The efficient redesign of bacteria for biotechnological purposes, such as biofuel production, waste disposal or specific biocatalytic functions, requires a quantitative systems-level understanding of energy supply, carbon, and redox metabolism. The measurement of transcript levels, metabolite concentrations and metabolic fluxes per se gives an incomplete picture. An appreciation of the interdependencies between the different measurement values is essential for systems-level understanding. Mathematical modeling has the potential to provide a coherent and quantitative description of the interplay between gene expression, metabolite concentrations, and metabolic fluxes. Escherichia coli undergoes major adaptations in central metabolism when the availability of oxygen changes. Thus, an integrated description of the oxygen response provides a benchmark of our understanding of carbon, energy, and redox metabolism. We present the first comprehensive model of the central metabolism of E. coli that describes steady-state metabolism at different levels of oxygen availability. Variables of the model are metabolite concentrations, gene expression levels, transcription factor activities, metabolic fluxes, and biomass concentration. We analyze the model with respect to the production capabilities of central metabolism of E. coli. In particular, we predict how precursor and biomass concentration are affected by product formation.
SEEK ID: https://fairdomhub.org/publications/231
PubMed ID: 24723921
Projects: SUMO
Publication type: Not specified
Journal: Front Microbiol
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Date Published: 27th Mar 2014
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I am interested in the coupling of global regulation and metabolism in E. coli. To analyze this I construct and analyze defined mutant strains. These strains are characterized in bioreactor experiments of different types (batch, conti, pulse ...) and measurements on the level of metabolites, mRNA, and protein are applied. For all projects there are cooperation partners that use the data in modeling approaches either from the MPI Magdeburg or from the SUMO consortium.
Projects: SUMO
Institutions: University of Stuttgart
I'm interested in the application and development of methods of systems theory in biology (systems biology). In particulary I work on the following topics: Thermodynamic constraints on biochemical network; Model reduction; Modeling and Analysis of metabolic regulation.
Projects: SUMO
Institutions: University of Sheffield
The major theme of the research in my laboratory is bacterial gene regulation. We are interested in signal perception mechanisms (in particular oxygen); signal transduction (ligand induced protein confromational changes); interaction of transcription factors with the core transcription machinery; interactions between transcription factors to integrate multiple signals; and the influence of promoter architectures on these events. We are also interested in aome aspects of post-transcriptional ...
Projects: SUMO
Institutions: University of Stuttgart
Tools: Matlab, Copasi, Flux balance analysis, Dynamic modelling
I recently joined the Institute for System Dynamics as a PhD student. I'm currently working on a dynamic model of nitrate respiration in E. coli.
Projects: SUMO
Institutions: University of Sheffield
Expertise: Escherichia coli, Microbiology Biochemistry Molecular biology Genetics Enzymology Synthetic biology Regulatory metabolic networks, Bacterial Cell Biology, Cellular biology of metals
Tools: Biochemistry and protein analysis, Transcriptomics, Spectroscopy and structural analysis, molecular biological techniques (RNA/DNA techniques
Work in my laboratory is focussed on microbial physiology - the study of how bacteria and other microorganisms work. Although rooted in the tradition of bacterial growth and intermediary metabolism, microbial physiology now embraces molecular biology, genetics, biochemistry, and indeed any discipline that can shed light on bacterial function. Much of our experimental work is conducted with Escherichia coli, the pre-eminent ‘model’ organism with unrivalled ease of genetic and physiological ...
Projects: SUMO
Institutions: University of Sheffield
I am a post-doctoral research associate working in Sheffield in the SUMO consortium. My research focuses on transcriptional regulation in E. coli, with particular emaphasis on the transcriptomic analysis of steady-state chemostat cultures using both microarray and qRT-PCR approaches.
Previous experience, especially that gained during my PhD, involved work on Salmonella physiology and lag phase growth, focusing particularly on gene-expression and transcriptional regulation. Other techniques used ...
Projects: SUMO
Institutions: University of Stuttgart
From 2005 to 2008 I was group leader at the Institute for System Dynamics at the University of Stuttgart. Since 2008 I am now Professor of Systems Biology at the University of Luxembourg.
The research of the Systems Biology Group at the University of Luxembourg is focussed in the area of experimental and theoretical systems biology. We are applying different modelling techniques (mainly ODE and logical) to biological systems to develop suitable computational models. The analysis of these models ...
Projects: SUMO
Institutions: University of Stuttgart
Expertise: Mathematical modelling, Nonlinear Dynamics, Parameter estimation
PI of the SUMO work package "Detailed kinetic modelling, identification and analysis of the citric acid cycle and respiratory chains of E. coli". Director of the Institute for System Dynamics, Universität Stuttgart, Germany.
