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General Information
Manuscript title Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.
PubMed ID 21092096
Journal Microbial Cell Factories
Year 2010
Authors Tuty AA Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden and Kazuyuki Shimizu
Affiliations Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Japan
Keywords Specific Growth Rate, Flux Balance Analysis, Oxidative Pentose Phosphate Pathway, Main Metabolic Pathway, Isotopomer Distribution
Full text article Kadir_2010.pdf
Project name not specified


Experiment Description
Organism Escherichia coli
Strain K-12 BW25113 and ppc, pyk mutants
Data type time-series data of metabolites
Data units g/L
Execution date not specified


Experimental Details
Temperature (°C) 37.0
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) not specified
Medium composition

M9 sythetic medium: 48 mM Na2HPO4, 22 mM KH2PO4, 10 mM NaCl, 40 mM (NH4)zSO4 and 4 g/l of glucose. Components filter-sterilized separatory and then added (per liter of final volume): 1 ml 1 M MgSO4, 1 ml vitamin B1 (1 mgl stock), 1 ml 0.1 mM CaCl2, and 10 ml trace element solution containing (per liter): 0.55g CaCl2 1g FeCl3, 0.1 mg/l MnCl2.4H2O, 0.17 g ZnCl2, 0.043 g CuCl2.2H2O, 0.06 g CoCl2.2H2O, and 0.06 g Na2MoO4.2H2O).

General protocol information Sampling method: 5ml from the culture broth

Quenching procedure: 15ml of 60% (v/v) aqueous methanol containing 70mM HEPES at -80ºC

Extraction technique: enzymatic, perchloric acid

Sample analyzing method: enzymatic

Methods description - Notes

Cells were separated from the culture by centrifugation at 10,000 ×g for 15 min at 0°C. To extract intracellular metabolites from the cell pellet, 500 ml of 50% methanol was added, and the cells were re-suspended by vortexing the mixture. Then 2 ml of 35% of perchloric acid ...

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Data file
KIMODATAID38_v1.xlsx Preview file
Alternative format(s)
KIMODATAID38_wt_timeseries.csv Preview
KIMODATAID38_pyk_timeseries.csv Preview
KIMODATAID38_ppc_timseries.csv Preview
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Plain text: metadataDataEntryID38.txt
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Submission and curation

Entered by: Administrator KiMoSysFirst name: Administrator
Affiliation: INESC-ID/IST
Homepage: http://kdbio.inesc-id.pt/kimosys
Interests: mathematical modeling, accessible data, use of data

Created: 2013-04-24 14:37:13 UTC

Updated: 2020-04-24 16:10:29 UTC

Version: 1

Status: (reviewed) 2013-12-06 17:17:38 UTC

Views: 14

Downloads: 1




Associated Models

Here we can find relevant models associated with Data EntryID 38:

Model
EntryID
Model name Category Model Type Data used for Access Json
16 glycolysis Escherichia coli model Metabolism ordinary differential equations Model validation {"id":16,"organism_id":38,"comments":"","sbml_file_name":"Kadir_2010.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"21092096","dilution_rate":"—","name_of_model":"glycolysis Escherichia coli model","manuscript_title":"Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.","authors":"Tuty AA Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden and Kazuyuki Shimizu","journal":"Microbial Cell Factories","affiliation":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan","project_name":"","biomodels_id":"","keywords":"Escherichia coli, single-gene knockouts, main central metabolism and TCA","software":"http://www.matlab.com (MATLAB)","control":"2018-07-21T20:34:09.507Z","main_organism":"Escherichia coli","year":2010,"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
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 http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html. ","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
45 Batch kinetic model of Escherichia coli Metabolism ordinary differential equations Model building {"id":45,"organism_id":null,"comments":"Kinetic model source: http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html.","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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