Regulation of transcription by acetate in Escherichia coli: in vivo and in vitro comparisons.

Acetate, even at neutral pH, induces changes in gene expression that allow Escherichia coli to adapt to the diverse chemical stresses of the gastrointestinal tract. These include differential effects on transcription, including both activation and repression. The in vivo studies presented here show that cyclopropane fatty acid synthase transcription induced by neutral acetate proceeds via both the sigma70 and sigma38 forms of RNA polymerase. Upstream DNA elements are required in both cases, but in vitro studies demonstrate that the binding of regulatory factors is not needed. Sigma70 promoters respond towards acetate with very significant differences in vitro, with effects ranging from inhibition to lack of effect to weak stimulation to strong stimulation. By contrast, the effects of acetate on sigma38 transcription at these same promoters in vitro are generally stimulatory. Thus, acetate directly alters transcription complexes in vitro in ways that lead to significant differential transcription, contributing to the diverse effects that are known to allow adaptation in vivo.