title: Structure and function of the Escherichia coli protein YmgB: a protein critical for biofilm formation and acid-resistance.
abstract: The Escherichia coli gene cluster ymgABC was identified in transcriptome studies to have a role in biofilm development and stability. In this study, we showed that YmgB represses biofilm formation in rich medium containing glucose, decreases cellular motility, and protects the cell from acid indicating that YmgB has a major role in acid-resistance in E. coli. Our data show that these phenotypes are potentially mediated through interactions with the important cell signal indole. In addition, gel mobility-shift assays suggest that YmgB may be a non-specific DNA-binding protein. Using nickel-enrichment DNA microarrays, we showed that YmgB binds, either directly or indirectly, via a probable ligand, genes important for biofilm formation. To advance our understanding of the function of YmgB, we used X-ray crystallography to solve the structure of the protein to 1.8 A resolution. YmgB is a biological dimer that is structurally homologous to the E. coli gene regulatory protein Hha, despite having only 5% sequence identity. This supports our DNA microarray data showing that YmgB is a gene regulatory protein. Therefore, this protein, which clearly has a critical role in acid-resistance in E. coli, has been renamed as AriR for regulator of acid resistance influenced by indole.
authors.affiliation: Artie McFerrin Department of Chemical Engineering, Texas A & M University, College Station, TX 77843-3122, USA.
authors.forename: Jintae
authors.initials: J
authors.lastname: Lee
authors.forename: Rebecca
authors.initials: R
authors.lastname: Page
authors.forename: Rodolfo
authors.initials: R
authors.lastname: García-Contreras
authors.forename: Jeanne-Marie
authors.initials: JM
authors.lastname: Palermino
authors.forename: Xue-Song
authors.initials: XS
authors.lastname: Zhang
authors.forename: Ojus
authors.initials: O
authors.lastname: Doshi
authors.forename: Thomas K
authors.initials: TK
authors.lastname: Wood
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Peti
mesh_terms: D000143:Acids / Q000378:metabolism*; D000595:Amino Acid Sequence; D018441:Biofilms; D002465:Cell Movement / Q000502:physiology; D018360:Crystallography, X-Ray; D004268:DNA-Binding Proteins / Q000737:chemistry; D019281:Dimerization; D004926:Escherichia coli / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D006861:Hydrogen Peroxide / Q000378:metabolism; D007211:Indoles / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis; D016877:Oxidants / Q000378:metabolism; D020836:Protein Structure, Quaternary; D016415:Sequence Alignment; D013820:Thermolysin / Q000737:chemistry
chemical_list: D000143:Acids; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D007211:Indoles; D016877:Oxidants; C525027:YmgB protein, E coli; C079209:hha protein, E coli; D006861:Hydrogen Peroxide; D013820:Thermolysin