PMID: 32484956 , Related PDB ids: 6PMI, 6PMJ

Authors:

Shi W, Zhou W, Zhang B, Huang S, Jiang Y, Schammel A, Hu Y, Liu B

Title:

Structural basis of bacterial sigma(28) -mediated transcription reveals roles of the RNA polymerase zinc-binding domain.

Journal:

EMBO J. 2020 Jun 2:e104389. doi: 10.15252/embj.2020104389.

Abstract:

In bacteria, sigma(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 sigma(28) -dependent promoter recognition remains uncharacterized. Here, we report cryo-EM structures of E. coli sigma(28) -dependent transcribing complexes on a complete flagella-specific promoter. These structures reveal how sigma(28) -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 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 has the overall effect of facilitating closed-to-open isomerization of the RNAP-promoter complex by compensating for the weak interaction between sigma4 and -35 element. This suggests that ZBD relocation may be a general mechanism employed by sigma(70) family factors to enhance transcription from promoters with weak sigma4/-35 element interactions.