Skip to main content
PMC home page
Journal of Virology logoLink to Journal of Virology
. 1985 Mar;53(3):834–840. doi: 10.1128/jvi.53.3.834-840.1985

Three intergenic regions of coronavirus mouse hepatitis virus strain A59 genome RNA contain a common nucleotide sequence that is homologous to the 3' end of the viral mRNA leader sequence.

C J Budzilowicz, S P Wilczynski, S R Weiss
PMCID: PMC254715  PMID: 2983094

Abstract

cDNA clones that represent various portions of the coronavirus mouse hepatitis virus strain A59 genome RNA have been constructed. cDNAs were synthesized by transcription of genome RNA by using either oligo(dT) or random oligomers of calf thymus DNA as primers. These cDNAs were converted into double-stranded DNA and cloned into pBR322 by standard techniques. The resulting cloned viral DNA fragments were mapped to viral genes by hybridization with Northern blots of intracellular RNA from mouse hepatitis virus strain A59-infected cells. These cDNA clones map in six of the seven viral genes. Clone g344, 1.8 kilobases, is the largest and encompasses gene 5 (which encodes a nonstructural protein) and gene 6 (which encodes the E1 viral glycoprotein) as well as the intergenic regions preceding genes 5, 6, and 7. Sequencing of parts of this cloned DNA show that these three intergenic regions contain a common 11-nucleotide sequence. This sequence shares homology with the 3' end of the viral mRNA leader sequence. Thus, this common intergenic sequence may contain a binding site for a leader RNA that hybridizes to negative-strand viral RNA at the beginning of each gene to prime mRNA synthesis. The different degrees of homology between the leader and its putative binding site may influence the differential rates of transcription of the various viral mRNAs.

