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

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.