of turnip yellow mosaic virus RNA. Proc Natl Acad Sci U S A 99:13465–13470 [CrossRef]
   [Google Scholar]
4. Bodaghi S., Ngon A Yassi M., Dodds J. A. 2000; Heterogeneity in the 3′-terminal untranslated region of tobacco mild green mosaic tobamoviruses from Nicotiana glauca resulting in variants with three or six pseudoknots. J Gen Virol 81:577–586
   [Google Scholar]
5. Bozarth C. S., Weiland J. J., Dreher T. W. 1992; Expression of ORF-69 of turnip yellow mosaic virus is necessary for viral spread in plants. Virology 187:124–130 [CrossRef]
   [Google Scholar]
6. Bransom K. L., Dreher T. W. 1994; Identification of the essential cysteine and histidine residues of the turnip yellow mosaic virus protease. Virology 198:148–154 [CrossRef]
   [Google Scholar]
7. Bransom K. L., Wallace S. E., Dreher T. W. 1996; Identification of the cleavage site recognized by the turnip yellow mosaic virus protease. Virology 217:404–406 [CrossRef]
   [Google Scholar]
8. Chen J., Li W. X., Xie D., Peng J. R., Ding S. W. 2004; Viral virulence protein suppresses RNA silencing-mediated defense but upregulates the role of microRNA in host gene expression. Plant Cell 16:1302–1313 [CrossRef]
   [Google Scholar]
9. Coutts R. H. A., Livieratos I. C. 2003; A rapid method for sequencing the 5′- and 3′-termini of dsRNA viral templates using RLM-Race. J Phytopathol 151:525–527 [CrossRef]
   [Google Scholar]
10. Devereux J., Haeberli P., Smithies O. 1984; A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res 12:387–395 [CrossRef]
    [Google Scholar]
11. Dunn D. B., Hitchborn J. H. 1965; The use of bentonite in the purification of plant viruses. Virology 25:171–192 [CrossRef]
    [Google Scholar]
12. Felden B., Florentz C., Giegé R., Westhof E. 1996; A central pseudoknotted three-way junction imposes tRNA-like mimicry and the orientation of three 5′ upstream pseudoknots in the 3′ terminus of tobacco mosaic virus RNA. RNA 2:201–212
    [Google Scholar]
13. Filichkin S. A., Bransom K. L., Goodwin J. B., Dreher T. W. 2000; The infectivities of turnip yellow mosaic virus genomes with altered tRNA mimicry are not dependent on compensating mutations in the viral replication protein. J Virol 74:8368–8375 [CrossRef]
    [Google Scholar]
14. Goodwin J. B., Skuzeski J. M., Dreher T. W. 1997; Characterization of chimeric turnip yellow mosaic virus genomes that are infectious in the absence of aminoacylation. Virology 230:113–124 [CrossRef]
    [Google Scholar]
15. Gultyaev A. P., van Batenburg E., Pleij C. W. A. 1994; Similarities between the secondary structure of satellite tobacco mosaic virus and tobamovirus RNAs. J Gen Virol 75:2851–2856 [CrossRef]
    [Google Scholar]
16. Gultyaev A. P., van Batenburg F. H. D., Pleij C. W. A. 1995; The computer simulation of RNA folding pathways using a genetic algorithm. J Mol Biol 250:37–51 [CrossRef]
    [Google Scholar]
17. Hellendoorn K., Mat A. W., Gultyaev A. P., Pleij C. W. A. 1996a; Secondary structure model of the coat protein gene of turnip yellow mosaic virus RNA: long, C-rich, single-stranded regions. Virology 224:43–54 [CrossRef]
    [Google Scholar]
18. Hellendoorn K., Michiels P. J., Buitenhuis R., Pleij C. W. A. 1996b; Protonatable hairpins are conserved in the 5′-untranslated region of tymovirus RNAs. Nucleic Acids Res 24:4910–4917 [CrossRef]
    [Google Scholar]
19. Hellendoorn K., Verlaan P. W., Pleij C. W. A. 1997; A functional role for the conserved protonatable hairpins in the 5′ untranslated region of turnip yellow mosaic virus RNA. J Virol 71:8774–8779
    [Google Scholar]
20. Kadare G., Rozanov M., Haenni A.-L. 1995; Expression of the turnip yellow mosaic virus proteinase in Escherichia coli and determination of the cleavage site within the 206 kDa protein. J Gen Virol 76:2853–2857 [CrossRef]
    [Google Scholar]
21. Kashiwazaki S., Scott K. P., Reavy B., Harrison B. D. 1995; Sequence analysis and gene content of potato mop top virus RNA 3: further evidence of heterogeneity in the genome organization of furoviruses. Virology 206:701–706 [CrossRef]
    [Google Scholar]
22. Koenig R., Lesemann D.-E. 2000; Ein Tymovirus aus den Zierpflanzen Diascia und Nemesia - wie zuverlässig ist die Serologie bei der Identifizierung von Pflanzenviren?. Phytomedizin 30:16–17
    [Google Scholar]
23. Koenig R., Pleij C. W. A., Beier C., Commandeur U. 1998; Genome properties of beet virus Q, a new furo-like virus from sugarbeet, determined from unpurified virus. J Gen Virol 79:2027–2036
