Rule-based modeling of transcriptional attenuation at the tryptophan operon

Authors:
Céline Kuttler;Cédric Lhoussaine;Mirabelle Nebut
Affiliations:
University of Lille, Cité Scientifique, Villeneuve d'Ascq Cedex, France;University of Lille, Cité Scientifique, Villeneuve d'Ascq Cedex, France;University of Lille, Cité Scientifique, Villeneuve d'Ascq Cedex, France
Venue:
Winter Simulation Conference
Year:
2009

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Abstract

Transcriptional attenuation at E. coli's tryptophan operon is a prime example of RNA-mediated gene regulation. In this paper, we present a discrete stochastic model of the fine-grained control of attenuation, based on chemical reactions. Stochastic simulation of our model confirms results that were previously obtained by master or differential equations. Our approach is easier to understand than master equations, although mathematically well founded. It is compact due to rule schemas that define finite sets of chemical reactions. Moreover, our model makes intense use of reaction rules with more than two reactants. As we show, such n-ary rules are essential to concisely capture the control of attenuation. Our model could not adequately be represented in object-centered modeling languages based on the pi-calculus, because these are limited to binary interactions.