Conserved sequences near the early transcription start sites of vaccinia virus.

Transcription start sites were determined for the herpes simplex virus thymidine kinase (HSV-TK) mRNA expressed by four vaccinia virus recombinants in which the upstream insertion of shotgun-isolated vaccinia genomic fragments of 156 to 379 bp promoted this expression. Two of these fragments were related in such a manner that 62 bp separated two divergent early transcription start sites. The region of imperfect dyad symmetry revealed in this fragment is proposed to result from the presence of two divergent early transcription signals of vaccinia virus. Subsequent comparison showed that domains with high sequence homologies to those depicted by the dyad symmetry existed at comparable locations in the sequences flanking both the HSV-TK mRNA start site of the other two recombinants and that of several early vaccinia genes. Maximum homologies among these conserved sequences was obtained when they were aligned discontinuously. These studies also revealed a late mRNA start site with no more than 10 bp of vaccinia sequences upstream.