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 International Conference on Complex Systems (ICCS2007)

The genetic network controlling E. coli metabolism as a dynamical system

Areejit Samal
Department of Physics, University of Delhi, India

Sanjay Jain
Department of Physics, University of Delhi, India

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     Last modified: June 30, 2007

Elucidating the architecture and dynamics of large scale genetic regulatory networks of cells is an important goal in systems biology. Recently a genetic network of 583 genes controlling E. coli metabolism has been constructed (M.W. Covert et al., Nature 2004) containing not only the connections between genes but also the boolean rule at each node that controls the gene switching on or off as a function of its inputs. We use computer simulations and graph theoretic analysis of this network to investigate system level properties of E. coli.
The system can be viewed as a set of 583 boolean variables in discrete time whose state at any given time instant is governed by the state at the previous time instant and by the state of the environment, the latter being determined by the presence or absence of 96 external metabolites. We have studied how the attractors of this dynamical system depend on the initial condition of the genes, and on various environmental conditions corresponding to buffered minimal media. We find that the system exhibits homeostasis in that its attractors, that turn out to be fixed points or low period cycles, are highly insensitive to initial conditions or perturbations of gene configurations for any given fixed environment. At the same time the attractors show a wide variation when external media are varied implying that the system mounts a highly flexible response to changed environmental conditions. The regulatory dynamics acts to enhance the cellular growth rate under changed media. We show how structural design features of the network such as acyclicity and modularity explain its dynamical behaviour.

Reference: Areejit Samal and Sanjay Jain, arxiv:q-bio.MN/0703059

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