Fig. 2
AhdI R-M system promoter regions. The arrangement of the promoter elements for AhdI CR and M promoters is based on the experimental information provided in [6]. The regions which are schematically shown correspond to (a) PCR promoter. Circles indicate C monomers, the rectangles indicates RNAP, while the arrows indicate transcriptionally active configurations. K2 – K5 denote the dissociation constants (see Additional file 1) corresponding to different promoter configurations (K1 denotes the dissociation constant of dimerization), where ω and ω’ denote, respectively, the binding cooperativity between the two C dimers bound to DNA, and between C dimer bound to the distal binding site and RNAP. C binds to the promoter as either dimer (K3) or tetramer (K4). The bound dimer recruits RNAP to the promoter (K5). On the other hand, the tetramer configuration corresponds to the repression, as it prevents RNAP binding to the promoter. b Transcription is repressed by DNA methylation due to M binding [6], i.e. M methylates specific sites in M promoter that overlap RNAP binding site – for simplicity this is in the figure represented as M being bound to the promoter DNA