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Structure paper

TitleStructural basis of ribosomal RNA transcription regulation.
Journal, issue, pagesNat Commun, Vol. 12, Issue 1, Page 528, Year 2021
Publish dateJan 22, 2021
AuthorsYeonoh Shin / M Zuhaib Qayyum / Danil Pupov / Daria Esyunina / Andrey Kulbachinskiy / Katsuhiko S Murakami /
PubMed AbstractRibosomal RNA (rRNA) is most highly expressed in rapidly growing bacteria and is drastically downregulated under stress conditions by the global transcriptional regulator DksA and the alarmone ppGpp. ...Ribosomal RNA (rRNA) is most highly expressed in rapidly growing bacteria and is drastically downregulated under stress conditions by the global transcriptional regulator DksA and the alarmone ppGpp. Here, we determined cryo-electron microscopy structures of the Escherichia coli RNA polymerase (RNAP) σ holoenzyme during rRNA promoter recognition with and without DksA/ppGpp. RNAP contacts the UP element using dimerized α subunit carboxyl-terminal domains and scrunches the template DNA with the σ finger and β' lid to select the transcription start site favorable for rapid promoter escape. Promoter binding induces conformational change of σ domain 2 that opens a gate for DNA loading and ejects σ from the RNAP cleft to facilitate open complex formation. DksA/ppGpp binding also opens the DNA loading gate, which is not coupled to σ ejection and impedes open complex formation. These results provide a molecular basis for the exceptionally active rRNA transcription and its vulnerability to DksA/ppGpp.
External linksNat Commun / PubMed:33483500 / PubMed Central
MethodsEM (single particle)
Resolution3.53 - 4.14 Å
Structure data

EMDB-21879, PDB-7khc:
Escherichia coli RNA polymerase and rrnBP1 promoter closed complex
Method: EM (single particle) / Resolution: 4.14 Å

EMDB-21880, PDB-7khb:
Escherichia coli RNA polymerase and rrnBP1 promoter open complex
Method: EM (single particle) / Resolution: 3.53 Å

EMDB-21881, PDB-7khi:
Escherichia coli RNA polymerase and rrnBP1 promoter complex with DksA/ppGpp
Method: EM (single particle) / Resolution: 3.62 Å

EMDB-21883, PDB-7khe:
Escherichia coli RNA polymerase and rrnBP1 promoter pre-open complex with DksA/ppGpp
Method: EM (single particle) / Resolution: 3.58 Å

Chemicals

ChemComp-1N7:
CHAPSO / detergent*YM

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-POP:
PYROPHOSPHATE 2-

ChemComp-G4P:
GUANOSINE-5',3'-TETRAPHOSPHATE

Source
  • Escherichia coli (E. coli)
  • escherichia coli (strain k12) (bacteria)
  • escherichia coli k-12 (bacteria)
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION / TRANSCRIPTION-DNA complex

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