Projects: SUMO
Institutions: Max Planck Institute for Dynamics of Complex Technical Systems
Projects: SUMO
Institutions: Max Planck Institute for Dynamics of Complex Technical Systems
Roles: Postdoc
Expertise: Microbiology, Molecular Biology, E. coli, Biotechnology
Tools: qRT-PCR, Bioreactor experiments/Fermentation (batch, Chemostat), Enzyme assays, 2D-PAGE
Institutions: University of Amsterdam
Professor Quantitative Microbial Physiology Dept Mol Mic Phys Swammerdam Inst Life Sc University of Amsterdam
Projects: SUMO
Institutions: University of Amsterdam
Expertise: Transcriptomics, Bacillus subtilis, Escherichia coli, stress responses
Tools: Chemostats, HPLC, phage transduction
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
Organisms: Escherichia coli, Escherichia coli K-12
This assay describes how to analyze gene expression rates via RT-PCR.
Submitter: Sonja Steinsiek
Assay type: Gene Expression Profiling
Technology type: qRT-PCR
Investigation: Steady state studies for different oxygen avail...
Organisms: Escherichia coli (chemostat)
SOPs: Evans Medium, SUMO chemostat conditions, SUMO mRNA isolation Epicentre
Data files: Gene expression rates at different aerobiosis l... and 3 hidden items
Snapshots: No snapshots
This document describes by-product formation rates measured in MG1655 at steady-state conditions in Infors-Multifors-Bioreactors.
Submitter: Sonja Steinsiek
Assay type: Metabolomics
Technology type: Technology Type
Investigation: Steady state studies for different oxygen avail...
Organisms: Escherichia coli (chemostat)
SOPs: DCW measurement, Evans Medium, Measurement of extracellular metabolites, SUMO chemostat conditions
Data files: 3 hidden items
Snapshots: No snapshots
This experiment uses a low-copy plasmid based system (MG1655 Δlac FF(-41.5)/RW50) for measuring FNR activity. Initial acetate calibration of the chemostat with the MG1655 Δlac strain was carried out, with β-galactosidase activity from the FF(-41.5)/RW50 reporter plasmid measured at 100%, 80%, 50%, 20% and 0% aerobiosis levels. Finally, the aerobiosis levels were re-determined by calculating the actual acetate flux in the sampled chemostat runs.
Note: the strain used (MG1655 Δlac) is not the same ...
Submitter: Michael Ederer
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Steady state studies for different oxygen avail...
Organisms: Escherichia coli (chemostat)
SOPs: DCW measurement, Evans Medium, SUMO B-galactosidase assay
Data files: FNR activity at different aerobiosis levels REC..., FNR reporter activity at different aerobiosis l...
Snapshots: No snapshots
The task of this assay is to determine the impact of oxygen availability on the concentrations of metabolites from different central metabolic pathways. The focus lies on metabolites connected to glycolysis, tri-carbon-acid-cycle and energy metabolism. All strains have been cultured and analysed according to the SOPs listed below
Submitter: Stefan Stagge
Assay type: Metabolomics
Technology type: Liquid Chromatography Mass Spectrometry
Investigation: Steady state studies for different oxygen avail...
Organisms: Escherichia coli (chemostat)
SOPs: DCW measurement, Quenching and Extraction of intracellular metab..., SUMO chemostat conditions
Data files: 3 hidden items
Snapshots: No snapshots
This assay describes the determination of concentrations and ratio of metabolites of adenine nucleotides (NAD and NADH). These metabolites have been extracted from Escherichia coli MG1655 and isgenic mutant strains.
Submitter: Stefan Stagge
Assay type: Metabolomics
Technology type: Initial Rate Experiment
Investigation: Steady state studies for different oxygen avail...
Organisms: Escherichia coli : K-12/MG1655 (wild-type / wild-type) (chemostat)
SOPs: 1 hidden item
Data files: 2 hidden items
Snapshots: No snapshots
This assay describes the determination of concentrations and ratio of metabolites of ubiquinones (oxidised and reduced form). These metabolites have been extracted from Escherichia coli MG1655 and isgenic mutant strains.
Submitter: Stefan Stagge
Assay type: Metabolomics
Technology type: HPLC
Investigation: Steady state studies for different oxygen avail...
Organisms: Escherichia coli : K-12/MG1655 (wild-type / wild-type) (chemostat)
SOPs: DCW measurement, Q/QH2 sampling, SUMO chemostat conditions
Data files: 091016 quinones complete data magdeburg, 091016 quinones complete data magdeburg
Snapshots: No snapshots
Glucose transporter mutants were analyzed under aerobic and aerobic conditions in batch cultures with glucose as substrate. Acetate formation rates and glucose consumption rates were measured, as well as extracellular cAMP concentrations.
Submitter: Sonja Steinsiek
Assay type: Extracellular Metabolite Concentration
Technology type: Technology Type
Investigation: Analysis of the glucose transport in Escherichi...
