Requirement of the 5'-end genomic sequence as an upstream cis-acting element for coronavirus subgenomic mRNA transcription - PubMed

Requirement of the 5'-end genomic sequence as an upstream cis-acting element for coronavirus subgenomic mRNA transcription

C L Liao et al. J Virol. 1994 Aug.

Abstract

We have developed a defective interfering (DI) RNA containing a chloramphenicol acetyltransferase reporter gene, placed behind an intergenic sequence, for studying subgenomic mRNA transcription of mouse hepatitis virus (MHV), a prototype coronavirus. Using this system, we have identified the sequence requirement for MHV subgenomic mRNA transcription. We show that this sequence requirement differs from that for RNA replication. In addition to the previously identified requirement for an intergenic (promoter) sequence, additional sequences from the 5' end of genomic RNA are required for subgenomic mRNA transcription. These upstream sequences include the leader RNA and a spacer sequence between the leader and intergenic sequence, which is derived from the 5' untranslated region and part of gene 1. The spacer sequence requirement is specific, since only the sequence derived from the 5' end of RNA genome, but not from other MHV genomic regions or heterologous sequences, could initiate subgenomic transcription from the intergenic sequence. These results strongly suggest that the wild-type viral subgenomic mRNAs (mRNA2 to mRNA7) and probably their counterpart subgenomic negative-sense RNAs cannot be utilized for mRNA amplification. Furthermore, we have demonstrated that a partial leader sequence present at the 5' end of genome, which lacks the leader-mRNA fusion sequence, could still support subgenomic mRNA transcription. In this case, the leader sequences of the subgenomic transcripts were derived exclusively from the wild-type helper virus, indicating that the MHV leader RNA initiates in trans subgenomic mRNA transcription. Thus, the leader sequence can enhance subgenomic transcription even when it cannot serve as a primer for mRNA synthesis. These results taken together suggest that the 5'-end leader sequence of MHV not only provides a trans-acting primer for mRNA initiation but also serves as a cis-acting element required for the transcription of subgenomic mRNAs. The identification of an upstream cis-acting element for MHV subgenomic mRNA synthesis defines a novel sequence requirement for regulating mRNA synthesis in RNA viruses.

Similar articles

• Coronavirus leader RNA regulates and initiates subgenomic mRNA transcription both in trans and in cis.

  Zhang X, Liao CL, Lai MM. Zhang X, et al. J Virol. 1994 Aug;68(8):4738-46. doi: 10.1128/JVI.68.8.4738-4746.1994. J Virol. 1994. PMID: 8035476 Free PMC article.

• The leader RNA of coronavirus mouse hepatitis virus contains an enhancer-like element for subgenomic mRNA transcription.

  Wang Y, Zhang X. Wang Y, et al. J Virol. 2000 Nov;74(22):10571-80. doi: 10.1128/jvi.74.22.10571-10580.2000. J Virol. 2000. PMID: 11044101 Free PMC article.

• Evidence for coronavirus discontinuous transcription.

  Jeong YS, Makino S. Jeong YS, et al. J Virol. 1994 Apr;68(4):2615-23. doi: 10.1128/JVI.68.4.2615-2623.1994. J Virol. 1994. PMID: 8139040 Free PMC article.

• A new model for coronavirus transcription.

  Sawicki SG, Sawicki DL. Sawicki SG, et al. Adv Exp Med Biol. 1998;440:215-9. doi: 10.1007/978-1-4615-5331-1_26. Adv Exp Med Biol. 1998. PMID: 9782283 Review.

• Coronavirus transcription: a perspective.

  Sawicki SG, Sawicki DL. Sawicki SG, et al. Curr Top Microbiol Immunol. 2005;287:31-55. doi: 10.1007/3-540-26765-4_2. Curr Top Microbiol Immunol. 2005. PMID: 15609508 Free PMC article. Review.

Cited by

• Intra-genome variability in the dinucleotide composition of SARS-CoV-2.

  Digard P, Lee HM, Sharp C, Grey F, Gaunt E. Digard P, et al. Virus Evol. 2020 Aug 13;6(2):veaa057. doi: 10.1093/ve/veaa057. eCollection 2020 Jul. Virus Evol. 2020. PMID: 33029383 Free PMC article.

• A Conserved Stem-Loop Structure within ORF5 Is a Frequent Recombination Hotspot for Porcine Reproductive and Respiratory Syndrome Virus 1 (PRRSV-1) with a Particular Modified Live Virus (MLV) Strain.

  Mötz M, Stadler J, Kreutzmann H, Ladinig A, Lamp B, Auer A, Riedel C, Rümenapf T. Mötz M, et al. Viruses. 2023 Jan 16;15(1):258. doi: 10.3390/v15010258. Viruses. 2023. PMID: 36680298 Free PMC article.

• A leaderless genome identified during persistent bovine coronavirus infection is associated with attenuation of gene expression.

  Ke TY, Liao WY, Wu HY. Ke TY, et al. PLoS One. 2013 Dec 12;8(12):e82176. doi: 10.1371/journal.pone.0082176. eCollection 2013. PLoS One. 2013. PMID: 24349214 Free PMC article.

• The 5' nontranslated region of potato virus X RNA affects both genomic and subgenomic RNA synthesis.

  Kim KH, Hemenway C. Kim KH, et al. J Virol. 1996 Aug;70(8):5533-40. doi: 10.1128/JVI.70.8.5533-5540.1996. J Virol. 1996. PMID: 8764066 Free PMC article.

• Polypyrimidine tract-binding protein binds to the leader RNA of mouse hepatitis virus and serves as a regulator of viral transcription.

  Li HP, Huang P, Park S, Lai MM. Li HP, et al. J Virol. 1999 Jan;73(1):772-7. doi: 10.1128/JVI.73.1.772-777.1999. J Virol. 1999. PMID: 9847386 Free PMC article.

References

Publication types

MeSH terms

Substances

LinkOut - more resources

• Full Text Sources

  • Atypon
  • Europe PubMed Central
  • PubMed Central