Systems Biology in Pseudomonas for Industrial Biocatalysis: Dynamic modeling and simulation of relevant physiological modules involved in biocatalytic reactions based on metabolite measurements

Pseudomonas is a BMBF Industrial Project
Funding Period:

01/10/2008 – 30/09/2011

Project description:

The project aims the reconstruction of metabolic and regulatory networks and further analysis of their topology and dynamics. The information source for this reconstruction is (1) the annotated genome and (2) transcriptome and proteome data. The metabolic network will be reconstructed from the annotated genome and as far as possible cross checked against the transcriptome and proteome data. This reconstruction includes the check for consistency of elementary and charge balances of the various transformation steps as a precondition for every method based on balancing chemical species. Topological analysis like, for example, detection of unused transformation steps, dead-ends, parallel routes, and elementary flux modes will be applied and a layout of the network performed. Together with the experimental groups time series of transcriptome profiling will be designed and performed. The measurements are then performed at transient conditions following the dynamic response to the stimulus of interest. The time dependent micro array data are afterwards used for reconstruction of regulatory networks. The project aims to apply network reverse engineering methods based on boolean algebra and deterministic differential equation approaches.

Michael Breuer


Bernhard Hauer

Inst. für Techn. Biochemie, University of Stuttgart

Matthias Reuss M., Siemann-Herzberg

Institut für Bioverfahrenstechnik, CSB, University of Stuttgart

Josef Altenbuchner

Institut für Industrielle Genetik, University of Stuttgart

Georg Sprenger

Institut für Mikrobiologie, University of Stuttgart

Dieter Jendrossek

Institut für Mikrobiologie, University of Stuttgart

K.-H. Engesser

Inst. für Siedlungswasserbau, Wassergüte- und Abfallwirtschaft, University of Stuttgart

Jürgen Pleiss, Vlada Urlacher

Institute für Technische Biochemie, University of Stuttgart

Armin Huber

Institut für Physiologie, Universität Hohenheim

Joachim W. Schmid

Insilico Biotechnology AG, Stuttgart

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