Kinetic model of Escherichia coli's electron transport chain (ETC) coupled to a simplified growth model Version 2
The model describes the electron transport chain (ETC) of Escherichia coli by ordinary differential equations. Also a simplified growth model based on an abstract reducing potential describing the balance of electron donor (glucose) and electron acceptors is coupled to the ETC. The model should reproduce and predict the regulation of the described system for different oxygen availability within the aerobiosis scale (glucose limited continuous culture<=>chemostat). Therefore oxygen is changed slowly over time (linear increase) and the simulated variables can be considered as steady-states for single fixed oxygen concentrations (anaerobic=> microaerobic=> aerobic) in the inflowing gas. Time=20000 corresponds to 100% aerobiosis (end of model validity). Different glucose concentrations Glcin and dilution rates Dil can be simulated by changing the corresponding parameters and the parameter JO2in100 for the maximal oxygen flow.
SEEK ID: https://fairdomhub.org/models/45?version=2
1 item is associated with this Model:- EcoliETC2.xml (SBML and XML document - 81.9 KB)
Organism: Escherichia coli
Model type: Ordinary differential equations (ODE)
Model format: SBML
Execution or visualisation environment: JWS Online
Model image: No image specified
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Created: 30th May 2011 at 08:09
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Version 2 (latest) Created 30th May 2011 at 08:09 by Sebastian Henkel
Model structure and parameters not changed, but previously incorrectly named model elements renamed.
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Projects: SUMO
Institutions: University of Stuttgart
Former: PhD student as research associate at the Institute for System Dynamics (ISYS), Universität Stuttgart, Germany. Engineering background→modelling, identification and analyses. Detailed kinetic modelling, identification and analysis of the TCA cycle (tricarboxylic acid cycle, citric acid cycle) and the ETC (electron transport chains, respiratory chains) of Escherichia coli. One of the SysMO-DB pals for SUMO. Now: Industrial affiliation
SysMO is a European transnational funding and research initiative on "Systems Biology of Microorganisms".
The goal pursued by SysMO was to record and describe the dynamic molecular processes going on in unicellular microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models.
Systems biology will raise biomedical and biotechnological research to a new quality level and contribute markedly to progress in understanding. Pooling European research ...
Projects: BaCell-SysMO, COSMIC, SUMO, KOSMOBAC, SysMO-LAB, PSYSMO, SCaRAB, MOSES, TRANSLUCENT, STREAM, SulfoSys, SysMO DB, SysMO Funders, SilicoTryp, Noisy-Strep
Web page: http://sysmo.net/
"Systems Understanding of Microbial Oxygen responses" (SUMO) investigates how Escherichia coli senses oxygen, or the associated changes in oxidation/reduction balance, via the Fnr and ArcA proteins, how these systems interact with other regulatory systems, and how the redox response of an E. coli population is generated from the responses of single cells. There are five sub-projects to determine system properties and behaviour and three sub-projects to employ different and complementary modelling ...
Programme: SysMO
Public web page: http://www.sysmo.net/index.php?index=55
Changing the oxygen availability leads to an adaptation of Escherichia coli at different biological levels. After pertubation of oxygen in chemostat experiments the microorganism(s) will come back to another steady state. This investigation deals with these stationary responses of Escherichia coli within the aerobiosis scale. The change for different biological variables, in different areas of the organism like the electron transport chain, the TCA cycle or globally is investigated by wildtype ...
Submitter: Michael Ederer
Studies: Basic regulatory principles of Escherichia coli’s electron transport cha..., Determination of the impact of specific enzyme reactions and regulatory ..., Quantitative analysis of catabolic carbon and electron fluxes in E. coli..., The Escherichia coli steady state response to oxygen: from molecular int...
Assays: Analysis of by-product formation rates in MG1655, Analysis of gene expression rates at different aerobiosis levels via RT-PCR, ArcA phosphorylation at different aerobiosis levels (steady states), Characterization of E. coli MG1655 and ∆sdhC and ∆frdA isogenic mutant s..., Determination of intracellular metabolite concentrations, Determination of intracellular redox state by means of NAD/NADH ratio, Determination of intracellular redox state by means of ubiquinones (oxd/..., FNR activity at different aerobiosis levels (steady state), Kinetic modelling of Escherichia coli's electron transport chain, Kinetic modelling of Escherichia coli's electron transport chain coupled..., Literature Data from Alexeeva et al., J. Bacteriol., 2000, 2002, 2003, Measurement of cytochrome numbers, Physiological measurements from Sheffield chemostat, Steady State Oxygen Response of E. coli WT and two Electron Transport Ch..., Transcriptional profiling of steady states at different aerobiosis levels
Goals:
- Understanding the regulatory principles of Escherichia coli’s electron transport chain (ETC) for varying oxygen conditions in glucose-limited continuous cultures (especially regulatory loops via the transcription factors FNR and ArcA).
- Explaining the observed phenomena in the measurement data.
- Predicting unmeasured variables especially of the gene expression regulatory loops.
Means:
- Experiments (chemostat experiments within the aerobiosis scale).
- Kinetic modelling (especially ...
Submitter: Sebastian Henkel
Biological problem addressed: Model Analysis Type
Investigation: Steady state studies for different oxygen avail...
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Date Published: 30th Sep 2014
Publication Type: Not specified
