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. 1989 Dec;63(12):5285–5292. doi: 10.1128/jvi.63.12.5285-5292.1989

High-frequency leader sequence switching during coronavirus defective interfering RNA replication.

S Makino 1, M M Lai 1
PMCID: PMC251194  PMID: 2555555

Abstract

A system was developed that exploited defective interfering (DI) RNAs of coronavirus to study the role of free leader RNA in RNA replication. A cDNA copy of mouse hepatitis virus DI RNA was placed downstream of the T7 RNA polymerase promoter to generate DI RNAs capable of extremely efficient replication in the presence of a helper virus. We demonstrated that, in the DI RNA-transfected cells, the leader sequence of these DI RNAs was switched to that of the helper virus during one round of replication. This high-frequency leader sequence exchange was not observed if a nine-nucleotide stretch of sequence (UUUAUAAAC) at the junction between the leader and the remaining DI sequence was deleted. This observation suggests that a free leader RNA generated from the genomic RNA of mouse hepatitis virus may participate in the replication of DI RNA.

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Selected References

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  1. 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]
  2. 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]
  3. 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]
  4. Hirano N., Fujiwara K., Hino S., Matumoto M. Replication and plaque formation of mouse hepatitis virus (MHV-2) in mouse cell line DBT culture. Arch Gesamte Virusforsch. 1974;44(3):298–302. doi: 10.1007/BF01240618. [DOI] [PubMed] [Google Scholar]
  5. Keck J. G., Soe L. H., Makino S., Stohlman S. A., Lai M. M. RNA recombination of murine coronaviruses: recombination between fusion-positive mouse hepatitis virus A59 and fusion-negative mouse hepatitis virus 2. J Virol. 1988 Jun;62(6):1989–1998. doi: 10.1128/jvi.62.6.1989-1998.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. 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]
  7. Koller B., Fromm H., Galun E., Edelman M. Evidence for in vivo trans splicing of pre-mRNAs in tobacco chloroplasts. Cell. 1987 Jan 16;48(1):111–119. doi: 10.1016/0092-8674(87)90361-8. [DOI] [PubMed] [Google Scholar]
  8. Krause M., Hirsh D. A trans-spliced leader sequence on actin mRNA in C. elegans. Cell. 1987 Jun 19;49(6):753–761. doi: 10.1016/0092-8674(87)90613-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. 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]
  10. 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]
  11. Lai M. M. Coronavirus leader-RNA-primed transcription: an alternative mechanism to RNA splicing. Bioessays. 1986 Dec;5(6):257–260. doi: 10.1002/bies.950050606. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Lai M. M., Makino S., Soe L. H., Shieh C. K., Keck J. G., Fleming J. O. Coronavirus: a jumping RNA transcription. Cold Spring Harb Symp Quant Biol. 1987;52:359–365. doi: 10.1101/sqb.1987.052.01.041. [DOI] [PubMed] [Google Scholar]
  13. 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]
  14. Lai M. M., Patton C. D., Stohlman S. A. Replication of mouse hepatitis virus: negative-stranded RNA and replicative form RNA are of genome length. J Virol. 1982 Nov;44(2):487–492. doi: 10.1128/jvi.44.2.487-492.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. 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]
  16. Langridge J., Langridge P., Bergquist P. L. Extraction of nucleic acids from agarose gels. Anal Biochem. 1980 Apr;103(2):264–271. doi: 10.1016/0003-2697(80)90266-3. [DOI] [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. Levis R., Weiss B. G., Tsiang M., Huang H., Schlesinger S. Deletion mapping of Sindbis virus DI RNAs derived from cDNAs defines the sequences essential for replication and packaging. Cell. 1986 Jan 17;44(1):137–145. doi: 10.1016/0092-8674(86)90492-7. [DOI] [PubMed] [Google Scholar]
