A Basal Promoter Element Recognized by Free RNA Polymerase σ Subunit Determines Promoter Recognition by RNA Polymerase Holoenzyme

SummaryDuring transcription initiation by bacterial RNA polymerase, the σ subunit recognizes the −35 and −10 promoter elements; free σ, however, does not bind DNA. We selected ssDNA aptamers that strongly and specifically bound free σA from Thermus aquaticus. A consensus sequence, GTA(C/T)AATGGGA, was required for aptamer binding to σA, with the TA(C/T)AAT segment making interactions similar to those made by the −10 promoter element (consensus sequence TATAAT) in the context of RNA polymerase holoenzyme. When in dsDNA form, the aptamers function as strong promoters for the T. aquaticus RNA polymerase σA holoenzyme. Recognition of the aptamer-based promoters depends on the downstream GGGA motif from the aptamers' common sequence, which is contacted by σA region 1.2 and directs transcription initiation even in the absence of the −35 promoter element. Thus, recognition of bacterial promoters is controlled by independent interactions of σ with multiple basal promoter elements.