A second functional RNA domain in the 5′ UTR of the Tomato bushy stunt virus genome: Intra- and interdomain interactions mediate viral RNA replication

RNA

Volumn 9, Issue 10, 2003, Pages 1232-1245

  Ray, Debashish ^a   Wu, Baodong ^a   White, K Andrew ^a  

^a YORK UNIVERSITY   (Canada)

Author keywords

(+) strand RNA virus; DI RNA; Plant virus; RNA replication; RNA structure; TBSV; Tombusviridae; Tombusvirus

Indexed keywords

DEFECTIVE INTERFERING RNA; RNA; UNCLASSIFIED DRUG;

5' UNTRANSLATED REGION; ARTICLE; COMPUTER ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT VIRUS; PRIORITY JOURNAL; RNA REPLICATION; RNA STRUCTURE; STRUCTURE ACTIVITY RELATION; TOMBUSVIRUS; VIRUS GENOME; VIRUS REPLICATION;

5' UNTRANSLATED REGIONS; BASE SEQUENCE; BLOTTING, NORTHERN; CONSERVED SEQUENCE; CUCUMIS SATIVUS; GENOME, VIRAL; LYCOPERSICON ESCULENTUM; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PROTOPLASTS; RNA STABILITY; RNA, VIRAL; SEQUENCE HOMOLOGY, NUCLEIC ACID; SUPPRESSION, GENETIC; TOMBUSVIRUS; VIRUS REPLICATION;

LYCOPERSICON ESCULENTUM; RNA VIRUSES; TOMATO BUSHY STUNT VIRUS; TOMBUSVIRIDAE; TOMBUSVIRUS;

EID: 0141520704     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.5630203     Document Type: Article

References (44)

