title: Links between Transcription, Environmental Adaptation and Gene Variability in Escherichia coli: Correlations between Gene Expression and Gene Variability Reflect Growth Efficiencies.
abstract: Gene expression is known to be the principle factor explaining how fast genes evolve. Highly transcribed genes evolve slowly because any negative impact caused by a particular mutation is magnified by protein abundance. However, gene expression is a phenotype that depends both on the environment and on the strains or species. We studied this phenotypic plasticity by analyzing the transcriptome profiles of four Escherichia coli strains grown in three different culture media, and explored how expression variability was linked to gene allelic diversity. Genes whose expression changed according to the media and not to the strains were less polymorphic than other genes. Genes for which transcription depended predominantly on the strain were more polymorphic than other genes and were involved in sensing and responding to environmental changes, with an overrepresentation of two-component system genes. Surprisingly, we found that the correlation between transcription and gene diversity was highly variable among growth conditions and could be used to quantify growth efficiency of a strain in a medium. Genetic variability was found to increase with gene expression in poor growth conditions. As such conditions are also characterized by down-regulation of all DNA repair systems, including transcription-coupled repair, we suggest that gene expression under stressful conditions may be mutagenic and thus leads to a variability in mutation rate among genes in the genome which contributes to the pattern of protein evolution.
authors.affiliation: INSERM, UMR 1137, Infection, Antimicrobiens, Modélisation, Evolution (IAME), Paris, France Faculté de Médecine, Universités Paris Diderot et Paris Nord-Sorbonne Paris Cité, Paris, France jean-paul.feugeas@inserm.fr olivier.tenaillon@inserm.fr.
authors.forename: Jean-Paul
authors.initials: JP
authors.lastname: Feugeas
authors.affiliation: INSERM, UMR 1137, Infection, Antimicrobiens, Modélisation, Evolution (IAME), Paris, France Faculté de Médecine, Universités Paris Diderot et Paris Nord-Sorbonne Paris Cité, Paris, France AP-HP, Unité de Transplantation, GH Pitié-Salpêtrière Charles Foix et Université Pierre et Marie Curie, Paris, France.
authors.forename: Jerome
authors.initials: J
authors.lastname: Tourret
authors.affiliation: INSERM, UMR 1137, Infection, Antimicrobiens, Modélisation, Evolution (IAME), Paris, France Faculté de Médecine, Universités Paris Diderot et Paris Nord-Sorbonne Paris Cité, Paris, France.
authors.forename: Adrien
authors.initials: A
authors.lastname: Launay
authors.affiliation: INSERM, UMR 1137, Infection, Antimicrobiens, Modélisation, Evolution (IAME), Paris, France Faculté de Médecine, Universités Paris Diderot et Paris Nord-Sorbonne Paris Cité, Paris, France.
authors.forename: Odile
authors.initials: O
authors.lastname: Bouvet
authors.affiliation: INRA, MIAT, Plateforme Bio-Informatique GenoToul, Castanet-Tolosan Cedex, France.
authors.forename: Claire
authors.initials: C
authors.lastname: Hoede
authors.affiliation: INSERM, UMR 1137, Infection, Antimicrobiens, Modélisation, Evolution (IAME), Paris, France Faculté de Médecine, Universités Paris Diderot et Paris Nord-Sorbonne Paris Cité, Paris, France AP-HP, Laboratoire de Génétique Moléculaire, GH Paris Nord Val de Seine, Paris, France.
authors.forename: Erick
authors.initials: E
authors.lastname: Denamur
authors.affiliation: INSERM, UMR 1137, Infection, Antimicrobiens, Modélisation, Evolution (IAME), Paris, France Faculté de Médecine, Universités Paris Diderot et Paris Nord-Sorbonne Paris Cité, Paris, France jean-paul.feugeas@inserm.fr olivier.tenaillon@inserm.fr.
authors.forename: Olivier
authors.initials: O
authors.lastname: Tenaillon
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics*; D004260:DNA Repair; D004268:DNA-Binding Proteins / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics* / Q000254:growth & development* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics; D019143:Evolution, Molecular; D015964:Gene Expression Regulation, Bacterial; D014644:Genetic Variation; D016296:Mutagenesis; D009154:Mutation; D014158:Transcription, Genetic; D015533:Transcriptional Activation
chemical_list: D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins
keywords: adaptation; evolution; mutation; transcription