Primary and secondary structural elements required for synthesis of barley yellow dwarf virus subgenomic RNA1

Journal of Virology

Volumn 73, Issue 4, 1999, Pages 2876-2885

  Koev, Gennadiy ^a   Mohan, B R ^a,b   Miller, W Allen ^a  

^a IOWA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ARTICLE; BARLEY YELLOW DWARF VIRUS; BASE PAIRING; BINDING SITE; GENE MAPPING; LUTEOVIRUS; NONHUMAN; PLANT VIRUS; PRIORITY JOURNAL; PROMOTER REGION; RNA BINDING; RNA REPLICATION; RNA SEQUENCE; RNA STRUCTURE; RNA SYNTHESIS; RNA TRANSCRIPTION; VIRUS EXPRESSION; VIRUS GENOME; VIRUS MUTATION;

EID: 0033014991     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/jvi.73.4.2876-2885.1999     Document Type: Article

References (49)

1. Andino, R., G. E. Rieckhof, and D. Baltimore. 1990. A functional ribonucleoprotein complex forms around the 5′ end of poliovirus RNA. Cell 63: 369-380.
2. Ansel-McKinney, P., and L. Gehrke. 1998. RNA determinants of a specific RNA-coat protein peptide interaction in alfalfa mosaic virus: conservation of homologous features in ilarvirus RNAs. J. Mol. Biol. 278:767-785.
3. Balmori, E., D. Gilmer, K. Richards, H. Guilley, and G. Jonard. 1993. Mapping the promoter for subgenomic RNA synthesis on beet necrotic yellow vein virus RNA 3. Biochimie 75:517-521.
4. Boccard, F., and D. Baulcombe. 1993. Mutational analysis of cis-acting sequences and gene function in RNA3 of cucumber mosaic virus. Virology 193:563-578.
5. Brown, D., and L. Gold. 1996. RNA replication by Qβ replicase: a working model. Proc. Natl. Acad. Sci. USA 93:11558-11562.
6. Carpenter, C. D., J.-W. Oh, C. Zhang, and A. E. Simon. 1995. Involvement of a stem-loop structure in the location of junction sites in viral RNA recombination. J. Mol. Biol. 245:608-622.
7. Chang, R.-Y., R. Krishnan, and D. A. Brian. 1996. The UCUAAAC promoter motif is not required for high-frequency leader recombination in bovine coronavirus defective interfering RNA. J. Virol. 70:2720-2729.
8. Chay, C. A., U. B. Gunasinge, S. P. Dinesh-Kumar, W. A. Miller, and S. M. Gray. 1996. Aphid transmission and systemic plant infection determinants of barley yellow dwarf luteovirus-PAV are contained in the coat protein readthrough domain and 17-kDa protein, respectively. Virology 219:57-65.
9. D'Arcy, C., L. Domier, and M. A. Mayo. Luteoviridae. In Seventh report of the International Committee on the Taxonomy of Viruses, in press. Elsevier, New York, N.Y.
10. Deiman, B. A. L. M., R. M. Kortlever, and C. W. A. Pleij. 1997. The role of the pseudoknot at the 3′ end of turnip yellow mosaic virus RNA in minusstrand synthesis by the viral RNA-dependent RNA polymerase. J. Virol. 71:5990-5996.
11. Di, R., S. P. Dinesh-Kumar, and W. A. Miller. 1993. Translational frame-shifting by barley yellow dwarf virus RNA (PAV serotype) in Escherichia coli and in eukaryotic cell-free extracts. Mol. Plant-Microbe interact. 6:444-452.
12. Dinesh-Kumar, S. P., V. Brault, and W. A. Miller. 1992. Precise mapping and in vitro translation of a trifunctional subgenomic RNA of barley yellow dwarf virus. Virology 187:711-722.
13. Dinesh-Kumar, S. P., and W. A. Miller. 1993. Control of start codon choice on a plant viral RNA encoding overlapping genes. Plant Cell 5:679-692.
14. Felden, B., H. Himeno, A. Muto, J. McCutcheon, J. Atkins, and R. F. Gesteland. 1997. Probing the structure of the Escherichia coli 10Sa RNA (tmRNA). RNA 3:89-103.
15. French, R., and P. Ahlquist. 1988. Characterization and engineering of sequences controlling in vivo synthesis of brome mosaic virus subgenomic RNA. J. Virol. 62:2411-2420.
16. Gargouri, R., R. L. Joshi, J. F. Bol, S. Astier-Manifacier, and A.-L. Haenni. 1989. Mechanism of synthesis of turnip yellow mosaic virus coat protein subgenomic RNA in vivo. Virology 171:386-393.
17. Johnston, J. C., and D. M. Rochon. 1995. Deletion analysis of the promoter for the cucumber necrosis virus 0.9-kb subgenomic RNA. Virology 214:100-109.
18. Kelly, L., W. L. Gerlach, and P. M. Waterhouse. 1994. Characterisation of the subgenomic RNAs of an Australian isolate of barley yellow dwarf luteovirus. Virology 202:565-573.
19. Lai, M. M. C., and D, Cavanagh. 1997. The molecular biology of coronaviruses. Adv. Virus Res. 48:1-100.
20. Landt, O., H.-P. Grunert, and U. Hahn. 1990. A general method for rapid site-directed mutagenesis using the polymerase chain reaction. Gene 96:125-128.
21. Lauber, E., H. Guilley, K. Richards, G. Jonard, and D. Gilmer. 1997. Conformation of the 3′-end of beet necrotic yellow vein benevirus RNA 3 analysed by chemical and enzymatic probing and mutagenesis. Nucleic Acids Res. 25:4723-4729.
