Structure and function of the Escherichia coli protein YmgB: a protein critical for biofilm formation and acid-resistance.
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.
Lee
Jintae
J
Artie McFerrin Department of Chemical Engineering, Texas A & M University, College Station, TX 77843-3122, USA.
Page
Rebecca
R
García-Contreras
Rodolfo
R
Palermino
Jeanne-Marie
JM
Zhang
Xue-Song
XS
Doshi
Ojus
O
Wood
Thomas K
TK
Peti
Wolfgang
W
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
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