Analysis of the CIS-Acting Elements of Coronavirus Transcription

Abstract

Mouse hepatitis virus (MHV), a coronavirus, is an enveloped virus containing a single-stranded, positive-sense RNA genome of approximately 31 kb (11, 13, 22). There are seven to eight species of virus-specific subgenomic mRNAs in MHV-infected cells. These subgenomic mRNAs comprise a 3’-coterminal nested-set (9, 14). In decreasing order of size, they are mRNAs 1 through 7 (9, 14). The 5’ end of the MHV genomic RNA contains a 72- to 77-nucleotide-long leader sequence (8, 10, 26). Within the 3’-region of the leader sequence there is a pentanucleotide sequence, UCUAA. This sequence repeats two to four times in different MHV strains (19). The MHV-specific genes are downstream from the leader, and each gene is separated by a special short stretch of sequence, the intergenic sequence. The intergenic sequences include the unique consensus sequence UCUAAAC or a sequence very similar sequence (25). All MHV mRNA species have a sequence identical to the 5’-end genomic leader sequence. These leader sequences are fused to the intergenic consensus sequence, which marks the start of each gene (8, 10, 25, 26). In most MHV genes the degree of intergenic sequence nucleotide homology with the leader sequence correlates with the amount of mRNA transcribed (25). This correlation is not observed in infectious bronchitis virus mRNA transcription (4). The site where the leader fuses with the mRNA is somewhere within the repeated pentanucleotide (UCUAA). The number of repeats in each given mRNA varies (19). The pentanucleotide repeats at the genomic leader sequence and at the intergenic region are identical, making identification of the fusion site of these two sequences difficult.