Domain 1.1 of the sigma(70) subunit of Escherichia coli RNA polymerase modulates the formation of stable polymerase/promoter complexes

The sigma 70 (sigma (70)) subunit of Escherichia coli RNA polymerase specif ies transcription from promoters that are responsible for basal gene expres sion during vegetative growth. When sigma (70) is present within polymerase holoenzyme, two of its domains, 2.4 and 4.2, interact with sequences withi n the -10 and -35 regions, respectively, of promoter DNA. However, in free sigma (70), DNA binding is prevented by domain 1.1, the N-terminal domain o f the protein. Previous work has demonstrated that the presence of domain 1 .1 is required for efficient transcription initiation at the lambda promote r P-R. 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 an d decay of stable, pretranscription complexes. We find that the absence of domain 1.1 does not render the polymerase defective at all of these promote rs. Depending on the promoter, the absence of domain 1.1 can promote or inh ibit transcription initiation by affecting the formation of stable pretrans cription complexes. However, domain 1.1 does not affect the stability of th ese 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 sigma (70) recognition seque nces. However, when domain 1.1 is absent, having this match becomes less im portant in determining how efficiently stable complexes are made. We sugges t that domain 1.1 influences initiation by constraining polymerase to asses s a promoter primarily by the fitness of its -10 and -35 regions to the can onical sequences. (C) 2001 Academic Press.