Nucleic Acids Research 2013-04-01

The σ70 region 1.2 regulates promoter escape by unwinding DNA downstream of the transcription start site.

Aleksandra Bochkareva, Nikolay Zenkin

Index: Nucleic Acids Res. 41(8) , 4565-72, (2013)

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Abstract

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 σ(70) region 1.2, present in all σ(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 σ(70) region 1.2 is assisted by the β-lobe domain, but does not involve the β'-rudder or the β'-switch-2, earlier proposed to participate in promoter escape. DNA sequence independence of this function of σ(70) region 1.2 suggests that it may be conserved in all σ(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 β-lobe and σ region 1.2.