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

Abstract

Expression of genes belonging to the pho regulon in Streptomyces coelicolor is positively regulated (as shown by comparing the wild-type and a ΔphoP 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 PhoPDBD 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 PhoPDBD. Deletion of 1 nt leaving a 10-nt direct repeat reduced drastically binding of PhoPDBD. 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 PhoPDBD in footprinting analyses. A cooperative binding of PhoPDBD molecules initiated at conserved core DRus appears to be the mechanism involved in binding of several PhoPDBD monomers to those complex operators. The information theory-based model that incorporates the positive or negative contribution to the binding of PhoPDBD of adjacent sequences has been used to deduce the structure of PHO boxes and the relevance of each DRu.