A positive-strand RNA virus with three very different subgenomic RNA promoters

Journal of Virology

Volumn 74, Issue 13, 2000, Pages 5988-5996

  Koev, Gennadiy ^a,b   Miller, W Allen ^a  

^a IOWA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

ARTICLE; GENE EXPRESSION; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; RNA REPLICATION; RNA STRUCTURE; RNA SYNTHESIS; RNA VIRUS; VIRUS GENE;

BASE SEQUENCE; CHROMOSOME MAPPING; HORDEUM; LUTEOVIRUS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PROMOTER REGIONS (GENETICS); PROTOPLASTS; RNA, VIRAL; SEQUENCE HOMOLOGY, NUCLEIC ACID; TREES; VIRUS REPLICATION;

EID: 0034044063     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.74.13.5988-5996.2000     Document Type: Article

References (53)

1. Adkins, S., R. W. Siegel, J. H. Sun, and C. C. Kao. 1997. Minimal templates directing accurate initiation of subgenomic RNA synthesis in vitro by the brome mosaic virus RNA-dependent RNA polymerase. RNA 3:634-647.
2. Allen, E., S. Wang, and W. A. Miller. 1999. Barley yellow dwarf virus RNA requires a cap-independent translation sequence because it lacks a 5′ cap. Virology 253:139-144.
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 (Paris) 75:517-521.
4. Barr, J. N., S. P. Whelan, and G. W. Wertz. 1997. cis-Acting signals involved in termination of vesicular stomatitis virus mRNA synthesis include the conserved AUAC and the U7 signal for polyadenylation. J. Virol. 71:8718-8725.
5. 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.
6. Brown, D., and L. Gold. 1996. RNA replication by Qβ replicase: a working model. Proc. Natl. Acad. Sci. USA 93:11558-11562.
7. 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.
8. 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.
9. 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.
10. 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.
11. Duggal, R., and E. Wimmer. 1999. Genetic recombination of poliovirus in vitro and in vivo: temperature-dependent alteration of crossover sites. Virology 258:30-41.
12. 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.
13. Harrison, G. P., M. S. Mayo, E. Hunter, and A. M. Lever. 1998. Pausing of reverse transcriptase on retroviral RNA templates is influenced by secondary structures both 5′ and 3′ of the catalytic site. Nucleic Acids Res. 26:3433-3442.
14. Hilf, M. E., A. V. Karasev, H. R. Pappu, D. J. Gumpf, C. L. Niblett, and S. M. Garnsey. 1995. Characterization of citrus tristeza virus subgenomic RNAs in infected tissue. Virology 208:576-582.
15. Huang, P., and M. M. C. Lai. 1999. Polypyrimidine tract-binding protein binds to the complementary strand of the mouse hepatitis virus 3′ untranslated region, thereby altering RNA conformation. J. Virol. 73:9110-9116.
16. Jaspars, E. M. J. 1999. Genome activation in alfamo-and ilarviruses. Arch. Virol. 144:843-863.
17. Johnston, J. C., and D. M. Rochon. 1995. Deletion analysis of the promoter for the cucumber necrosis virus 0.9-kb suhgenomic 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. Kim, K. H., and C. L. Hemenway. 1999. Long-distance RNA-RNA interactions and conserved sequence elements affect potato virus X plus-strand RNA accumulation. RNA 5:636-645.
20. Klarmann, G. J., C. A. Schauber, and B. D. Preston. 1993. Template-directed pausing of DNA synthesis by HIV-1 reverse transcriptase during polymerization of HIV-1 sequences in vitro. J. Biol. Chem. 268:9793-9802. (Erratum, 268:13754.)
21. Koev, G., B. R. Mohan, and W. A. Miller. 1999. Primary and secondary structural elements required for synthesis of barley yellow dwarf virus subgenomic RNA1. J. Virol. 73:2876-2885.
22. Koonin, E. V., and V. V. Dolja. 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. Lai, M. M., and D. Cavanagh. 1997. The molecular biology of coronaviruses. Adv. Virus Res. 48:1-100.
24. Lai, M. M. C. 1998. Cellular factors in the transcription and replication of viral RNA genomes: a parallel to DNA-dependent RNA transcription. Virology 244:1-12.
25. Lai, M. M. C. 1996. Recombination in large RNA viruses: coronaviruses. Semin. Virol. 7:381-388.