  19. Makino S., Fujioka N., Fujiwara K. Structure of the intracellular defective viral RNAs of defective interfering particles of mouse hepatitis virus. J Virol. 1985 May;54(2):329–336. doi: 10.1128/jvi.54.2.329-336.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Makino S., Lai M. M. Evolution of the 5'-end of genomic RNA of murine coronaviruses during passages in vitro. Virology. 1989 Mar;169(1):227–232. doi: 10.1016/0042-6822(89)90060-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Makino S., Shieh C. K., Keck J. G., Lai M. M. Defective-interfering particles of murine coronavirus: mechanism of synthesis of defective viral RNAs. Virology. 1988 Mar;163(1):104–111. doi: 10.1016/0042-6822(88)90237-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Makino S., Shieh C. K., Soe L. H., Baker S. C., Lai M. M. Primary structure and translation of a defective interfering RNA of murine coronavirus. Virology. 1988 Oct;166(2):550–560. doi: 10.1016/0042-6822(88)90526-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Makino S., Soe L. H., Shieh C. K., Lai M. M. Discontinuous transcription generates heterogeneity at the leader fusion sites of coronavirus mRNAs. J Virol. 1988 Oct;62(10):3870–3873. doi: 10.1128/jvi.62.10.3870-3873.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. 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]
  25. Makino S., Taguchi F., Fujiwara K. Defective interfering particles of mouse hepatitis virus. Virology. 1984 Feb;133(1):9–17. doi: 10.1016/0042-6822(84)90420-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Makino S., Taguchi F., Hirano N., Fujiwara K. Analysis of genomic and intracellular viral RNAs of small plaque mutants of mouse hepatitis virus, JHM strain. Virology. 1984 Nov;139(1):138–151. doi: 10.1016/0042-6822(84)90335-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. McMaster G. K., Carmichael G. G. Analysis of single- and double-stranded nucleic acids on polyacrylamide and agarose gels by using glyoxal and acridine orange. Proc Natl Acad Sci U S A. 1977 Nov;74(11):4835–4838. doi: 10.1073/pnas.74.11.4835. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Murphy W. J., Watkins K. P., Agabian N. Identification of a novel Y branch structure as an intermediate in trypanosome mRNA processing: evidence for trans splicing. Cell. 1986 Nov 21;47(4):517–525. doi: 10.1016/0092-8674(86)90616-1. [DOI] [PubMed] [Google Scholar]
  29. Patterson J. L., Holloway B., Kolakofsky D. La Crosse virions contain a primer-stimulated RNA polymerase and a methylated cap-dependent endonuclease. J Virol. 1984 Oct;52(1):215–222. doi: 10.1128/jvi.52.1.215-222.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Pedersen F. S., Haseltine W. A. A micromethod for detailed characterization of high molecular weight RNA. Methods Enzymol. 1980;65(1):680–687. doi: 10.1016/s0076-6879(80)65066-6. [DOI] [PubMed] [Google Scholar]
  31. Plotch S. J., Bouloy M., Ulmanen I., Krug R. M. A unique cap(m7GpppXm)-dependent influenza virion endonuclease cleaves capped RNAs to generate the primers that initiate viral RNA transcription. Cell. 1981 Mar;23(3):847–858. doi: 10.1016/0092-8674(81)90449-9. [DOI] [PubMed] [Google Scholar]
  32. 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]
  33. Soe L. H., Shieh C. K., Baker S. C., Chang M. F., Lai M. M. Sequence and translation of the murine coronavirus 5'-end genomic RNA reveals the N-terminal structure of the putative RNA polymerase. J Virol. 1987 Dec;61(12):3968–3976. doi: 10.1128/jvi.61.12.3968-3976.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Sutton R. E., Boothroyd J. C. Evidence for trans splicing in trypanosomes. Cell. 1986 Nov 21;47(4):527–535. doi: 10.1016/0092-8674(86)90617-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Tabor S., Richardson C. C. A bacteriophage T7 RNA polymerase/promoter system for controlled exclusive expression of specific genes. Proc Natl Acad Sci U S A. 1985 Feb;82(4):1074–1078. doi: 10.1073/pnas.82.4.1074. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Zimmern D., Kaesberg P. 3'-terminal nucleotide sequence of encephalomyocarditis virus RNA determined by reverse transcriptase and chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1978 Sep;75(9):4257–4261. doi: 10.1073/pnas.75.9.4257. [DOI] [PMC free article] [PubMed] [Google Scholar]

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