Structural basis of bacterial σ 28 ‐mediated transcription reveals roles of the RNA polymerase zinc‐binding domain

Abstract

In bacteria, σ²⁸ is the flagella‐specific sigma factor that targets RNA polymerase (RNAP ) to control the expression of flagella‐related genes involving bacterial motility and chemotaxis. However, the structural mechanism of σ²⁸‐dependent promoter recognition remains uncharacterized. Here, we report cryo‐EM structures of E. coli σ²⁸‐dependent transcribing complexes on a complete flagella‐specific promoter. These structures reveal how σ²⁸‐RNAP recognizes promoter DNA through strong interactions with the −10 element, but weak contacts with the −35 element, to initiate transcription. In addition, we observed a distinct architecture in which the β′ zinc‐binding domain (ZBD ) of RNAP stretches out from its canonical position to interact with the upstream non‐template strand. Further in vitro and in vivo assays demonstrate that this interaction has the overall effect of facilitating closed‐to‐open isomerization of the RNAP –promoter complex by compensating for the weak interaction between σ4 and −35 element. This suggests that ZBD relocation may be a general mechanism employed by σ⁷⁰ family factors to enhance transcription from promoters with weak σ4/−35 element interactions.