The carbon assimilation network in Escherichia coli is densely connected and largely sign-determined by directions of metabolic fluxes

Valentina Baldazzi 1 Delphine Ropers 1 Yves Markowicz 1, 2 Daniel Kahn 3, 4 Hans Geiselmann 1, 2 Hidde Jong 1, *
* Auteur correspondant
1 IBIS - Modeling, simulation, measurement, and control of bacterial regulatory networks
LAPM - Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble], Inria Grenoble - Rhône-Alpes, Institut Jean Roget
4 BAMBOO - An algorithmic view on genomes, cells, and environments
Inria Grenoble - Rhône-Alpes, LBBE - Laboratoire de Biométrie et Biologie Evolutive
Abstract : Gene regulatory networks consist of direct interactions but also include indirect interactions mediated by metabolites and signaling molecules. We describe how these indirect interactions can be derived from a model of the underlying biochemical reaction network, using weak time-scale assumptions in combination with sensitivity criteria from metabolic control analysis. We apply this approach to a model of the carbon assimilation network in Escherichia coli. Our results show that the derived gene regulatory network is densely connected, contrary to what is usually assumed. Moreover, the network is largely sign-determined, meaning that the signs of the indirect interactions are fixed by the flux directions of biochemical reactions, independently of specific parameter values and rate laws. An inversion of the fluxes following a change in growth conditions may affect the signs of the indirect interactions though. This leads to a feedback structure that is at the same time robust to changes in the kinetic properties of enzymes and that has the flexibility to accommodate radical changes in the environment.
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https://hal.inria.fr/hal-00793021
Contributeur : Gaëlle Rivérieux <>
Soumis le : jeudi 21 février 2013 - 14:32:55
Dernière modification le : lundi 5 novembre 2018 - 11:24:03

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  • HAL Id : hal-00793021, version 1

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Valentina Baldazzi, Delphine Ropers, Yves Markowicz, Daniel Kahn, Hans Geiselmann, et al.. The carbon assimilation network in Escherichia coli is densely connected and largely sign-determined by directions of metabolic fluxes. Actes des Journées Ouvertes Biologie, Informatique et Mathématiques (JOBIM 2010), 2010, Montpellier, France. pp.11-12, 2010. 〈hal-00793021〉

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