title: Importance of metabolic coupling for the dynamics of gene expression following a diauxic shift in Escherichia coli.
abstract: Gene regulatory networks consist of direct interactions, but also include indirect interactions mediated by metabolism. We investigate to which extent these indirect interactions arising from metabolic coupling influence the dynamics of the system. To this end, we build a qualitative model of the gene regulatory network controlling carbon assimilation in Escherichia coli, and use this model to study the changes in gene expression following a diauxic shift from glucose to acetate. In particular, we compare the relative variation in the steady-state concentrations of enzymes and transcription regulators during growth on glucose and acetate, as well as the dynamic response of gene expression to the exhaustion of glucose and the subsequent assimilation of acetate. We find significant differences between the dynamics of the system in the absence and presence of metabolic coupling. This shows that interactions arising from metabolic coupling cannot be ignored when studying the dynamics of gene regulatory networks.
authors.affiliation: INRA, Plantes et Systèmes de Culture Horticoles, Domaine St Paul, Site Agroparc, 84941 Avignon Cedex 9, France. valentina.baldazzi@avignon.inra.fr
authors.forename: Valentina
authors.initials: V
authors.lastname: Baldazzi
authors.forename: Delphine
authors.initials: D
authors.lastname: Ropers
authors.forename: Johannes
authors.initials: J
authors.lastname: Geiselmann
authors.forename: Daniel
authors.initials: D
authors.lastname: Kahn
authors.forename: Hidde
authors.initials: H
authors.lastname: de Jong
mesh_terms: D002244:Carbon / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology*; D053263:Gene Regulatory Networks / Q000502:physiology; D005943:Gluconeogenesis / Q000235:genetics; D005947:Glucose / Q000378:metabolism; D006019:Glycolysis / Q000235:genetics; D053858:Metabolic Networks and Pathways / Q000235:genetics; D008957:Models, Genetic
chemical_list: D002244:Carbon; D005947:Glucose