Cryo-EM structure of Escherichia coli σ70 RNAP and promoter DNA complex revealed a role of σ nonconserved region during the open complex formation

Abstract

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 {sigma}70 factor form the RNAP holoenzyme to express housekeeping genes. The {sigma}70 contains a large insertion at between the conserved regions 1.2 and 2.1, the {sigma} non-conserved region ({sigma}NCR), but its function remains to be elucidated. In this study, we determined the cryo-EM structures of the E. coli RNAP {sigma}70 holoenzyme and its complex with promoter DNA (open complex, RPo) at 4.2 and 5.75 [A] resolutions, respectively, to reveal native conformations of RNAP and DNA. The RPo structure presented here found an interaction between R157 residue in the {sigma}NCR 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 {sigma}NCR 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 {sigma}NCR and DNA interaction is conserved in proteobacteria and RNAP in other bacteria replace its role with a transcription factor.