Signal sensory systems that impact Σ54-dependent transcription

Alternative Sigma-factors of bacteria bind core RNA polymerase to program the specific promoter selectivity of the holoenzyme. Signal-responsive changes in the availability of different Sigma-factors redistribute the RNA polymerase among the distinct promoter classes in the genome for appropriate adaptive, developmental and survival responses. The Sigma 54-factor is structurally and functionally distinct from all other Sigma-factors. Consequently, binding of Sigma 54 to RNA polymerase confers unique features on the cognate holoenzyme, which requires activation by an unusual class of mechano-transcriptional activators, whose activities are highly regulated in response to environmental cues. This review summarizes the current understanding of the mechanisms of transcriptional activation by Sigma 54-RNA polymerase and highlights the impact of global regulatory factors on transcriptional efficiency from Sigma 54-dependent promoters. These global factors include the DNA-bending proteins IHF and CRP, the nucleotide alarmone ppGpp, and the RNA polymerase-targeting protein DksA.