DNA supercoiling contributes to disconnect σs accumulation from σs-dependent transcription in Escherichia coli

The sigma(S) subunit of RNA polymerase is a key regulator of Escherichia coli transcription in stress conditions. sigma(S) accumulates in cells subjected to stresses such as an osmotic upshift or the entry into stationary phase. We show here that, at elevated osmolarity, sigma(S) accumulates long before the beginning of the sigma(S) -dependent induction of osmE (p) , one of its target promoters. A combination of in vivo and in vitro evidence indicates that a high level of DNA negative supercoiling inhibits transcription by Esigma(S). The variations in superhelical densities occurring as a function of growth conditions can modulate transcription of a subset of sigma(S) targets and thereby contribute to the temporal disconnection between the accumulation of sigma(S) and sigma(S)-driven transcription. We propose that, in stress conditions leading to the accumulation of sigma(S) without lowering the growth rate, the level of DNA supercoiling acts as a checkpoint that delays the shift from the major (Esigma(70)) to the general stress (Esigma(S)) transcriptional machinery, retarding the induction of a subset of the sigma(S) regulon until the conditions become unfavourable enough to cause entry into stationary phase.