Full text

PDF
834

Images in this article

836Image
on p.836
836Image
on p.836

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Armstrong J., Niemann H., Smeekens S., Rottier P., Warren G. Sequence and topology of a model intracellular membrane protein, E1 glycoprotein, from a coronavirus. Nature. 1984 Apr 19;308(5961):751–752. doi: 10.1038/308751a0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Armstrong J., Smeekens S., Rottier P. Sequence of the nucleocapsid gene from murine coronavirus MHV-A59. Nucleic Acids Res. 1983 Feb 11;11(3):883–891. doi: 10.1093/nar/11.3.883. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Armstrong J., Smeekens S., Spaan W., Rottier P., van der Zeijst B. Cloning and sequencing the nucleocapsid and E1 genes of coronavirus. Adv Exp Med Biol. 1984;173:155–162. doi: 10.1007/978-1-4615-9373-7_16. [DOI] [PubMed] [Google Scholar]
  4. Baric R. S., Stohlman S. A., Lai M. M. Characterization of replicative intermediate RNA of mouse hepatitis virus: presence of leader RNA sequences on nascent chains. J Virol. 1983 Dec;48(3):633–640. doi: 10.1128/jvi.48.3.633-640.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Biggin M. D., Gibson T. J., Hong G. F. Buffer gradient gels and 35S label as an aid to rapid DNA sequence determination. Proc Natl Acad Sci U S A. 1983 Jul;80(13):3963–3965. doi: 10.1073/pnas.80.13.3963. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Brayton P. R., Lai M. M., Patton C. D., Stohlman S. A. Characterization of two RNA polymerase activities induced by mouse hepatitis virus. J Virol. 1982 Jun;42(3):847–853. doi: 10.1128/jvi.42.3.847-853.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Cheley S., Anderson R., Cupples M. J., Chan E. C., Morris V. L. Intracellular murine hepatitis virus-specific RNAs contain common sequences. Virology. 1981 Jul 30;112(2):596–604. doi: 10.1016/0042-6822(81)90305-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Gough N. M., Webb E. A., Cory S., Adams J. M. Molecular cloning of seven mouse immunoglobulin kappa chain messenger ribonucleic acids. Biochemistry. 1980 Jun 10;19(12):2702–2710. doi: 10.1021/bi00553a026. [DOI] [PubMed] [Google Scholar]
  9. Jacobs L., Spaan W. J., Horzinek M. C., van der Zeijst B. A. Synthesis of subgenomic mRNA's of mouse hepatitis virus is initiated independently: evidence from UV transcription mapping. J Virol. 1981 Aug;39(2):401–406. doi: 10.1128/jvi.39.2.401-406.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Lai M. M., Baric R. S., Brayton P. R., Stohlman S. A. Characterization of leader RNA sequences on the virion and mRNAs of mouse hepatitis virus, a cytoplasmic RNA virus. Proc Natl Acad Sci U S A. 1984 Jun;81(12):3626–3630. doi: 10.1073/pnas.81.12.3626. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Lai M. M., 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 Sep;39(3):823–834. doi: 10.1128/jvi.39.3.823-834.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Lai M. M., Patton C. D., Baric R. S., Stohlman S. A. Presence of leader sequences in the mRNA of mouse hepatitis virus. J Virol. 1983 Jun;46(3):1027–1033. doi: 10.1128/jvi.46.3.1027-1033.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Lai M. M., Patton C. D., Stohlman S. A. Further characterization of mRNA's of mouse hepatitis virus: presence of common 5'-end nucleotides. J Virol. 1982 Feb;41(2):557–565. doi: 10.1128/jvi.41.2.557-565.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Lai M. M., Stohlman S. A. RNA of mouse hepatitis virus. J Virol. 1978 May;26(2):236–242. doi: 10.1128/jvi.26.2.236-242.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Lehrach H., Diamond D., Wozney J. M., Boedtker H. RNA molecular weight determinations by gel electrophoresis under denaturing conditions, a critical reexamination. Biochemistry. 1977 Oct 18;16(21):4743–4751. doi: 10.1021/bi00640a033. [DOI] [PubMed] [Google Scholar]
  16. Leibowitz J. L., Weiss S. R., Paavola E., Bond C. W. Cell-free translation of murine coronavirus RNA. J Virol. 1982 Sep;43(3):905–913. doi: 10.1128/jvi.43.3.905-913.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. 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 Oct 15;114(1):39–51. doi: 10.1016/0042-6822(81)90250-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. MANAKER R. A., PICZAK C. V., MILLER A. A., STANTON M. F. A hepatitis virus complicating studies with mouse leukemia. J Natl Cancer Inst. 1961 Jul;27:29–51. [PubMed] [Google Scholar]
  19. Messing J., Crea R., Seeburg P. H. A system for shotgun DNA sequencing. Nucleic Acids Res. 1981 Jan 24;9(2):309–321. doi: 10.1093/nar/9.2.309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Niemann H., Heisterberg-Moutsis G., Geyer R., Klenk H. D., Wirth M. Glycoprotein E1 of MHV-A59: structure of the O-linked carbohydrates and construction of full length recombinant cDNA clones. Adv Exp Med Biol. 1984;173:201–213. doi: 10.1007/978-1-4615-9373-7_20. [DOI] [PubMed] [Google Scholar]
  21. Ou J. H., Rice C. M., Dalgarno L., Strauss E. G., Strauss J. H. Sequence studies of several alphavirus genomic RNAs in the region containing the start of the subgenomic RNA. Proc Natl Acad Sci U S A. 1982 Sep;79(17):5235–5239. doi: 10.1073/pnas.79.17.5235. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Rigby P. W., Dieckmann M., Rhodes C., Berg P. Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I. J Mol Biol. 1977 Jun 15;113(1):237–251. doi: 10.1016/0022-2836(77)90052-3. [DOI] [PubMed] [Google Scholar]
  23. Rottier P. J., Spaan W. J., Horzinek M. C., van der Zeijst B. A. Translation of three mouse hepatitis virus strain A59 subgenomic RNAs in Xenopus laevis oocytes. J Virol. 1981 Apr;38(1):20–26. doi: 10.1128/jvi.38.1.20-26.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Siddell S., Wege H., ter Meulen V. The structure and replication of coronaviruses. Curr Top Microbiol Immunol. 1982;99:131–163. doi: 10.1007/978-3-642-68528-6_4. [DOI] [PubMed] [Google Scholar]
  25. Skinner M., Siddell S. Nucleotide sequencing of mouse hepatitis virus strain JHM messenger RNA 7. Adv Exp Med Biol. 1984;173:163–171. doi: 10.1007/978-1-4615-9373-7_17. [DOI] [PubMed] [Google Scholar]
  26. Spaan W. J., Rottier P. J., Horzinek M. C., van der Zeijst B. A. Sequence relationships between the genome and the intracellular RNA species 1, 3, 6, and 7 of mouse hepatitis virus strain A59. J Virol. 1982 May;42(2):432–439. doi: 10.1128/jvi.42.2.432-439.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Spaan W., Delius H., Skinner M. A., Armstrong J., Rottier P., Smeekens S., Siddell S. G., van der Zeijst B. Transcription strategy of coronaviruses: fusion of non-contiguous sequences during mRNA synthesis. Adv Exp Med Biol. 1984;173:173–186. doi: 10.1007/978-1-4615-9373-7_18. [DOI] [PubMed] [Google Scholar]
  28. Strauss E. G., Strauss J. H. Replication strategies of the single stranded RNA viruses of eukaryotes. Curr Top Microbiol Immunol. 1983;105:1–98. doi: 10.1007/978-3-642-69159-1_1. [DOI] [PubMed] [Google Scholar]
  29. Taylor J. M., Illmensee R., Summers J. Efficeint transcription of RNA into DNA by avian sarcoma virus polymerase. Biochim Biophys Acta. 1976 Sep 6;442(3):324–330. doi: 10.1016/0005-2787(76)90307-5. [DOI] [PubMed] [Google Scholar]
  30. Thomas P. S. Hybridization of denatured RNA and small DNA fragments transferred to nitrocellulose. Proc Natl Acad Sci U S A. 1980 Sep;77(9):5201–5205. doi: 10.1073/pnas.77.9.5201. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Weiss S. R., Leibowitz J. L. Characterization of murine coronavirus RNA by hybridization with virus-specific cDNA probes. J Gen Virol. 1983 Jan;64(Pt 1):127–133. doi: 10.1099/0022-1317-64-1-127. [DOI] [PubMed] [Google Scholar]

Articles from Journal of Virology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES