Leader switching occurs during the rescue of defective RNAs by heterologous strains of the coronavirus infectious bronchitis virus

Journal of General Virology

Volumn 81, Issue 3, 2000, Pages 791-801

  Stirrups, Kathleen ^a,b   Shaw, Kathleen ^a   Evans, Sharon ^a   Dalton, Kevin ^a,c   Cavanagh, David ^a   Britton, Paul ^a  

^a INSTITUTE FOR ANIMAL HEALTH   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; RNA; SIGNAL PEPTIDE;

5' UNTRANSLATED REGION; ARTICLE; AVIAN INFECTIOUS BRONCHITIS VIRUS; CORONAVIRUS; COW; HELPER VIRUS; MURINE HEPATITIS CORONAVIRUS; PRIORITY JOURNAL; RNA REPLICATION; RNA STRUCTURE; SEQUENCE ANALYSIS;

AVES; AVIAN INFECTIOUS BRONCHITIS VIRUS; BOVINAE; BOVINE CORONAVIRUS; CORONAVIRUS; MURINAE; MURINE HEPATITIS VIRUS; RNA VIRUSES;

EID: 0033956460     PISSN: 00221317     EISSN: None     Source Type: Journal    
DOI: 10.1099/0022-1317-81-3-791     Document Type: Article

References (43)

