Structural Basis of σ54 Displacement and Promoter Escape in Bacterial Transcription

Gene transcription is a fundamental cellular process carried out by RNA polymerase (RNAP). Transcription initiation is highly regulated and in bacteria, transcription initiation is mediated by {sigma} factors, which recruit RNA polymerase (RNAP) to the promoter DNA region and facilitate open complex formation, where double stranded DNA is opening up into a transcription bubble and template strand DNA is in position for initial RNA synthesis. During initial transcription, DNA downstream of the transcription start site is fed into the active site of RNAP, whilst the upstream promoter DNA remains tethered to the RNAP via the {sigma} factor, resulting in a build-up of tension. In order to progress to the processive elongation state, RNAP must escape from the promoter, and displace or dissociate the {sigma} factor. Bacteria s factors can be broadly separated into two classes with the majority belong to the s70 class, represented by the {sigma}70 that regulate housekeeping genes. {sigma}54 forms a class on its own and regulate stress response genes. Extensive studies on {sigma}70 have revealed the molecular mechanisms of {sigma}70 promoter escape while how {sigma}54 transitions from initial transcription to elongation is unknown. Here we present a series of cryo electron microscopy structures of the {sigma}54 factor with progressively longer RNA, revealing the molecular mechanism of {sigma}54 displacement and promoter escape. Our data show that the initial instability is driven by DNA scrunching, and the final displacement steps are driven by both RNA extension and DNA scrunching.