The displacement of the σ70 finger in initial transcription is highly heterogeneous and promoter-dependent

Journal article

Most bacterial sigma factors (σ) contain a highly conserved structural module, the 'σ-finger', which forms a loop that protrudes towards the RNA polymerase active centre in the open complex and has been implicated in pre-organization of template DNA, abortive initiation of short RNAs, initiation pausing, and promoter escape. Here, we introduce a novel single-molecule FRET (smFRET) assay to monitor σ-finger motions during transcription initiation and promoter escape. By performing real-time smFRET measurements, we determine that for all promoters studied, displacement occurs before promoter escape and can occur either before or after a clash with the extending RNA. We show that the kinetics of σ-finger displacement are highly dependent on the promoter, with implications for transcription kinetics and regulation. Analogous mechanisms may operate in the similar modules present across all kingdoms of life.

Authors: Wang, A; Fletcher, A; Mukherjee, P; Grainger, DC; Mazumder, A

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Oxford University Press
• Journal: Nucleic Acids Research
• Volume: 53
• Issue: 17
• Pages: gkaf857
• Publication date: 2025-09-01
• DOI: 10.1093/nar/gkaf857
• EISSN: 1362-4962
• ISSN: 0305-1048
• Pmid: 40966499
• Language: English
• Keywords: Bacterial Proteins; Transcription Initiation, Genetic; Escherichia coli; Promoter Regions, Genetic; Single Molecule Imaging; Gene Expression Regulation, Bacterial; Fluorescence Resonance Energy Transfer; DNA-Directed RNA Polymerases; Kinetics; Sigma Factor; Transcription, Genetic