A BULGED STEM-LOOP STRUCTURE IN THE 3'-UNTRANSLATED REGION OF THE GENOME OF THE CORONAVIRUS MOUSE HEPATITIS-VIRUS IS ESSENTIAL FOR REPLICATION

The 3' untranslated region (UTR) of the positive-sense RNA genome of t he coronavirus mouse hepatitis virus (MHV) contains sequences that are necessary for the synthesis of negative-strand viral RNA as well as s equences that may be crucial for both genomic and subgenomic positive- strand RNA synthesis. We have found that the entire 3' UTR of MHV coul d be replaced by the 3' UTR of bovine coronavirus (BCV), which diverge s overall by 31% in nucleotide sequence. This exchange between two vir uses that are separated by a species barrier was carried out by target ed RNA recombination. Our results define regions of the two 3' UTRs th at are functionally equivalent despite having substantial sequence sub stitutions, deletions, or insertions with respect to each other. More significantly, our attempts to generate an unallowed substitution of a particular portion of the BCV 3' UTR for the corresponding region of the MHV 3' UTR led to the discovery of a bulged stem-loop RNA secondar y structure, adjacent to the stop codon of the nucleocapsid gene, that is essential for MHV viral RNA replication.