A pseudoknot in a preactive form of a viral RNA is part of a structural switch activating minus-strand synthesis

Journal of Virology

Volumn 80, Issue 18, 2006, Pages 9181-9191

  Zhang, Jiuchun ^a   Zhang, Guohua ^a   Guo, Rong ^a   Shapiro, Bruce A ^b   Simon, Anne E ^a  

^a Bldg 142   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA DIRECTED RNA POLYMERASE; SATELLITE RNA; UNTRANSLATED RNA; VIRUS RNA;

ARTICLE; CELL METABOLISM; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; IN VITRO STUDY; IN VIVO STUDY; MOLECULAR MODEL; NONHUMAN; PLANT VIRUS; PRIORITY JOURNAL; PSEUDOKNOT; RNA CLEAVAGE; RNA CONFORMATION; RNA SEQUENCE; RNA STRUCTURE; RNA SYNTHESIS; RNA TRANSCRIPTION; RNA TRANSLATION; RNA VIRUS; STRUCTURAL GENOMICS; STRUCTURE ANALYSIS; TURNIP CRINKLE VIRUS;

BASE SEQUENCE; GENE EXPRESSION REGULATION, VIRAL; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; PLANT VIRUSES; RNA; RNA, SATELLITE; RNA, VIRAL; VIRUS REPLICATION; VIRUSES;

TURNIP CRINKLE VIRUS;

EID: 33748509730     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.00295-06     Document Type: Article

References (43)

