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.
| Original language | English (US) |
|---|---|
| Article number | e104389 |
| Journal | EMBO Journal |
| Volume | 39 |
| Issue number | 14 |
| DOIs | |
| State | Published - Jul 15 2020 |
Bibliographical note
Funding Information:The cryo-EM data were collected at the cryo-electron microscopy facility in the Hormel Institute, University of Minnesota, which is funded by the Hormel Foundation. This work was supported by the start-up funding granted to B.L. from the Hormel Institute, University of Minnesota, and the National Natural Science Foundation of China to Y.H. (#31670134). Support from the Youth Innovation Promotion Association, CAS, to Y.H. and help from the Core Facility and Technical Support of Wuhan Institute of Virology in radioactive and fluorescent tests are also acknowledged.
Funding Information:
The cryo‐EM data were collected at the cryo‐electron microscopy facility in the Hormel Institute, University of Minnesota, which is funded by the Hormel Foundation. This work was supported by the start‐up funding granted to B.L. from the Hormel Institute, University of Minnesota, and the National Natural Science Foundation of China to Y.H. (#31670134). Support from the Youth Innovation Promotion Association, CAS, to Y.H. and help from the Core Facility and Technical Support of Wuhan Institute of Virology in radioactive and fluorescent tests are also acknowledged.
Publisher Copyright:
© 2020 The Authors
Keywords
- Cryo-EM
- ZBD relocation
- flagellar gene regulation
- transcription initiation complex
- σ