title: Mechanism for attenuation of DNA binding by MarR family transcriptional regulators by small molecule ligands.
abstract: Members of the multiple antibiotic resistance regulator (MarR) family control gene expression in a variety of metabolic processes in bacteria and archaea. Hypothetical uricase regulator (HucR), which belongs to the ligand-responsive branch of the MarR family, regulates uricase expression in Deinococcus radiodurans by binding a shared promoter region between uricase and HucR genes. We show here that HucR responds only to urate and, to a lesser extent, to xanthine by attenuated DNA binding, compared to other intermediates of purine degradation. Using molecular-dynamics-guided mutational analysis, we identified the ligand-binding site in HucR. Electrophoretic mobility shift assays and intrinsic Trp fluorescence have identified W20 from the N-terminal helix and R80 from helix 3, which serves as a scaffold for the DNA recognition helix, as being essential for ligand binding. Using structural data combined with in silico and in vitro analyses, we propose a mechanism for the attenuation of DNA binding in which a conformational change initiated by charge repulsion due to a bound ligand propagates to DNA recognition helices. This mechanism may apply generally to MarR homologs that bind anionic phenolic ligands.
authors.affiliation: Department of Biological Sciences, Louisiana State University, Baton Rouge, 70803, USA.
authors.forename: Inoka C
authors.initials: IC
authors.lastname: Perera
authors.forename: Yong-Hwan
authors.initials: YH
authors.lastname: Lee
authors.forename: Steven P
authors.initials: SP
authors.lastname: Wilkinson
authors.forename: Anne
authors.initials: A
authors.lastname: Grove
mesh_terms: D001426:Bacterial Proteins / Q000037:antagonists & inhibitors / Q000378:metabolism*; D001665:Binding Sites; D004269:DNA, Bacterial / Q000378:metabolism*; D034301:Deinococcus / Q000235:genetics* / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects; D007700:Kinetics; D008024:Ligands; D008958:Models, Molecular; D050505:Mutant Proteins / Q000378:metabolism; D009875:Operator Regions, Genetic / Q000235:genetics; D011485:Protein Binding / Q000187:drug effects; D017433:Protein Structure, Secondary; D014158:Transcription, Genetic / Q000187:drug effects; D014527:Uric Acid / Q000737:chemistry / Q000494:pharmacology; D019820:Xanthine / Q000737:chemistry / Q000494:pharmacology
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D008024:Ligands; D050505:Mutant Proteins; D019820:Xanthine; D014527:Uric Acid