Comparative Analysis of the Interactions of Escherichia Coli σS and σ70 RNA Polymerase Holoenzyme with the Stationary-Phase-Specific bolAp1 Promoter

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Abstract
We have investigated the interactions of Escherichia coli σ70 and σS holoenzyme RNA polymerases (EσS and Eσ70) with the stationary-phase-specific bolAp1 promoter by various footprinting methods in vitro. EσS and Eσ70 have been shown to transcribe the bolAp1 promoter in vitro. We have determined the effects of salt and holoenzyme concentrations on EσS and Eσ70 open complex formation at the bolAp1 promoter in vitro. We have obtained a high-resolution hydroxyl radical (OH·) footprint of EσS and Eσ70 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 °C, both holoenzymes produced similar but not identical patterns of reactivities.