In vitro and in vivo studies of the RNA conformational switch in alfalfa mosaic virus

Journal of Virology

Volumn 84, Issue 3, 2010, Pages 1423-1429

  Chen, Shih Cheng ^a   Olsthoorn, René C L ^a  

^a LEIDEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

SINDBIS VIRUS NONSTRUCTURAL PROTEIN 4; TRANSFER RNA; VIRUS RNA;

3' UNTRANSLATED REGION; ADENYLATION; ALFALFA MOSAIC VIRUS; ARTICLE; BINDING AFFINITY; GENE CONTROL; GENE REPLICATION; GENE SWITCHING; GENETIC VARIABILITY; HUMAN; IN VITRO STUDY; IN VIVO STUDY; PRIORITY JOURNAL; PROTEIN STRUCTURE; PROTEIN SYNTHESIS; RNA CONFORMATION; RNA TRANSLATION;

3' UNTRANSLATED REGIONS; ALFALFA MOSAIC VIRUS; BASE SEQUENCE; DNA PRIMERS; NUCLEIC ACID CONFORMATION; RNA, VIRAL; VIRUS REPLICATION;

ALFALFA MOSAIC VIRUS;

EID: 73949116974     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.01443-09     Document Type: Article

References (31)

1. Aparicio, F., M. Vilar, E. Perez-Payá, and V. Pallás. 2003. The coat protein of prunus necrotic ringspot virus specifically binds to and regulates the conformation of its genomic RNA. Virology 313:213-223.
2. Bernstein, D. S., N. Buter, C. Stumpf, and M. Wickens. 2002. Analyzing RNA-protein complexes using a yeast three-hybrid system. Methods 26:123-141.
3. Bol, J. F. 2005. Replication of alfamo- and ilarviruses: role of the coat protein. Annu. Rev. Phytopathol. 43:39-62.
4. Chen, S. C., A. P. Gultyaev, C. W. A. Pleij, and R. C. L. Olsthoorn. 2009. A secondary structure model for the 3′-untranslated region of ilarvirus RNAs. In Z. Feng and M. Long (ed.), Viral genomes: diversity, properties and parameters. Nova Science Publishers, Hauppage, NY.
5. de Graaff, M., M. R. Man in't Veld, and E. M. J. Jaspars. 1995. In vitro evidence that the coat protein of alfalfa mosaic virus plays a direct role in the regulation of plus and minus RNA synthesis: implications for the life cycle of alfalfa mosaic virus. Virology 208:583-589.
6. Deiman, B. A. L. M., P. W. G. Verlaan, and C. W. A. Pleij. 2000. In vitro transcription by the turnip yellow mosaic virus RNA polymerase: a comparison with the alfalfa mosaic virus and brome mosaic virus replicases. J. Virol. 74:264-271.
7. Reference deleted.
8. Gultyaev, A. P., F. H. D. van Batenburg, and C. W. A. Pleij. 1999. An approximation of loop free energy values of RNA H-pseudoknots. RNA 5:609-617.
9. Guogas, L. M., S. M. Laforest, and L. Gehrke. 2005. Coat protein activation of alfalfa mosaic virus replication is concentration dependent. J. Virol. 79: 5752-5761.
10. Haasnoot, J. 2002. Requirements for promoter activity in alfalfa mosaic and brome mosaic viruses. Ph.D. thesis. Leiden University, Leiden, The Netherlands.
11. Hook, B., D. Bernstein, B. Zhang, and M. Wickens. 2005. RNA-protein interactions in the yeast three-hybrid system: affinity, sensitivity, and enhanced library screening. RNA 11:227-233.
12. Houser-Scott, F., M. L. Baer, K. F. Liem, Jr., J. M. Cai, and L. Gehrke. 1994. Nucleotide sequence and structural determinants of specific binding of coat protein or coat protein peptides to the 3′ untranslated region of alfalfa mosaic virus RNA 4. J. Virol. 68:2194-2205.
13. Jaeger, S., G. Eriani, and F. Martin. 2004. The results and prospects of the yeast three-hybrid system. FEBS Lett. 556:7-12.
