Inter-sigmulon communication through topological promoter coupling

Divergent transcription from within bacterial intergenic regions frequently involves promoters dependent on alternative σ-factors. This is the case for the non-overlapping σ(70)- and σ(54)-dependent promoters that control production of the substrate-responsive regulator and enzymes for (methyl)phenol catabolism. Here, using an array of in vivo and in vitro assays, we identify transcription-driven supercoiling arising from the σ(54)-promoter as the mechanism underlying inter-promoter communication that results in stimulation of the activity of the σ(70)-promoter. The non-overlapping ‘back-to-back’ configuration of a powerful σ(54)-promoter and weak σ(70)-promoter within this system offers a previously unknown means of inter-sigmulon communication that renders the σ(70)-promoter subservient to signals that elicit σ(54)-dependent transcription without it possessing a cognate binding site for the σ(54)-RNA polymerase holoenzyme. This mode of control has the potential to be a prevalent, but hitherto unappreciated, mechanism by which bacteria adjust promoter activity to gain appropriate transcriptional control.