The σ subunit of RNA polymerase contacts the leading ends of transcripts 9-13 bases long on the λ P_R promoter but not on T7 A1

The σ subunit of RNA polymerase is responsible for specific initiation of RNA synthesis at promoter sites on DNA. σ dissociates shortly after initiation. Photoaffinity-labeling experiments performed on transcription complexes with two different DNA promoters, which have highly homologous control sequences upstream from the transcribed regions, have revealed that the σ subunit of RNA polymerase is contacted by the 5′ ends of quite different lengths of nascent RNA in each transcription complex. On the other hand, the labeling of subunits ββ′ is quite similar for both promoters, and the α subunit is not labeled in either case. The results of transcription experiments on the phage λP_R promoter show that σ can be photoaffinity labeled by RNA chains that are 9-13 nucleotides long and thus remains associated with the core enzyme at least to that point. But on the A1 promoter of phage T7 DNA, photoaffinity labeling of σ ceases with the trinucleotide. Thus release of σ from the vicinity of nascent RNA depends not merely on the length but on the sequence of the transcript. For the T7 A1 promoter, σ labeling ceases while the leading end of the RNA is still base paired to the DNA template; thus, it appears that there is at least one site on the enzyme that interacts with the growing transcript/template hybrid, in a sequence-dependent way, to effect σ release. Similarities with the results of Hansen and McClure [Hansen, U. M., & McClure, W. R. (1980) J. Biol. Chem. 255, 9564-9570] for σ dissociation from transcription complexes on poly[d(A-T)] are discussed, with the observation that the RNA/DNA hybrids formed on T7 A1 show an alternating pattern of bridging hydrogen bond donors and acceptors in the major groove that exactly matches the one formed on poly[d(A-T)]. This property is not shared by λP_R.