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TitleConcerted transformation of a hyper-paused transcription complex and its reinforcing protein.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 3040, Year 2024
Publish dateApr 8, 2024
AuthorsPhilipp K Zuber / Nelly Said / Tarek Hilal / Bing Wang / Bernhard Loll / Jorge González-Higueras / César A Ramírez-Sarmiento / Georgiy A Belogurov / Irina Artsimovitch / Markus C Wahl / Stefan H Knauer /
PubMed AbstractRfaH, a paralog of the universally conserved NusG, binds to RNA polymerases (RNAP) and ribosomes to activate expression of virulence genes. In free, autoinhibited RfaH, an α-helical KOW domain ...RfaH, a paralog of the universally conserved NusG, binds to RNA polymerases (RNAP) and ribosomes to activate expression of virulence genes. In free, autoinhibited RfaH, an α-helical KOW domain sequesters the RNAP-binding site. Upon recruitment to RNAP paused at an ops site, KOW is released and refolds into a β-barrel, which binds the ribosome. Here, we report structures of ops-paused transcription elongation complexes alone and bound to the autoinhibited and activated RfaH, which reveal swiveled, pre-translocated pause states stabilized by an ops hairpin in the non-template DNA. Autoinhibited RfaH binds and twists the ops hairpin, expanding the RNA:DNA hybrid to 11 base pairs and triggering the KOW release. Once activated, RfaH hyper-stabilizes the pause, which thus requires anti-backtracking factors for escape. Our results suggest that the entire RfaH cycle is solely determined by the ops and RfaH sequences and provide insights into mechanisms of recruitment and metamorphosis of NusG homologs across all life.
External linksNat Commun / PubMed:38589445 / PubMed Central
MethodsEM (single particle)
Resolution2.6 - 3.4 Å
Structure data

17626

8pdy

EMDB-17626, PDB-8pdy:
E. coli RNA polymerase paused at ops site
Method: EM (single particle) / Resolution: 2.8 Å

17632

8pen

EMDB-17632, PDB-8pen:
fully recruited RfaH bound to E. coli transcription complex paused at ops site (alternative state of RfaH)
Method: EM (single particle) / Resolution: 3.1 Å

17646

8pfg

EMDB-17646: transcription complex paused at ops site and bound to autoinhibited RfaH, not fully complementary scaffold
PDB-8pfg: autoinhibited RfaH bound to E. coli transcription complex paused at ops site (encounter complex), not fully complementary scaffold
Method: EM (single particle) / Resolution: 3.1 Å

17647

8pfj

EMDB-17647, PDB-8pfj:
fully recruited RfaH bound to E. coli transcription complex paused at ops site (not fully complementary scaffold; alternative state of RfaH)
Method: EM (single particle) / Resolution: 3.4 Å

17657

8ph9

EMDB-17657, PDB-8ph9:
E. coli RNA polymerase paused at ops site (non-complementary scaffold)
Method: EM (single particle) / Resolution: 3.0 Å

17668

8phk

EMDB-17668: E. coli transcription complex paused at ops site with fully recruited RfaH
PDB-8phk: fully recruited RfaH bound to E. coli transcription complex paused at ops site
Method: EM (single particle) / Resolution: 3.1 Å

17679

8pib

EMDB-17679, PDB-8pib:
autoinhibited RfaH bound to E. coli transcription complex paused at ops site (encounter complex)
Method: EM (single particle) / Resolution: 2.6 Å

17681

8pid

EMDB-17681, PDB-8pid:
backtracked E. coli transcription complex paused at ops site and bound to RfaH
Method: EM (single particle) / Resolution: 3.0 Å

17685

8pil

EMDB-17685, PDB-8pil:
E. coli transcription complex paused at ops site and bound to RfaH and NusA
Method: EM (single particle) / Resolution: 3.2 Å

17686

8pim

EMDB-17686, PDB-8pim:
fully recruited RfaH bound to E. coli transcription complex paused at ops site (not complementary scaffold)
Method: EM (single particle) / Resolution: 3.4 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

Source
  • escherichia coli (E. coli)
KeywordsTRANSCRIPTION / transcription complex / pause at ops site / DNA hairpin / pausing / recruited RfaH / ops hairpin / RfaH / ops / ops site / encounter complex / backtracking / NusA

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