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-Structure paper
| タイトル | Real-time capture of σ transcription initiation intermediates reveals mechanism of ATPase-driven activation by limited unfolding. |
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| ジャーナル・号・ページ | Nat Commun, Vol. 16, Issue 1, Page 7138, Year 2025 |
| 掲載日 | 2025年8月4日 |
 著者 | Andreas U Mueller / Nina Molina / B Tracy Nixon / Seth A Darst /  |
| PubMed 要旨 | Bacterial σ factors bind RNA polymerase (E) to form holoenzyme (Eσ), conferring promoter specificity to E and playing a key role in transcription bubble formation. σ is unique among σ factors in ...Bacterial σ factors bind RNA polymerase (E) to form holoenzyme (Eσ), conferring promoter specificity to E and playing a key role in transcription bubble formation. σ is unique among σ factors in its structure and functional mechanism, requiring activation by specialized AAA+ ATPases. Eσ forms an inactive promoter complex where the N-terminal σ region I (σ-RI) threads through a small DNA bubble. On the opposite side of the DNA, the ATPase engages σ-RI within the pore of its hexameric ring. Here, we perform kinetics-guided structural analysis of de novo formed Eσ initiation complexes and engineer a biochemical assay to measure ATPase-mediated σ-RI translocation during promoter melting. We show that the ATPase exerts mechanical action to translocate about 30 residues of σ-RI through the DNA bubble, disrupting inhibitory structures of σ to allow full transcription bubble formation. A local charge switch of σ-RI from positive to negative may help facilitate disengagement of the otherwise processive ATPase, allowing subsequent σ disentanglement from the DNA bubble. |
 リンク | Nat Commun / PubMed:40759887 / PubMed Central |
| 手法 | EM (単粒子) |
| 解像度 | 2.6 - 4.6 Å |
| 構造データ |  EMDB-48574: Mycobacterial open-gate proteasome in complex with engineered NtrC1  EMDB-48576: de novo SigN RNA polymerase open complex (RPo), consensus map  EMDB-48577: de novo SigN RNA polymerase open complex (RPo), SigN focus map  EMDB-48578: de novo SigN RNA polymerase NTP-bound open complex (RPo+2A), consensus map  EMDB-48579: de novo SigN RNA polymerase NTP-bound open complex (RPo+2A), SigN focus map  EMDB-48580: de novo SigN RNA polymerase transcription initiation intermediate with pre-catalytic bEBP state (RPi1 open ring), consensus map  EMDB-48581: de novo SigN RNA polymerase transcription initiation intermediate with pre-catalytic bEBP state (RPi1 open ring), SigN focus map  EMDB-48582: de novo SigN RNA polymerase transcription initiation intermediate with pre-catalytic bEBP state (RPi1 open ring), bEBP focus map  EMDB-48583: de novo SigN RNA polymerase transcription initiation intermediate with post-catalytic bEBP state (RPi1 closed ring), consensus map  EMDB-48584: de novo SigN RNA polymerase transcription initiation intermediate with post-catalytic bEBP state (RPi1 closed ring), SigN focus map  EMDB-48585: de novo SigN RNA polymerase transcription initiation intermediate with post-catalytic bEBP state (RPi1 closed ring), bEBP focus map EMDB-48586, PDB-9mse: EMDB-48587, PDB-9msf: EMDB-48588, PDB-9msg: EMDB-48589, PDB-9msh: EMDB-48590, PDB-9msj: |
| 化合物 |  ChemComp-ATP:  ChemComp-MG:  ChemComp-POP:  ChemComp-ZN:  ChemComp-HOH:  ChemComp-ADP: |
| 由来 |
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 キーワード | TRANSCRIPTION / sigma N / sigma 54 / ATPase / bacterial enhancer binding protein / transcription initiation / intermediate / TRANSFERASE/DNA / TRANSFERASE-DNA complex |
escherichia coli (大腸菌)
aquifex aeolicus vf5 (バクテリア)