PMID: 29581236

Authors:

Narayanan A, Vago FS, Li K, Qayyum MZ, Yernool D, Jiang W, Murakami KS

Title:

Cryo-EM structure of Escherichia coli sigma(70) RNAP and promoter DNA complex revealed a role of sigma non-conserved region during the open complex formation.

Journal:

J Biol Chem. 2018 Mar 26. pii: RA118.002161. doi: 10.1074/jbc.RA118.002161.

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 sigma70 factor form the RNAP holoenzyme to express housekeeping genes. The sigma70 contains a large insertion at between the conserved regions 1.2 and 2.1, the sigma non-conserved region (sigmaNCR), but its function remains to be elucidated. In this study, we determined the cryo-EM structures of the E. coli RNAP sigma70 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 sNCR 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 sNCR and DNA interaction by the amino acid substitutions (R157A/E) influences the DNA opening around the transcription start site and therefore decreases the transcription activity of RNAP. We propose that the sNCR and DNA interaction is conserved in proteobacteria and RNAP in other bacteria replace its role with a transcription factor.