Sequencing of coronavirus IBV genomic RNA: a 195-base open reading frame encoded by mRNA B (original) (raw)

Abstract

DNA sequencing of genomic cDNA clones of avian infectious bronchitis virus (IBV) has been carried out. 770 bases have been determined which include genomic sequences spanning the 5' termini of the two smallest mRNAs of the 3'-coterminal “nested” set: mRNA A and mRNA B. This region contains the complete coding sequences for mRNA B which are additional to those present in mRNA A. Two open reading frames are present, predicting proteins of _M_rs 7500 and 9500.

Keywords: Avian infectious bronchitis virus, cDNA clones, recombinant DNA

Abbreviations: bp, base pairs; IBV, infectious bronchitis virus; kb, kilobases or kilobase pairs; MHV, murine hepatitis virus; mRNA, messenger RNA; ORF, open reading frame

Communicated by K. Chater

References

  1. Armstrong J., Smeekens S., Rottier P. Sequence of the nucleocapsid gene from murine coronavirus MHV-A59. Nucl. Acids Res. 1983;11:883–891. doi: 10.1093/nar/11.3.883. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Baric S., Stohlman S., Lai M.M.C. Characterization of replicative intermediate RNA of mouse hepatitis virus: presence of leader sequences on nascent chains. J. Virol. 1983;48:633–640. doi: 10.1128/jvi.48.3.633-640.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Brown T.D.K., Boursnell M.E.G. Avian infectious bronchitis virus genomic RNA contains sequence homologies at the intergenic boundaries. Virus Res. 1984;1:15–24. [Google Scholar]
  4. Cavanagh D. Structural polypeptides of coronavirus IBV. J. Gen. Virol. 1981;53:93–103. doi: 10.1099/0022-1317-53-1-93. [DOI] [PubMed] [Google Scholar]
  5. Holmes D.S., Quigley M. A rapid boiling method for the preparation of bacterial plasmids. Anal. Biochem. 1981;114:193–197. doi: 10.1016/0003-2697(81)90473-5. [DOI] [PubMed] [Google Scholar]
  6. Kozak M. Comparison of initiation of protein synthesis in prokaryotes, eukaryotes and organelles. Microbiol. Revs. 1983;47:1–45. doi: 10.1128/mr.47.1.1-45.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Lai M.M.C., Brayton P.R., Armen R.C., Patton C.D., Pugh C., Stohlman S.A. Mouse hepatitis virus A59: mRNA structure and genetic localization of the sequence divergence from hepatotropic strain MHV-3. J. Virol. 1981;39:823–834. doi: 10.1128/jvi.39.3.823-834.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Lai M.M.C., Patton C.D., Stohlman S. Further characterisation of mRNAs of mouse hepatitis virus: presence of common 5'-end nucleotides. J. Virol. 1982;41:557–565. doi: 10.1128/jvi.41.2.557-565.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Lai M.M.C., Patton C.D., Baric R.S., Stohlman S. Presence of leader sequences in the mRNA of mouse hepatitis virus. J. Virol. 1983;46:1027–1033. doi: 10.1128/jvi.46.3.1027-1033.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Larson R., Messing J. Apple II computer software for DNA and protein sequence data. DNA. 1983;2:31–35. doi: 10.1089/dna.1.1983.2.31. [DOI] [PubMed] [Google Scholar]
  11. Leibowitz J.L., Wilhelmsen K.C., Bond C.W. The virus-specific intracellular RNA species of two murine coronaviruses: MHV-A59 and MHV-JHM. Virology. 1981;114:39–51. doi: 10.1016/0042-6822(81)90250-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Maniatis T., Fritsch E.F., Sambrook J. Cold Spring Harbor Laboratory; Cold Spring Harbor, NY: 1982. (Molecular Cloning— A Laboratory Manual). [Google Scholar]
  13. Maxam A.M., Gilbert W. Sequencing end-labelled DNA with base-specific chemical cleavages. In: Grossman L., Moldave K., editors. Vol. 65. Academic Press; New York: 1980. pp. 499–560. (Methods in Enzymology). Part 1. [DOI] [PubMed] [Google Scholar]
  14. Messing J., Vieira J. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene. 1982;19:259–268. doi: 10.1016/0378-1119(82)90015-4. [DOI] [PubMed] [Google Scholar]
  15. Rottier P., Spaan W.J.M., Horzinek M.C, Van der Zeijst B.A.M. Translation of three mouse hepatitis virus strain A59 subgenomic RNAs in Xenopus laevis oocytes. J. Virol. 1981;38:20–26. doi: 10.1128/jvi.38.1.20-26.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Siddell S. Coronavirus JHM: coding assignments of subgenomic mRNAs. J. Gen. Virol. 1983;64:113–125. doi: 10.1099/0022-1317-64-1-113. [DOI] [PubMed] [Google Scholar]
  17. Siddell S., Wege H., Barthel A., Ter Meulen V. Coronavirus JHM: cell-free synthesis of structural protein p60. J. Virol. 1980;33:10–17. doi: 10.1128/jvi.33.1.10-17.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Siddell S., Wege H., Ter Meulen V. The biology of coronaviruses. J. Gen. Virol. 1983;64:761–776. doi: 10.1099/0022-1317-64-4-761. [DOI] [PubMed] [Google Scholar]
  19. Skinner M., Siddell S. Coronavirus JHM: nucleotide sequence of the mRNA that encodes nucleocapsid protein. Nucl. Acids Res. 1983;11:5045–5054. doi: 10.1093/nar/11.15.5045. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Spaan W., Delius H., Skinner M., Armstrong J., Rottier P., Smeekens S., Van der Zeijst A.M., Siddell S.G. Coronavirus mRNA synthesis involves fusion of non-contiguous sequences. EMBO J. 1983;2:1839–1844. doi: 10.1002/j.1460-2075.1983.tb01667.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Staden R. Graphic methods to determine the function of nucleic acid sequences. Nucl. Acids Res. 1984;12:521–538. doi: 10.1093/nar/12.1part2.521. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Stern D.F., Kennedy S.I.T. Coronavirus multiplication strategy I. Identification and characterisation of virus-specified RNA. J. Virol. 1980;34:665–674. doi: 10.1128/jvi.34.3.665-674.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Stern D.F., Kennedy S.I.T. Coronavirus multiplication strategy, II. Mapping the avian infectious bronchitis virus intracellular RNA species to the genome. J. Virol. 1980;36:440–449. doi: 10.1128/jvi.36.2.440-449.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Stern D.F., Burgess L., Sefton B.M. Structural analysis of virion proteins of the avian coronavirus infectious bronchitis virus. J. Virol. 1982;42:208–219. doi: 10.1128/jvi.42.1.208-219.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Stern D.F., Sefton B.M. Coronavirus multiplication: locations of virion proteins on the avian infectious bronchitis virus genome. J. Virol. 1984 doi: 10.1128/jvi.50.1.22-29.1984. in press. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Swank R.T., Munkres K.D. Molecular weight analysis of oligopeptides by electrophoresis in polyacrylamide gel with sodium dodecyl sulfate. Anal. Biochem. 1971;39:462–477. doi: 10.1016/0003-2697(71)90436-2. [DOI] [PubMed] [Google Scholar]
  27. Twigg A.J., Sherratt D. Trans-complementable copy-number mutants of plasmid ColEl. Nature. 1980;283:216–218. doi: 10.1038/283216a0. [DOI] [PubMed] [Google Scholar]