Transcription termination by vaccinia RNA polymerase entails recognition of specific phosphates in the nascent RNA.

Vaccinia virus RNA polymerase terminates transcription downstream of a UUUUUNU signal in the nascent RNA. Transduction of the RNA signal to the elongating polymerase requires a termination factor (vaccinia termination factor/capping enzyme) and is coupled to the hydrolysis of ATP. It was shown previously that incorporation of 5-bromouracil or 5-iodouracil within the UUUUUNU element abolishes termination by preventing factor-dependent release of the nascent chain from the polymerase elongation complex. Here, we report that termination is prevented by phosphorothioate substitution at UMP residues in the nascent RNA. In contrast, phosphorothioate substitution at AMP, CMP, and GMP nucleotides does not inhibit termination. Thus, the action of a eukaryotic termination factor entails recognition of the nucleotide bases and the phosphate groups of the target sequence in nascent RNA.