Factors directing the RNA-dependent RNA polymerase jump during discontinuous transcription in coronaviruses

It has been 23 years since it was learned that coronavirus subgenomic messenger RNAs are unusual among virus messenger RNAs in that they are 5' and 3' co-terminal with the plus-strand RNA viral genome. Although it is generally agreed that the co-terminal structure is the result of a discontinuous transcription process whereby the RNA-dependent RNA polymerase (RdRP) jumps in a high-frequency (sequence) similarity-assisted manner (resembling copy-choice recombination) from a donor to an acceptor RNA strand, it is not known what mechanisms direct the Rd.Rp to jump. Here, with the use of a bovine coronavirus minireplicon (a defective interfering RNA), it is documented that (1) group 2 corona virus RNA replication signals recognized by the viral RdRps (among six group 2 coronaviruses studied) are common whereas the transcription signals directing discontinuous transcription are not, (2) a 22-nt region of sequence identity is sufficient to direct the RdRp to jump from the positive-strand minireplicon donor to the positive-strand virus genome acceptor as long as it occurs within the precisely restricted window of nts 33 to 97 within the 5'-proximal region of the 31032-nt genome, (3) a 22-nt region of sequence identity is sufficient to direct the RdRp to jump from the positive-strand minireplicon donor to the virus negative-strand antigenome as long as it occurs within the precisely restricted window of nts 35 to 123 from the 3' end of the antigenome, and (4) the 22- nt region of sequence identity can dire.ct the RdRp jump to yield a subgenomic messenger RNA with a leader as short as 33 nt, but no shorter. These results show that specific RNA structural elements direct the RdRp jump during the required intermolecular recombination events (i.e. discontinuous transcription) in the process of coronavirus replication. Rational drug designs for interrupting these elements may lead to therapeutic molecules for treating coronavirus infection, including infection by the SARS coronavirus which to date appears to be a group 2 member.