Importance of the positive-strand RNA secondary structure of a murine coronavirus defective interfering RNA internal replication signal in positive-strand RNA synthesis

Journal of Virology

Volumn 72, Issue 10, 1998, Pages 7926-7933

  Repass, John F ^a   Makino, Shinji ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE; RIBONUCLEASE; VIRUS RNA;

ARTICLE; BASE PAIRING; CORONAVIRUS; NONHUMAN; PRIORITY JOURNAL; RNA ANALYSIS; RNA REPLICATION; RNA STRUCTURE; RNA SYNTHESIS; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; VIRUS GENOME;

EID: 0031694636     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/jvi.72.10.7926-7933.1998     Document Type: Article

References (31)

1. Barrera, I., U. Schuppli, J. M. Sogo, and H. Weber. 1993. Different mechanisms of recognition of bacteriophage Qβ plus and minus strand RNAs by Qβ replicase. J. Mol. Biol. 232:512-521.
2. Baudin, F., C. Bach, S. Cusack, and R. W. H. Ruigrok. 1994. Structure of influenza virus RNP. 1. Influenza virus nucleoprotein melts secondary structure in panhandle RNA and exposes the bases to the solvent. EMBO J. 13:3158-3165.
3. Bonilla, P. J., A. E. Gorbalenya, and S. R. Weiss. 1994. Mouse hepatitis virus strain A59 RNA polymerase gene ORF 1a: heterogeneity among MHV strains. Virology 198:736-740.
4. de Groot, R. J., R. G. van der Most, and W. J. M. Spaan. 1992. The fitness of defective interfering murine coronavirus DI-a and its derivatives is decreased by nonsense and frame shift mutations. J. Virol. 66:5898-5905.
5. Furuya, T., and M. M. C. Lai. 1993. Three different cellular proteins bind to complementary sites on the 5′-end-positive and 3′-end-negative strands of mouse hepatitis virus RNA. J. Virol. 67:7215-7222.
6. Hirano, N., K. Fujiwara, S. Hino, and M. Matsumoto. 1974. Replication and plaque formation of mouse hepatitis virus (MHV-2) in mouse cell line DBT culture. Arch. Gesamte Virusforsch. 44:298-302.
7. Jacobson, S. J., D. A. Konings, and P. Sarnow. 1993. Biochemical and genetic evidence for a pseudoknot structure at the 3′ terminus of the poliovirus RNA genome and its role in viral RNA amplification. J. Virol. 67:2961-2971.
8. Joo, M., S. Banerjee, and S. Makino. 1996. Replication of murine coronavirus defective interfering RNA from negative-strand transcripts. J. Virol. 70:5769-5776.
9. Joo, M., and S. Makino. 1992. Mutagenic analysis of the coronavirus intergenie consensus sequence. J. Virol. 66:6330-6337.
10. Kim, Y.-N., Y. S. Jeong, and S. Makino. 1993. Analysis of cis-acting sequences essential for coronavirus defective interfering RNA replication. Virology 197:53-63.
11. Kim, Y.-N., and S. Makino. 1995. Characterization of a murine coronavirus defective interfering RNA internal cis-acting replication signal. J. Virol. 69:4963-4971.
12. Lai, M. M. C., P. R. Brayton, R. C. Armen, C. D. Patton, C. Pugh, and S. A. Stohlman. 1981. Mouse hepatitis virus A59: mRNA structure and genetic localization of the sequence divergence from hepatotropic strain MHV-3. J. Virol. 39:823-834.
13. Lai, M. M. C., and S. A. Stohlman. 1978. RNA of mouse hepatitis virus. J. Virol. 26:236-242.
14. Lee, H. J., C.-K. Shieh, A. E. Gorbalenya, E. V. Eugene, N. La Monica, J. Tuler, A. Bagdzhadzhyan, and M. M. C. Lai. 1991. The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase. Virology 180:567-582.
15. Li, H. P., X. Zhang, R. Duncan, L. Comai, and M. M. C. Lai. 1997. Heterogeneous nuclear ribonucleoprotein A1 binds to the transcription-regulatory region of mouse hepatitis virus RNA. Proc. Natl. Acad. Sci. USA 94:9544-9549.
16. Lin, Y.-J., and M. M. C. Lai. 1993. Deletion mapping of a mouse hepatitis virus defective interfering RNA reveals the requirement of an internal and discontinuous sequence for replication. J. Virol. 67:6110-6118.
17. Luytjes, W., H. Gerritsma, and W. J. M. Spaan. 1996. Replication of synthetic defective interfering RNAs derived from coronavirus mouse hepatitis virus-A59. Virology 216:174-183.
18. Makino, S., N. Fujioka, and K. Fujiwara. 1985. Structure of the intracellular defective viral RNAs of defective interfering particles of mouse hepatitis virus. J. Virol. 54:329-336.
19. Makino, S., M. Joo, and J. K. Makino. 1991. A system for study of coronavirus mRNA synthesis: a regulated, expressed subgenomic defective interfering RNA results from intergenic site insertion. J. Virol. 65:6031-6041.
20. Makino, S., and M. M. C. Lai. 1989. High-frequency leader sequence switching during coronavirus defective interfering RNA replication. J. Virol. 63: 5285-5292.
21. Makino, S., C.-K. Shieh, L. H. Soe, S. C. Baker, and M. M. C. Lai. 1988. Primary structure and translation of a defective interfering RNA of murine coronavirus. Virology 166:550-560.
22. Masters, P. S., C. A. Koetzner, C. A. Kerr, and Y. Heo. 1994. Optimization of targeted RNA recombination and mapping of a novel nucleocapsid gene mutation in the coronavirus mouse hepatitis virus. J. Virol. 68:328-337.
23. Meyer, F., H. Weber, and C. Weissman. 1981. Interactions of Qβ replicase with Qβ RNA. J. Mol. Biol. 153:631-660.
24. Pachuk, C. J., P. J. Bredenbeek, P. W. Zoltick, W. J. M. Spaan, and S. R. Weiss. 1989. Molecular cloning of the gene encoding the putative polymerase of mouse hepatitis virus, strain A59. Virology 171:141-148.
25. Schuppli, D., I. Barrera, and H. Weber. 1994. Identification of replication elements on bacteriophage Qβ minus strand RNA that are essential for template activity with Qβ replicase. J. Mol. Biol. 243:811-815.
26. Stern, S., D. Moazed, and H. F. Noller. 1988. Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension. Methods Enzymol. 164:481-489.
27. van der Most, R. G., P. J. Bredenbeek, and W. J. M. Spaan. 1991. A domain at the 3′ end of the polymerase gene is essential for encapsidation of coronavirus defective interfering RNAs. J. Virol. 65:3219-3226.
28. Winship, P. R. 1989. An improved method for directly sequencing PCR material using dimethyl sulfoxide. Nucleic Acids Res. 17:1266.
29. Yu, W., and J. Leibowitz. 1995. A conserved motif at the 3′ end of mouse hepatitis virus genomic RNA required for host protein binding and viral RNA replication. Virology 214:128-138.
30. Yu, W., and J. Leibowitz. 1995. Specific binding of host cellular proteins to multiple sites within the 3′ end of mouse hepatitis virus genomic RNA. J. Virol. 69:2016-2023.
31. Zuker, M., and P. Steigler. 1981. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 9:133-148.