{"database":"FAIRDOMHub","file_versions":[],"scores":null,"additional":{"omics_type":["Models"],"submitter":["Sebastian Henkel"],"full_dataset_link":["https://fairdomhub.org/models/45?version=2"],"ModelFormat":["SBML"],"submitter_affiliation":["University of Stuttgart"],"repository":["FAIRDOMHub"],"pubmed_abstract":["For adaptation between anaerobic, micro-aerobic and aerobic conditions Escherichia coli's metabolism and in particular its electron transport chain (ETC) is highly regulated. Although it is known that the global transcriptional regulators FNR and ArcA are involved in oxygen response it is unclear how they interplay in the regulation of ETC enzymes under micro-aerobic chemostat conditions. Also, there are diverse results which and how quinones (oxidised/reduced, ubiquinone/other quinones) are controlling the ArcBA two-component system. In the following a mathematical model of the E. coli ETC linked to basic modules for substrate uptake, fermentation product excretion and biomass formation is introduced. The kinetic modelling focusses on regulatory principles of the ETC for varying oxygen conditions in glucose-limited continuous cultures. The model is based on the balance of electron donation (glucose) and acceptance (oxygen or other acceptors). Also, it is able to account for different chemostat conditions due to changed substrate concentrations and dilution rates. The parameter identification process is divided into an estimation and a validation step based on previously published and new experimental data. The model shows that experimentally observed, qualitatively different behaviour of the ubiquinone redox state and the ArcA activity profile in the micro-aerobic range for different experimental conditions can emerge from a single network structure. The network structure features a strong feed-forward effect from the FNR regulatory system to the ArcBA regulatory system via a common control of the dehydrogenases of the ETC. The model supports the hypothesis that ubiquinone but not ubiquinol plays a key role in determining the activity of ArcBA in a glucose-limited chemostat at micro-aerobic conditions."],"pubmed_title":["Basic regulatory principles of Escherichia coli's electron transport chain for varying oxygen conditions."],"pubmed_authors":["Henkel Sebastian G SG, Ter Beek Alexander A, Steinsiek Sonja S, Stagge Stefan S, Bettenbrock Katja K, de Mattos M Joost Teixeira MJ, Sauter Thomas T, Sawodny Oliver O, Ederer Michael M"],"description_synonyms":["Alkalescens-Dispar Group, Diffusely Adherent Escherichia coli, Bacterium coli, Couple, Escherichia/Shigella coli, postnatal development., Enteroinvasive E. coli, growth pattern, non-developmental growth, postnatal growth, bacterium E3, E coli, Coupled, growth and development, EAggEC, Enteroaggregative E. coli, Coupling, E. coli, Eschericia coli, Enteroaggregative Escherichia coli, development, Bacterium coli commune, Diffusely Adherent E. coli, Bacillus coli, Escherchia coli, Enteroinvasive Escherichia coli, Enterococcus coli, growth"],"pubmed_title_synonyms":["Alkalescens-Dispar Group, O2, Diffusely Adherent Escherichia coli, Disauerstoff, dioxygen, Bacterium coli, Oxygen 16, Escherichia/Shigella coli, Enteroinvasive E. coli, O, Oxygen-16, bacterium E3, E coli, E-948, 8O, EAggEC, Enteroaggregative E. coli, oxygen, E. coli, Eschericia coli, Enteroaggregative Escherichia coli, Oxygen, Bacterium coli commune, [OO], dioxygene, Diffusely Adherent E. coli, Sauerstoff, Bacillus coli, Escherchia coli, oxigeno, Dioxygen., Enteroinvasive Escherichia coli, Enterococcus coli, oxygene, E948, E 948, OXYGEN MOLECULE, molecular oxygen"],"pubmed_abstract_synonyms":["biochemical pathways, Metabolic Process, Activity, Feature, Glukose, Metabolic Concepts, bacterium E3, Monohydrate, sci, (DL)-Isomer, clefted, Social Controls, prevention, Roles, responsivity, GRP1, oxigeno, Dextrose, Grp1, ubiquinols, Concepts, HOW, How, ubiquinol 1, ubiquinol 0, excretion, Enterococcus coli, Metabolism