14. Jaeger, S., G. Eriani, and F. Martin. 2004. Critical residues for RNA discrimination of the histone hairpin binding protein (HBP) investigated by the yeast three-hybrid system. FEBS Lett. 556:265-270.
15. Jaspars, E. M. J. 1999. Genome activation in alfamo- and ilarviruses. Arch. Virol. 144:843-863.
16. Krab, I. M., C. Caldwell, D. R. Gallie, and J. F. Bol. 2005. Coat protein enhances translational efficiency of alfalfa mosaic virus RNAs and interacts with the eIF4G component of initiation factor eIF4F. J. Gen. Virol. 86:1841-1849.
17. Neeleman, L., R. C. L. Olsthoorn, H. J. M. Linthorst, and J. F. Bol. 2001. Translation of a nonpolyadenylated viral RNA is enhanced by binding of viral coat protein or polyadenylation of the RNA. Proc. Natl. Acad. Sci. U. S. A. 98:14286-14291.
18. Neeleman, L., H. J. M. Linthorst, and J. F. Bol. 2004. Efficient translation of alfamovirus RNAs requires the binding of coat protein dimers to the 3′ termini of the viral RNAs. J. Gen. Virol. 85:231-240.
19. Olsthoorn, R. C. L., and J. F. Bol. 2002. Role of an essential triloop hairpin and flanking structures in the 3′ untranslated region of Alfalfa mosaic virus RNA in in vitro transcription. J. Virol. 76:8747-8756.
20. 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.
21. 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.
22. Quadt, R., H. J. Rosdorff, T. W. Hunt, and E. M. J. Jaspars. 1991. Analysis of the protein composition of alfalfa mosaic virus RNA-dependent RNA polymerase. Virology 182:309-315.
23. Reusken, C. B. E. M., and J. F. Bol. 1996. Structural elements of the 3′-terminal coat protein binding site in alfalfa mosaic virus RNAs. Nucleic Acids Res. 24:2660-2665.
24. Reusken, C. B. E. M., L. Neeleman, and J. F. Bol. 1994. The 3′-untranslated region of alfalfa mosaic virus RNA 3 contains at least two independent binding sites for viral coat protein. Nucleic Acids Res. 22:1346-1353.
25. Sengupta, D. J., B. Zhang, B. Kraemer, P. Pochart, S. Fields, and M. Wickens. 1996. A three-hybrid system to detect RNA-protein interactions in vivo. Proc. Natl. Acad. Sci. U. S. A. 93:8496-8501.
26. van der Heijden, M. W., J. E. Carette, P. J. Reinhoud, A. Haegi, and J. F. Bol. 2001. Alfalfa mosaic virus replicase proteins P1 and P2 interact and colocalize at the vacuolar membrane. J. Virol. 75:1879-1987.
27. van der Vossen, E. A. G., L. Neeleman, and J. F. Bol. 1994. Early and late functions of alfalfa mosaic virus coat protein can be mutated separately. Virology 202:891-903.
28. Vlot, A. C., L. Neeleman, H. J. M. Linthorst, and J. F. Bol. 2001. Role of the 3′-untranslated regions of alfalfa mosaic virus RNAs in the formation of a transiently expressed replicase in plants and in the assembly of virions. J. Virol. 75:6440-6449.
29. Zuidema, D. 1983. Specific binding sites on RNAs and coat protein of alfalfa mosaic virus involved in genome activation. Ph.D. thesis. Leiden University, Leiden, The Netherlands.
30. Zuidema, D., R. H. Cool, and E. M. J. Jaspars. 1984. Minimum requirements for specific binding of RNA and coat protein of alfalfa mosaic virus. Virology 136:282-292.
31. Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction Nucleic Acids Res. 31:3406-3415.