+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

Role of nucleotides immediately flanking the transcription-regulating sequence core in coronavirus subgenomic mRNA synthesis



Role of nucleotides immediately flanking the transcription-regulating sequence core in coronavirus subgenomic mRNA synthesis



Journal of Virology 79(4): 2506-2516



The generation of subgenomic mRNAs in coronavirus involves a discontinuous mechanism of transcription by which the common leader sequence, derived from the genome 5' terminus, is fused to the 5' end of the mRNA coding sequence (body). Transcription-regulating sequences (TRSs) precede each gene and include a conserved core sequence (CS) surrounded by relatively variable sequences (5' TRS and 3' TRS). Regulation of transcription in coronaviruses has been studied by reverse-genetics analysis of the sequences immediately flanking a unique CS in the Transmissible gastroenteritis virus genome (CS-S2), located inside the S gene, that does not lead to detectable amounts of the corresponding mRNA, in spite of its canonical sequence. The transcriptional inactivity of CS-S2 was genome position independent. The presence of a canonical CS was not sufficient to drive transcription, but subgenomic synthesis requires a minimum base pairing between the leader TRS (TRS-L) and the complement of the body TRS (cTRS-B) provided by the CS and its adjacent nucleotides. A good correlation was observed between the free energy of TRS-L and cTRS-B duplex formation and the levels of subgenomic mRNA S2, demonstrating that base pairing between the leader and body beyond the CS is a determinant regulation factor in coronavirus transcription. In TRS mutants with increasing complementarity between TRS-L and cTRS-B, a tendency to reach a plateau in DeltaG values was observed, suggesting that a more precise definition of the TRS limits might be proposed, specifically that it consists of the central CS and around 4 nucleotides flanking 5' and 3' the CS. Sequences downstream of the CS exert a stronger influence on the template-switching decision according to a model of polymerase strand transfer and template switching during minus-strand synthesis.

Please choose payment method:






(PDF emailed within 0-6 h: $19.90)

Accession: 012526450

Download citation: RISBibTeXText

PMID: 15681451

DOI: 10.1128/jvi.79.4.2506-2516.2005


Related references

Requirement of the 5'-end genomic sequence as an upstream cis-acting element for coronavirus subgenomic mRNA transcription. Journal of Virology 68(8): 4727-4737, 1994

The Stability of the Duplex between Sense and Antisense Transcription-Regulating Sequences Is a Crucial Factor in Arterivirus Subgenomic mRna Synthesis. Journal of Virology 77(2): 1175-1183, 2003

The stability of the duplex between sense and antisense transcription-regulating sequences is a crucial factor in arterivirus subgenomic mRNA synthesis. Journal of Virology 77(2): 1175-1183, 2003

Identification of a noncanonical signal for transcription of a novel subgenomic mRNA of mouse hepatitis virus: implication for the mechanism of coronavirus RNA transcription. Virology 278(1): 75-85, 2000

Coronavirus leader RNA regulates and initiates subgenomic mRNA transcription both in trans and in cis. Journal of Virology 68(8): 4738-4746, 1994

The 3' untranslated region of coronavirus RNA is required for subgenomic mRNA transcription from a defective interfering RNA. Journal of Virology 70(10): 7236-7240, 1996

Investigation of the control of coronavirus subgenomic mRNA transcription by using T7-generated negative-sense RNA transcripts. Journal of Virology 69(10): 6219-6227, 1995

The leader RNA of coronavirus mouse hepatitis virus contains an enhancer-like element for subgenomic mRNA transcription. Journal of Virology 74(22): 10571-10580, 2000

Structure and functional relevance of a transcription-regulating sequence involved in coronavirus discontinuous RNA synthesis. Journal of Virology 85(10): 4963-4973, 2011

Coronavirus transcription mediated by sequences flanking the transcription consensus sequence. Virology 217(1): 311-322, 1996

The leader sequence of the subgenomic mRNA's of Rous sarcoma virus is approximately 390 nucleotides. Journal of Virology 41(2): 527-534, 1982

Importance of coronavirus negative-strand genomic RNA synthesis prior to subgenomic RNA transcription. Virus Research 57(1): 35-42, 1998

Sequence motifs involved in the regulation of discontinuous coronavirus subgenomic RNA synthesis. Journal of Virology 78(2): 980-994, 2004

Sequence Motifs Involved in the Regulation of Discontinuous Coronavirus Subgenomic Rna Synthesis. Journal of Virology 78(2): 980-994, 2004

Effect of intergenic consensus sequence flanking sequences on coronavirus transcription. Journal of Virology 67(6): 3304-3311, 1993