Organisms: Escherichia coli : MG1655 (del LAM;del rph-1 / pyrimidine starvation ) (batch)
SOPs: Measurement of extracellular metabolites and 1 hidden item
Data files: Growth, by-product formation and glucose consum..., Growth, yield and cAMP excretion under anaerobi...
Snapshots: No snapshots
MG1655 and mutant strains with defects in glucose transport systems were analyzed in aerobic and anaerobic batch cultures.
Submitter: Sonja Steinsiek
Assay type: Gene Expression Profiling
Technology type: Technology Type
Investigation: Analysis of the glucose transport in Escherichi...
Organisms: No organisms
SOPs: SUMO mRNA isolation Epicentre and 1 hidden item
Data files: Transcription of glucose uptake transport syste..., Transcription of glucose uptake transport syste...
Snapshots: No snapshots
ArcA phosphorylation in chemostat cultures grown at different aerobiosis levels was quantitated by Phos-tag SDS-PAGE gel analysis and subsequent immunodetection of ArcA.
Submitter: Matthew Rolfe
Assay type: Experimental Assay Type
Technology type: SDS-PAGE
Investigation: Steady state studies for different oxygen avail...
Organisms: Escherichia coli : MG1655 (del LAM;del rph-1 / pyrimidine starvation ) (chemostat)
SOPs: Determination of protein phosphorylation levels..., Evans Medium, SUMO chemostat conditions
Data files: No Data files
Snapshots: No snapshots
This data file shows results from the different chemostat experiments.Gene expression rates are presented.
Creators: Katja Bettenbrock, Sonja Steinsiek
Submitter: Katja Bettenbrock
Measurement of by-product formation rates, substrate consumption rates and extracellular concentrations of cAMP under aerobic batch conditions with glucose as substrate.
Creator: Sonja Steinsiek
Submitter: Sonja Steinsiek
Transcription of glucose uptake transport systems in a mutant background under anaerobic batch conditions.
Creator: Sonja Steinsiek
Submitter: Sonja Steinsiek
Transcription of glucose uptake transport systems in a mutant background under aerobic batch conditions.
Creator: Sonja Steinsiek
Submitter: Sonja Steinsiek
Measurement of by-product formation rates, substrate consumption rates and extracellular concentrations of cAMP under anaerobic batch conditions with glucose as substrate.
Creator: Sonja Steinsiek
Submitter: Sonja Steinsiek
A .pdf files showing graphs of FNR activity at varying aerobiosis levels
Top graph shows no acetate re-calibration Bottom graph shows data with acetate re-calibration
Creator: Matthew Rolfe
Submitter: The JERM Harvester
This .csv file shows FNR activity at different aerobiosis levels
Columns a_old Desired aerobiosis level (Aerobiosis units or %AAU) Bgal_activity Average FNR reporter activity (Miller units) Bgal_STDEV STDEV of FNR reporter activities (Miller units) rDOT(μM) Dissolved oxygen tension (μM) DCW DCW (g/L) [acetate] Extracellular acetate concentration (mM) Qacetate Acetate flux (mmoles/h/gDCW) a_new Actual aerobiosis level in sampled chemostat
Creator: Matthew Rolfe
Submitter: The JERM Harvester
his document contains data for quinone concentrations and ratios of ubichinon and menachinon.These data have been generated for analysis of MG1655 at steady-state conditions in Infors-Multifors-Bioreactors. All measurements have been done in Amsterdam at the group of Prof. Joost Teixeira de Mattos.
Duplicates of samples for quinones were taken after 20 hours of steady state conditions. Chemostat experiments were carried out in Infors-Bioreactors at 0, 20, 50, 80, 100 and 120% aerobiosis. All data ...
Creators: Stefan Stagge, Alexander Ter Beek
Submitter: The JERM Harvester
This is the csv version of the file: 091016 quinones complete data magdeburg
This document contains data for quinone concentrations and ratios of ubichinon and menachinon.These data have been generated for analysis of MG1655 at steady-state conditions in Infors-Multifors-Bioreactors. All measurements have been done in Amsterdam at the group of Prof. Joost Teixeira de Mattos.
Duplicates of samples for quinones were taken after 20 hours of steady state conditions. Chemostat experiments were carried ...
Creators: Stefan Stagge, Alexander Ter Beek
Submitter: The JERM Harvester
The model describes the catabolism of Escherichia coli and its regulation. The metabolic reactions are modeled by the thermokinetic model formalism. The model is simplified by assuming rapid equilibrium of many reactions. Regulation is modeled by phenomenological laws describing the activation or repression of enzymes and genes in dependence of metabolic signals. The model is intended to describe the behavior of E. coli in a chemostat culture in depedence on the oxygen supply.
The model is described ...
Creators: Michael Ederer, David Knies
Submitter: Michael Ederer
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Organism: Escherichia coli
Investigations: Steady state studies for different oxygen avail...