    [Google Scholar]
24. Koenig R., Pleij C. W. A., Huth W. 1999; Molecular characterization of a new furovirus mainly infecting rye. Arch Virol 144:2125–2140 [CrossRef]
    [Google Scholar]
25. Koenig R., Pleij C. W. A., Büttner G. 2000; Structure and variability of the 3′ end of RNA 3 of beet soil-borne pomovirus – a virus with uncertain pathogenic effects. Arch Virol 145:1173–1181 [CrossRef]
    [Google Scholar]
26. Koenig R., Pleij C. W. A., Loss S., Burgermeister W., Aust H., Schiemann J. 2004; Molecular characterisation of potexviruses isolated from three different genera in the family Cactaceae . Arch Virol 149:903–914 [CrossRef]
    [Google Scholar]
27. Koenig R., Pleij C. W. A., Lesemann D.-E., Loss S., Vetten H. J. 2005; Molecular characterization of Anagyris vein yellowing virus, Plantago mottle virus and Scrophularia mottle virus – comparison of various approaches for tymovirus classification. Arch Virol (in press
    [Google Scholar]
28. Koonin E. V., Dolja V. V. 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 [CrossRef]
    [Google Scholar]
29. Mans R. M., Pleij C. W. A., Bosch L. 1991; tRNA-like structures. Structure, function and evolutionary significance. Eur J Biochem 201:303–324 [CrossRef]
    [Google Scholar]
30. Meshi T., Ohno T., Iba H., Okada Y. 1981; Nucleotide sequence of a cloned cDNA copy of TMV (cowpea strain) RNA, including the assembly origin, the coat protein cistron, and the 3′ non-coding region. Mol Gen Genet 184:20–25 [CrossRef]
    [Google Scholar]
31. Nameki N., Asahara H., Shimizu M., Okada N., Himeno H. 1995; Identity elements of Saccharomyces cerevisiae tRNA^His . Nucleic Acids Res 23:389–394 [CrossRef]
    [Google Scholar]
32. Pleij C. W. A., Abrahams J. P., van Belkum A., Rietveld K., Bosch L. 1987; The spatial folding of the 3′ noncoding region of aminoacylatable plant viral RNAs. In Positive Strand RNA Viruses , UCLA Symposia on Molecular and Cellular Biology , New Series . vol 54 pp  299–316 Edited by Brinton M. A., Rueckert R. New York: Alan Riss;
33. Rietveld K., van Poelgeest R., Pleij C. W. A., van Boom J. H., Bosch L. 1982; The tRNA-like structure at the 3′ terminus of turnip yellow mosaic virus RNA. Differences and similarities with canonical tRNA. Nucleic Acids Res 10:1929–1946 [CrossRef]
    [Google Scholar]
34. Rietveld K., Linschooten K., Pleij C. W. A., Bosch L. 1984; The three-dimensional folding of the tRNA-like structure of tobacco mosaic virus RNA. A new building principle applied twice. EMBO J 3:2613–2619
    [Google Scholar]
35. Rudinger J., Florentz C., Giegé R. 1994; Histidylation by yeast HisRS of tRNA or tRNA-like structure relies on residues −1 and 73 but is dependent on the RNA context. Nucleic Acids Res 22:5031–5037 [CrossRef]
    [Google Scholar]
36. Ruiz del Pino M., Moreno A., Garcia de Lacoba M., Castillo-Lluva S., Gilardi P., Serra M. T., Garcia-Luque I. 2003; Biological and molecular characterization of P101 isolate, a tobamoviral pepper strain from Bulgaria. Arch Virol 148:2115–2135 [CrossRef]
    [Google Scholar]
37. Seigner L. 2003; Schäden an Zierpflanzen durch INSV und Nemesiavirus. Das Magazin für Zierpflanzenbau 19:47–49
    [Google Scholar]
38. Shimamoto I., Sonoda S., Vazquez P., Minaka N., Nishiguchi M. 1998; Nucleotide sequence analysis of the 3′ terminal region of a wasabi strain of crucifer tobamovirus genomic RNA: subgrouping of crucifer tobamoviruses. Arch Virol 143:1801–1813 [CrossRef]
    [Google Scholar]
39. Shirako Y., Wilson T. M. A. 1993; Complete nucleotide sequence and organization of the bipartite RNA genome of soil-borne wheat mosaic virus. Virology 195:16–32 [CrossRef]
    [Google Scholar]
40. Skelton A. L., Jarvis B., Koenig R., Lesemann D.-E., Mumford R. A. 2004; The isolation and identification of a tymovirus from Nemesia in the UK. Plant Pathol 53:798 [CrossRef]
    [Google Scholar]
41. Skuzeski J. M., Bozarth C. S., Dreher T. W. 1996; The turnip yellow mosaic virus tRNA-like structure cannot be replaced by generic tRNA-like elements or by heterologous 3′ untranslated regions known to enhance mRNA expression and stability. J Virol 70:2107–2115
    [Google Scholar]
42. van Belkum A., Abrahams J. P., Pleij C. W. A., Bosch L. 1985; Five pseudoknots are present at the 204 nucleotides long 3′ noncoding region of tobacco mosaic virus RNA. Nucleic Acids Res 13:7673–7686 [CrossRef]
    [Google Scholar]