Stem-loop IV in the 5′ untranslated region is a cis-acting element in bovine coronavirus defective interfering RNA replication

Journal of Virology

Volumn 79, Issue 19, 2005, Pages 12434-12446

  Raman, Sharmila ^a   Brian, David A ^a,b  

^a UNIVERSITY OF TENNESSEE   (United States)

^b UNIVERSITY OF TENNESSEE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL PROTEIN; DEFECTIVE INTERFERING RNA; RNA; UNCLASSIFIED DRUG; VIRUS PROTEIN;

ARTICLE; CORONAVIRUS; CROSS LINKING; DEFECTIVE VIRUS; GEL MOBILITY SHIFT ASSAY; GENE MAPPING; GENETIC CONSERVATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; RNA REPLICATION; SARS CORONAVIRUS; SEQUENCE HOMOLOGY; UNTRANSLATED REGION; VIRUS GENOME;

5' UNTRANSLATED REGIONS; BASE SEQUENCE; CELL LINE; CORONAVIRUS, BOVINE; DEFECTIVE VIRUSES; ELECTROPHORETIC MOBILITY SHIFT ASSAY; HUMANS; MOLECULAR SEQUENCE DATA; MOLECULAR WEIGHT; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; PROTEINS; RNA, VIRAL; SARS VIRUS; VIRUS REPLICATION;

BOVINE CORONAVIRUS; CORONAVIRUS; SARS CORONAVIRUS;

EID: 25144448646     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.79.19.12434-12446.2005     Document Type: Article

References (42)

