Repository » Data AccessID 96

Detail View - Data AccessID 96

Backimage Back

General Information info

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 Downloadarticle Toya_2010.pdf
Project name not specified

Experiment Description info

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 info

Temperature (0C) 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). Intracellular metabolites: sample preparation was carried out using the modified method described by Ohashi et al. [1] An aliquot of culture broth containing 0.015 g of cells was passed through a 0.45‐μm pore size filter (Millipore). The cells on the filter were 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 internal standard. Quantities of 4 mL of chloroform and 1.6 mL of Milli‐Q water were added to the solution, which was then fully mixed. The solution was centrifuged at 2,300g for 5 min at 4°C, and the separated methanol layer was filtered by centrifugation through a Millipore 5‐kDa cutoff filter to remove high‐molecular‐weight compounds. The filtrate was lyophilized and then dissolved in 50 μL of Milli‐Q water before CE‐TOFMS analysis. CE‐TOFMS experiments were performed on an Agilent CE capillary electrophoresis system (Agilent Technologies, Germany) and an Agilent G3250AA LC/MSD TOF system (Agilent Technologies, Palo Alto, CA). The CE‐TOFMS conditions used for anionic metabolite analysis have been described elsewhere [2,3]. All measurements were performed three times.
------------------------------------------References--------------------------------------- [1] Sohashi Y, Hirayama A, Ishikawa T, Nakamura S, Shimizu K, Ueno Y, Tomita M, Soga T. Depiction of metabolome changes in histidine‐starved Escherichia coli by CE‐TOFMS. Mol Biosyst. 2008; 4: 135–147. http://doi.org/fsn7dx [2] Soga T, Baran R, Suematsu M, Ueno Y, Ikeda S, Sakurakawa T, Kakazu Y, Ishikawa T, Robert M, Nishioka T, Tomita M. Differential metabolomics reveals ophthalmic acid as an oxidative stress biomarker indicating hepatic glutathione consumption. J Biol Chem. 2006; 281: 16768–16776. http://doi.org/fch7nt [3] Soga T, Ohashi Y, Ueno Y, Naraoka H, Tomita M, Nishioka T. Quantitative metabolome analysis using capillary electrophoresis mass spectrometry. J Proteome Res. 2003; 2: 488–494. http://doi.org/fgcc2v

Data file
Downloadmetabolites KIMODATAID96_v1.xlsx
Alternative format(s)
no file uploaded
Cite|Share

Organism


Related Data: AccessID 30 | AccessID 35 | AccessID 41 | AccessID 44 | AccessID 51 | AccessID 54 | AccessID 63 | AccessID 64 | AccessID 65 | AccessID 67 | AccessID 68 | AccessID 74 | AccessID 75 | AccessID 78 | AccessID 79 | AccessID 80 | AccessID 86 | AccessID 87 | AccessID 92 | AccessID 101 | AccessID 102 | AccessID 103 | AccessID 104 | AccessID 105 | AccessID 106 | AccessID 107 | AccessID 108 | AccessID 109 | AccessID 110 | AccessID 112 | AccessID 116 | AccessID 118 | AccessID 119 | AccessID 125 | AccessID 126


Submission and curation info

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 2018-07-13 11:15:07 UTC

Updated 2018-07-13 11:19:10 UTC

Version 1

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




Associated Models


Here we can find relevant models associated with Data EntryID 96:

Model
EntryID
Model name Category Model Type Data used for Access Json
38
Authors: Nusrat Jahan, Kazuhiro Maeda, Yu Matsuoka, Yurie Sugimoto and Hiroyuki Kurata

Original paper: Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli

E. coli Central Carbon Metabolism Metabolism ordinary differential equations Model building and Model validation Visto4 {"affiliation":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680\u20114 Kawazu, Iizuka, Fukuoka 820\u20118502, Japan","article_file_name":null,"authors":"Nusrat Jahan, Kazuhiro Maeda, Yu Matsuoka, Yurie Sugimoto and Hiroyuki Kurata","biomodels_id":"","category":"Metabolism","combine_archive_content_type":"application/octet-stream","combine_archive_file_name":"COMBINE_KIMOMODELID38.omex","combine_archive_file_size":6603649,"combine_archive_updated_at":"2018-07-23T21:38:00Z","comments":"MATLAB version of the model is available at http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html. ","control":"2018-07-20T16:47:46Z","dilution_rate":"0.2, 0.4, 0.5 and 0.7","id":38,"journal":"Microbial Cell Factories","keywords":"Systems biology, Rational design, Dynamic model, Enzyme kinetics, Transcription factor, Signal transduction, Allosteric enzyme","main_organism":"Escherichia coli","manuscript_title":"Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli","model_name":"E. coli Central Carbon Metabolism","model_type":"ordinary differential equations","organism_id":null,"project_name":"","pubmed_id":"27329289","review_journal_id":null,"sbml_file_name":"Jahan_2016.pdf","software":"MATLAB2007 or higher","used_for":"---\n- Model building\n- Model validation\n","year":2016} Administrator KiMoSys
40
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: http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html.","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
45
Authors: Hiroyuki Kurata and Yurie Sugimoto

Original paper: Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures

Batch kinetic model of Escherichia coli Metabolism ordinary differential equations Model building Visto4 {"affiliation":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan","article_file_name":null,"authors":"Hiroyuki Kurata and Yurie Sugimoto","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: http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html.","control":null,"dilution_rate":"\u2014","id":45,"journal":"Journal of Bioscience and Bioengineering","keywords":"Kinetic model, Synthetic biology, Central carbon metabolism, Dynamic simulation, Escherichia coli","main_organism":"Escherichia coli","manuscript_title":"Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures","model_name":"Batch kinetic model of Escherichia coli","model_type":"ordinary differential equations","organism_id":null,"project_name":"","pubmed_id":"29054464","review_journal_id":null,"sbml_file_name":"Kurata_2018.pdf","software":"MATLAB (MathWorks)","used_for":"---\n- Model building\n","year":2018} Administrator KiMoSys



Associate models to data

- Several models can be associated.

Add New Model



Backimage Back | Top