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General Information info

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 Downloadarticle Zhu_2005.pdf
Project name not specified

Experiment Description info

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 info

Temperature (0C) 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).

Data file
Downloadmetabolites KIMODATAID101_v1.xlsx
Alternative format(s)
no file uploaded


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Submission and curation info

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 2018-07-19 14:34:29 UTC

Version 1

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

Associated Models

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Model name Category Model Type Data used for Access Json
Authors: Yu Matsuoka and Hiroyuki Kurata

Original paper: Modeling and simulation of the redox regulation of the metabolism in Escherichia coli at different oxygen concentrations.

E. coli redox regulation model Metabolism ordinary differential equations Model building and Model validation Visto4 {"affiliation":" Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan","article_file_name":null,"authors":"Yu Matsuoka and Hiroyuki Kurata","biomodels_id":"","category":"Metabolism","combine_archive_content_type":null,"combine_archive_file_name":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"comments":"Kinetic model source:","control":"2018-07-20T16:25:00Z","dilution_rate":"\u2014","id":40,"journal":"Biotechnology for Biofuels","keywords":"Kinetic modeling, Fermentation, Dissolved oxygen limitation, Redox regulation, ArcA, Fnr, Respiratory chain, NADH/NAD+ ratio, Escherichia coli ","main_organism":"Escherichia coli","manuscript_title":"Modeling and simulation of the redox regulation of the metabolism in Escherichia coli at different oxygen concentrations.","model_name":"E. coli redox regulation model","model_type":"ordinary differential equations","organism_id":null,"project_name":"","pubmed_id":"28725263","review_journal_id":null,"sbml_file_name":"Matsuoka_2017.pdf","software":"MATLAB (MathWorks) was used for all simulations.","used_for":"---\n- Model building\n- Model validation\n","year":2017} Administrator KiMoSys

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