Structure and Function of the Escherichia coli Protein YmgB

A Protein Critical for Biofilm Formation and Acid-resistance

Jintae Lee, Rebecca Page, Rodolfo García-Contreras, Jeanne Marie Palermino, Xue Song Zhang, Ojus Doshi, Thomas Keith Wood, Wolfgang Peti

Research output: Contribution to journalArticle

48 Citations (Scopus)

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 Å 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.

Original languageEnglish (US)
Pages (from-to)11-26
Number of pages16
JournalJournal of Molecular Biology
Volume373
Issue number1
DOIs
StatePublished - Oct 12 2007

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Escherichia coli Proteins
Biofilms
Escherichia coli
Acids
Oligonucleotide Array Sequence Analysis
Proteins
X Ray Crystallography
DNA-Binding Proteins
Electrophoretic Mobility Shift Assay
Multigene Family
Nickel
Transcriptome
Cell Movement
Gels
Ligands
Phenotype
Glucose
Genes
indole

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology

Cite this

Lee, Jintae ; Page, Rebecca ; García-Contreras, Rodolfo ; Palermino, Jeanne Marie ; Zhang, Xue Song ; Doshi, Ojus ; Wood, Thomas Keith ; Peti, Wolfgang. / Structure and Function of the Escherichia coli Protein YmgB : A Protein Critical for Biofilm Formation and Acid-resistance. In: Journal of Molecular Biology. 2007 ; Vol. 373, No. 1. pp. 11-26.
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Structure and Function of the Escherichia coli Protein YmgB : A Protein Critical for Biofilm Formation and Acid-resistance. / Lee, Jintae; Page, Rebecca; García-Contreras, Rodolfo; Palermino, Jeanne Marie; Zhang, Xue Song; Doshi, Ojus; Wood, Thomas Keith; Peti, Wolfgang.

In: Journal of Molecular Biology, Vol. 373, No. 1, 12.10.2007, p. 11-26.

Research output: Contribution to journalArticle

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