Target genes and structure of the direct repeats in the DNA-binding sequences of the response regulator PhoP in Streptomyces coelicolor

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Abstract
Expression of genes belonging to the pho regulon in Streptomyces coelicolor is positively regulated (as shown by comparing the wild-type and a Δ phoP mutant) by binding of the response regulator PhoP to 11-nt direct repeats (DRus). These sequences have been found in over 100 genes of Streptomyces coelicolor ; 20 of them were cloned and the binding of PhoP DBD to most of their promoters has been shown by electrophoretic mobility shift assays. Deletion experiments showed that at least two DRus are required for proper binding of PhoP DBD . Deletion of 1 nt leaving a 10-nt direct repeat reduced drastically binding of PhoP DBD . Three different types of operators have been identified. Complex operators (class III) contain up to six DRus, some of them with poor conservation of the 11-nt consensus sequence, which however were protected by PhoP DBD in footprinting analyses. A cooperative binding of PhoP DBD molecules initiated at conserved core DRus appears to be the mechanism involved in binding of several PhoP DBD monomers to those complex operators. The information theory-based model that incorporates the positive or negative contribution to the binding of PhoP DBD of adjacent sequences has been used to deduce the structure of PHO boxes and the relevance of each DRu.