Domain 1.1 of the σ70 Subunit of Escherichia coli RNA Polymerase Modulates the Formation of Stable Polymerase/Promoter Complexes

The sigma 70 (σ70) subunit of Escherichia coli RNA polymerase specifies transcription from promoters that are responsible for basal gene expression during vegetative growth. When σ70 is present within polymerase holoenzyme, two of its domains, 2.4 and 4.2, interact with sequences within the −10 and −35 regions, respectively, of promoter DNA. However, in free σ70, DNA binding is prevented by domain 1.1, the N-terminal domain of the protein. Previous work has demonstrated that the presence of domain 1.1 is required for efficient transcription initiation at the lambda promoter PR. To investigate whether this is a general property of domain 1.1, we have used five promoters to compare polymerases with and without domain 1.1 in in vitro transcription assays, and in assays assessing the formation and decay of stable, pretranscription complexes. We find that the absence of domain 1.1 does not render the polymerase defective at all of these promoters. Depending on the promoter, the absence of domain 1.1 can promote or inhibit transcription initiation by affecting the formation of stable pretranscription complexes. However, domain 1.1 does not affect the stability of these complexes once they are formed. For polymerases containing domain 1.1, the efficiency of stable complex formation correlates with how well the −10 and −35 regions of a promoter match the ideal σ70 recognition sequences. However, when domain 1.1 is absent, having this match becomes less important in determining how efficiently stable complexes are made. We suggest that domain 1.1 influences initiation by constraining polymerase to assess a promoter primarily by the fitness of its −10 and −35 regions to the canonical sequences.