Advertisement

The Complete Nucleotide Sequence of Avian Infectious Bronchitis Virus: Analysis of the Polymerase-Coding Region

  • M. E. G. Boursnell
  • T. D. K. Brown
  • I. J. Foulds
  • P. F. Green
  • F. M. Tomley
  • M. M. Binns
Chapter
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 218)

Abstract

Avian infectious bronchitis virus (IBV) is the type species of the family Coronaviridae (Siddell et al., 1983). It has a large positive-stranded RNA genome which has been estimated at 20–24 kilobases (Lomniczi & Kennedy, 1977). As with other coronaviruses, a number of subgenomic messenger RNA species are produced in infected cells which form a 3′-coterminal nested set (Stern & Kennedy, 1980a; 1980b). In the case of IBV there are six mRNA species in total, which are designated mRNAs A-F, mRNA A being the smallest, and mRNA F being of genome size. mRNAs A, C and E encode the three main structural components of the virion, the nucleocapsid polypeptide, the membrane polypeptide and the precursor polypeptide to the spike (Stern & Sefton, 1984). mRNA D encodes at least one product, a 12.4 kilodalton polypeptide of unknown function (Smith et al., this volume), but no product has yet been detected for mRNA B. The coding regions of mRNAs A-E are situated in the 3′-most 7.3 kilobases of the IBV genome, the nucleotide sequence of which has been determined previously from cDNA clones (Boursnell et al., 1984, 1985a, 1985b; Boursnell & Brown, 1984; Binns et al., 1985b).

