Evolution of virus-derived sequences for high-level replication of a subviral RNA

Virology

Volumn 351, Issue 2, 2006, Pages 476-488

  Zhang, Jiuchun ^a   Zhang, Guohua ^a   McCormack, John C ^a   Simon, Anne E ^a  

^a University of Maryland   (United States)

Author keywords

RNA conformational switch; RNA replication promoters; RNA virus evolution; Satellite RNA; Turnip crinkle virus

Indexed keywords

COAT PROTEIN; RNA DIRECTED RNA POLYMERASE; SATELLITE RNA; VIRUS RNA;

ARTICLE; CONTROLLED STUDY; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; PREDICTION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; RNA CONFORMATION; RNA REPLICATION; TERMINAL SEQUENCE; VIRUS REPLICATION; WILD TYPE;

BASE SEQUENCE; CAPSID PROTEINS; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, VIRAL; PLANT VIRUSES; PROMOTER REGIONS (GENETICS); PROTEIN BINDING; RNA, VIRAL; VIRUS REPLICATION;

TURNIP CRINKLE VIRUS;

EID: 33746275193     PISSN: 00426822     EISSN: 10960341     Source Type: Journal    
DOI: 10.1016/j.virol.2006.03.011     Document Type: Article

References (51)

1. Barry J.K., and Miller W.A. A -1 ribosomal frameshift element that requires base pairing across four kilobases suggests a mechanism of regulating ribosome and replicase traffic on a viral RNA. Proc. Natl. Acad. Sci. U.S.A. 99 (2002) 11133-11138
2. Barton D.J., O'Donnell B.J., and Flanegan J.B. 5′ cloveleaf in poliovirus RNA is a cis-acting replication element required for negative-strand synthesis. EMBO J. 20 (2001) 1439-1448
3. Brown D.M., Kauder S.E., Cornell C.T., Jang G.M., Racaniello V.R., and Semler B.L. Cell-dependent role for the poliovirus 3′ noncoding region in positive-strand RNA synthesis. J. Virol. 78 (2004) 1344-1351
4. Carpenter C.D., and Simon A.E. In vivo restoration of biologically active 3′ ends of virus-associated RNAs by nonhomologous RNA recombination and replacement of a terminal motif. J. Virol. 70 (1996) 478-486
5. Chandrika R., Rabindran S., Lewandowski D.J., Manjunath K.L., and Dawson W.O. Full-length tobacco mosaic virus RNAs and defective RNAs have different 3′ replication signals. Virology 273 (2000) 198-209
6. Chao L., Rang C.U., and Wong L.E. Distribution of spontaneous mutants and inferences about the replication mode of the RNA bacteriophage φ{symbol}6. J. Virol. 76 (2002) 3276-3281
7. David C., Gargouri-Bouzid R., and Haenni A.L. RNA replication of plant viruses containing an RNA genome. Prog. Nucleic Acid Res. Mol. Biol. 42 (1992) 157-227
8. Dreher T.W. Functions of the 3′-untranslated regions of positive strand RNA viral genomes. Annu. Rev. Phytopathol. 37 (1999) 151-174
9. French R., and Ahlquist P. Intercistronic as well as terminal sequences are required for efficient amplification of brome mosaic virus RNA3. J. Virol. 61 (1987) 1457-1465
10. Frolov I., Hardy R., and Rice C.M. Cis-acting RNA elements at the 5′ end of Sindbis virus genome RNA regulate minus- and plus-strand RNA synthesis. RNA 7 (2001) 1638-1651
11. Guan H. Replication and 3′-end repair of a subviral RNA associated with turnip crinkle virus. Ph. D. Dissertation (2000), University of Massachusetts, Amherst
12. Herold J., and Andino R. Poliovirus RNA replication requires genome circularization through a protein-protein bridge. Mol. Cell 7 (2001) 581-591
