CHARACTERIZATIONS OF CORONAVIRUS CIS-ACTING RNA ELEMENTS AND THE TRANSCRIPTION STEP AFFECTING ITS TRANSCRIPTION EFFICIENCY

Seven to eight species of viral subgenomic mRNAs are produced in coron avirus-infected cells, These mRNAs are produced in different quantitie s, and their molar ratios remain constant during viral replication. We studied RNA elements that affect coronavirus transcription efficiency by characterizing a series of cloned coronavirus mouse hepatitis viru s (MHV) defective interfering (DI) RNAs containing an inserted interge nic sequence, from which subgenomic DI RNA is transcribed in MHV-infec ted cells. Certain combinations oi upstream and downstream flanking se quences of the intergenic sequence suppressed subgenomic DI RNA transc ription, yet changing one of the flanking sequences to a different seq uence eliminated transcription suppression. The suppressive effect of certain combinations of flanking sequences, but not all combinations, could be counteracted by altering the intergenic sequence. Thus, the c ombination of intergenic sequence and flanking sequence affected trans cription efficiency. We also characterized another set of DI RNAs desi gned to clarity which transcription step determines the relative molar ratios of coronavirus mRNAs. Our study indicated that if subgenomic m RNAs were exclusively synthesized from negative-strand genomic RNA, th en the relative molar ratios of coronavirus mRNAs were most likely det ermined alter synthesis of the genomic-sized template RNA. If negative -strand subgenomic RNAs were templates for subgenomic mRNAs, then the relative molar ratios of coronavirus mRNAs probably were determined af ter synthesis of the genomic-sized template RNA used for subgenomic-si zed RNA transcription but prior to the completion of the synthesis oi subgenomic-sized RNAs containing the leader sequence. The relative mol ar ratios of coronavirus mRNAs, therefore, seem to have been establish ed prior to a putative replicon-type amplification of subgenomic mRNAs . (C) 1998 Academic Press.