An optimal cis-replication stem-loop IV in the 5′ untranslated region of the mouse coronavirus genome extends 16 nucleotides into open reading frame 1

Journal of Virology

Volumn 85, Issue 11, 2011, Pages 5593-5605

  Guan, Bo Jhih ^a   Wu, Hung Yi ^a,b   Brian, David A ^a  

^a UNIVERSITY OF TENNESSEE   (United States)

^b NATIONAL CHUNG HSING UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; VIRUS RNA;

5' UNTRANSLATED REGION; ANIMAL CELL; ARTICLE; CONTROLLED STUDY; CORONAVIRUS; EVOLUTIONARY ADAPTATION; GENE SEQUENCE; MOUSE; MURINE HEPATITIS CORONAVIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PLASMID; PRIORITY JOURNAL; RNA STRUCTURE; SEQUENCE ALIGNMENT; VIRAL GENETICS; VIRUS GENOME; VIRUS MUTATION; VIRUS REPLICATION; WILD TYPE;

5' UNTRANSLATED REGIONS; ANIMALS; CELL LINE; CORONAVIRUS, BOVINE; MICROBIAL VIABILITY; MURINE HEPATITIS VIRUS; OPEN READING FRAMES; RECOMBINATION, GENETIC; RNA, VIRAL; VIRAL PLAQUE ASSAY; VIRUS REPLICATION;

BOVINE CORONAVIRUS; CORONAVIRUS; MURINE HEPATITIS VIRUS; SARS CORONAVIRUS;

EID: 79956143000     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.00263-11     Document Type: Article

References (42)

