In this study, we highlight the role of the discriminator as a global sensor of supercoiling variations and propose the first quantitative regulatory model of this principle, based on the specific step of promoter opening during transcription initiation. It defines the predictive rule by which SC quantitatively modulates the expression rate of bacterial promoters, depending on the G/C content of their discriminator and independently from promoter-specific regulatory proteins.

DNA supercoiling is an essential mechanism of bacterial chromosome compaction, whose level is mainly regulated by topoisomerase I and DNA gyrase. Inhibiting either of these enzymes with antibiotics leads to global supercoiling modifications and subsequent changes in global gene expression. In previous studies, genes responding to DNA relaxation induced by DNA gyrase inhibition were categorised as ‘supercoiling-sensitive’. Here, we studied the opposite variation of DNA supercoiling in the phytopathogen Dickeya dadantii using the non-marketed antibiotic seconeolitsine. We showed that the drug is active against topoisomerase I from this species, and analysed the first transcriptomic response of a Gram-negative bacterium to topoisomerase I inhibition. We find that the responding genes essentially differ from those observed after DNA relaxation, and further depend on the growth phase. We characterised these genes at the functional level, and also detected distinct patterns in terms of expression level, spatial and orientational organisation along the chromosome. Altogether, these results highlight that the supercoiling-sensitivity is a complex feature, which depends on the action of specific topoisomerases, on the physiological conditions, and on their genomic context. Based on previous in vitro expression data of several promoters, we propose a qualitative model of SC-dependent regulation that accounts for many of the contrasting transcriptomic features observed after DNA gyrase or topoisomerase I inhibition.

DNA supercoiling acts as a basal transcriptional regulator, which contributes to the quick and global transcriptional response of bacteria to many environmental changes. In spite of this importance, mechanistic models explaining the differential response of promoters to global topological variations of the chromosome remain essentially lacking. Here, we present the first quantitative transcriptional regulatory model by DNA supercoiling, focusing on the specific step of promoter opening during transcription initiation. Based on the known physico-chemical properties of DNA denaturation, it involves only one global adjustable parameter and is yet able to predict the global supercoiling response of promoters in a wide range of bacteria, based on the sequence content of their "discriminator" element. We first show that it quantitatively predicts both \emph{in vitro} and \emph{in vivo} data from transcription assays focusing on individual model promoters. We then assess the universality of the mechanism by analyzing transcriptomes of phylogenetically distant bacteria under conditions of supercoiling variation: (1) by gyrase-inhibiting antibiotics, (2) by biologically relevant environmental stresses, (3) naturally acquired and inherited in the longest-running evolution experiment. The model robustly predicts a significant contribution of the entire transcriptomic response to transient or inherited supercoiling variations in various species. This study strongly suggests that the proposed physical mechanism is used as an ubiquitous regulatory mechanism in the whole prokaryotic kingdom, based on the fundamental mechanical properties of the double-helix. Importance: DNA supercoiling acts as a global yet underestimated transcriptional regulator in bacteria. We propose the first quantitative model of this regulation mode, based on the specific step of promoter opening during transcription initiation, explaining the differential response of promoters to global topological variations of the chromosome. In contrast to classical mechanisms requiring dedicated regulatory molecules to bind target promoters, we show that global deformations of the DNA template itself underpin a selective response of each particular promoter, according to its "discriminator" sequence, by modulating the ability of RNA Polymerase to initiate transcription. This study defines the first systematic rule underpinning the ubiquitous regulatory action of DNA supercoiling on the core transcriptional machinery, in particular in response to quick environmental changes.

DNA supercoiling is an essential mechanism of bacterial chromosome compaction, whose level is mainly regulated by topoisomerase I and DNA gyrase. Inhibiting either of these enzymes with antibiotics leads to global supercoiling modifications and subsequent changes in global gene expression. In previous studies, genes responding to DNA relaxation induced by gyrase inhibition were categorized as "supercoiling-sensitive". Here, we studied the opposite variation of DNA supercoiling in the phytopathogen Dickeya dadantii using the non-marketed antibiotic seconeolitsine, and obtained the first transcriptomic response of a Gram-negative bacterium to topoisomerase I inhibition. We find that the responding genes essentially differ from those observed after DNA relaxation, and further depend on the growth phase. We characterised these genes at the functional level, and also detected distinct patterns in their spatial and orientational organisation along the chromosome. Altogether, these results suggest that the "supercoiling-sensitivity" is not an intrinsic property of promoters, but depends on the action of specific topoisomerases, on the physiological conditions, and on their genomic context. Based on previous in vitro expression data of several promoters, we propose a qualitative model of SC-dependent regulation that accounts for many of the contrasting transcriptomic features observed after gyrase or topoisomerase I inhibition.