Summary information and primary citation
- PDB-id
-
9msj;
DSSR-derived features in text and
JSON formats
- Class
- transcription
- Method
- cryo-EM (3.1 Å)
- Summary
- De novo sign RNA polymerase ntp-bound open complex
(rpo+2a)
- Reference
-
Mueller AU, Molina N, Nixon BT, Darst SA (2025):
"Real-time
capture of sigma N transcription initiation intermediates
reveals mechanism of ATPase-driven activation by limited
unfolding." Nat Commun, 16,
7138. doi: 10.1038/s41467-025-61837-4.
- Abstract
- 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<sub>N</sub> is unique among σ factors in its
structure and functional mechanism, requiring activation by
specialized AAA+ ATPases. Eσ<sub>N</sub> forms
an inactive promoter complex where the N-terminal
σ<sub>N</sub> region I
(σ<sub>N</sub>-RI) threads through a small DNA
bubble. On the opposite side of the DNA, the ATPase engages
σ<sub>N</sub>-RI within the pore of its
hexameric ring. Here, we perform kinetics-guided structural
analysis of de novo formed Eσ<sub>N</sub>
initiation complexes and engineer a biochemical assay to
measure ATPase-mediated σ<sub>N</sub>-RI
translocation during promoter melting. We show that the
ATPase exerts mechanical action to translocate about 30
residues of σ<sub>N</sub>-RI through the DNA
bubble, disrupting inhibitory structures of
σ<sub>N</sub> to allow full transcription
bubble formation. A local charge switch of
σ<sub>N</sub>-RI from positive to negative may
help facilitate disengagement of the otherwise processive
ATPase, allowing subsequent σ<sub>N</sub>
disentanglement from the DNA bubble.
