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Nucleic Acids Res. 2013 Apr;41(8):4565-72. doi: 10.1093/nar/gkt116. Epub 2013 Feb 20.

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

Author information

  • 1Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Baddiley-Clark Building, Richardson Road, Newcastle upon Tyne NE2 4AX, UK.

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.

PMID:
23430153
[PubMed - indexed for MEDLINE]
PMCID:
PMC3632114
Free PMC Article

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