Qualitative simulation of the carbon starvation response in Escherichia coli.

Delphine Ropers 1 Hidde de Jong 1 Michel Page Dominique Schneider Johannes Geiselmann
1 HELIX - Computer science and genomics
Inria Grenoble - Rhône-Alpes, LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
Abstract : In case of nutritional stress, like carbon starvation, Escherichia coli cells abandon their exponential-growth state to enter a more resistant, non-growth state called stationary phase. This growth-phase transition is controlled by a genetic regulatory network integrating various environmental signals. Although E. coli is a paradigm of the bacterial world, it is little understood how its response to carbon starvation conditions emerges from the interactions between the different components of the regulatory network. Using a qualitative method that is able to overcome the current lack of quantitative data on kinetic parameters and molecular concentrations, we model the carbon starvation response network and simulate the response of E. coli cells to carbon deprivation. This allows us to identify essential features of the transition between exponential and stationary phase and to make new predictions on the qualitative system behavior following a carbon upshift.
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Submitted on : Wednesday, September 12, 2007 - 6:06:44 PM
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Delphine Ropers, Hidde de Jong, Michel Page, Dominique Schneider, Johannes Geiselmann. Qualitative simulation of the carbon starvation response in Escherichia coli.. BioSystems, Elsevier, 2006, 84 (2), pp.124-52. ⟨10.1016/j.biosystems.2005.10.005⟩. ⟨hal-00171698⟩

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