Negative Cooperativity of Uric Acid Binding to the Transcriptional Regulator HucR from Deinococcus radiodurans

• Published in: Journal of molecular biology 2005-07, Vol.350 (4), p.617-630
• Main Authors: Wilkinson, Steven P., Grove, Anne
• Format: Article
• Language: English
• Subjects: Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Circular Dichroism; Deinococcus - genetics; Deinococcus - metabolism; Deinococcus radiodurans; DNA - metabolism; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; Gene Expression Regulation, Bacterial - physiology; intrinsic fluorescence; ligand; MarR; Mutation; oxidative stress; Protein Binding; Protein Structure, Tertiary; Repressor Proteins - genetics; Repressor Proteins - metabolism; Spectrometry, Fluorescence; Uric Acid - metabolism; winged helix-turn-helix
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2005.05.027

Members of the MarR family of winged helix transcriptional regulators have been shown to regulate multidrug and oxidative stress response, pathogenesis, and catabolism of aromatic compounds. Many respond to anionic lipophilic compounds in their capacity to bind DNA, and the co-crystal structure of MarR bound to salicylate revealed two ligand-binding pockets, SAL-A and SAL-B. The MarR homolog, HucR, from Deinococcus radiodurans has been shown to repress expression of a predicted uricase, and DNA-binding by HucR is antagonized by uric acid, the substrate of uricase. We provide a biochemical investigation of DNA-binding and uric acid-binding by HucR. Equilibrium analytical ultracentrifugation indicates that HucR exists as a dimer. Intrinsic fluorescence spectra suggest that the association of the HucR dimer with its cognate DNA involves conformational flexibility in the globular interior and/or dimerization domain of the protein, and near-UV circular dichroism spectra indicate a concomitant change in the helical twist of the DNA duplex. DNA-binding affinity, measured by electrophoretic mobility-shift assays, for HucR mutants bearing single amino acid substitutions suggests the importance of the β-hairpin “wing” in DNA binding. Analysis of intrinsic fluorescence spectra demonstrates that uric acid induces conformational changes in HucR and binds with an apparent K d=11.6(±3.7) μM and a Hill coefficient of 0.7±0.1, indicating negative cooperativity. Fluorescence and DNA-binding properties of the HucR variants indicate that SAL-A is a low-affinity, uric acid-binding site and that negative cooperativity exists between homologous, high-affinity sites. The conservation of residues comprising site SAL-A suggests that it is a low-affinity, ligand-binding site in MarR homologs. Mechanistic considerations suggest that HucR is regulated by uric acid to maintain optimal cellular levels of this scavenger of free radicals in response to oxidative stress and DNA damage.