The Cooperative Binding Energetics of CytR and cAMP Receptor Protein Support a Quantitative Model of Differential Activation and Repression of CytR-Regulated Class III Escherichia coli Promoters

cAMP receptor protein (CRP) and CytR mediate positive and negative control of nine genes in Escherichia coli, most of which are involved in nucleoside catabolism and recycling. Five promoters share a common architecture in which tandem CRP sites flank an intervening CytR operator (CytO). CytR and CRP bind cooperatively to these promoters to form a three-protein, DNA-bound complex that controls activation and repression, the levels of which vary markedly among the promoters. To understand the specific combinatorial control mechanisms that are responsible for this outcome, we have used quantitative DNase I footprinting to generate individual site isotherms for each site of protein-DNA interaction. The intrinsic affinities of each transcription factor for its respective site and the specific patterns of cooperativity and competition underlying the molecular interactions at each promoter were determined by a global analysis of these titration data. Here we present results obtained for nupGP and tsxP2, adding to results published previously for deoP2, udpP, and cddP. These data allowed us to correlate the reported levels of activation, repression, and induction with the ligation states of these five promoters under physiologically relevant conditions. A general pattern of transcriptional regulation emerges that allows for complex patterns of regulation in this seemingly simple system.