Systems Biology of Microorganisms: Systems Understanding of Microbial Oxygen-Dependent and Independent Catabolism

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This project is part of the European Transnational Funding and Research Initiative

University of Stuttgart
Institute for System Dynamics
Pfaffenwaldring 9
70569 Stuttgart

Sebastian Henkel
Tel.: +49 - 711 - 685 69898

Michael Ederer
Tel.: +49 - 711 - 685 6619

Funding Period:

01.05.2010 – 30.04.2013

Project description:

Escherichia coli exhibits a versatile metabolism (incorporating aerobic respiratory, anaerobic respiratory and fermentative metabolic modes) plus numerous and sometimes complex regulatory networks to achieve optimal growth and survival. One such adaptation that has been widely studied is the response of E. coli to the provision (or not) of oxygen and/or alternative terminal electron acceptors. In the SysMO project, SUMO2 (Systems Understanding of Microbial Oxygen-Dependent and Independent Catabolism), we assembled an interdisciplinary team to undertake a comprehensive, quantitative systems-based analysis of the responses to varying degrees of the availability of oxygen, other electron acceptors and the carbon source.
Our aim in SUMO2 is to obtain a complete, quantitative description of the integrated catabolic subsystems of E. coli, from regulation to energy conservation.
Our work plan for SUMO2 is centred on these three interlinked Themes: (1) system dynamics during transition to anaerobic respiration and in response to pulses of electron acceptors; (2) adaptive responses to different catabolic modes; (3) multi-scale and multi-level modelling of catabolism. Our workplan embraces the systems biological cycle of iterative experiments and modelling, in which models guide the experimental work; this will enable us to realise our ultimate goal, which is a coherent model of catabolism.

Robert Poole, Jeff Green

Department of Molecular Biology and Biotechnology, University of Sheffield (UK)

Mike Holcombe

Department of Computer Science, University of Sheffield (UK)

Joost Teixeira de Mattos

Swammerdam Institute for Life Sciences, Universiteit van Amsterdam (NL)

Guido Sanguinetti

Institute for Adaptive and Neural Computation, The University of Edinburgh (UK)

Katja Bettenbrock, Andreas Kremling

Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg (DE)

Oliver Sawodny, Michael Ederer

Institute for System Dynamics (ISYS), CSB, University of Stuttgart (DE)

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