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TitleStructural basis of bacterial σ -mediated transcription reveals roles of the RNA polymerase zinc-binding domain.
Journal, issue, pagesEMBO J, Vol. 39, Issue 14, Page e104389, Year 2020
Publish dateJul 15, 2020
AuthorsWei Shi / Wei Zhou / Baoyue Zhang / Shaojia Huang / Yanan Jiang / Abigail Schammel / Yangbo Hu / Bin Liu /
PubMed AbstractIn bacteria, σ 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 ...In bacteria, σ 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 σ -dependent promoter recognition remains uncharacterized. Here, we report cryo-EM structures of E. coli σ -dependent transcribing complexes on a complete flagella-specific promoter. These structures reveal how σ -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 σ family factors to enhance transcription from promoters with weak σ4/-35 element interactions.
External linksEMBO J / PubMed:32484956 / PubMed Central
MethodsEM (single particle)
Resolution3.86 - 3.91 Å
Structure data

20394

6pmi

EMDB-20394, PDB-6pmi:
Sigm28-transcription initiation complex with specific promoter at the state 1
Method: EM (single particle) / Resolution: 3.86 Å

20395

6pmj

EMDB-20395, PDB-6pmj:
Sigm28-transcription initiation complex with specific promoter at the state 2
Method: EM (single particle) / Resolution: 3.91 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

Source
  • escherichia coli (E. coli)
  • escherichia coli o157:h7 (bacteria)
  • escherichia coli o45:k1 (strain s88 / expec) (bacteria)
  • escherichia coli (strain k12) (bacteria)
KeywordsTRANSCRIPTION / sigma28 / transcription initiation complex / RpoF / ZNR domain

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