13. Isken O., Grassmann C.W., Yu H., and Behrens S.E. Complex signals in the genomic 3′ nontranslated region of bovine viral diarrhea virus coordinate translation and replication of the viral RNA. RNA 10 (2004) 1637-1652
14. Khromykh A.A., Meka H., Guyatt K.J., and Westaway E.G. Essential role of cyclization sequences in flavivirus RNA replication. J. Virol. 75 (2001) 6719-6728
15. Klovins J., and van Duin J. A long-range pseudoknot in Qβ is essential for replication. J. Mol. Biol. 294 (1999) 875-884
16. Koev G., Liu S., Beckett R., and Miller W.A. The 3′-terminal structure required for replication of barley yellow dwarf virus RNA contains an embedded 3′ end. Virology 292 (2002) 114-126
17. Kong Q., Wang J., and Simon A.E. Satellite RNA-mediated resistance to turnip crinkle virus in Arabidopsis involves a reduction in virus movement. Plant Cell 9 (1997) 2051-2063
18. Li X.H., and Simon A.E. In vivo accumulation of a turnip crinkle virus defective interfering RNA is affected by alterations in size and sequence. J. Virol. 65 (1991) 4582-4590
19. Li X.H., Heaton L., Morris T.J., and Simon A.E. Defective interfering RNAs of turnip crinkle virus intensify viral symptoms and are generated de novo. Proc. Natl. Acad. Sci. U.S.A. 86 (1989) 9173-9177
20. McCormack J.C., and Simon A.E. Biased hypermutagenesis associated with mutations in an untranslated hairpin of an RNA virus. J. Virol. 78 (2004) 7813-7817
21. Monkewich S., Lin H.-X., Fabian M.R., Xu W., Na H., Ray D., Chernysheva O.A., Nagy P., and White K.A. The p92 polymerase coding region contains an internal RNA element required at an early step in tombusvirus genome replication. J. Virol. 79 (2005) 4848-4858
22. Na H., and White A. Structure and prevalence of replication silencer-3′ terminus RNA interactions in Tombusviridae. Virology 345 (2006) 305-316
23. Nagashima S., Sasaki J., and Taniguchi K. The 5′-terminal region of the Aichi virus genome encodes cis-acting replication elements required for positive- and negative-strand RNA synthesis. J. Virol. 79 (2005) 6918-6931
24. Nagy P.D., Carpenter C.D., and Simon A.E. A novel 3′ end repair mechanism in an RNA virus. Proc. Natl. Acad. Sci. U.S.A. 94 (1997) 1113-1118
25. Nagy P.D., Pogany J., and Simon A.E. RNA elements required for RNA recombination function as replication enhancers in vitro and in vivo in a plus-strand RNA virus. EMBO J. 18 (1999) 5653-5665
26. Olsthoorn R.C., Mertens S., Brederode F.T., and Bol J.F. A conformational switch at the 3′ end of a plant virus RNA regulates viral replication. EMBO J. 18 (1999) 4856-4864
27. Panavas T., and Nagy P.D. The RNA replication enhancer element of tombusvirus contains two interchangeable hairpins that are functional during plus-strand synthesis. J. Virol. 77 (2003) 258-269
28. Panaviene Z., Panavas T., and Nagy P.D. Role of an internal and two 3′-terminal RNA elements in assembly of tombusvirus replicase. J. Virol. 79 (2005) 10608-10618
29. Pogany J., Fabian M.R., White K.A., and Nagy P.D. Functions of novel replication enhancer and silencer elements in tombusvirus replication. EMBO J. 22 (2003) 5602-5611
30. Rajendran K.S., Pogany J., and Nagy P.D. Comparison of turnip crinkle virus RNA-dependent RNA polymerase preparations expressed in Escherichia coli or derived from infected plants. J. Virol. 76 (2002) 1707-1717
31. Ray D., and White K.A. An internally located RNA hairpin enhances replication of tomato bushy stunt virus RNAs. J. Virol. 77 (2003) 245-257
