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Nucleic Acids Research Advance Access originally published online on January 10, 2008
Nucleic Acids Research 2008 36(4):1358-1368; doi:10.1093/nar/gkm1150
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Nucleic Acids Research, 2008, Vol. 36, No. 4 1358-1368
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Molecular Biology

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

Alberto Sola-Landa1, Antonio Rodríguez-García1, Alexander Kristian Apel1,2 and Juan F. Martín1,2,*

1Instituto de Biotecnología de León (INBIOTEC), Parque Científico de León, Av. Real, 1, 24006 and 2Área de Microbiología. Fac. CC. Biológicas y Ambientales, Universidad de León, Campus de Vegazana, s/n, 24071, León, Spain

*To whom correspondence should be addressed. Tel: +34 987 291 505/+34 987 210 308; Fax: +34 987 291 506/+34 987 210 388; Email: jf.martin{at}unileon.es

Received July 19, 2007. Revised December 11, 2007. Accepted December 12, 2007.

Expression of genes belonging to the pho regulon in Streptomyces coelicolor is positively regulated (as shown by comparing the wild-type and a {Delta}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 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.


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