1. Almazan, F., C. Galan, and L. Enjuanes. 2004. The nucleoprotein is required for efficient coronavirus genome replication. J. Virol. 78:12683-12688.
2. Andino, R., G. E. Rieckhof, P. L. Achacoso, and D. Baltimore. 1993. Polio-virus RNA synthesis utilizes an RNP complex formed around the 5′-end of viral RNA. EMBO J. 12:3587-3598.
3. Andino, R., G. E. Rieckhof, and D. Baltimore. 1990. A functional ribonucleo-protein complex forms around the 5′ end of poliovirus RNA. Cell 63:369-380.
4. Barton, D. J., B. J. O'Donnell, and J. B. Flanegan. 2001. 5′ cloverleaf in poliovirus RNA is a cis-acting replication element required for negative-strand synthesis. EMBO J 20:1439-1448.
5. Bedard, K. M., B. L. Walter, and B. L. Semler. 2004. Multimerization of poly(rC) binding protein 2 is required for translation initiation mediated by a viral IRES. RNA 10:1266-1276.
6. Blyn, L. B., J. S. Towner, B. L. Semler, and E. Ehrenfeld. 1997. Requirement of poly(rC) binding protein 2 for translation of poliovirus RNA. J. Virol. 71:6243-6246.
7. Chang, R. Y., M. A. Hofmann, P. B. Sethna, and D. A. Brian. 1994. A cis-acting function for the coronavirus leader in defective interfering RNA replication. J. Virol. 68:8223-8231.
8. Chang, R. Y., R. Krishnan, and D. A. Brian. 1996. The UCUAAAC promoter motif is not required for high-frequency leader recombination in bovine coronavirus defective interfering RNA. J. Virol. 70:2720-2729.
9. Chen, J., A. Noueiry, and P. Ahlquist. 2001. Brome mosaic virus protein 1a recruits viral RNA2 to RNA replication through a 5′-proximal RNA2 signal. J. Virol. 75:3207-3219.
10. Fabian, M. R., and K. A. White. 2004. 5′-3′ RNA-RNA interaction facilitates cap- and poly(A) tail-independent translation of tomato bushy stunt virus mRNA: a potential common mechanism for tombusviridae. J. Biol. Chem. 279:28862-28872.
11. Frolov, I., R. Hardy, and C. M. Rice. 2001. cis-acting RNA elements at the 5′ end of Sindbis virus genome RNA regulate minus- and plus-strand RNA synthesis. RNA 7:1638-1651.
12. Gamarnik, A. V., and R. Andino. 2000. Interactions of viral protein 3CD and poly(rC) binding protein with the 5′ untranslated region of the poliovirus genome. J. Virol. 74:2219-2226.
13. Gamarnik, A. V., and R. Andino. 1998. Switch from translation to RNA replication in a positive-stranded RNA virus. Genes Dev. 12:2293-2304.
14. Gamarnik, A. V., and R. Andino. 1997. Two functional complexes formed by KH domain containing proteins with the 5′ noncoding region of poliovirus RNA. RNA 3:882-892.
15. Goebel, S. J., J. Taylor, and P. S. Masters. 2004. The 3′ cis-acting genomic replication element of the severe acute respiratory syndrome coronavirus can function in the murine coronavirus genome. J. Virol. 78:7846-7851.
16. Guo, L., E. M. Allen, and W. A. Miller. 2001. Base-pairing between untranslated regions facilitates translation of uncapped, nonpolyadenylated viral RNA. Mol. Cell 7:1103-1109.
17. Herold, J., and R. Andino. 2001. Poliovirus RNA replication requires genome circularization through a protein-protein bridge. Mol. Cell 7:581-591.
18. Hofmann, M. A., R. Y. Chang, S. Ku, and D. A. Brian. 1993. Leader-mRNA junction sequences are unique for each subgenomic mRNA species in the bovine coronavirus and remain so throughout persistent infection. Virology 196:163-171.
19. Huang, P., and M. M. Lai. 1999. Polypyrimidine tract-binding protein binds to the complementary strand of the mouse hepatitis virus 3′ untranslated region, thereby altering RNA conformation. J. Virol. 73:9110-9116.
20. 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.
21. Kim, K. H., and C. L. Hemenway. 1999. Long-distance RNA-RNA interactions and conserved sequence elements affect potato virus X plus-strand RNA accumulation. RNA 5:636-645.
22. Li, H. P., P. Huang, S. Park, and M. M. Lai. 1999. Polypyrimidine tract-binding protein binds to the leader RNA of mouse hepatitis virus and serves as a regulator of viral transcription. J. Virol. 73:772-777.
23. Makino, S., and M. M. Lai. 1989. High-frequency leader sequence switching during coronavirus defective interfering RNA replication. J. Virol. 63:5285-5292.
24. Mathews, D. H., J. Sabina, M. Zuker, and D. H. Turner. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288:911-940.
25. Miller, E. D., C. A. Plante, K. H. Kim, J. W. Brown, and C. Hemenway. 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.
26. Nelson, G. W., S. A. Stohlman, and S. M. Tahara. 2000. High affinity interaction between nucleocapsid protein and leader/intergenic sequence of mouse hepatitis virus RNA. J. Gen. Virol. 81:181-188.
27. Parsley, T. B., J. S. Towner, L. B. Blyn, E. Ehrenfeld, and B. L. Semler. 1997. Poly(rC) binding protein 2 forms a ternary complex with the 5′-terminal sequences of poliovirus RNA and the viral 3CD proteinase. RNA 3:1124-1134.
28. Raman, S., P. Bouma, G. D. Williams, and D. A. Brian. 2003. Stem-loop III in the 5′ untranslated region is a cis-acting element in bovine coronavirus defective interfering RNA replication. J. Virol. 77:6720-6730.
29. Ray, D., H. Na, and K. A. White. 2004. Structural properties of a multifunctional T-shaped RNA domain that mediate efficient tomato bushy stunt virus RNA replication. J. Virol. 78:10490-10500.
30. Schelle, B., N. Karl, B. Ludewig, S. G. Siddell, and V. Thiel. 2005. Selective replication of coronavirus genomes that express nucleocapsid protein. J. Virol. 79:6620-6630.
31. Senanayake, S. D., and D. A. Brian. 1999. Translation from the 5′ untranslated region (UTR) of mRNA 1 is repressed, but that from the 5′ UTR of mRNA 7 is stimulated in coronavirus-infected cells. J. Virol. 73:8003-8009.
32. Snijder, E. J., P. J. Bredenbeek, J. C. Dobbe, V. Thiel, J. Ziebuhr, L. L. Poon, Y. Guan, M. Rozanov, W. J. Spaan, and A. E. Gorbalenya. 2003. Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage. J. Mol. Biol. 331:991-1004.
33. Spagnolo, J. F., and B. G. Hogue. 2000. Host protein interactions with the 3′ end of bovine coronavirus RNA and the requirement of the poly(A) tail for coronavirus defective genome replication. J. Virol. 74:5053-5065.
34. Teterina, N. L., D. Egger, K. Bienz, D. M. Brown, B. L. Semler, and E. Ehrenfeld. 2001. Requirements for assembly of poliovirus replication complexes and negative-strand RNA synthesis. J. Virol. 75:3841-3850.
35. Thomson, A. M., J. T. Rogers, C. E. Walker, J. M. Staton, and P. J. Leedman. 1999. Optimized RNA gel-shift and UV cross-linking assays for characterization of cytoplasmic RNA-protein interactions. BioTechniques 27:1032-1042.
36. Van Den Born, E., A. P. Gultyaev, and E. J. Snijder. 2004. Secondary structure and function of the 5′-proximal region of the equine arteritis virus RNA genome. RNA 10:424-437.
37. Vlot, A. C., and J. F. Bol. 2003. The 5′ untranslated region of alfalfa mosaic virus RNA 1 is involved in negative-strand RNA synthesis. J. Virol. 77: 11284-11289.
38. Walter, B. L., T. B. Parsley, E. Ehrenfeld, and B. L. Semler. 2002. Distinct poly(rC) binding protein KH domain determinants for poliovirus translation initiation and viral RNA replication. J. Virol. 76:12008-12022.
39. Woo, P. C., S. K. Lau, C. M. Chu, K. H. Chan, H. W. Tsoi, Y. Huang, B. H. Wong, R. W. Poon, J. J. Cai, W. K. Luk, L. L. Poon, S. S. Wong, Y. Guan, J. S. Peiris, and K. Y. Yuen. 2005. Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. J. Virol. 79:884-895.
40. Wu, H. Y., J. S. Guy, D. Yoo, R. Vlasak, E. Urbach, and D. A. Brian. 2003. Common RNA replication signals exist among group 2 coronaviruses: evidence for in vivo recombination between animal and human coronavirus molecules. Virology 315:174-183.
41. You, S., B. Falgout, L. Markoff, and R. Padmanabhan. 2001. 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. 276:15581-15591.
42. Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31:3406-3415.