Structural basis of bacterial σ²⁸-mediated transcription reveals roles of the RNA polymerase zinc-binding domain

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.