A general role of zinc binding domain revealed by structures of σ28-dependent transcribing complexes

In bacteria, {sigma}28 is the flagella-specific sigma factor that controls the expression of flagella-related genes involving bacterial motility and chemotaxis. However, its transcriptional mechanism remains largely unclear. Here we report cryo-EM structures of {sigma}28-dependent transcribing complexes on a complete flagella-specific DNA promoter. The structures reveal how {sigma}28-RNA polymerase (RNAP) recognizes promoter DNA through strong interaction with -10 element but weak contact with -35 element to initiate transcription. In addition, we observed a distinct architecture in which the {beta}' 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 facilitates the isomerization of RNAP-promoter closed to open complex due to compensating the weak interaction between {sigma}4/-35 element, and suggest that ZBD-relocation is a general mechanism employed by the {sigma}70-family factors to enhance transcription from promoters with weak {sigma}4/-35 element interactions.