1. Brantl, S. 2004. Bacterial gene regulation: from transcription attenuation to riboswitches and ribozymes. Trends Microbiol. 12:473-475.
2. Brown, D. M., S. E. Kauder, C. T. Cornell, G. M. Jang, V. R. Racaniello, and B. Semler. 2004. Cell-dependent role for the poliovirus 3′ noncoding region in positive-strand RNA synthesis. J. Virol. 78:1344-1351.
3. Chao, L., C. U. Rang, and L. E. Wong. 2002. Distribution of spontaneous mutants and inferences about the replication mode of the RNA bacteriophage Φ6. J. Virol. 76:3276-3281.
4. Dutkiewicz, M., and J. Ciesiolka. 2005. Structural characterization of the highly conserved 98-base sequence at the 3′ end of HCV RNA genome and the complementary sequence located at the 5′ end of the replicative viral strand. Nucleic Acids Res. 33:693-703.
5. Goebel, S. J., B. Hsue, T. F. Dombrowski, and P. S. Masters. 2004. Characterization of the RNA components of a putative molecular switch in the 3′ untranslated region of the murine coronavirus genome. J. Virol. 78:669-682.
6. Greatorex, J. 2004. The retroviral RNA dimer linkage: different structures may reflect different roles. Retrovirology 1:22.
7. Hacker, D. L., I. T. D. Petty, N. Wei, and T. J. Morris. 1992. Turnip crinkle virus genes required for RNA replication and virus movement. Virology 186:1-8.
8. Huthoff, H., and B. Berkhout. 2001. Two alternating structures of the HIV-1 leader RNA. RNA 7:143-157.
9. Kasprzak, W., and B. A. Shapiro. 1999. Stem Trace: an interactive visual tool for comparative RNA structure analysis. Bioinformatics 15:16-31.
10. Ke, A. L., K. H. Zhou, F. Ding, J. H. D. Cate, and J. A. Doudna. 2004. A conformational switch controls hepatitis delta virus ribozyme catalysis. Nature 429:201-204.
11. Khromykh, A. A., H. Meka, K. J. Guyatt, and E. G. Westaway. 2001. Essential role of cyclization sequences in flavivirus RNA replication. J. Virol. 75:6719-6728.
12. Klovins, J., V. Berzins, and J. Van Duin. 1998. A long-range interaction in Qβ RNA that bridges the thousand nucleotides between the M-site and the 3′ end is required for replication. RNA 4:948-957.
13. Koev, G., S. J. Liu, R. Beckett, and W. A. Miller. 2002. The 3′-terminal structure required for replication of barley yellow dwarf virus RNA contains an embedded 3′ end. Virology 292:114-126.
14. Kong, Q., J. Wang, and A. E. Simon. 1997. Satellite RNA-mediated resistance to turnip crinkle virus in Arabidopsis involves a reduction in virus movement. Plant Cell 9:2051-2063.
15. McCormack, J. C., and A. E. Simon. 2004. Biased hypermutagenesis associated with mutations in an untranslated hairpin of an RNA virus. J. Virol. 78:7813-7817.
16. Nagel, J. H. A., and C. W. A. Pleij. 2002. Self-induced structural switches in RNA. Biochimie 84:913-923.
17. Nagy, P. D., J. Pogany, and A. E. Simon. 1999. RNA elements required for RNA recombination function as replication enhancers in vitro and in vivo in a plus-strand RNA virus. EMBO J. 18:5653-5665.
18. Olsthoorn, R. C. L., S. Mertens, F. T. Brederode, and J. F. Bol. 1999. A conformational switch at the 3′ end of a plant virus RNA regulates viral replication. EMBO J. 18:4856-4864.
19. Paillart, J.-C., M. Dettenhofer, X.-F. Yu, C. Ehresmann, B. Ehresmann, and R. Marquet. 2004. First snapshots of the HIV-1 RNA structure in infected cells and in virions. J. Biol. Chem. 279:48397-48403.
20. Pan, J., D. Thirumalai, and S. A. Woodson. 1997. Folding of RNA involves parallel pathways. J. Mol. Biol. 273:7-13.
21. Panaviene, Z., T. Panavas, and P. D. Nagy. 2005. Role of an internal and two 3′-terminal RNA elements in assembly of tombusvirus replicase. J. Virol. 79:10608-10618.
22. Petrillo, J. E., G. Rocheleau, B. Kelley-Clarke, and L. Gehrke. 2005. Evaluation of the conformational switch model for alfalfa mosaic virus RNA replication. J. Virol. 79:5743-5751.
23. Rajendran, K. S., J. Pogany, and P. D. Nagy. 2002. Comparison of turnip crinkle virus RNA-dependent RNA polymerase preparations expressed in Escherichia coli or derived from infected plants. J. Virol. 76:1707-1717.
24. Schuppli, D., J. Georgijevic, and H. Weber. 2000. Synergism of mutations in bacteriophage Qβ RNA affecting host factor dependence of Qβ replicase. J. Mol. Biol. 295:149-154.
25. Shapiro, B. A., and J. Navetta. 1994. A massively parallel genetic algorithm for RNA secondary structure prediction. J. Supercomput. 8:195-207.
26. Shapiro, B. A., and J.-C. Wu. 1996. An annealing mutation operator in the genetic algorithm for RNA folding. Comput. Appl. Biosci. 12:171-180.
27. Shapiro, B. A., and W. Kasprzak. 1996. STRUCTURELAB: a heterogeneous bioinformatics system for RNA structure analysis. J. Mol. Graph. 14:194-205.
28. Shapiro, B. A., J.-C. Wu, D. Bengali, and M. Potts. 2001a. The massively parallel genetic algorithm for RNA folding: MIMD implementation and population variation. Bioinformatics 17:137-148.
29. Shapiro, B. A., D. Bengali, W. Kasprzak, and J.-C. Wu. 2001b. RNA folding pathway functional intermediates: their prediction and analysis. J. Mol. Biol. 312:27-44.
30. Simon, A. E., and S. H. Howell. 1986. The virulent satellite RNA of turnip crinkle virus has a major domain homologous to the 3′-end of the helper virus genome. EMBO J. 5:3423-3428.
31. Simon, A. E., M. J. Roossinck, and Z. Havelda. 2004. Plant virus satellite and defective interfering RNAs: new paradigms for a new century. Annu. Rev. Phytopathol. 42:415-447.
32. Song, C., and A. E. Simon. 1994. RNA-dependent RNA polymerase from plants infected with turnip crinkle virus can transcribe (+)- and (-)-strands of virus-associated RNAs. Proc. Natl. Acad. Sci. USA 91:8792-8796.
33. Song, C., and A. E. Simon. 1995. Requirement of a 3′-terminal stem-loop in in vitro transcription by an RNA-dependent RNA polymerase. J. Mol. Biol. 254:6-14.
34. Song, S. I., and W. A. Miller. 2004. cis and trans requirements of rolling circle replication of a satellite RNA. J. Virol. 78:3072-3082.
35. Sun, X., G. Zhang, and A. E. Simon. 2005. Short internal sequences involved in RNA replication and virion accumulation in a subviral RNA of turnip crinkle virus. J. Virol. 79:512-524.
36. Sun, X., and A. E. Simon. 2006. A cis-replication element functions in both orientations to enhance replication of turnip crinkle virus. Virology 352:39-51.
37. van Dijk, A. A., E. V. Makeyevt, and D. H. Bamford. 2004. Initiation of viral RNA-dependent RNA polymerization. J. Gen. Virol. 85:1077-1093.
38. Woodson, S. A. 2005. Metal ions and RNA folding: a highly charged topic with a dynamic future. Curr. Opin. Chem. Biol. 9:104-109.
39. Zhang, G., and A. E. Simon. 2003. A multifunctional turnip crinkle virus replication enhancer revealed by in vivo functional SELEX. J. Mol. Biol. 326:35-48.
40. Zhang, G., J. Zhang, and A. E. Simon. 2004. Repression and derepression of minus-strand synthesis in a plus-strand RNA virus replicon. J. Virol. 78:7619-7633.
41. Zhang, G., J. Zhang, A. T. George, T. Baumstark, and A. E. Simon. 2006. Conformational changes involved in initiation of minus-strand synthesis of a virus-associated RNA. RNA 12:147-162.
42. Zhang, J., R. Stuntz, and A. E. Simon. 2004. Analysis of a viral replication repressor: sequence requirements for a large symmetrical internal loop. Virology 326:90-102.
43. Zhang, J., and A. E. Simon. 2005. Importance of sequence and structural elements within a viral replication repressor. Virology 333:301-315.