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

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 σ(70), 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