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PMID: 18187507 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

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

Nucleic acids research ·Vol. 36 ·No. 4 ·2008-03-00 ·Pages 1358-68

Sola-Landa A, Rodríguez-García A, Apel AK, Martín JF

Abstract

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

MeSH Terms
Bacterial Proteins/metabolism Base Sequence Binding Sites Consensus Sequence DNA Footprinting DNA, Bacterial/chemistry Gene Expression Regulation, Bacterial Operator Regions, Genetic Phosphates/metabolism Promoter Regions, Genetic Repetitive Sequences, Nucleic Acid Sequence Analysis, DNA Streptomyces coelicolor/genetics,metabolism
Chemicals
Bacterial Proteins DNA, Bacterial Phosphates PhoP protein, Bacteria
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Sola-Landa Alberto
Instituto de Biotecnología de León (INBIOTEC), Parque Científico de León, Av. Real, 1, 24006, León, Spain.
Rodríguez-García Antonio
Apel Alexander Kristian
Martín Juan F
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkm1150
Published
2008-03-00
Epub
2008-00-10
Pages
1358-68
Language
English
Region
England
NLM ID
0411011
PMCID
PMC2275107
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkm1150 PMC Full Text View journal details
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