1. Andino, R., Rieckhof, G.E., and Baltimore, D.A. 1990. A functional ribonucleoprotein complex forms around the 5′ end of poliovirus RNA. Cell 63: 369-380.
2. Barton, D.J., O'Donnell, B.J., and Flanegan, J.B. 2001. 5′ cloverleaf in poliovirus RNA is a cis-acting replication element required for negative-strand synthesis. EMBO J. 20: 1439-1448.
3. Belsham, G.J. and Sonenberg, N. 1996. RNA-protein interactions in regulation of picornaviras RNA translation. Microbiol. Rev. 60: 499-511.
4. Bink, H.H., Hellendoorn, K., van der Meulen, J., and Pleij, C.W. 2002. Protonation of non-Watson-Crick base pairs and encapsidation of turnip yellow mosaic virus RNA. Proc. Natl. Acad. Sci. 99: 13465-13470.
5. Buck, K.W. 1996. Comparison of the replication of positive-stranded RNA viruses of plants and animals. Adv. Virus Res. 47: 159-251.
6. Chang, Y.C., Borja, M., Scholthof, H.B., Jackson, A.O., and Morris, T.J. 1995. Host effects and sequences essential for accumulation of defective interfering RNAs of cucumber necrosis and tomato bushy stunt tombusviruses. Virology 210: 41-53.
7. Chen, J., Noueiry, A., and Ahlquist P. 2001. Brome mosaic virus Protein la recruits viral RNA2 to RNA replication through a 5′ proximal RNA2 signal. J. Virol. 75: 3207-3219.
8. Fujimura, T. and Esteban, R. 2000. Recognition of RNA encapsidation signal by the yeast L-A double-stranded RNA virus. J. Biol. Chem. 275: 37118-37126.
9. Gallie, D.R. 2001. Cap-independent translation conferred by the 5′ leader of tobacco etch virus is eukaryotic initiation factor 4G dependent. J. Virol. 75: 12141-12152.
10. Guan, H., Song, C., and Simon, A.E. 1997. RNA promoters located on (-)-strands of a subviral RNA associated with turnip crinkle virus. RNA 3: 1401-1412.
11. Guan, H., Carpenter, C.D., and Simon, A.E. 2000a. Analysis of cis-acting sequences involved in plus-strand synthesis of a turnip crinkle virus-associated satellite RNA identifies a new carmovirus replication element. Virology 268: 345-354.
12. -. 2000b. Requirement of a 5′-proximal linear sequence on minus strands for plus-strand synthesis of a satellite RNA associated with turnip crinkle virus. Virology 268: 355-363.
13. Guo, L., Allen, E.M., and Miller, W.A. 2001. Base-pairing between untranslated regions facilitates translation of uncapped, nonpolyadenylated viral RNA. Mol. Cell 7: 1103-1109.
14. Hearne, P.Q., Knorr, D.A., Hillman, B.I., and Morris, T.J. 1990. The complete genome structure and synthesis of infectious RNA from clones of tomato bushy stunt virus. Virology 177: 141-151.
15. Herold, J. and Andino, R. 2001. Poliovirus RNA replication requires genome circularization through a protein-protein bridge. Mol. Cell 7: 581-591.
16. Luo, G., Xin, S., and Cai, Z. 2003. Role of the 5′-proximal stem-loop structure of the 5′ untranslated region in replication and translation of hepatitis C virus RNA. J. Virol. 77: 3312-3318.
17. Mason, P.W., Bezborodova, S.V., and Henry, T.M. 2002. Identification and characterization of a cis-acting replication element (cre) adjacent to the internal ribosome entry site of foot-and-mouth disease virus. J. Virol. 76: 9686-9694.
18. Mathews, D.H., Sabina, J., Zuker, M., and Turner, D.H. 1999. Expanded sequence dependence of thermodynamic parameters provides robust prediction of RNA secondary structure. J. Mol. Biol. 288: 911-940.
19. Miller, J.S., Damude, H., Robbins, M.A., Reade, R.D., and Rochon, D.M. 1997. Genome structure of cucumber leaf spot virus: Sequence analysis suggests it belongs to a distinct species within the Tombusviridae. Virus Res. 52: 51-60.
20. Miller, E.D., Plante, C.A., Kim, K.H., Brown, J.W., and Hemenway, C. 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.
21. Nagy, P.D. and Pogany, J. 2000. Partial purification and characterization of Cucumber necrosis virus and Tomato bushy stunt virus RNA-dependent RNA polymerases: Similarities and differences in template usage between Tombusvirus and Carmovirus RNA-dependent RNA polymerases. Virology 276: 279-288.
22. Oster, S.K., Wu, B., and White, K.A. 1998. Uncoupled expression of p33 and p92 permits amplification of tomato bushy stunt virus RNAs. J. Virol. 72: 5845-5851.
23. Panavas, T. and Nagy, P.D. 2003. The RNA replication enhancer element of Tombusviruses contains two interchangeable hairpins that are functional during plus-strand synthesis. J. Virol. 77: 258-269.
24. Panavas, T., Pogany, J., and Nagy, P.D. 2002a. Analysis of minimal promoter sequences for plus-strand synthesis by the Cucumber necrosis virus RNA-dependent RNA polymerase. Virology 296: 263-274.
25. -. 2002b. Internal initiation by the cucumber necrosis virus RNA-dependent RNA polymerase is facilitated by promoter-like sequences. Virology 296: 275-287.
26. Ray, D. and White, K.A. 1999. Enhancer-like properties of an RNA element that modulates Tombusvirus RNA accumulation. Virology 256: 162-171.
27. -. 2003. An internally located RNA hairpin enhances replication of Tomato bushy stunt virus RNAs. J. Virol. 77: 245-257.
28. Rubino, L. and Russo, M. 1997. Molecular analysis of the pothos latent virus genome. J. Gen. Virol. 78: 1219-1226.
29. Russo, M., Burgyan, J., and Martelli, G.P. 1994. Molecular biology of Tombusviridae. Adv. Virus Res. 44: 381-428.
30. Sarnow, P. 2003. Viral internal ribosome entry site elements: Novel ribosome-RNA complexes and roles in viral pathogenesis. J. Virol. 77: 2801-2806.
31. Sasaki, J. and Taniguchi, K. 2003. The 5′-end sequence of the genome of Aichi virus, a picornavirus, contains an element critical for viral RNA encapsidation. J. Virol. 77: 3542-3548.
32. Sit, T.L., Leclerc, D., and AbouHaidar, M.G. 1994. The minimal 5′ sequence for in vitro initiation of papaya mosaic potexvirus assembly. Virology 199: 238-242.
33. Valcarcel, J. and Gebauer, F. 1997. Post-transcriptional regulation: The dawn of PTB. Curr. Biol. 7: R705-R708.
34. Vagner, S., Galy, B., and Pyronnet, S. 2001. Irresistible IRES. Attracting the translation machinery to internal ribosome entry sites. EMBO Rep. 2: 893-898.
35. van Marle, G., Dobbe, J.C., Gultyaev, A.P., Luytjes, W., Spaan, W.J., and Snijder, E.J. 1999. Arterivirus discontinuous mRNA transcription is guided by base pairing between sense and antisense transcription-regulating sequences. Proc. Natl. Acad. Sci. 96: 12056-12061.
36. Varani, G. and McClain, W.H. 2000. The GU wobble base pair. A fundamental building block of RNA structure crucial to RNA function in diverse biological systems. EMBO Rep. 1: 18-23.
37. White, K.A. 1996. Formation and evolution of tombusvirus defective interfering RNAs. Sem. Virol. 7: 409-416.
38. White, K.A. and Morris, T.J. 1994a. Enhanced competitiveness of Tomato bushy stunt virus defective interfering RNAs by segment duplication or nucleotide insertion. J. Virol. 68: 6092-6096.
39. -. 1994b. Nonhomologous RNA recombination in tombusviruses: Generation and evolution of defective interfering RNAs by stepwise deletions. J. Virol. 68: 14-24.
40. Witherell, G.W., Gott, J.M., and Uhlenbeck, O.C. 1991. Specific interaction between RNA phage coat proteins and RNA. Prog. Nucleic Acid Res. Mol. Biol. 40: 185-220.
41. Wu, B. and White, K.A. 1998. Formation and amplification of a novel tombusvirus defective RNA which lacks the 5′ nontranslated region of the viral genome. J. Virol. 72: 9897-9905.
42. -. 1999. A primary determinant of cap-independent translation is located in the 3′-proximal region of the Tomato bushy stunt virus genome. J. Virol. 73: 8982-8988.
43. Wu, B., Vanti, W.B., and White, K.A. 2001. An RNA domain within the 5′ untranslated region of the Tomato bushy stunt virus genome modulates viral RNA replication. J. Mol. Biol. 305: 741-756.
44. Zuker, M., Mathews, D.H., and Turner, D.H. 1999. Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide. In RNA biochemistry and bio/technology (eds. J. Barciszewski and B.F.C. Clark), pp. 11-43. Kluwer Academic Publishers, Dordrecht/Norwell, MA.