Inter-sigmulon communication through topological promoter coupling

Abstract

Divergent transcription from within bacterial intergenic regions frequently involves promoters dependent on alternative σ-factors. This is the case for the non-overlapping σ70- and σ54-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 σ54-promoter as the mechanism underlying inter-promoter communication that results in stimulation of the activity of the σ70-promoter. The non-overlapping ‘back-to-back’ configuration of a powerful σ54-promoter and weak σ70-promoter within this system offers a previously unknown means of inter-sigmulon communication that renders the σ70-promoter subservient to signals that elicit σ54-dependent transcription without it possessing a cognate binding site for the σ54-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.

The ancestral stringent response potentiator, DksA has been adapted throughout Salmonella evolution to orchestrate the expression of metabolic, motility, and virulence pathways

“…Gel retardation assay was carried out according to. 81 A 1,100 bp DNA fragment corresponding to the regulatory region upstream from hilA was generated using the primers hilA_prom_Fw and hilA_prom_Rev listed in Table S3B. 75 ng of the DNA probe was incubated at 4°C for 60 min with 1 unit of E. coli RNAP holoenzyme (New-England Biolabs) and increasing amounts (0.017 to 0.7 µg) of purified His-DksA in the Binding buffer [35 mM Tris-Ac (pH 7.9), 70 mM KAc, 5 mM MgAc 2 , 20 mM NH 4 Ac, 1 mM DTT].…”

Transient and dynamic DNA supercoiling potently stimulates the leu-500 promoter in Escherichia coli

“…Although these two transient supercoiled domains may be relaxed by DNA topoisomerases or cancel each other by diffusion (13,14,16,24), they should have great influence on nearby DNA transactions, such as transcription. Indeed, several cases (25)(26)(27)(28)(29) demonstrated that transcription coupled DNA supercoiling (TCDS) 2 plays important roles in divergently coupled promoters/transcriptions in which two neighboring promoters initiate transcription in opposite directions. For example, in the ilvYC operon of E. coli, the ilvY promoter is divergently coupled to the ilvC promoter (28).…”