title: Interactions between genotype and environment drive the metabolic phenotype within Escherichia coli isolates.
abstract: To gain insights into the adaptation of the Escherichia coli species to different environments, we monitored protein abundances using quantitative proteomics and measurements of enzymatic activities of central metabolism in a set of five representative strains grown in four contrasted culture media including human urine. Two hundred and thirty seven proteins representative of the genome-scale metabolic network were identified and classified into pathway categories. We found that nutrient resources shape the general orientation of metabolism through coordinated changes in the average abundances of proteins and in enzymatic activities that all belong to the same pathway category. For example, each culture medium induces a specific oxidative response whatever the strain. On the contrary, differences between strains concern isolated proteins and enzymes within pathway categories in single environments. Our study confirms the predominance of genotype by environment interactions at the proteomic and enzyme activity levels. The buffering of genetic variation when considering life-history traits suggests a multiplicity of evolutionary strategies. For instance, the uropathogenic isolate CFT073 shows a deregulation of iron demand and increased oxidative stress response.
authors: Univ Paris-Sud, UMR de Génétique Végétale INRA/Univ Paris-Sud/CNRS, Ferme du Moulon, 91190, Gif-sur-Yvette, France.|INSERM, IAME, UMR 1137, F-75018, Paris, France.|Univ Paris Diderot, Sorbonne Paris Cité, F-75018, Paris, France.
authors: Victor
authors: V
authors: Sabarly
authors: INSERM, IAME, UMR 1137, F-75018, Paris, France.|Univ Paris Diderot, Sorbonne Paris Cité, F-75018, Paris, France.
authors: Cécile
authors: C
authors: Aubron
authors: INSERM, IAME, UMR 1137, F-75018, Paris, France.|Univ Paris Diderot, Sorbonne Paris Cité, F-75018, Paris, France.
authors: Jérémy
authors: J
authors: Glodt
authors: INRA, UMR de Génétique Végétale INRA/Univ Paris-Sud/CNRS, Ferme du Moulon, 91190, Gif-sur-Yvette, France.
authors: Thierry
authors: T
authors: Balliau
authors: CNRS, UMR de Génétique Végétale INRA/Univ Paris-Sud/CNRS, Ferme du Moulon, 91190, Gif-sur-Yvette, France.
authors: Olivier
authors: O
authors: Langella
authors: INRA, UMR MICALIS, PAPPSO, batiment 526, Domaine de Vilvert, 78352, Jouy en Josas cedex, France.
authors: Didier
authors: D
authors: Chevret
authors: Service de Biochimie, Hormonologie, Hôpital Robert Debré, Paris, France.
authors: Odile
authors: O
authors: Rigal
authors: CNRS, UMR de Génétique Végétale INRA/Univ Paris-Sud/CNRS, Ferme du Moulon, 91190, Gif-sur-Yvette, France.
authors: Aurélie
authors: A
authors: Bourgais
authors: INSERM, IAME, UMR 1137, F-75018, Paris, France.|Univ Paris Diderot, Sorbonne Paris Cité, F-75018, Paris, France.
authors: Bertrand
authors: B
authors: Picard
authors: Univ Paris-Sud, UMR de Génétique Végétale INRA/Univ Paris-Sud/CNRS, Ferme du Moulon, 91190, Gif-sur-Yvette, France.
authors: Dominique
authors: D
authors: de Vienne
authors: INSERM, IAME, UMR 1137, F-75018, Paris, France.|Univ Paris Diderot, Sorbonne Paris Cité, F-75018, Paris, France.
authors: Erick
authors: E
authors: Denamur
authors: INSERM, IAME, UMR 1137, F-75018, Paris, France.|Univ Paris Diderot, Sorbonne Paris Cité, F-75018, Paris, France.
authors: Odile
authors: O
authors: Bouvet
authors: Univ Paris-Sud, UMR de Génétique Végétale INRA/Univ Paris-Sud/CNRS, Ferme du Moulon, 91190, Gif-sur-Yvette, France.
authors: Christine
authors: C
authors: Dillmann
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D005075:Biological Evolution; D003470:Culture Media / Q000378:metabolism; D004777:Environment; D004926:Escherichia coli / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000145:classification / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics; D005838:Genotype; D006801:Humans; D007501:Iron / Q000378:metabolism*; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D010084:Oxidation-Reduction; D018384:Oxidative Stress / Q000502:physiology*; D010641:Phenotype; D040901:Proteomics
chemical_list: D003470:Culture Media; D029968:Escherichia coli Proteins; D007501:Iron