Effect of intergenic consensus sequence flanking sequences on coronavirus transcription

Insertion of a region, including the 18-nucleotide-long intergenic sequence between genes 6 and 7 of mouse hepatitis virus (MHV) genomic RNA, into an MHV defective interfering (DI) RNA leads to transcription of subgenomic DI RNA in helper virus-infected cells (S. Makino, M. Joo, and J. K. Makino, J. Virol. 66:6031-6041, 1991). In this study, the subgenomic DI RNA system was used to determine how sequences flanking the intergenic region affect MHV RNA transcription and to identify the minimum intergenic sequence required for MHV transcription. DI cDNAs containing the intergenic region between genes 6 and 7, but with different lengths of upstream or downstream flanking sequences, were constructed. All DI cDNAs had an 18-nucleotide-long intergenic region that was identical to the 3′ region of the genomic leader sequence, which contains two UCUAA repeat sequences. These constructs included 0 to 1,440 nucleotides of upstream flanking sequence and 0 to 1,671 nucleotides of downstream flanking sequence. An analysis of intracellular genomic DI RNA and subgenomic DI RNA species revealed that there were no significant differences in the ratios of subgenomic to genomic DI RNA for any of the DI RNA constructs. DI cDNAs which lacked the intergenic region flanking sequences and contained a series of deletions within the 18-nucleotide-long intergenic sequence were constructed to determine the minimum sequence necessary for subgenomic DI RNA transcription. Small amounts of subgenomic DI RNA were synthesized from genomic DI RNAs with the intergenic consensus sequences UCUAAAC and GCUAAAC, whereas no subgenomic DI RNA transcription was observed from DI RNAs containing UCUAAAG and GCTAAAG sequences. These analyses demonstrated that the sequences flanking the intergenic sequence between genes 6 and 7 did not play a role in subgenomic DI RNA transcription regulation and that the UCUAAAC consensus sequence was sufficient for subgenomic DI RNA transcription.