The interaction between σS , the stationary phase σ factor, and the core enzyme of Escherichia coli RNA polymerase.

Abstract Background: The RNA polymerase holoenzyme of Escherichia coli is composed of a core enzyme (subunit structure α₂ ββ′) associated with one of the σ subunits, required for promoter recognition. Different σ factors compete for core binding. Among the seven σ factors present in E. coli , σ⁷⁰ controls gene transcription during the exponential phase, whereas σ^S regulates the transcription of genes in the stationary phase or in response to different stresses. Using labelled σ^S and σ⁷⁰ , we compared the affinities of both σ factors for core binding and investigated the structural changes in the different subunits involved in the formation of the holoenzymes. Results: Using native polyacrylamide gel electrophoresis, we demonstrate that σ^S binds to the core enzyme with fivefold reduced affinity compared to σ⁷⁰ . Using iron chelate protein footprinting, we show that the core enzyme significantly reduces polypeptide backbone solvent accessibility in regions 1.1, 2.5, 3.1 and 3.2 of σ^S , while increasing the accessibility in region 4.1 of σ^S . We have also analysed the positioning of σ^S on the holoenzyme by the proximity-dependent protein cleavage method using σ^S derivatives in which FeBABE was tethered to single cysteine residues at nine different positions. Protein cutting patterns are observed on the β and β′ subunits, but not α. Regions 2.5, 3.1 and 3.2 of σ^S are close to both β and β′ subunits, in agreement with iron chelate protein footprinting data. Conclusions: A comparison between these results using σ^S and previous data from σ⁷⁰ indicates similar contact patterns on the core subunits and similar characteristic changes associated with... [ABSTRACT FROM AUTHOR]