title: Identification of the target DNA sequence and characterization of DNA binding features of HlyU, and suggestion of a redox switch for hlyA expression in the human pathogen Vibrio cholerae from in silico studies.
abstract: HlyU, a transcriptional regulator common in many Vibrio species, activates the hemolysin gene hlyA in Vibrio cholerae, the rtxA1 operon in Vibrio vulnificus and the genes of plp-vah1 and rtxACHBDE gene clusters in Vibrio anguillarum. The protein is also proposed to be a potential global virulence regulator for V. cholerae and V. vulnificus. Mechanisms of gene control by HlyU in V. vulnificus and V. anguillarum are reported. However, detailed elucidation of the interaction of HlyU in V. cholerae with its target DNA at the molecular level is not available. Here we report a 17-bp imperfect palindrome sequence, 5'-TAATTCAGACTAAATTA-3', 173 bp upstream of hlyA promoter, as the binding site of HlyU. This winged helix-turn-helix protein binds necessarily as a dimer with the recognition helices contacting the major grooves and the β-sheet wings, the minor grooves. Such interactions enhance hlyA promoter activity in vivo. Mutations affecting dimerization as well as those in the DNA-protein interface hamper DNA binding and transcription regulation. Molecular dynamic simulations show hydrogen bonding patterns involving residues at the mutation sites and confirmed their importance in DNA binding. On binding to HlyU, DNA deviates by ∼68º from linearity. Dynamics also suggest a possible redox control in HlyU.
authors.affiliation: Bioinformatics Centre, Bose Institute, P1/12CIT Scheme VIIM, Kolkata 700054, India.
authors.forename: Debadrita
authors.initials: D
authors.lastname: Mukherjee
authors.affiliation: Department of Biochemistry, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata 700054, India.
authors.forename: Aritrika
authors.initials: A
authors.lastname: Pal
authors.affiliation: Department of Biochemistry, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata 700054, India.
authors.forename: Devlina
authors.initials: D
authors.lastname: Chakravarty
authors.affiliation: Bioinformatics Centre, Bose Institute, P1/12CIT Scheme VIIM, Kolkata 700054, India Department of Biochemistry, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata 700054, India pinak@boseinst.ernet.in.
authors.forename: Pinak
authors.initials: P
authors.lastname: Chakrabarti
mesh_terms: D000596:Amino Acids / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D004269:DNA, Bacterial / Q000235:genetics* / Q000378:metabolism; D019281:Dimerization; D005798:Genes, Bacterial; D010084:Oxidation-Reduction; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic; D014734:Vibrio cholerae / Q000235:genetics*
chemical_list: D000596:Amino Acids; D001426:Bacterial Proteins; D004269:DNA, Bacterial; D014157:Transcription Factors; C084286:hlyU protein, Vibrio cholerae