TY - JOUR T1 - Cryo-EM structure of <em>Escherichia coli</em> σ<sup>70</sup> RNAP and promoter DNA complex revealed a role of σ non-conserved region during the open complex formation JF - bioRxiv DO - 10.1101/256826 SP - 256826 AU - Anoop Narayanan AU - Frank S. Vago AU - Kungpeng Li AU - M. Zuhaib Qayyum AU - Dinesh Yernool AU - Wen Jiang AU - Katsuhiko S. Murakami Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/01/30/256826.abstract N2 - First step of gene expression is transcribing the genetic information stored in DNA to RNA by the transcription machinery including RNA polymerase (RNAP). In Escherichia coli, a primary σ70 factor form the RNAP holoenzyme to express housekeeping genes. The σ70 contains a large insertion at between the conserved regions 1.2 and 2.1, the σ non-conserved region (σNCR), but its function remains to be elucidated. In this study, we determined the cryo-EM structures of the E. coli RNAP σ70 holoenzyme and its complex with promoter DNA (open complex, RPo) at 4.2 and 5.75 Å resolutions, respectively, to reveal native conformations of RNAP and DNA. The RPo structure presented here found an interaction between R157 residue in the σNCR and promoter DNA just upstream of the −10 element, which was not observed in a previously determined E. coli RNAP transcription initiation complex (RPo plus short RNA) structure by X-ray crystallography due to restraint of crystal packing effect. Disruption of the σNCR and DNA interaction by the amino acid substitution (R157E) influences the DNA opening around the transcription start site and therefore decreases the transcription activity of RNAP. We propose that the σNCR and DNA interaction is conserved in proteobacteria and RNAP in other bacteria replace its role with a transcription factor. ER -