Rule-Based Modeling of Transcriptional Attenuation at the Tryptophan Operon

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 for this phenomenon based on chemical reactions. Our model is compact and intelligible, due to n-ary reactions (which preclude object-centric approaches) and to rule schemas that define finite sets of chemical reactions. Stochastic simulations with our model confirm results that were previously obtained by master equations or differential equations. In addition, our approach permits to reflect mutation experiments by simple model modifications, and to re-use model components for transcriptional attenuation in other genes and organisms. Keywords. Systems biology, riboswitch, rule-based modeling languages, stochastic simulation, kappa.

• Type: Journal
• Year: 2010
• Where: TCSB
• Authors: Céline Kuttler, Cédric Lhoussaine, Mirabelle Nebut
• Keywords: Computational Biology, Model, Stochastic Simulation, TCSB 2010, Transcriptional Attenuation