Structural basis of bacterial ?28-mediated transcription reveals roles of the RNA polymerase zinc-binding domain

In bacteria, ?28 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 ?28-dependent promoter recognition remains uncharacterized. Here we report cryo-EM structures of E. coli ?28-dependent transcribing complexes on a complete flagella-specific promoter. These structures reveal how ?28-RNAP recognizes promoter DNA through strong interactions with the ?10 element, but weak contacts with the ?35 sequence element, to initiate transcription. In addition, we observed a distinct architecture in which the ?? 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 ?4/?35 element. This suggests that ZBD relocation may be a general mechanism employed by ?70-family factors to enhance transcription from promoters with weak ?4/?35 element interactions.