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TitleMechanisms of DNA opening revealed in AAA+ transcription complex structures.
Journal, issue, pagesSci Adv, Vol. 8, Issue 51, Page eadd3479, Year 2022
Publish dateDec 21, 2022
AuthorsFuzhou Ye / Forson Gao / Xiaojiao Liu / Martin Buck / Xiaodong Zhang /
PubMed AbstractGene transcription is carried out by RNA polymerase (RNAP) and requires the conversion of the initial closed promoter complex, where DNA is double stranded, to a transcription-competent open promoter ...Gene transcription is carried out by RNA polymerase (RNAP) and requires the conversion of the initial closed promoter complex, where DNA is double stranded, to a transcription-competent open promoter complex, where DNA is opened up. In bacteria, RNAP relies on σ factors for its promoter specificities. Using a special form of sigma factor (σ), which forms a stable closed complex and requires its activator that belongs to the AAA+ ATPases (ATPases associated with diverse cellular activities), we obtained cryo-electron microscopy structures of transcription initiation complexes that reveal a previously unidentified process of DNA melting opening. The σ amino terminus threads through the locally opened up DNA and then becomes enclosed by the AAA+ hexameric ring in the activator-bound intermediate complex. Our structures suggest how ATP hydrolysis by the AAA+ activator could remove the σ inhibition while helping to open up DNA, using σ amino-terminal peptide as a pry bar.
External linksSci Adv / PubMed:36542713 / PubMed Central
MethodsEM (single particle)
Resolution3.4 - 4.5 Å
Structure data

14171

7qv9

EMDB-14171, PDB-7qv9:
CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-14172: CryoEM structure of bacterial transcription intermediate complex mediated by activator protein PspF
Method: EM (single particle) / Resolution: 4.2 Å

14190

7qwp

EMDB-14190, PDB-7qwp:
CryoEM structure of bacterial transcription close complex (RPc)
Method: EM (single particle) / Resolution: 3.4 Å

14200

7qxi

EMDB-14200, PDB-7qxi:
Cryo-EM structure of RNA polymerase-sigma54 holo enzyme with promoter DNA closed complex
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-14206: Cryo-EM structure of RNA polymerase-sigma54 holoenzyme with promoter DNA and transcription activator PspF intermedate complex
Method: EM (single particle) / Resolution: 4.5 Å

EMDB-14207: Cryo-EM structure of RNA polymerase-sigma54 holoenzyme with promoter DNA and transcription activator PspF intermedate complex
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-14208: Cryo-EM structure of RNA polymerase-sigma54 holoenzyme with promoter DNA and transcription activator PspF intermedate complex
Method: EM (single particle) / Resolution: 4.3 Å

Chemicals

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-AF3:
ALUMINUM FLUORIDE

Source
  • escherichia coli k-12 (bacteria)
  • klebsiella pneumoniae (bacteria)
KeywordsTRANSCRIPTION / RNA polymerase / AAA protein / transcription regulation / cryoEM / Cryo EM / transcription close complex / sigma54

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