Pseudomonas aeruginosa SutA wedges RNAP lobe domain open to facilitate promoter DNA unwinding

Abstract Pseudomonas aeruginosa ( Pae ) SutA adapts bacteria to hypoxia and nutrition-limited environment during chronic infection by increasing transcription activity of an RNA polymerase (RNAP) holoenzyme comprising the stress-responsive σ factor σ S (RNAP-σ S ). SutA shows no homology to previously characterized RNAP-binding proteins. The structure and mode of action of SutA remain unclear. Here we determined cryo-EM structures of Pae RNAP-σ S holoenzyme, Pae RNAP-σ S holoenzyme complexed with SutA, and Pae RNAP-σ S transcription initiation complex comprising SutA. The structures show SutA pinches RNAP-β protrusion and facilitates promoter unwinding by wedging RNAP-β lobe open. Our results demonstrate that SutA clears an energetic barrier to facilitate promoter unwinding of RNAP-σ S holoenzyme.