Recognition of bacterial promoter ‐10 region by σ subunit of RNA polymerase

Abstract

RNA polymerase (RNAP), a bacterial cell regulation target, binds promoters, then opens DNA near the transcription start site. The crucial step in DNA promoter melting is −10 element (consensus sequence T−12A−11T−10A−9A−8T−7) recognition by the RNAP sigma (σ) subunit. X‐ray crystallography reveals details of ‐10 element recognition by σ. Single stranded (ss) DNA with the TATAAT sequence is draped across a σ conserved surface, with a 90° turn between the −11 and −10. Specific interactions occur with the most conserved bases: T‐12, A‐11, and T‐7, especially A‐11 and T‐7, which are flipped out of ss DNA and buried in σ pockets. A hydrophobic pocket tightly fits A‐11 between σ R246 and Y253. A‐11 hydrogen bonds with σ K241, F242 and E243. T‐7 fits in a large hydrophilic σ pocket with three ordered waters. T‐7 hydrogen bonds with L209 and N206 and has water‐mediated interactions with several σ residues. Less important central bases, ‐10T, ‐9A and ‐8A, point away from σ and make few or no base‐specific contacts with the protein. The structure reveals insights into initiation of transcription bubble formation and suggests interesting ideas for rational antimicrobial design. The Leonia High School SMART (Students Modeling a Research Topic) Team partnered with a researcher to create a physical model of σ interacting with the DNA ‐10 element using 3D printing technology. Supported by a grant from HHMI Pre‐College Program.