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. 1988 Nov 25;16(22):10849–10860. doi: 10.1093/nar/16.22.10849

Differential premature termination of transcription as a proposed mechanism for the regulation of coronavirus gene expression.

D A Konings 1, P J Bredenbeek 1, J F Noten 1, P Hogeweg 1, W J Spaan 1
PMCID: PMC338943  PMID: 2905039

Abstract

We propose that the different subgenomic mRNA levels of coronaviruses are controlled through differential premature termination of transcription, and are modulated by the relative strength of transcriptional initiation/blockage events. We present the complete set of sequences covering the leader encoding and intergenic regions of the MHV-A59 strain. A computer-assisted analysis of the two now complete sets of these sequences of strain IBV-M42 and MHV-A59 shows that, in contrast to the previous theory, differences amongst stabilities of intermolecular base-pairings between the leader and the intergenic regions are not sufficient to determine the mRNA gradients in both MHV and IBV infected cells. Neither can the accessibility of the interacting regions on the leader and the negative stranded genome, as revealed by secondary structure analysis, explain the mRNA levels. The nested gene organisation itself, on the other hand, could be responsible for observed mRNA levels gradually increasing with gene order. Relatively slow new initiation events at intergenic regions are proposed to block elongation of passing transcripts which, via temporary pausing, can cause premature termination of transcription. This effects longer transcripts more than shorter ones.

