title: GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli.
abstract: In several Gram-positive and Gram-negative bacteria glutamate decarboxylases play an important role in the maintenance of cellular homeostasis in acid environments. Here, new insight is brought to the regulation of the acid response in Escherichia coli. Overexpression of yhiE, similarly to overexpression of gadX, a known regulator of glutamate decarboxylase expression, leads to increased resistance of E. coli strains under high acid conditions, suggesting that YhiE is a regulator of gene expression in the acid response. Target genes of both YhiE (renamed GadE) and GadX were identified by a transcriptomic approach. In vitro experiments with GadE purified protein provided evidence that this regulator binds to the promoter region of these target genes. Several of them are clustered together on the chromosome and this chromosomal organization is conserved in many E. coli strains. Detailed structural (in silico) analysis of this chromosomal region suggests that the promoters of the corresponding genes are preferentially denatured. These results, along with the G+C signature of the chromosomal region, support the existence of a fitness island for acid adaptation on the E. coli chromosome.
authors.affiliation: Unité de Génétique des Génomes Bactériens, URA CNRS 2185, Institut Pasteur, France.
authors.forename: Florence
authors.initials: F
authors.lastname: Hommais
authors.affiliation: Unité de Génétique des Génomes Bactériens, URA CNRS 2185, Institut Pasteur, France.
authors.forename: Evelyne
authors.initials: E
authors.lastname: Krin
authors.affiliation: Génopole - plateau puces à ADN, URA CNRS 2185, Institut Pasteur, France.
authors.forename: Jean-Yves
authors.initials: JY
authors.lastname: Coppée
authors.affiliation: Génopole - plateau puces à ADN, URA CNRS 2185, Institut Pasteur, France.
authors.forename: Céline
authors.initials: C
authors.lastname: Lacroix
authors.affiliation: Unité de Bio-informatique Structurale, URA CNRS 2185, Institut Pasteur, France.
authors.forename: Edouard
authors.initials: E
authors.lastname: Yeramian
authors.affiliation: Unité de Génétique des Génomes Bactériens, URA CNRS 2185, Institut Pasteur, France.
authors.forename: Antoine
authors.initials: A
authors.lastname: Danchin
authors.affiliation: Unité de Génétique des Génomes Bactériens, URA CNRS 2185, Institut Pasteur, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Bertin
mesh_terms: D051777:AraC Transcription Factor / Q000235:genetics / Q000378:metabolism*; D001482:Base Composition; D001483:Base Sequence; D002874:Chromosome Mapping; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism*; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D005968:Glutamate Decarboxylase / Q000235:genetics / Q000378:metabolism; D006801:Humans; D006863:Hydrogen-Ion Concentration; D005810:Multigene Family; D011401:Promoter Regions, Genetic; D014157:Transcription Factors
chemical_list: D051777:AraC Transcription Factor; D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; C479562:GadE protein, E coli; C446316:GadX protein, E coli; D014157:Transcription Factors; D005968:Glutamate Decarboxylase