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Structure paper

TitleA general mechanism for transcription bubble nucleation in bacteria.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 120, Issue 14, Page e2220874120, Year 2023
Publish dateApr 4, 2023
AuthorsAndreas U Mueller / James Chen / Mengyu Wu / Courtney Chiu / B Tracy Nixon / Elizabeth A Campbell / Seth A Darst /
PubMed AbstractBacterial transcription initiation requires σ factors for nucleation of the transcription bubble. The canonical housekeeping σ factor, σ, nucleates DNA melting via recognition of conserved bases ...Bacterial transcription initiation requires σ factors for nucleation of the transcription bubble. The canonical housekeeping σ factor, σ, nucleates DNA melting via recognition of conserved bases of the promoter -10 motif, which are unstacked and captured in pockets of σ. By contrast, the mechanism of transcription bubble nucleation and formation during the unrelated σ-mediated transcription initiation is poorly understood. Herein, we combine structural and biochemical approaches to establish that σ, like σ, captures a flipped, unstacked base in a pocket formed between its N-terminal region I (RI) and extra-long helix features. Strikingly, RI inserts into the nascent bubble to stabilize the nucleated bubble prior to engagement of the obligate ATPase activator. Our data suggest a general paradigm of transcription initiation that requires σ factors to nucleate an early melted intermediate prior to productive RNA synthesis.
External linksProc Natl Acad Sci U S A / PubMed:36972428 / PubMed Central
MethodsEM (single particle)
Resolution2.6 - 3.1 Å
Structure data

EMDB-28783: EsN-dhsU36mm2 full map (map 1)
Method: EM (single particle) / Resolution: 2.6 Å

EMDB-28784: EsN-dhsU36mm2 local map (map 2)
Method: EM (single particle) / Resolution: 3.0 Å

28785

8f1j

EMDB-28785: EsN-dhsU36mm2 composite map
PDB-8f1j: SigN RNA polymerase early-melted intermediate bound to mismatch DNA fragment dhsU36mm2 (-12A)
Method: EM (single particle) / Resolution: 2.6 Å

EMDB-28786: EsN-dhsU36duplex full map (map 1)
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-28790: EsN-dhsU36duplex local map (map 2)
Method: EM (single particle) / Resolution: 3.1 Å

28791

8f1k

EMDB-28791: EsN-dhsU36duplex composite map
PDB-8f1k: SigN RNA polymerase early-melted intermediate bound to full duplex DNA fragment dhsU36 (-12T)
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-28792: EsN-dhsU36mm1 full map (map 1)
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-28794: EsN-dhsU36mm1 local map (map 2)
Method: EM (single particle) / Resolution: 3.0 Å

28797

8f1i

EMDB-28797: EsN-dhsU36mm1 composite map
PDB-8f1i: SigN RNA polymerase early-melted intermediate bound to mismatch fragment dhsU36mm1 (-12T)
Method: EM (single particle) / Resolution: 3.0 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-HOH:
WATER / Water

Source
  • escherichia coli (E. coli)
  • aquifex aeolicus (bacteria)
KeywordsTRANSCRIPTION/DNA / promoter-bound / initiation / DNA melting / transcription bubble nucleation / TRANSCRIPTION / TRANSCRIPTION-DNA complex

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