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Selected References

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

  1. Banerjee A. K. Transcription and replication of rhabdoviruses. Microbiol Rev. 1987 Mar;51(1):66–87. doi: 10.1128/mr.51.1.66-87.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Baric R. S., Shieh C. K., Stohlman S. A., Lai M. M. Analysis of intracellular small RNAs of mouse hepatitis virus: evidence for discontinuous transcription. Virology. 1987 Feb;156(2):342–354. doi: 10.1016/0042-6822(87)90414-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. 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]
  4. Baric R. S., Stohlman S. A., Razavi M. K., Lai M. M. Characterization of leader-related small RNAs in coronavirus-infected cells: further evidence for leader-primed mechanism of transcription. Virus Res. 1985 Jul;3(1):19–33. doi: 10.1016/0168-1702(85)90038-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Boursnell M. E., Brown T. D., Foulds I. J., Green P. F., Tomley F. M., Binns M. M. Completion of the sequence of the genome of the coronavirus avian infectious bronchitis virus. J Gen Virol. 1987 Jan;68(Pt 1):57–77. doi: 10.1099/0022-1317-68-1-57. [DOI] [PubMed] [Google Scholar]
  6. Brayton P. R., Stohlman S. A., Lai M. M. Further characterization of mouse hepatitis virus RNA-dependent RNA polymerases. Virology. 1984 Feb;133(1):197–201. doi: 10.1016/0042-6822(84)90439-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Brown T. D., Boursnell M. E., Binns M. M. A leader sequence is present on mRNA A of avian infectious bronchitis virus. J Gen Virol. 1984 Aug;65(Pt 8):1437–1442. doi: 10.1099/0022-1317-65-8-1437. [DOI] [PubMed] [Google Scholar]
  8. Brown T. D., Boursnell M. E., Binns M. M., Tomley F. M. Cloning and sequencing of 5' terminal sequences from avian infectious bronchitis virus genomic RNA. J Gen Virol. 1986 Feb;67(Pt 2):221–228. doi: 10.1099/0022-1317-67-2-221. [DOI] [PubMed] [Google Scholar]
  9. Budzilowicz C. J., Wilczynski S. P., Weiss S. R. 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. J Virol. 1985 Mar;53(3):834–840. doi: 10.1128/jvi.53.3.834-840.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Freier S. M., Kierzek R., Jaeger J. A., Sugimoto N., Caruthers M. H., Neilson T., Turner D. H. Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci U S A. 1986 Dec;83(24):9373–9377. doi: 10.1073/pnas.83.24.9373. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Gubler U., Hoffman B. J. A simple and very efficient method for generating cDNA libraries. Gene. 1983 Nov;25(2-3):263–269. doi: 10.1016/0378-1119(83)90230-5. [DOI] [PubMed] [Google Scholar]
  12. Hogeweg P., Hesper B. Energy directed folding of RNA sequences. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):67–74. doi: 10.1093/nar/12.1part1.67. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. 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]
  14. Keck J. G., Stohlman S. A., Soe L. H., Makino S., Lai M. M. Multiple recombination sites at the 5'-end of murine coronavirus RNA. Virology. 1987 Feb;156(2):331–341. doi: 10.1016/0042-6822(87)90413-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. 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]
  16. Lai M. M., Baric R. S., Makino S., Keck J. G., Egbert J., Leibowitz J. L., Stohlman S. A. Recombination between nonsegmented RNA genomes of murine coronaviruses. J Virol. 1985 Nov;56(2):449–456. doi: 10.1128/jvi.56.2.449-456.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. 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]
  18. 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]
  19. 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]
  20. Makino S., Stohlman S. A., Lai M. M. Leader sequences of murine coronavirus mRNAs can be freely reassorted: evidence for the role of free leader RNA in transcription. Proc Natl Acad Sci U S A. 1986 Jun;83(12):4204–4208. doi: 10.1073/pnas.83.12.4204. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Meinkoth J., Wahl G. Hybridization of nucleic acids immobilized on solid supports. Anal Biochem. 1984 May 1;138(2):267–284. doi: 10.1016/0003-2697(84)90808-x. [DOI] [PubMed] [Google Scholar]
  22. Sanger F., Coulson A. R., Barrell B. G., Smith A. J., Roe B. A. Cloning in single-stranded bacteriophage as an aid to rapid DNA sequencing. J Mol Biol. 1980 Oct 25;143(2):161–178. doi: 10.1016/0022-2836(80)90196-5. [DOI] [PubMed] [Google Scholar]
  23. Sawicki S. G., Sawicki D. L. Coronavirus minus-strand RNA synthesis and effect of cycloheximide on coronavirus RNA synthesis. J Virol. 1986 Jan;57(1):328–334. doi: 10.1128/jvi.57.1.328-334.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Shapiro D. J., Blume J. E., Nielsen D. A. Regulation of messenger RNA stability in eukaryotic cells. Bioessays. 1987 May;6(5):221–226. doi: 10.1002/bies.950060507. [DOI] [PubMed] [Google Scholar]
  25. Shieh C. K., Soe L. H., Makino S., Chang M. F., Stohlman S. A., Lai M. M. The 5'-end sequence of the murine coronavirus genome: implications for multiple fusion sites in leader-primed transcription. Virology. 1987 Feb;156(2):321–330. doi: 10.1016/0042-6822(87)90412-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Spaan W. J., Rottier P. J., Horzinek M. C., van der Zeijst B. A. Isolation and identification of virus-specific mRNAs in cells infected with mouse hepatitis virus (MHV-A59). Virology. 1981 Jan 30;108(2):424–434. doi: 10.1016/0042-6822(81)90449-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. 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]
  28. Spaan W., Delius H., Skinner M., Armstrong J., Rottier P., Smeekens S., van der Zeijst B. A., Siddell S. G. Coronavirus mRNA synthesis involves fusion of non-contiguous sequences. EMBO J. 1983;2(10):1839–1844. doi: 10.1002/j.1460-2075.1983.tb01667.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Stern D. F., Kennedy S. I. Coronavirus multiplication strategy. I. Identification and characterization of virus-specified RNA. J Virol. 1980 Jun;34(3):665–674. doi: 10.1128/jvi.34.3.665-674.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Stern D. F., Kennedy S. I. Coronavirus multiplication strategy. II. Mapping the avian infectious bronchitis virus intracellular RNA species to the genome. J Virol. 1980 Nov;36(2):440–449. doi: 10.1128/jvi.36.2.440-449.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Stern D. F., Sefton B. M. Synthesis of coronavirus mRNAs: kinetics of inactivation of infectious bronchitis virus RNA synthesis by UV light. J Virol. 1982 May;42(2):755–759. doi: 10.1128/jvi.42.2.755-759.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. 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]
  33. Wilhelmsen K. C., Leibowitz J. L., Bond C. W., Robb J. A. The replication of murine coronaviruses in enucleated cells. Virology. 1981 Apr 15;110(1):225–230. doi: 10.1016/0042-6822(81)90027-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Williams A. L., Jr, Tinoco I., Jr A dynamic programming algorithm for finding alternative RNA secondary structures. Nucleic Acids Res. 1986 Jan 10;14(1):299–315. doi: 10.1093/nar/14.1.299. [DOI] [PMC free article] [PubMed] [Google Scholar]

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