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General Information
Manuscript title 13C‐metabolic flux analysis for batch culture of Escherichia coli and its pyk and pgi gene knockout mutants based on mass isotopomer distribution of intracellular metabolites.
PubMed ID 20730757
Journal Biotechnology Progress
Year 2010
Authors Yoshihiro Toya, Nobuyoshi Ishii, Kenji Nakahigashi, Takashi Hirasawa, Tomoyoshi Soga, Masaru Tomita, Kazuyuki Shimizu
Affiliations Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan
Keywords 13C-metabolic flux analysis, batch culture, Escherichia coli, Pyk mutant, Pgi
Full text article Toya_2010.pdf
Project name not specified

Experiment Description
Organism Escherichia coli
Strain Wild‐type E. coli BW25113, Pyk and Pgi mutants
Data type time-series data of metabolites
Data units g/L and mM
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) 1.2
Biomass concentration (g/L) 1 OD600 = 0.3 g/L
Medium composition

Synthetic medium (48 mM Na2HPO4, 22 mM KH2PO4, 10 mM NaCl, 45 mM (NH4)2SO4, 4 g/L glucose) supplemented with 1 mM MgSO4, 1 mg/mL thiamine, 0.056 mg/L CaCl2, 0.08 mg/L FeCl3, 0.01 mg/L MnCl2·4H2O, 0.017 mg/L ZnCl2, 0.0043 mg/L CuCl2·2H2O, 0.006 mg/L CoCl2·2H2O, and 0.06 mg/L Na2MoO4·2H2O.

General protocol information Sampling method: An aliquot of culture broth containing 0.015 g of cells was passed through a 0.45‐μm pore size filter.

Quenching procedure: cells washed with 20 mL of Milli‐Q water at 37°C and metabolism was stopped by submerging in 4 mL of methanol at 4°C containing 2 μM 2‐(N‐morpholino)ethanesulfonic acid, 2 μM trimesate, 2 μM methionine sulfone and 2 μM 3‐aminopyrrolidine as standard.

Extraction technique: chloroform-methanol

Sample analyzing method: CE-TOF-MS

Methods description - Notes

Extracellular metabolites: glucose and acetate, were measured by enzymatic assay kits (F‐kit, Roche Diagnostics, 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: 2018-07-13 11:15:07 UTC

Updated: 2020-04-24 16:10:35 UTC

Version: 1

Status: (reviewed) 2018-07-13 11:16:17 UTC

Views: 3

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Associated Models

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Model name Category Model Type Data used for Access Json
38 E. coli Central Carbon Metabolism Metabolism ordinary differential equations Model building and Model validation {"id":38,"organism_id":null,"comments":"MATLAB version of the model is available at ","sbml_file_name":"Jahan_2016.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"27329289","dilution_rate":"0.2, 0.4, 0.5 and 0.7","name_of_model":"E. coli Central Carbon Metabolism","manuscript_title":"Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli","authors":"Nusrat Jahan, Kazuhiro Maeda, Yu Matsuoka, Yurie Sugimoto and Hiroyuki Kurata","journal":"Microbial Cell Factories","affiliation":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680‑4 Kawazu, Iizuka, Fukuoka 820‑8502, Japan","project_name":"","biomodels_id":"","keywords":"Systems biology, Rational design, Dynamic model, Enzyme kinetics, Transcription factor, Signal transduction, Allosteric enzyme","software":"MATLAB2007 or higher","control":"2018-07-20T16:47:46.311Z","main_organism":"Escherichia coli","year":2016,"combine_archive_file_name":"COMBINE_KIMOMODELID38.omex","combine_archive_content_type":"application/octet-stream","combine_archive_file_size":6603649,"combine_archive_updated_at":"2018-07-23T21:38:00.461Z","review_journal_id":null,"doi":null} Administrator KiMoSys
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
45 Batch kinetic model of Escherichia coli Metabolism ordinary differential equations Model building {"id":45,"organism_id":null,"comments":"Kinetic model source:","sbml_file_name":"Kurata_2018.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n","model_type":"ordinary differential equations","pubmed_id":"29054464","dilution_rate":"—","name_of_model":"Batch kinetic model of Escherichia coli","manuscript_title":"Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures","authors":"Hiroyuki Kurata and Yurie Sugimoto","journal":"Journal of Bioscience and Bioengineering","affiliation":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan","project_name":"","biomodels_id":"","keywords":"Kinetic model, Synthetic biology, Central carbon metabolism, Dynamic simulation, Escherichia coli","software":"MATLAB (MathWorks)","control":null,"main_organism":"Escherichia coli","year":2018,"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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