Keywords

Codon Usage Homology Region Vesicular Stomatitis Virus Infectious Bronchitis Virus Mouse Hepatitis Virus 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. Ambartsumyan, N. S. and Mazo, A. M., 1980, Elimination of the secondary structure effect in gel sequencing of nucleic acids. FEBS Letters, 114: 265–268.PubMedCrossRefGoogle Scholar
  2. Atkins, J. F., Elseviers, D. and Gorini, L., 1972, Low activity of beta-galactosidase in frameshift mutants of Escherichia coli. Proc. Natl. Acad. Sci. USA, 69: 1192–1195.PubMedCrossRefGoogle Scholar
  3. Bankier, A. and Barrell, B. G. Shotgun DNA sequencing, in: “Techniques in the Life Sciences (Biochemistry)” vol. B5, “Techniques in Nucleic Acid Biochemistry”, pp. B508, 1-34 ed. R. A. Flavell, Elsevier Science Publishers, Ireland (1983).Google Scholar
  4. Biggin, M., Farrell, P. J. and Barrell, B. G., 1984, Transcription and DNA sequence of the BamHl L fragment of B95-8 Epstein-Barr virus. EMBO J., 3: 1083–1090.PubMedGoogle Scholar
  5. Binns, M. M., Boursnell, M. E. G., Foulds, I. J. and Brown, T. D. K., 1985a, The use of a random priming procedure to generate cDNA libraries of infectious bronchitis virus, a large RNA virus, J.Virol., Meths 11: 265–269.CrossRefGoogle Scholar
  6. Binns, M. M., Boursnell, M. E. G., Cavanagh, D., Pappin, D. J. C. and Brown, T. D. K., 1985b, Cloning and sequencing of the gene encoding the spike protein of the coronavirus IBV, J.Gen.Virol., 66: 719–726.PubMedCrossRefGoogle Scholar
  7. Boursnell, M. E. G. and Brown, T. D. K., 1984, Sequencing of coronavirus IBV genomic RNA: a 195-base open reading frame encoded by mRNA B. Gene, 29: 87–92.PubMedCrossRefGoogle Scholar
  8. Boursnell, M. E. G., Brown, T. D. K. and Binns, M. M., 1984, Sequence of the membrane protein gene from avian coronavirus IBV, Virus Research, 1: 303–313.PubMedCrossRefGoogle Scholar
  9. Boursnell, M. E. G., Binns, M. M., Foulds, I. J. and Brown, T. D. K., 1985a, Sequences of the nucleocapsid genes from two strains of avian infectious bornchitis virus, J.Gen.Virol., 66: 573–580.PubMedCrossRefGoogle Scholar
  10. Boursnell, M. E. G., Binns, M. M. and Brown, T. D. K., 1985b, Sequencing of coronavirus IBV genomic RNA: three open reading frames in the 5′ ‘unique’ region of mRNA D, J. Gen.Virol., 66: 2253–2258.PubMedCrossRefGoogle Scholar
  11. Boursnell, M. E. G., Brown, T. D. K., Foulds, I. J., Green, P. F., Tomley, F. M. and Binns, M. M., 1986, The complete sequence of the genome of infectious bronchitis virus (IBV). J.Gen.Virol., (in press).Google Scholar
  12. Brayton, P. R., Lai, M. M. C., Patton, C. D. and Stohlman, S. A., 1982, Characterisation of two polymerase activities induced by mouse hepatitis virus, J.Virol., 42: 847–853.PubMedGoogle Scholar
  13. Brayton, P. R., Stohlman, S. A. and Lai, M. M. C., 1984, Further characterisation of mouse hepatitis virus RNA-dependent RNA polymerases, Virology, 133: 197–201.PubMedCrossRefGoogle Scholar
  14. Brown, T. D. K. and Boursnell, M. E. G., 1984, Avian infectious bronchitis virus genomic RNA contains sequence homologies at the intergenic boundaries, Virus Research, 1: 15–24.CrossRefGoogle Scholar
  15. Brown, T. D. K., Boursnell, M. E. G., Binns, M. M. and Tomley, F. M., 1986, Cloning and sequencing of 5′ terminal sequences from avian infectious bronchitis virus genomic RNA, J. Gen. Virol., 67: 221–228.PubMedCrossRefGoogle Scholar
  16. Caton, A. J., Brownlee, G. G., Yewdell, J. W. and Gerhard, W., 1982, The antigenic structure of the influenza virus A/PR/8/34 hemagglutinin (Hl subtype), Cell, 31: 417–427.PubMedCrossRefGoogle Scholar
  17. Devereux, J., Haeberli, P. and Smithies, O., 1984, A comprehensive set of sequence analysis programs for the VAX, Nucl. Acids Res., 12: 387–395.PubMedCrossRefGoogle Scholar
  18. Fox, T. D. and Weiss-Brummer, B., 1980, Leaky +1 and −1 frameshift mutations at the same site in a yeast mitochondrial gene, Nature, 288: 60–63.PubMedCrossRefGoogle Scholar
  19. George, D. G., Barker, W. C. and Hunt, L. T., 1986, The protein identification resource (PIR), Nucl. Acids Res., 14: 11–15.PubMedCrossRefGoogle Scholar
  20. Germino, J. and Bastia, D., 1982, Primary structure of the replication initiation protein of plasmid R6K, Proc. Natl. Acad. Sci. USA, 79: 5475–5479.PubMedCrossRefGoogle Scholar
  21. Herman, R. C., 1986, Internal initiation of translation on the vesicular stomatitis virus phosphoprotein mRNA yields a second protein, J.Virol., 58: 797–804.PubMedGoogle Scholar
