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Real-time capture of σN transcription initiation intermediates reveals mechanism of ATPase-driven activation by limited unfolding
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Real-time capture of σN transcription initiation intermediates reveals mechanism of ATPase-driven activation by limited unfolding
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Journal Article
Real-time capture of σN transcription initiation intermediates reveals mechanism of ATPase-driven activation by limited unfolding
2025
Overview
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
N
is unique among σ factors in its structure and functional mechanism, requiring activation by specialized AAA+ ATPases. Eσ
N
forms an inactive promoter complex where the N-terminal σ
N
region I (σ
N
-RI) threads through a small DNA bubble. On the opposite side of the DNA, the ATPase engages σ
N
-RI within the pore of its hexameric ring. Here, we perform kinetics-guided structural analysis of de novo formed Eσ
N
initiation complexes and engineer a biochemical assay to measure ATPase-mediated σ
N
-RI translocation during promoter melting. We show that the ATPase exerts mechanical action to translocate about 30 residues of σ
N
-RI through the DNA bubble, disrupting inhibitory structures of σ
N
to allow full transcription bubble formation. A local charge switch of σ
N
-RI from positive to negative may help facilitate disengagement of the otherwise processive ATPase, allowing subsequent σ
N
disentanglement from the DNA bubble.
Bacterial transcription with σ
N
requires activation by specialized AAA+ ATPases. Here, the authors visualize transient structural intermediates and engineer a biochemical assay to show that these ATPases partially unfold σ
N
to initiate transcription.
Publisher
Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
Subject
/ 38/70
/ Adenosine Triphosphatases - genetics
/ Adenosine Triphosphatases - metabolism
/ Bacterial Proteins - chemistry
/ Bacterial Proteins - genetics
/ Bacterial Proteins - metabolism
/ DNA
/ DNA-Directed RNA Polymerases - chemistry
/ DNA-Directed RNA Polymerases - genetics
/ DNA-Directed RNA Polymerases - metabolism
/ Escherichia coli - metabolism
/ Humanities and Social Sciences
/ Kinetics
/ Proteins
/ Science
