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

• Published in: The Journal of biological chemistry Vol. 293; no. 19; p. 7367
• Main Authors: Narayanan, Anoop, Vago, Frank S, Li, Kunpeng, Qayyum, M Zuhaib, Yernool, Dinesh, Jiang, Wen, Murakami, Katsuhiko S
• Format: Journal Article
• Language: English
• Published: United States 11.05.2018
• Subjects: Cryoelectron Microscopy - methods; DNA, Bacterial - chemistry; DNA, Bacterial - genetics; DNA-Binding Proteins - metabolism; DNA-Directed RNA Polymerases - chemistry; DNA-Directed RNA Polymerases - metabolism; Escherichia coli - enzymology; Escherichia coli - genetics; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - metabolism; Genes, Bacterial; Genes, Essential; Nucleic Acid Conformation; Promoter Regions, Genetic; Protein Binding; Protein Conformation; Sigma Factor - chemistry; Sigma Factor - metabolism; Transcription Initiation Site; Transcription, Genetic; transcription; σ non-conserved region; open complex; promoter DNA; promoter; structural biology; RNA polymerase; cryo-EM; cryo-electron microscopy
• ISSN: 1083-351X

First step of gene expression is transcribing the genetic information stored in DNA to RNA by the transcription machinery including RNA polymerase (RNAP). In , a primary σ factor forms the RNAP holoenzyme to express housekeeping genes. The σ contains a large insertion between the conserved regions 1.2 and 2.1, the σ non-conserved region (σ ), but its function remains to be elucidated. In this study, we determined the cryo-EM structures of the RNAP σ 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 σ and promoter DNA just upstream of the -10 element, which was not observed in a previously determined RNAP transcription initiation complex (RPo plus short RNA) structure by X-ray crystallography because of restraint of crystal packing effects. Disruption of the σ 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 σ and DNA interaction is conserved in proteobacteria, and RNAP in other bacteria replaces its role with a transcription factor.