32. Simon A.E. Genus Carmovirus (Tombusviridae) (2001), The Springer Index of Viruses, Springer Verlag
33. Simon A.E., and Howell S.H. The virulent satellite RNA of turnip crinkle virus has a major domain homologous to the 3′ end of the helper virus genome. EMBO J. 5 (1986) 3423-3428
34. Simon A.E., Roossinck M.J., and Havelda Z. Plant virus satellite and defective interfering RNAs: new paradigms for a new century. Annu. Rev. Phytopathol. 42 (2004) 415-447
35. Song C., and Simon A.E. RNA-dependent RNA polymerase from plants infected with turnip crinkle virus can transcribe (+) and (-)-strands of virus-assocciated RNAs. Proc. Natl. Acad. Sci. U.S.A. 91 (1994) 8792-8796
36. Song C., and Simon A.E. Requirement of a 3′-terminal stem-loop in in vitro transcription by an RNA dependent RNA polymerase. J. Mol. Biol. 254 (1995) 6-14
37. Sun, X., Simon, A.E., A cis-replication element functions in both orientations to enhance replication of turnip crinkle virus. Manuscript in revision.
38. van den Born E., Posthuma C.C., Gultyaev A.P., and Snijder E.J. Discontinuous subgenomic RNA synthesis in arteriviruses is guided by an RNA hairpin structure located in the genomic leader region. J. Virol. 79 (2005) 6312-6324
39. van Dijk A.A., Makeyev E.V., and Bamford D.H. Initiation of viral RNA-dependent RNA polymerization. J. Gen. Virol. 85 (2004) 1077-1093
40. Vlot A.C., and Bol J.F. The 5′ untranslated region of alfalfa mosaic virus RNA1 is involved in negative-strand RNA synthesis. J. Virol. 77 (2003) 11284-11289
41. Wang J., and Simon A.E. Symptom attenuation by a satellite RNA in vivo is dependent on reduced levels of virus coat protein. Virology 259 (1999) 234-245
42. Wang J., and Simon A.E. 3′-end stem-loops of the subviral RNAs associated with turnip crinkle virus are involved in symptom modulation and coat protein binding. J. Virol. 74 (2000) 6528-6537
43. White K.A., and Morris T.J. Defective and defective interfering RNAs of monopartite plus-strand RNA plant viruses. Cur. Top. Microbiol. Immunol. 239 (1999) 1-17
44. You S., Falgout B., Markoff L., and Padmanabhan R. In vitro RNA synthesis from exogenous Dengue viral RNA templates requires long-range interactions between 5′- and 3′-terminal regions that influence RNA structure. J. Biol. Chem. 276 (2001) 15581-15591
45. Zhang G., and Simon A.E. A multifunctional turnip crinkle virus replication enhancer revealed by in vivo functional SELEX. J. Mol. Biol. 326 (2003) 35-48
46. Zhang J., and Simon A.E. Importance of sequence and structural elements within a viral replication repressor. Virology 333 (2005) 301-315
47. Zhang G., Zhang J., and Simon A.E. Repression and derepression of minus-strand synthesis in a plus-strand RNA virus replicon. J. Virol. 78 (2004) 7619-7633
48. Zhang J., Stuntz R., and Simon A.E. Analysis of a viral replication repressor: sequence requirements in the large symmetrical loop. Virology 326 (2004) 90-102
49. Zhang G., Zhang J., George A.T., Baumstark T., and Simon A.E. Conformational changes involved in initiation of minus-strand synthesis of a virus-associated RNA. RNA 12 (2006) 147-162
50. Zhang., J., Zhang, G., Guo, R., Shapiro, B., Simon, A.E., A pseudoknot in pre-active form of a viral RNA is part of a structural switch that activates minus-strand synthesis. Manuscript submitted for publication.
51. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31 (2003) 3406-3415