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General Information
Manuscript title Effect of a single-gene knockout on the metabolic regulation in Escherichia coli for D-lactate production under microaerobic condition.
PubMed ID 15781419
Journal Metabolic Engineering
Year 2005
Authors Jiangfeng Zhu, Kazuyuki Shimizu
Affiliations Department of Biochemical Engineering & Science, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
Keywords Escherichia coli, Enzyme activity, Metabolite concentration, Metabolic flux analysis, Lactate production, Pyruvate metabolism
Full text article Zhu_2005.pdf
Project name not specified

Experiment Description
Organism Escherichia coli
Strain BW25113, pflA, pta, ppc, adhE and pykF mutants
Data type metabolites at steady-state
Data units yield on glucose (g/g)%
Execution date not specified

Experimental Details
Temperature (°C) 37
pH 7.0
Carbon source glucose
Culture mode batch
Process condition aerobic
Dilution rate (h⁻¹)
Working volume (L) 1.0
Biomass concentration (g/L) See worksheet for the different strains. Cell dry weight was determined by measuring the optical density at 600 nm.
Medium composition

Reactor medium was a minimal medium containing (per liter) 2 g of Na2SO4, 2.5 g of (NH4)2SO4, 0.5 g of NH4Cl, 7.3 g of K2HPO4, 3.6 g of NaH2PO4. The following components were sterilized by passing through a 0.2 μm pore-size filter (per liter of final medium): 3 ml of 1 M MgSO4, and 3 ml trace element solution containing (per liter) 0.5 g of CaCl2·H2O, 0.18 g of ZnSO4·7H2O, 0.1 g of MnSO4·H2O, 21.1 g of Na2EDTA, 16.7 g of FeCl3·6H2O, 0.16 g of CuSO4·5H2O and 0.18 g of CoCl2·6H2O. Glucose was used as a carbon source and the initial concentration was about 10 g/L.

General protocol information Sampling method: Samples were centrifuged for 10 min at 4 °C and 6000×g to remove the cells for extracellular metabolite analysis.

Quenching procedure:

Extraction technique: not used

Sample analyzing method: enzymatic

Methods description - Notes

The concentrations of D-lactate, acetate, formate and succinate were measured using capillary electrophoresis (CE) (Agilent, Germany).

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Submission and curation

Entered by: Administrator KiMoSysFirst name: Administrator
Affiliation: INESC-ID/IST
Interests: mathematical modeling, accessible data, use of data

Created: 2018-07-19 14:32:27 UTC

Updated: 2020-04-24 16:10:36 UTC

Version: 1

Status: (reviewed) 2018-07-19 14:34:40 UTC

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Downloads: 52

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Model name Category Model Type Data used for Access Json
40 E. coli redox regulation model Metabolism ordinary differential equations Model building and Model validation {"id":40,"organism_id":null,"comments":"Kinetic model source:","sbml_file_name":"Matsuoka_2017.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"28725263","dilution_rate":"—","name_of_model":"E. coli redox regulation model","manuscript_title":"Modeling and simulation of the redox regulation of the metabolism in Escherichia coli at different oxygen concentrations.","authors":"Yu Matsuoka and Hiroyuki Kurata","journal":"Biotechnology for Biofuels","affiliation":" Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan","project_name":"","biomodels_id":"","keywords":"Kinetic modeling, Fermentation, Dissolved oxygen limitation, Redox regulation, ArcA, Fnr, Respiratory chain, NADH/NAD+ ratio, Escherichia coli ","software":"MATLAB (MathWorks) was used for all simulations.","control":"2018-07-20T16:25:00.495Z","main_organism":"Escherichia coli","year":2017,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Administrator KiMoSys

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