1. Ausubel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A. & Struhl, K. (1987). Current Protocols In Molecular Biology. New York: John Wiley and Sons.
2. Binns, M. M., Boursnell, M. E. G., Cavanagh, D., Pappain, D. J. C. & Brown, T. D. K. (1985). Cloning and sequencing of the gene encoding the spike protein of the coronavirus IBV. Journal of General Virology 66, 719-726.
3. Binns, M. M., Boursnell, M. E. G., Tomley, F. M. & Brown, T. D. K. (1986). Comparison of the spike precursor sequences of coronavirus IBV strains M41 and 6/82 with that of IBV Beaudette. Journal of General Virology 67, 2825-2831.
4. Bonfield, J. K., Smith, K. F. & Staden, R. (1995). A new DNA sequence assembly program. Nucleic Acids Research 24, 4992-4999.
5. Boursnell, M. E. G., Brown, T. D. K., Foulds, I. J., Green, P. F., Tomley, F. M. & Binns, M. M. (1987). Completion of the sequence of the genome of the coronavirus avian infectious bronchitis virus. Journal of General Virology 68, 57-77.
6. Brian, D. A. & Spaan, W. J. M. (1997). Recombination and coronavirus defective interfering RNAs. Seminars in Virology 8, 101-111.
7. Chang, R. Y., Hofmann, M. A., Sethna, P. B. & Brian, D. A. (1994). A cis-acting function for the coronavirus leader in defective interfering RNA replication. Journal of Virology 68, 8223-8231.
8. Chang, R. Y., Krishnan, R. & Brian, D. A. (1996). The UCUAAAC promoter motif is not required for high-frequency leader recombination in bovine coronavirus defective interfering RNA. Journal of Virology 70, 2720-2729.
9. Darbyshire, J. H., Rowell, J. G., Cook, J. K. A. & Peters, R. W. (1979). Taxonomic studies on strains of avian infectious bronchitis virus using neutralisation tests in tracheal organ cultures. Archives of Virology 61, 227-238.
10. Davelaar, F. G., Kouwenhoven, B. & Burger, A. G. (1984). Occurrence and significance of infectious bronchitis virus variant strains in egg and broiler production in the Netherlands. Veterinary Quarterly 6, 114-120.
11. Devereux, J., Haeberli, P. & Smithies, O. (1984). A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Research 12, 387-395.
12. de Vries, A. A. F., Horzinek, M. C., Rottier, P. J. M. & de Groot, R. J. (1997). The genome organisation of the Nidovirales: similarities and differences between arteri-, toro- and coronaviruses. Seminars in Virology 8, 33-47.
13. Feinberg, A. P. & Vogelstein, B. (1983). A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Analytical Biochemistry 132, 6-13.
14. Hiscox, J. A., Mawditt, K. L., Cavanagh, D. & Britton, P. (1995). Investigation of the control of coronavirus subgenomic mRNA transcription by using T7-generated negative-sense RNA transcripts. Journal of Virology 69, 6219-6227.
15. Hofmann, M. A., Sethna, P. B. & Brian, D. A. (1990). Bovine coronavirus mRNA replication continues throughout persistent infection in cell culture. Journal of Virology 64, 4108-4114.
16. Jaeger, J. A., Turner, D. H. & Zuker, M. (1989). Improved predictions of secondary structures for RNA. Proceedings of the National Academy of Sciences, USA 86, 7706-7710.
17. Jaeger, J. A., Turner, D. H. & Zuker, M. (1990). Predicting optimal and suboptimal secondary structure for RNA. Methods in Enzymology 183, 281-306.
18. Kottier, S. A., Cavanagh, D. & Britton, P. (1995). Experimental evidence of recombination in coronavirus infectious bronchitis virus. Virology 213, 569-580.
19. Kusters, J. G., Niesters, H. G. M., Lenstra, J. A., Horzinek, M. C. & Van Der Zeijst, B. A. M. (1989). Phylogeny of antigenic variants of avian coronavirus IBV. Virology 169, 217-221.
20. Lai, M. M. & Cavanagh, D. (1997). The molecular biology of coronaviruses. Advances in Virus Research 48, 1-100.
21. Makino, S. & Lai, M. M. C. (1989). High-frequency leader sequence switching during coronavirus defective interfering RNA replication. Journal of Virology 63, 5285-5292.
22. Makino, S., Stohlman, S. A. & Lai, M. M. C. (1986). Leader sequences of murine coronavirus mRNAs can be freely reassorted: evidence for the role of free leader RNA in transcription. Proceedings of the National Academy of Sciences, USA 83, 4204-4208.
23. Makino, S., Shieh, C., Keck, J. G. & Lai, M. M. C. (1988a). Defective-interfering particles of murine coronavirus: mechanism of synthesis of defective viral RNAs. Virology 163, 104-111.
24. Makino, S., Shieh, C.-K., Soe, L. H., Baker, S. C. & Lai, M. M. C. (1988b). Primary structure and translation of a defective interfering RNA of murine coronavirus. Virology 166, 550-560.
25. Makino, S., Yokomori, K. & Lai, M. M. C. (1990). Analysis of efficiently packaged defective Interfering RNAs of murine coronavirus: localization of a possible RNA-packaging signal. Journal of Virology 64, 6045-6053.
26. Maruyama, I. N., Rakow, T. L. & Maruyama, H. I. (1995). cRACE: a simple method for identification of the 5′ end of mRNAs. Nucleic Acids Research 23, 3796-3797.
27. Matzura, O. & Wennborg, A. (1996). RNAdraw: an integrated program for RNA secondary structure calculation and analysis under 32-bit Microsoft Windows. Computer Applications in the Biosciences 12, 247-249.
28. Mendez, A., Smerdou, C., Izeta, A., Gebauer, F. & Enjuanes, L. (1996). Molecular characterization of transmissible gastroenteritis coronavirus defective interfering genomes: packaging and heterogeneity. Virology 217, 495-507.
29. Nicholas, K. B. & Nicholas, H. B., Jr (1997). GeneDoc: a tool for editing and annotating multiple sequence alignments, 2.4.002 edn: Distributed by author (http://www.cris.com/∼ketchup/genedoc. html).
30. Niesters, H. G. M., Lenstra, J. A., Spaan, W. J. M., Zijderveld, A. J., Bleumink-Pluym, N. M. C., Hong, F., Van Scharrenburg, G. J. M., Horzinek, M. C. & Van Der Zeijst, B. A. M. (1986). The peplomer protein sequence of the M41 strain of coronavirus IBV and its comparison with Beaudette strains. Virus Research 5, 253-263.
31. Pénzes, Z. (1995). Defective replicating RNAs of coronavirus infectious bronchitis virus: investigation of replication and genome packaging signals. PhD thesis, University of Hertfordshire, UK.
32. Pénzes, Z., Tibbles, K., Shaw, K., Britton, P., Brown, T. D. K. & Cavanagh, D. (1994). Characterization of a replicating and packaged defective RNA of avian coronavirus infectious bronchitis virus. Virology 203, 286-293.
33. Pénzes, Z., Wroe, C., Brown, T. D., Britton, P. & Cavanagh, D. (1996). Replication and packaging of coronavirus infectious bronchitis virus defective RNAs lacking a long open reading frame. Journal of Virology 70, 8660-8668.
34. Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989). Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
35. Sawicki, S. G. & Sawicki, D. L. (1990). Coronavirus transcription: subgenomic mouse hepatitis virus replicative intermediates function in RNA synthesis. Journal of Virology 64, 1050-1056.
36. Siddell, S. G. (1995). The Coronaviridae. In The Coronaviridae, pp. 1-10. Edited by S. G. Siddell. New York: Plenum.
37. Stern, D. F. & Kennedy, S. I. T. (1980). Coronavirus multiplication strategy. I. Identification and characterization of virus-specific RNA. Journal of Virology 34, 665-674.
38. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. (1997). The Clustal X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25, 4876-4882.
39. van der Most, R. G. & Spaan, W. J. M. (1995). Coronavirus replication, transcription, and RNA recombination. In The Coronaviridae, pp. 11-31. Edited by S. G. Siddell. New York: Plenum.
40. van der Most, R. G., Bredenbeek, P. J. & Spaan, W. J. M. (1991). A domain at the 3′ end of the polymerase gene is essential for encapsidation of coronavirus defective interfering RNAs. Journal of Virology 65, 3219-3226.
41. Zuker, M. (1989a). Computer prediction of RNA structure. Methods in Enzymology 180, 262-288.
42. Zuker, M. (1989b). On finding all suboptimal foldings of an RNA molecule. Science 244, 48-52.
43. Zuker, M. & Stiegler, P. (1981). Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Research 9, 133-148.