Analysis of the CIS-Acting Elements of Coronavirus Transcription

  • Myungsoo Joo
  • Shinji Makino
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 342)


Mouse hepatitis virus (MHV), a coronavirus, is an enveloped virus containing a single-stranded, positive-sense RNA genome of approximately 31 kb (11, 13, 22). There are seven to eight species of virus-specific subgenomic mRNAs in MHV-infected cells. These subgenomic mRNAs comprise a 3’-coterminal nested-set (9, 14). In decreasing order of size, they are mRNAs 1 through 7 (9, 14). The 5’ end of the MHV genomic RNA contains a 72- to 77-nucleotide-long leader sequence (8, 10, 26). Within the 3’-region of the leader sequence there is a pentanucleotide sequence, UCUAA. This sequence repeats two to four times in different MHV strains (19). The MHV-specific genes are downstream from the leader, and each gene is separated by a special short stretch of sequence, the intergenic sequence. The intergenic sequences include the unique consensus sequence UCUAAAC or a sequence very similar sequence (25). All MHV mRNA species have a sequence identical to the 5’-end genomic leader sequence. These leader sequences are fused to the intergenic consensus sequence, which marks the start of each gene (8, 10, 25, 26). In most MHV genes the degree of intergenic sequence nucleotide homology with the leader sequence correlates with the amount of mRNA transcribed (25). This correlation is not observed in infectious bronchitis virus mRNA transcription (4). The site where the leader fuses with the mRNA is somewhere within the repeated pentanucleotide (UCUAA). The number of repeats in each given mRNA varies (19). The pentanucleotide repeats at the genomic leader sequence and at the intergenic region are identical, making identification of the fusion site of these two sequences difficult.


Consensus Sequence Intergenic Region Flank Sequence Leader Sequence Single Nucleotide Substitution 
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.


  1. 1.
    Baker, S. C., and M. M. C. Lai. EMBO J. 9:4173–4179. (1990).PubMedGoogle Scholar
  2. 2.
    Baric, R. S., K. Fu, M. C. Schaad, and S. A. Stohlman. Virology 177:646–656. (1990).PubMedCrossRefGoogle Scholar
  3. 3.
    Baric, R. S., S. A. Stohlman, and M. M. C. Lai. J. Virol. 48:633 (1983).PubMedGoogle Scholar
  4. 4.
    Brown, T. D. K., M. E. G. Boursnell, M. M. Binns, and F. M. Tomley, J. Gen. Virol. 67:221 (1986).PubMedCrossRefGoogle Scholar
  5. 5.
    Higuchi, R. Recombinant PCR, in “PCR Protocols,” M.A. Innis, D. H. Gelfand, J. J. Sninsky and T. J. White eds. Academic Press, San Diego (1990).Google Scholar
  6. 6.
    Jeong Y. S., and S. Makino. J. Virol. 66: 3339 (1992).PubMedGoogle Scholar
  7. 7.
    Lai, M. M. C. Annu. Rev. Microbiol. 44:303 (1990).PubMedCrossRefGoogle Scholar
  8. 8.
    Lai, M. M. C., R. S. Baric, P. R. Brayton, and S. A. Stohlman. Proc. Natl. Acad. Sci. USA 81: 3626 (1984).PubMedCrossRefGoogle Scholar
  9. 9.
    Lai, M. M. C., P. R. Brayton, R. C. Armen, C. D. Patton, C. Pugh, and S. A. Stohlman. J. Virol. 39: 823 (1981).PubMedGoogle Scholar
  10. 10.
    Lai, M. M. C., C. D. Patton, R. S. Banc, and S. A. Stohlman. J. Virol. 46: 1027 (1983).PubMedGoogle Scholar
  11. 11.
    Lai, M. M. C., and S. A. Stohlman. J. Virol. 26: 236 (1978).PubMedGoogle Scholar
  12. 12.
    La Monica, N., K. Yokomori, and M. M. C. Lai. Virology 188:402 (1992).PubMedCrossRefGoogle Scholar
  13. 13.
    Lee, H.-J., C.-K. Shieh, A. E. Gorbalenya, E. V. Eugene, N. La Monica, J. Tuler, A. Bagdzhadzhyan, and M. M. C. Lai. Virology 180:567 (1991).PubMedCrossRefGoogle Scholar
  14. 14.
    Leibowitz, J. L., K. C. Wilhelmsen, and C. W. Bond.Virology 114: 39 (1981).PubMedCrossRefGoogle Scholar
  15. 15.
    Makino, S., J. G. Keck, S. A. Stohlman, and M. M. C. Lai. J. Virol. 57:729 (1986).PubMedGoogle Scholar
  16. 16.
    Makino, S., M. Joo, and J. K. Makino. J. Virol. 65.:6031 (1991).PubMedGoogle Scholar
  17. 17.
    Makin, S., and M. M. C. Lai. Virology 169:227 (1989).CrossRefGoogle Scholar
  18. 18.
    Makin, S., and M. M. C. Lai. J. Virol. 63: 5285 (1989).Google Scholar
  19. 19.
    Makino, S., L. H. Soe, C.-K. Shieh, and M. M. C. Lai. J. Viol. 62:3870 (1988).Google Scholar
  20. 20.
    Makino, S., F. Taguchi, N. Hirano, and K. Fujiwara. Virology 139: 138 (1984).PubMedCrossRefGoogle Scholar
  21. 21.
    Makino, S., K. Yokomori, and M. M. C. Lai. J. Virol. 64:6045 (1990).PubMedGoogle Scholar
  22. 22.
    Pachuk, C. J., P. J. Bredenbeek, P. W. Zoltick, W. J. M. Spaan, and S. R. Weiss. Virology 171:141(1989).PubMedCrossRefGoogle Scholar
  23. 23.
    Sawicki, S. G., and D. L. Sawicki. J. Virol. 64:1050 (1990).PubMedGoogle Scholar
  24. 24.
    Shieh, C.-K., H.-J. Lee, K. Yokomori, N. La Monica, S. Makino, and M. M. C. Lai. J. Virol. 63:3729 (1989).PubMedGoogle Scholar
  25. 25.
    Shieh, C.-K., L. H. Soe, S. Makino, M.-F. Chang, S. A. Stohlman, and M. M. C. Lai. Virology 156: 321 (1987).PubMedCrossRefGoogle Scholar
  26. 26.
    Spaan, W., H. Delius, M. Skinner, J. Armstrong, P. Rottier, S. Smeekens, B. A. M. van der Zeijst, and S. G. Siddell. EMBO J. 2: 1939 (1983).Google Scholar
  27. 27.
    Winship P. R. 1989. Nucleic Acids Res. 17:1266 (1989).PubMedCrossRefGoogle Scholar
  28. 28.
    Yokomori, K., L. R. Banner, and M. M. C. Lai. Virology 183:647 (1991).PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 1994

Authors and Affiliations

  • Myungsoo Joo
    • 1
  • Shinji Makino
    • 1
  1. 1.Department of MicrobiologyThe University of Texas at AustinAustinUSA

Personalised recommendations