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

Nucleic Acids Research
Alberto Sola-LandaJuan F Martín

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 o...Continue Reading

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Citations

Jun 10, 2011·Nucleic Acids Research·Santosh ChauhanJaya Sivaswami Tyagi
Sep 4, 2008·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Shu WangCong Zhao Zhou
Jan 8, 2010·BMC Genomics·Kay NieseltElizabeth M H Wellington
Jun 25, 2014·Future Microbiology·Fernando Santos-BeneitJuan F Martín
Oct 7, 2017·Applied Microbiology and Biotechnology·María Ordóñez-RoblesAntonio Rodríguez-García
Feb 28, 2009·Environmental Microbiology·Rahat ZaheerTurlough M Finan
May 25, 2012·Applied Microbiology and Biotechnology·Juan F MartínEllizabeth M H Wellington
Aug 25, 2015·Applied Microbiology and Biotechnology·Renjun YangJilun Li
Apr 3, 2012·Applied Microbiology and Biotechnology·Emmanuelle DarbonMarie-Joëlle Virolle
Feb 24, 2011·Microbial Biotechnology·Juan F MartínAntonio Rodríguez-García
May 26, 2011·Natural Product Reports·Gilles P van Wezel, Kenneth J McDowall
Dec 9, 2014·Virulence·Samuel Mohammed ChekababCharles M Dozois
Jan 20, 2016·Journal of Basic Microbiology·Ines BoukhrisMarie-Joëlle Virolle
May 24, 2020·Scientific Reports·Aaron Millan-OropezaMarie-Joelle Virolle
May 31, 2012·Molecular Genetics and Genomics : MGG·Lorena T Fernández-MartínezJuan F Martín
Jan 11, 2019·Applied Microbiology and Biotechnology·Carlos Barreiro, Miriam Martínez-Castro

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Methods Mentioned

BETA
footprinting
PCR
electrophoretic mobility

Software Mentioned

delila
lister
scan
dalvec
makelogo
encode
multiscan
rseq
makebk
ri

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