1. Brian, D. A., and R. S. Baric. 2005. Coronavirus genome structure and replication. Curr. Top. Microbiol. Immunol. 287:1-30.
2. Brockway, S. M., and M. R. Denison. 2005. Mutagenesis of the murine hepatitis virus nsp1-coding region identifies residues important for protein processing, viral RNA synthesis, and viral replication. Virology 340:209-223.
3. Brown, C. G., K. S. Nixon, S. D. Senanayake, and D. A. Brian. 2007. An RNA stem-loop within the bovine coronavirus nsp1 coding region is a cis-acting element in defective interfering RNA replication. J. Virol. 81:7716-7724.
4. Chang, R. Y., and D. A. Brian. 1996. cis requirement for N-specific protein sequence in bovine coronavirus defective interfering RNA replication. J. Virol. 70:2201-2207.
5. 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.
6. 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.
7. Chen, S. C., and R. C. Olsthoorn. 2010. Group-specific structural features of the 5′-proximal sequences of coronavirus genomic RNAs. Virology 401:29-41.
8. Chen, W., and R. S. Baric. 1996. Molecular anatomy of mouse hepatitis virus persistence: coevolution of increased host cell resistance and virus virulence. J. Virol. 70:3947-3960.
9. Chen, W., V. J. Madden, C. R. Bagnell, Jr., and R. S. Baric. 1997. Hostderived intracellular immunization against mouse hepatitis virus infection. Virology 228:318-332.
10. Chouljenko, V. N., X. Q. Lin, J. Storz, K. G. Kousoulas, and A. E. Gorbalenya. 2001. Comparison of genomic and predicted amino acid sequences of respiratory and enteric bovine coronaviruses isolated from the same animal with fatal shipping pneumonia. J. Gen. Virol. 82:2927-2933.
11. Denison, M. R., et al. 2004. Cleavage between replicase proteins p28 and p65 of mouse hepatitis virus is not required for virus replication. J. Virol. 78: 5957-5965.
12. Gaertner, D. J., D. F. Winograd, S. R. Compton, F. X. Paturzo, and A. L. Smith. 1993. Development and optimization of plaque assays for rat coronaviruses. J. Virol. Methods 43:53-64.
13. 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.
14. Goebel, S. J., T. B. Miller, C. J. Bennett, K. A. Bernard, and P. S. Masters. 2007. A hypervariable region within the 3′ cis-acting element of the murine coronavirus genome is nonessential for RNA synthesis but affects pathogenesis. J. Virol. 81:1274-1287.
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. Gorbalenya, A. E., L. Enjuanes, J. Ziebuhr, and E. J. Snijder. 2006. Nidovirales: evolving the largest RNA virus genome. Virus Res. 117:17-37.
17. Gustin, K. M., B. J. Guan, A. Dziduszko, and D. A. Brian. 2009. Bovine coronavirus nonstructural protein 1 (p28) is an RNA binding protein that binds terminal genomic cis-replication elements. J. Virol. 83:6087-6097.
18. Hirano, N., K. Fujiwara, and M. Matumoto. 1976. Mouse hepatitis virus (MHV-2). Plaque assay and propagation in mouse cell line DBT cells. Jpn. J. Microbiol. 20:219-225.
19. Hofmann, M. A., S. D. Senanayake, and D. A. Brian. 1993. A translationattenuating intraleader open reading frame is selected on coronavirus mRNAs during persistent infection. Proc. Natl. Acad. Sci. U. S. A. 90:11733-\11737.
20. Hofmann, M. A., P. B. Sethna, and D. A. Brian. 1990. Bovine coronavirus mRNA replication continues throughout persistent infection in cell culture. J. Virol. 64:4108-4114.
21. Hsue, B., T. Hartshorne, and P. S. Masters. 2000. Characterization of an essential RNA secondary structure in the 3′ untranslated region of the murine coronavirus genome. J. Virol. 74:6911-6921.
22. Hsue, B., and P. S. Masters. 1997. A bulged stem-loop structure in the 3′ untranslated region of the genome of the coronavirus mouse hepatitis virus is essential for replication. J. Virol. 71:7567-7578.
23. Johnson, R. F., et al. 2005. Effect of mutations in the mouse hepatitis virus 3′(+)42 protein binding element on RNA replication. J. Virol. 79:14570-14585.
24. Kang, H., M. Feng, M. E. Schroeder, D. P. Giedroc, and J. L. Leibowitz. 2006. Putative cis-acting stem-loops in the 5′ untranslated region of the severe acute respiratory syndrome coronavirus can substitute for their mouse hepatitis virus counterparts. J. Virol. 80:10600-10614.
25. Li, L., et al. 2008. Structural lability in stem-loop 1 drives a 5′ UTR-3′ UTR interaction in coronavirus replication. J. Mol. Biol. 377:790-803.
26. Lin, Y. J., C. L. Liao, and M. M. Lai. 1994. Identification of the cis-acting signal for minus-strand RNA synthesis of a murine coronavirus: implications for the role of minus-strand RNA in RNA replication and transcription. J. Virol. 68:8131-8140.
27. Liu, P., et al. 2009. Mouse hepatitis virus stem-loop 2 adopts a uYNMG(U)a-like tetraloop structure that is highly functionally tolerant of base substitutions. J. Virol. 83:12084-12093.
28. Liu, P., et al. 2007. A U-turn motif-containing stem-loop in the coronavirus 5′ untranslated region plays a functional role in replication. RNA 13:763-780.
29. Makino, S., and M. M. Lai. 1989. High-frequency leader sequence switching during coronavirus defective interfering RNA replication. J. Virol. 63:5285-5292.
30. Masters, P. S. 2006. The molecular biology of coronaviruses. Adv. Virus Res. 66:193-292.
31. 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.
32. 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.
33. Raman, S., and D. A. Brian. 2005. Stem-loop IV in the 5′ untranslated region is a cis-acting element in bovine coronavirus defective interfering RNA replication. J. Virol. 79:12434-12446.
34. 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.
35. Tinoco, I., Jr., et al. 1973. Improved estimation of secondary structure in ribonucleic acids. Nat. New Biol. 246:40-41.
36. Williams, G. D., R. Y. Chang, and D. A. Brian. 1999. A phylogenetically conserved hairpin-type 3′ untranslated region pseudoknot functions in coronavirus RNA replication. J. Virol. 73:8349-8355.
37. Wu, H. Y., and D. A. Brian. 2007. 5′-proximal hot spot for an inducible positive-to-negative-strand template switch by coronavirus RNA-dependent RNA polymerase. J. Virol. 81:3206-3215.
38. Wu, H. Y., et al. 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.
39. Wu, H. Y., A. Ozdarendeli, and D. A. Brian. 2006. Bovine coronavirus 5′-proximal genomic acceptor hotspot for discontinuous transcription is 65 nucleotides wide. J. Virol. 80:2183-2193.
40. Yount, B., M. R. Denison, S. R. Weiss, and R. S. Baric. 2002. Systematic assembly of a full-length infectious cDNA of mouse hepatitis virus strain A59. J. Virol. 76:11065-11078.
41. Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31:3406-3415.
42. Zust, R., T. B. Miller, S. J. Goebel, V. Thiel, and P. S. Masters. 2008. Genetic interactions between an essential 3′ cis-acting RNA pseudoknot, replicase gene products, and the extreme 3′ end of the mouse coronavirus genome. J. Virol. 82:1214-1228.