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Rule-based Modeling of Transcriptional Attenuation at the Tryptophan Operon

Authors: Céline Kuttler, Cédric Lhoussaine, and Mirabelle Nebut

Published in: Dagstuhl Seminar Proceedings, Volume 9091, Formal Methods in Molecular Biology (2009)

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 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.

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Céline Kuttler, Cédric Lhoussaine, and Mirabelle Nebut. Rule-based Modeling of Transcriptional Attenuation at the Tryptophan Operon. In Formal Methods in Molecular Biology. Dagstuhl Seminar Proceedings, Volume 9091, pp. 1-22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)

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@InProceedings{kuttler_et_al:DagSemProc.09091.6,
  author =	{Kuttler, C\'{e}line and Lhoussaine, C\'{e}dric and Nebut, Mirabelle},
  title =	{{Rule-based Modeling of Transcriptional Attenuation at the Tryptophan Operon}},
  booktitle =	{Formal Methods in Molecular Biology},
  pages =	{1--22},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2009},
  volume =	{9091},
  editor =	{Rainer Breitling and David Roger Gilbert and Monika Heiner and Corrado Priami},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09091.6},
  URN =		{urn:nbn:de:0030-drops-19938},
  doi =		{10.4230/DagSemProc.09091.6},
  annote =	{Keywords: Systems biology, rule-based modeling languages, stochastic simulation, kappa.}
}

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Rule-based Modeling of Transcriptional Attenuation at the Tryptophan Operon

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