Abstract
We propose a formal modeling language for reaction networks with partial kinetic information. The language has a graphical syntax reminiscent to Petri nets. The kinetics of reactions need to be described only partially, so that the language can be used to model the regulation of metabolic networks. We present a qualitative reasoning method based on abstract interpretation of the steady state semantics of reaction networks modeled in our language. In particular, we can predict changes of influxes that lead to expected changes of outfluxes.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Brinsmade, S.R., Kleijn, R.J., Sauer, U., Sonenshein, A.L.: Regulation of CodY Activity through Modulation of Intracellular Branched-Chain Amino Acid Pools. J. Bacteriol. 192(24), 6357–6368 (2010)
Coutte, F., Niehren, J., Dhali, D., John, M., Versari, C., Jacques, P.: Knockout prediction in surfactin precursors biosynthetic pathway for its overproduction. J. Biotechnology. (to appear)
Forbus, K.D.: Qualitative reasoning. In: Tucker, A.B. (ed.) The Computer Science and Engineering Handbook, pp. 715–733. CRC Press (1997)
Grandoni, J.A., Zahler, S.A., Calvo, J.M.: Transcriptional regulation of the ilv-leu operon of Bacillus subtilis. J. Bacteriol. 174(10), 3212–3219 (1992)
John, M., Nebut, M., Niehren, J.: Knockout prediction for reaction networks with partial kinetic information. In: Giacobazzi, R., Berdine, J., Mastroeni, I. (eds.) VMCAI 2013. LNCS, vol. 7737, pp. 355–374. Springer, Heidelberg (2013)
Jungreuthmayer, C., Zanghellini, J.: Designing optimal cell factories: integer programming couples elementary mode analysis with regulation. BMC Syst. Biol. 6(1), 103 (2012)
Mäder, U., Hennig, S., Hecker, M., Homuth, G.: Transcriptional organization and posttranscriptional regulation of the Bacillus subtilis branched-chain amino acid biosynthesis genes. J. bacteriol. 186(8), 2240–2252 (2004)
Mäder, U., Schmeisky, A.G., Flórez, L.A., Stülke, J.: Subtiwiki – a comprehensive community resource for the model organism bacillus subtilis. Nucleic Acids Res. 40(D1), 278–287 (2012)
Molle, V., Nakaura, Y., Shivers, R.P., Yamaguchi, H., Losick, R., Fujita, Y., Sonenshein, A.L.: Additional targets of the Bacillus subtilis global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysis. J. bacteriol. 185(6), 1911–1922 (2003)
Orth, J.D., Thiele, I., Palsson, B.O.: What is flux balance analysis? Nat. Biotechnol. 28(3), 245–248 (2010)
Otero, J.M., Nielsen, J.: Industrial systems biology. Industrial Biotechnology: Sustainable Growth and Economic Success (2010)
Papin, J.A., Stelling, J., Price, N.D., Klamt, S., Schuster, S., Palsson, B.O.: Comparison of network-based pathway analysis methods. Trends Biotechnol. 22(8), 400–405 (2004)
Price, N.D., Reed, J.L., Palsson, B.O.: Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat. Rev. Microbiol. 2(11), 886–897 (2004)
Shivers, R.P., Sonenshein, A.L.: Activation of the Bacillus subtilis global regulator CodY by direct interaction with branched-chain amino acids. Mol. Microbiol. 53(2), 599–611 (2004)
Sohn, S.B., Kim, T.Y., Park, J.M., Lee, S.Y.: In silico genome-scale metabolic analysis of Pseudomonas putida kt2440 for polyhydroxyalkanoate synthesis, degradation of aromatics and anaerobic survival. Biotechnol. J. 5(7), 739–750 (2010)
Tojo, S., Satomura, T., Morisaki, K., Deutscher, J., Hirooka, K., Fujita, Y.: Elaborate transcription regulation of the Bacillus subtilis ilv-leu operon involved in the biosynthesis of branched-chain amino acids through global regulators of CcpA, CodY and TnrA. Mol. Microbiol. 56(6), 1560–1573 (2005)
Villapakkam, A.C., Handke, L.D., Belitsky, B.R., Levdikov, V.M., Wilkinson, A.J., Sonenshein, A.L.: Genetic and Biochemical Analysis of the Interaction of B. subtilis CodY with Branched-Chain Amino Acids. J. Bacteriol. 191(22), 6865–6876 (2009)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer International Publishing Switzerland
About this paper
Cite this paper
Niehren, J., John, M., Versari, C., Coutte, F., Jacques, P. (2015). Qualitative Reasoning for Reaction Networks with Partial Kinetic Information. In: Roux, O., Bourdon, J. (eds) Computational Methods in Systems Biology. CMSB 2015. Lecture Notes in Computer Science(), vol 9308. Springer, Cham. https://doi.org/10.1007/978-3-319-23401-4_14
Download citation
DOI: https://doi.org/10.1007/978-3-319-23401-4_14
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-23400-7
Online ISBN: 978-3-319-23401-4
eBook Packages: Computer ScienceComputer Science (R0)