Comparative analysis of the interactions of Escherichia coli sigma(S) and sigma(70) RNA polymerase holoenzyme with the stationary-phase-specific bolAp1 promoter

We have investigated the interactions of Escherichia coli sigma(70) and sigma(S) holoenzyme RNA polymerases (E sigma(S) and E sigma(70)) with the stationary-phase-specific bolAp1 promoter by various footprinting methods in vitro. E sigma(S) and E sigma(70) have been shown to transcribe the bolAp1 promoter in vitro. We have determined the effects of salt and holoenzyme concentrations on E sigma(S) and E sigma(70) open complex formation at the bolAp1 promoter in vitro. We have obtained a high-resolution hydroxyl radical (OH) footprint of E sigma(S) and E sigma(70) on the bolAp1 promoter. The OH footprinting data show remarkable similarities between the footprints of the heparin-resistant transcription complexes of the two holoenzymes which have the same +1 transcription start site. However, there are distinctive differences in the protection patterns in the region between -20 and -10 of the bolAp1 promoter. KMnO4 reactivity assays reveal that, at 37 degrees C, both holoenzymes produced similar but not identical patterns of reactivities.