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Importance of metabolic coupling for the dynamics of gene expression following a diauxic shift in E. 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 E. 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 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.
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https://hal.inria.fr/inria-00593109
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Submitted on : Friday, May 13, 2011 - 12:23:31 PM
Last modification on : Tuesday, May 10, 2022 - 3:00:39 PM
Long-term archiving on: : Sunday, August 14, 2011 - 3:04:15 AM

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  • HAL Id : inria-00593109, version 1
  • PRODINRA : 317603

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Valentina Baldazzi, Delphine Ropers, Johannes Geiselmann, Daniel Kahn, Hidde de Jong. Importance of metabolic coupling for the dynamics of gene expression following a diauxic shift in E. coli. [Research Report] RR-7617, INRIA. 2011. ⟨inria-00593109⟩

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