Summary
The adaptation of the growth of Escherichia coli to the availability of a carbon source is controlled by a complex genetic regulatory network whose functioning is still little understood. Using a qualitative method based on piecewise-linear differential equations, which is able to overcome the current lack of quantitative data on kinetic parameters and molecular concentrations, we model the carbon starvation response network and simulate the response of E. coli cells to carbon deprivation. This allows us to identify essential features of the transition between exponential and stationary phase and to make new predictions on the qualitative system behavior, following a carbon upshift.
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
Preview
Unable to display preview. Download preview PDF.
References
Balke, V., Gralla, J.: Changes in the linking number of supercoiled DNA accompany growth transitions in Escherichia coli.J. Bacteriol., 169, 4499–506 (1987).
Ball, C., Osuna, R., Ferguson, K., Johnson, R.: Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli. J. Bacteriol., 174, 8043–56 (1992).
Batt, G., Ropers, D., de Jong, H., Geiselmann, J, Mateescu, R., page, M., Schneider, D.: Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli. Bioinformatics, 21, 19–28 (2005).
Casey, R., de Jong, H., Gouzé, J.-L.: Piecewise-linear models of genetic regulatory networks: equilibria and their stability. J. Math. Biol., 52, 27–56 (2006).
Dennis, P., Ehrenberg, M., Bremer, H.: Control of rRNA synthesis in Escherichia coli:a systems biology approach. Microbiol Mol. Biol. Rev., 68, 639–68 (2004).
Drlica, K.: Bacterial topoisomerases and the control of DNA supercoiling. Trends Genet., 6, 433–7 (1990).
Glass, L., Kauffman, S.: The logical analysis of continuous, non-linear biochemical control networks. J. Theor. Biol., 39, 103–29 (1973).
Gonzalez-Gil, G., Bringmann, P., Kahmann, R.: Fis is a regulator of metabolism in Escherichia coli. Mol. Microbiol., 22, 21–9 (1996).
Gonzalez-Gil, G., Kahmann, R., Muskhelishvili, G.: Regulation of crptranscription by oscillation between distinct nucleoprotein complexes. EMBO J., 17, 2877–85 (1998).
Gouz’e, J.-L., Sari, T.: A class of piecewise linear differential equations arising in biological models. Dynam. Syst., 17, 299–316 (2003).
Hatfield, G., Benham, C.: DNA topology-mediated control of global gene expression in Escherichia coli.Annu. Rev. Genet., 36, 175–203 (2002).
Hengge-Aronis, R.: The general stress response in Escherichia coli. In: Storz, G., Hengge-Aronis, R. (eds.) Bacterial Stress Responses, 161–77. ASM Press (2000).
Huisman, G., Siegele D.A., Zambrano, M.M., Kolter, R.: Morphological and physiological changes during stationary phase. In: Neidhardt et al., F. (ed.) Escherichia coliand Salmonella: Cellular and Molecular Biology, 1672–82. ASM Press (1996).
de Jong, H., Geiselmann, J., Batt, G., Hernandez, C., Page, M.: Qualitative simulation of the initiation of sporulation in Bacillus subtilis. Bull. Math. Biol., 66, 261–99 (2004).
de Jong, H., Geiselmann, J., Hernandez, C., Page, M.: Genetic network analyzer: qualitative simulation of genetic regulatory networks. Bioinformatics, 19, 336–44 (2003).
de Jong, H., Gouzé, J.-L., Hernandez, C., Page, M., Sari, T., Geiselmann, J.: Qualitative simulation of genetic regulatory networks using piecewise-linear models. Bull. Math. Biol., 66, 301–40 (2004).
Keseler, I.M., Collado-Vides, J., Gama-Castro, S., Ingraham, J., Paley, S., Paulsen, I.T., Peralta-Gil, M., Karp, P.D.: EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res., 33, D334–7 (2005).
Kohn, K.: Molecular interaction maps as information organizers and simulation guides. Chaos, 11, 84–97 (2001).
Kremling, A., Bettenbrock, K., Laube, B., Jahreis, K., Lengeler, J.W., Gilles, E.D.: The organization of metabolic reaction networks: III. Application for diauxic growth on glucose and lactose. Metab. Eng., 3, 362–79 (2001).
Kremling, A., Gilles, E.: The organization of metabolic reaction networks: II. Signal processing in hierarchical structured functional units. Metab. Eng., 3, 138–50 (2001).
McAdams, H., Arkin, A.: Simulation of prokaryotic genetic circuits. Annu. Rev. Biophys. Biomol. Struct., 27, 199–224 (1998).
Ninnemann, O., Koch, C., Kahmann, R.: The E. coli fispromoter is subject to stringent control and autoregulation. EMBO J., 11, 1075–83 (1992).
Page, M., de Jong, H.: Search of steady states of piecewise-linear differential models of generic regulatory networks. Submitted.
Paul, B., Ross, W., Gaal, T., Gourse, R.: rRNA transcription in Escherichia coli. Annu. Rev. Genet., 38, 749–770 (2004).
Pratt, T.S, Steiner, T., Feldman, L.S., Walker, K.A., Osuna, R.: Deletion analysis of the $fis $promoter region in Escherichia coli: antagonistic effects of integration host factor and Fis. J. Bacteriol., 179, 6367–77 (1997).
Ropers, D., de Jong, H., Page, M., Schneider, D., Geiselmann, J.: Qualitative simulation of the carbon starvation response in Escherichia coli. BioSystems, in press (2006).
Saier, Jr, M.J., Ramseier, T.M., Reizer, J.: Regulation of carbon utilization. In: Neidhardt, F.C., Curtiss III, R., Ingraham, J.L., Lin, E.C.C., Low, K.B., Magasanik, B., Reznikoff, W.S., Riley, M., Schaechter, M., Umbarger, H.E. (eds.) Escherichia coli and Salmonella: Cellular and Molecular Biology, 1325–43. ASM Press, Washington D.C. (1996).
Salgado, H., Gama-Castro, S., Martinez-Antonio, A., Diaz-Peredo, E., Sánchez-Solano, F., Peralta-Gil, M., Garcia-Alonso, D., Jiménz-Jacinto, V., et al.: RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucleic Acids Res., 1, D303–6 (2004).
Thomas, R., d’Ari, R.Biological Feedback. CRC Press (1990).
Usseglio Viretta, A., Fussenegger, M.: Modeling the quorum sensing regulatory network of human-pathogenic Pseudomonas aeruginosa. Biotechnol. Prog., 20, 670–8 (2004).
Wick, L., Egli, T.: Molecular components of physiological stress responses in Escherichia coli. Adv. Biochem. Eng. Biotechnol., 89, 1–45 (2004).
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 springer
About this chapter
Cite this chapter
Ropers, D., Jong, H.d., Gouzé, JL., Page, M., Schneider, D., Geiselmann, J. (2007). Piecewise-Linear Models of Genetic Regulatory Networks: Analysis of the Carbon Starvation Response in Escherichia coli . In: Deutsch, A., Brusch, L., Byrne, H., Vries, G.d., Herzel, H. (eds) Mathematical Modeling of Biological Systems, Volume I. Modeling and Simulation in Science, Engineering and Technology. Birkhäuser Boston. https://doi.org/10.1007/978-0-8176-4558-8_8
Download citation
DOI: https://doi.org/10.1007/978-0-8176-4558-8_8
Publisher Name: Birkhäuser Boston
Print ISBN: 978-0-8176-4557-1
Online ISBN: 978-0-8176-4558-8
eBook Packages: Mathematics and StatisticsMathematics and Statistics (R0)