Region 1.2 of the RNA polymerase σ subunit controls recognition of the -10 promoter element

Abstract

Recognition of the -10 promoter consensus element by region 2 of the bacterial RNA polymerase σ subunit is a key step in transcription initiation. σ also functions as an elongation factor, inducing transcription pausing by interacting with transcribed DNA non-template strand sequences that are similar to the -10 element sequence. Here, we show that the region 1.2 of Escherichia coli σ70, whose function was heretofore unknown, is strictly required for efficient recognition of the non-template strand of -10-like pause-inducing DNA sequence by σ region 2, and for σ-dependent promoter-proximal pausing. Recognition of the fork-junction promoter DNA by RNA polymerase holoenzyme also requires σ region 1.2 and thus resembles the pause-inducing sequence recognition. Our results, together with available structural data, support a model where σ region 1.2 acts as a core RNA polymerase-dependent allosteric switch that modulates non-template DNA strand recognition by σ region 2 during transcription initiation and elongation. © 2007 European Molecular Biology Organization | All Rights Reserved.