The Σ70 region 1.2 regulates promoter escape by unwinding DNA downstream of the transcription start site

The mechanisms of abortive synthesis and promoter escape during initiation of transcription are poorly understood. Here, we show that, after initiation of RNA synthesis, non-specific interaction of Sigma(70) region 1.2, present in all Sigma(70) family factors, with the non-template strand around position -4 relative to the transcription start site facilitates unwinding of the DNA duplex downstream of the transcription start site. This leads to stabilization of short RNA products and allows their extension, i.e. promoter escape. We show that this activity of Sigma(70) region 1.2 is assisted by the beta-lobe domain, but does not involve the beta'-rudder or the beta'-switch-2, earlier proposed to participate in promoter escape. DNA sequence independence of this function of Sigma(70) region 1.2 suggests that it may be conserved in all Sigma(70) family factors. Our results indicate that the abortive nature of initial synthesis is caused, at least in part, by failure to open the downstream DNA by the beta-lobe and Sigma region 1.2.