26. 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.
27. 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.
28. Levis, R., S. Schlesinger, and H. V. Huang. 1990. Promoter for Sindbis virus RNA-dependent subgenomic RNA transcription. J. Virol. 64:1726-1733.
29. Lin, Y.-J., X. Zhang, R.-C. Wu, and M. M. C. Lai. 1996. The 3′ untranslated region of coronavirus RNA is required for subgenomic mRNA transcription from a defective interfering RNA. J. Virol. 70:7236-7240.
30. Maia, I. G., K. Seron, A.-L. Haenni, and F. Bernardi. 1996. Gene expression from viral RNA genomes. Plant Mol. Biol. 32:367-391.
31. Mathews, D. H., J. Sabina, M. Zuker, and D. H. Turner. 1999. Expanded sequence dependence of thermodynamic parameters provides robust prediction of RNA secondary structure. J. Mol. Biol. 288:911-940.
32. Mayo, M. A., and C. J. D'Arcy. 1999. Family Luteoviridae: a reclassification of luteoviruses, p. 15-22. In H. G. Smith and H. Barker (ed.), The Luteoviridae. CABI Publishing, Wallingford, Oxon, England.
33. Miller, E. D., C. A. Plante, K. H. Kim, J. W. Brown, and C. L. Hemenway. 1998. Stem-loop structure in the 5′ region of potato virus X genome required for plus-strand RNA accumulation. J. Mol. Biol. 284:591-608.
34. Miller, W. A. 1999. Luteoviridae, p. 901-908. In R. G. Webster and A. Granoff (ed.), Encyclopedia of virology, 2nd ed. Academic Press, London, England.
35. Miller, W. A., S. P. Dinesh-Kumar, and C. P. Paul. 1995. Luteovirus gene expression. Crit. Rev. Plant Sci. 14:179-211.
36. 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.
37. 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.
38. 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.
39. 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.
40. Sit, T. L., A. A. Vaewhongs, and S. A. Lommel. 1998. RNA-mediated trans-activation of transcription from a viral RNA. Science 281:829-832.
41. Tuerk, C., P. Gauss, C. Thermes, D. R. Groebe, M. Gayle, N. Guild, G. Stormo, Y. d'Aubenton-Carafa, O. C. Uhlenbeck, I. Tinoco, Jr., et al. 1988. CUUCGG hairpins: extraordinarily stable RNA secondary structures associated with various biochemical processes. Proc. Natl. Acad. Sci. USA 85: 1364-1368.
42. van der Kuyl, A. C., K. Langereis, C. J. Houwing, E. M. Jaspars, and J. F. Bol. 1990. cis-Acting elements involved in replication of alfalfa mosaic virus RNAs in vitro. Virology 253:327-336.
43. 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.
44. van Marle, G., W. Luytjes, R. G. van der Most, T. van der Straalen, and W. J. Spaan. 1995. Regulation of coronavirus mRNA transcription. J. Virol. 69: 7851-7856.
45. Wang, J., C. D. Carpenter, and A. E. Simon. 1999. Minimal sequence and structural requirements of a subgenomic RNA promoter for turnip crinkle virus. Virology 253:327-336.
46. 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.
47. Wang, S., L. Guo, E. Allen, and W. A. Miller. 1999. A potential mechanism for selective control of cap-independent translation by a viral RNA sequence in cis and in trans. RNA 5:728-738.
48. Wang, S., and W. A. Miller. 1995. A sequence located 4.5 to 5 kilobases from the 5′ end of the barley yellow dwarf virus (PAV) genome strongly stimulates translation of uncapped mRNA. J. Biol. Chem. 270:13446-13452.
49. Wang, S. P., K. S. Browning, and W. A. Miller. 1997. A viral sequence in the 3′ untranslated region mimics a 5′ cap in facilitating translation of uncapped mRNA. EMBO J. 16:4107-4116.
50. White, K. A., and T. J, Morris. 1995. RNA determinants of junction site selection in RNA virus recombinants and defective interfering RNAs. RNA 1:1029-1040.
51. 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.
52. Zhang, G., V. Slowinski, and K. A. White. 1999. Subgenomic mRNA regulation by a distal RNA element in a (+)-strand RNA virus. RNA 5:550-561.
53. Zuker, M., D. H. Mathews, and D. H. Turner. 1999. Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide, p. 11-43. In J. Barciszewski and B. F. C. Clark (ed.), RNA biochemistry and biotechnology. Kluwer Academic Publishers, Dordrecht, The Netherlands.