  22. Jacks, J. and Varmus, H. E., 1985, Expression of the rous sarcoma virus pol gene by ribosomal frameshifting, Science, 230: 1237–1242.PubMedCrossRefGoogle Scholar
  23. Kamer, G. and Argos, P., 1984, Primary structure comparison of RNA-dependent polymerases from plant, animal and bacterial viruses, Nucl. Acids Res., 12: 7269–7282.PubMedCrossRefGoogle Scholar
  24. Kanehisa, M. I., 1982, Los Alamos sequence analysis package for nucleic acids and proteins, Nucl. Acids Res., 10: 183–196.PubMedCrossRefGoogle Scholar
  25. Kastelein, R. A., Remaut, E., Fiers, W. and van Duin, J., 1982, Lysis gene expression of RNA phage MS2 depends on a frameshift during translation of the overlapping coat protein gene, Nature, 295: 35–41.PubMedCrossRefGoogle Scholar
  26. Korneluk, R. G., Quan, F. and Gravel, R. A., 1985, Rapid and reliable dideoxy sequencing of double-stranded DNA, Gene, 40: 317–323.PubMedCrossRefGoogle Scholar
  27. Kozak, M., 1983, Comparison of initiation of protein synthesis in procaryotes, eucaryotes and organelles, Microbiol.Revs., 47: 1–45.Google Scholar
  28. Kyte, J. and Doolittle, R. F., 1982, A simple method for displaying the hydropathic character of a protein, J.Mol.Biol., 157: 105–132.PubMedCrossRefGoogle Scholar
  29. Lipman, D. J. and Pearson, W. R., 1985, Rapid and sensitive protein similarity searches, Science, 227: 1141–1435.CrossRefGoogle Scholar
  30. Lomniczi, B., 1977, Biological properties of avian coronavirus RNA, J.Gen.Virol., 36: 531–533.PubMedCrossRefGoogle Scholar
  31. Lomniczi, B. and Kennedy, I., 1977, Genome of infectious bronchitis virus, J.Virol., 24: 99–107.PubMedGoogle Scholar
  32. Maxam, A. M. and Gilbert, W., 1980, Sequencing end-labelled DNA with base-specific chemical cleavages, ln “Methods in Enzymology”, L. Grossman and K. Moldave, Eds., Vol. 65, Part 1, Academic Press, New York, pp. 499–560.Google Scholar
  33. Mizusawa, S., Nishimura, S. and Seela, F., 1986, Improvement of the dideoxy chain termination method of DNA sequencing by use of deoxy-7-deazaguanosine triphosphate in place of dGTP, Nucl. Acids Res., 14: 1319–1324.PubMedCrossRefGoogle Scholar
  34. Schochetman, G., Stevens, R. H. and Simpson, R. W., 1977, Presence of infectious polyadenylated RNA in the coronavirus avian bronchitis virus, Virol., 77: 772–782.CrossRefGoogle Scholar
  35. Schubert, M., Harmison, G. G. and Meier, E., 1984, Primary structure of the vesicular stomatitis virus polymerase (L) gene: evidence for a high frequency of mutations, J.Virol., 51: 505–514.PubMedGoogle Scholar
  36. Siddell, S. G., Anderson, R., Cavanagh, D., Fujiwara, K., Klenk, H. D., MacNaughton, M. R., Pensaert, M., Stohlman, S. A., Sturman, L. and van der Zeijst, B. A. M., 1983, Coronaviridae, Intervirology, 20: 181–189.PubMedCrossRefGoogle Scholar
  37. Southern, E. M., 1975, Detection of specific sequences among DNA fragments separated by gel electrophoresis, J.Mol.Biol., 98: 503–517.PubMedCrossRefGoogle Scholar
  38. Staden, R., 1982, An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences, Nucl. Acids Res., 10: 2951–2961.PubMedCrossRefGoogle Scholar
  39. Staden, R., 1984, A computer program to enter DNA gel reading data into a computer, Nucl. Acids Res., 12: 499–503.PubMedCrossRefGoogle Scholar
  40. Steinhauer, D. A. and Holland, J. J., 1986, Direct method for quantitation of extreme polymerase error frequencies at selected single base sites in viral RNA, J.Virol. 57: 219–228.PubMedGoogle Scholar
  41. Stern, D. F. and Kennedy, S. I. T., 1980a, Coronavirus multiplication strategy. I. Identification and characterisation of virus-specified RNA, J.Virol., 34: 665–674.PubMedGoogle Scholar
  42. Stern, D. F. and Kennedy, S. I. T., 1980b, Coronavirus multiplication strategy. II. Mapping the avian infectious bronchitis virus intracellular RNA species to the genome, J.Virol., 36: 440–449.PubMedGoogle Scholar
  43. Stern, D. F. and Sefton, B. M., 1984, Coronavirus multiplication: the locations of genes for the virion proteins on the avian infectious bronchitis virus genome, J.Virol., 50: 22–29.PubMedGoogle Scholar
  44. Strauss, E. G. and Strauss, J. H., 1983, Replication strategies of the single stranded RNA viruses of eukaryotes, Curr. Topics in Microbiol. and Immunol., 105: 1–98.CrossRefGoogle Scholar

Copyright information

© Plenum Press, New York 1987

Authors and Affiliations

  • M. E. G. Boursnell
    • 1
  • T. D. K. Brown
    • 1
  • I. J. Foulds
    • 1
  • P. F. Green
    • 1
  • F. M. Tomley
    • 1
  • M. M. Binns
    • 1
  1. 1.Houghton Poultry Research StationHoughton, Huntingdon, CambridgeshireEngland, UK

Personalised recommendations