title: Insulation and wiring specificity of BceR-like response regulators and their target promoters in Bacillus subtilis.
abstract: BceRS and PsdRS are paralogous two-component systems in Bacillus subtilis controlling the response to antimicrobial peptides. In the presence of extracellular bacitracin and nisin, respectively, the two response regulators (RRs) bind their target promoters, PbceAor PpsdA, resulting in a strong up-regulation of target gene expression and ultimately antibiotic resistance. Despite high sequence similarity between the RRs BceR and PsdR and their known binding sites, no cross-regulation has been observed between them. We therefore investigated the specificity determinants of PbceAand PpsdAthat ensure the insulation of these two paralogous pathways at the RR-promoter interface. In vivo and in vitro analyses demonstrate that the regulatory regions within these two promoters contain three important elements: in addition to the known (main) binding site, we identified a linker region and a secondary binding site that are crucial for functionality. Initial binding to the high-affinity, low-specificity main binding site is a prerequisite for the subsequent highly specific binding of a second RR dimer to the low-affinity secondary binding site. In addition to this hierarchical cooperative binding, discrimination requires a competition of the two RRs for their respective binding site mediated by only slight differences in binding affinities.
authors.affiliation: Department Biology I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, Martinsried, 82152, Germany.
authors.forename: Chong
authors.initials: C
authors.lastname: Fang
authors.affiliation: Department Biology I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, Martinsried, 82152, Germany.|Institute of Science and Technology (IST) Austria, Am Campus 1, Klosterneuburg, A-3400, Austria.
authors.forename: Anna
authors.initials: A
authors.lastname: Nagy-Staroń
authors.affiliation: Department Biology I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, Martinsried, 82152, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Grafe
authors.affiliation: Department Biology I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, Martinsried, 82152, Germany.|Munich Center for Integrated Protein Science (CiPSM) at the Department Biology I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, Martinsried, 82152, Germany.
authors.forename: Ralf
authors.initials: R
authors.lastname: Heermann
authors.affiliation: Department Biology I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, Martinsried, 82152, Germany.|Munich Center for Integrated Protein Science (CiPSM) at the Department Biology I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, Martinsried, 82152, Germany.
authors.forename: Kirsten
authors.initials: K
authors.lastname: Jung
authors.affiliation: Department Biology I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, Martinsried, 82152, Germany.|Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
authors.forename: Susanne
authors.initials: S
authors.lastname: Gebhard
authors.affiliation: Department Biology I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, Martinsried, 82152, Germany.|Institute of Microbiology, Technische Universität (TU) Dresden, 01062, Dresden, Germany.
authors.forename: Thorsten
authors.initials: T
authors.lastname: Mascher
mesh_terms: D018528:ATP-Binding Cassette Transporters / Q000378:metabolism; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001412:Bacillus subtilis / Q000235:genetics / Q000378:metabolism*; D001414:Bacitracin / Q000378:metabolism; D001426:Bacterial Proteins / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects; D008969:Molecular Sequence Data; D009561:Nisin / Q000378:metabolism; D011401:Promoter Regions, Genetic; D011485:Protein Binding / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid; D015854:Up-Regulation
chemical_list: D018528:ATP-Binding Cassette Transporters; D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D001414:Bacitracin; D009561:Nisin