Cryo-EM structure of Escherichia coli ⁷⁰ RNA polymerase and promoter DNA complex revealed a role of non-conserved region during the open complex formation

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 primary⁷⁰ factor forms the RNAP holoenzyme to express housekeeping genes. The ⁷⁰ contains a large insertion between the conserved regions 1.2 and 2.1, the non-conserved region (_NCR), but its function remains to be elucidated. In this study, we determined the cryo-EM structures of the E. coli RNAP⁷⁰ 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 the_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 because of restraint of crystal packing effects. Disruption of the_NCR and DNA interaction by the amino acid substitutions (R157A/R157E) influences the DNA opening around the transcription start site and therefore decreases the transcription activity of RNAP. We propose that the _NCR and DNA interaction is conserved in proteobacteria, and RNAP in other bacteria replaces its role with a transcription factor.