22. Lehto, K., G. L. Grantham, and W. O. Dawson. 1990. Insertion of sequences containing the coat protein subgenomic RNA promoter and leader in front of the tobacco mosaic virus 30K ORF delays its expression and causes defective cell-to-cell movement. Virology 174:145-157.
23. Levis, R., S. Schlesinger, and H. V. Huang. 1990. Promoter for Sindbis virus RNA-dependent subgenomic RNA transcription. J. Virol. 64:1725-1733.
24. Marsh, L. E., T. W. Dreher, and T. C. Hall. 1988. Mutational analysis of the core and modulator sequences of the BMV RNA3 subgenomic promoter. Nucleic Acids Res. 16:981-995.
25. Miller, J. S., and M. A. Mayo. 1991. The location of the 5′ end of the potato leafroll luteovirus subgenomic coat protein mRNA. J. Gen. Virol, 72:2633-2638.
26. Miller, W. A. Luteoviridae. In R. G. Webster and A. Granoff (ed.), Encyclopedia of virology, 2nd ed., in press. Academic Press. London, United Kingdom.
27. Miller, W. A., C. M. Brown, and S. Wang. 1997. New punctuation for the genetic code: luteovirus gene expression. Semin. Virol. 8:3-13.
28. Miller, W. A., S. P. Dinesh-Kumar, and C. P. Paul. 1995. Luteovirus gene expression. Crit. Rev. Plant Sci. 14:179-211.
29. Miller, W. A., T. W. Dreher, and T. C. Hall. 1985. Synthesis of brome mosaic virus subgenomic RNA in vitro by internal initiation on (-) sense genomic RNA. Nature 313:68-70.
30. Miller, W. A., G. Koev, and B. R. Mohan. 1997. Are there risks associated with transgenic resistance to luteoviruses? Plant Dis. 81:700-710.
31. Miller, W. A., and L. Rasochova. 1997. Barley yellow dwarf viruses. Annu. Rev. Phytopathol. 35;167-190.
32. Miller, W. A., and S. L. Silver. 1991. Alternative tertiary structure attenuates self-cleavage of the ribozyme in the satellite RNA of barley yellow dwarf virus. Nucleic Acids Res. 19:5313-5320.
33. Mohan, B. R., S. P. Dinesh-Kumar, and W. A. Miller. 1995. Genes and cis-acting sequences involved in replication of barley yellow dwarf virus-PAV RNA. Virology 212:186-195.
34. Nagy, P. D., and J. J. Bujarski. 1993. Targeting the site of RNA-RNA recombination in brome mosaic virus with antisense sequences. Proc. Natl. Acad. Sci. USA 90:6390-6394.
35. Nagy, P. D., C. Zhang, and A. E. Simon. 1998. Dissecting RNA recombination in vitro: role of RNA sequences and the viral replicase. EMBO J. 17:2392-2403.
36. Parsley, T. B., J. S. Towner, L. B. Blyn, E. Ehrenfeld, and B. L. Semler. 1997. Poly (rC) binding protein 2 forms a ternary complex with the 5′-terminal sequences of poliovirus RNA and the viral 3CD proteinase. RNA 3:1124-1134.
37. Platt, T. 1981. Termination of transcription and its regulation in the tryptophan operon of E. coli. Cell 24:10-23.
38. Pogue, G. P., and T. C. Hall. 1992. The requirement for a 5′ stem-loop structure in brome mosaic virus replication supports a new model for viral positive-strand RNA initiation. J. Virol. 66:674-684.
39. Proutski, V., E. A. Gould, and E. C. Holmes. 1997. Secondary structure of the 3′ untranslated region of flaviviruses: similarities and differences. Nucleic Acids Res. 25:1194-1202.
40. Rohll, J. B., D. H. Moon, D. J. Evans, and J. W. Almond. 1995. The 3′ untranslated region of picornavirus RNA: features required for efficient genome replication. J. Virol. 69:7835-7844.
41. Seeley, K. A., D. H. Byrne, and J. T. Colbert. 1992. Red light-independent instability of oat phytochrome mRNA in vivo. Plant Cell 4:29-38.
42. Siegel, R. W., S. Adkins, and C. C. Kao. 1997. Sequence-specific recognition of a subgenomic RNA promoter by a viral RNA polymerase. Proc. Natl. Acad. Sci. USA 94:11238-11243.
43. Sit, T. L., A. A. Vaewhongs, and S. A. Lommel. 1998. RNA-mediated transactivation of transcription from a viral RNA. Science 281:829-832.
44. Tacke, E., D. Prufer, F. Salamini, and W. Rohde. 1990. Characterization of a potato leafroll luteovirus suhgenomic RNA: differential expression by internal translation initiation and UAG suppression. J. Gen. Virol. 71:2265-2272.
45. van der Vossen, E. A., T. Notenboom, and J. F. Bol. 1995. Characterization of sequences controlling the synthesis of alfalfa mosaic virus subgenomic RNA in vivo. Virology 212:663-672.
46. Massov, V. V., G. Zuber, B. Felden, J. P. Behr, and R. Giege. 1995. Cleavage of tRNA with imidazole and spermine imidazole constructs: a new approach for probing RNA structure. Nucleic Acids Res. 23:3161-3167.
47. Wang, J., and A. E. Simon. 1997. Analysis of the two subgenomic RNA promoters for turnip crinkle virus in vivo and in vitro. Virology 232:174-186.
48. Zavriev, S. K., C. M. Hickey, and S. A. Lommel. 1996. Mapping of the red clover necrotic mosaic virus subgenomic RNA. Virology 216:407-410.
49. Zuker, M. 1989. On finding all suboptimal foldings of an RNA molecule. Science 244:48-52.