Concept, E948, ubiquinol 7, Phenomenon, prevention and control, ubiquinol 9, Formal Social Controls, l(3)j5D5, IKKg, multicellular organismal biosynthetic process, KEY, Key, 24B, strong, single-organism biosynthetic process, Escherichia/Shigella coli, enzymes, reference sample, catabolism, O, PTPSTEP, Oxygen-16, ARCA, stru, hypoplasia, E coli, beta-particle, metabolic process resulting in cell growth, l(3)S053606, CG10293, DL-glucose, Fast, E. coli, Social, Eschericia coli, Enteroaggregative Escherichia coli, preventive measures, arca, Oxygen, l(3)j5B5, glucose, e, [OO], e-, l(2)k08110, Role Concepts, biotransformation, Catabolism, GPH, single-organism behavior, 0904/17, preventive therapy, anatomical protrusion, subdivided, Process, metabolism resulting in cell growth, Positrons, Enteroaggregative E. coli, Fermentations, results, DmIKKgamma, Role Concept, Diffusely Adherent E. coli, Sauerstoff, SZ1, dIKK, Fast Electron, 3.1.3.48, Kenny, Role, secretion, (alpha-D)-Isomer, ubiquinone hydroquinone, autosomal recessive, forked, D-Glucose, Diffusely Adherent Escherichia coli, Disauerstoff, dioxygen, divided, Enteroinvasive E. coli, Step, CG11628, IKK-gamma, Control, common, Striatum-enriched protein-tyrosine phosphatase, Electron, Controls, septate, Features, beta(-), experimental procedures, DmelCG16910, D Glucose, spine, STEP, Biocatalyst, anon-EST:Liang-2.39, Glucose Monohydrate, Regulation, ubiquinol 6 (ubiquinol 30), Dioxygen, Regulations, gluco-hexose, GRP1/cytohesin 1, experimental, conformation, Glucose, Processes, Biocatalysts, P62, e(-), E-948, 8O, electron, Metabolic Processes, excreted substance, dIKK-gamma, protrusion, CG11633, cytohesin/GRP1, dioxygene, reduced, resilient, Metabolism, Escherchia coli, tough, DmIKK-gamma, Enteroinvasive Escherichia coli, tiny, dmIKKgamma, IKK[[gamma]], Metabolism Phenomena, cerebellar ataxia, reactivity, anatomical systems, methods, l(3)s2612, Coenzyme Q, experimental section, Elektron, l(2)SH2 0323, Metabolic Concept, Enzyme, Neural-specific protein-tyrosine phosphatase, IKK, DmelCG10293, Characteristics, ubiquinol 50, Anhydrous, molecular oxygen, Controlled, Electrons, Positron, Alkalescens-Dispar Group, small, Controlling, Bacterium coli, Oxygen 16, waste substance, (beta-D)-Isomer, degradation, Formal Social Control, clone 2.39, Negatron, portion of excreted substance, Negatrons, stepk, enzyme activity, EAggEC, qkr, l(3)S090417, oxygen, Concept, Metabolic Phenomena, Metabolism Concepts, IKKgamma, uptake, Characteristic, Social Control, Bacillus coli, KH93F, Phenomena, feed, oxygene, Fast Electrons, metabolism, l(2)SH0323, OXYGEN MOLECULE, Metabolic Phenomenon, who, CYH1, O2, multicellular organism metabolic process, biodegradation, negatron, Metabolic, underdeveloped, Dmikkgamma, prophylaxis, Glc., Who/How, CG16910, Anhydrous Dextrose, beta, DmelCG11628, Bacterium coli commune, Biomasses, control, qkr[93F], regulation, response, E 948, General activity, hypothesis, Anabolism, Glc"],"name_synonyms":["Alkalescens-Dispar Group, Diffusely Adherent Escherichia coli, Bacterium coli, Couple, Escherichia/Shigella coli, postnatal development., Enteroinvasive E. coli, growth pattern, non-developmental growth, postnatal growth, bacterium E3, E coli, Coupled, growth and development, EAggEC, Enteroaggregative E. coli, Coupling, E. coli, Eschericia coli, Enteroaggregative Escherichia coli, development, Bacterium coli commune, Diffusely Adherent E. coli, Bacillus coli, Escherchia coli, Enteroinvasive Escherichia coli, Enterococcus coli, growth"],"additional_accession":[]},"is_claimable":false,"name":"Kinetic model of Escherichia coli's electron transport chain (ETC) coupled to a simplified growth model","description":"Kinetic model of Escherichia coli's electron transport chain (ETC) coupled to a simplified growth model","dates":{"created":"2011-05-30","publication":"2011-05-30","submission":"2011-05-30","last_modified":"2011-05-30"},"accession":"45","cross_references":{"pubmed":["25268772"]}}