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General Information info

Manuscript title Analysis of Escherichia coli Anaplerotic Metabolism and Its Regulation Mechanisms From the Metabolic Responses to Altered Dilution Rates and Phosphoenolpyruvate Carboxykinase Knockout.
PubMed ID 12966569
Journal Biotechnology and Bioengineering
Year 2003
Authors Yang C, Hua Q, Baba T, Mori H, Shimizu K
Affiliations Metabolome Unit, Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan.
Keywords Escherichia coli; metabolic flux; 13C labeling; anaplerotic reaction; phosphoenolpyruvate carboxykinase; in vivo regulation
Full text article Downloadarticle Yang2003.pdf
Project name not specified

Experiment Description info

Organism Escherichia coli
Strain W3110 and pck mutant
Data type flux measurements
Data units (mmol/g-dry cell weight/h)
Execution date not specified

Experimental Details info

Temperature (0C) 37
pH 7.0
Carbon source glucose,
Culture mode chemostat
Process condition aerobic
Dilution rate (h-1) 0.1, 0.32, 0.55 (WT ) and 0.1 (pck)
Working volume (L) 1.0
Biomass concentration (g/L) see worksheet.
Medium composition

Medium containing (per liter): 5.0 g of glucose, 1.0 g of NH4Cl, 2.7 g of (NH4)2SO4,6.8gofNa2HPO4,3.0gofKH2PO4, 0.6 g of NaCl, 0.2 g ofMgSO4 7H2O, 1.0 µg of thiamine HCl, 2.0 µL of polypropylene glycol 2000 as an antiform agent, and 10 mL of trace element solution [1].

General protocol information Flux analysis method: 13C constrained MFA

Platform: NMR

Methods description - Notes

MFA analysis: The carbon flux distribution in the bioreaction network was determined as a best fit to all extracellular flux measurements, the macromolecular biomass composition, and the relative intensities of the 13C-13C scalar coupling multiplets of the aforementioned 47 carbon positions of aminoacids and glycerol determined by 2D [13C,1H]-COSY. Theflux quantification was performed by a least-squares parameter fitting approach in the mathematical framework. Exchanges fluxes viareversible reactions were quantitatively considered in the flux calculations. Initially, the isotopomer balances of all metabolites in the bioreaction network are calculated from a random initial flux distribution. Relative 13C multiplet intensities are then simulated from this isotopomer distribution and compared to the experimental values. The quality of the fit was judged by the X2 (error) value. Multiple calculations were performed from different random starting points, and the best solution that was reproducibly attained was presented as the estimated result of flux distribution. A statistical error analysis of the estimated fluxes was included in the calculations. Moreover, the flux estimates were compared with the results of flux ratio analysis, since both methods employed are very different and thus flux ratio analysis can serve as an independent verification of the flux estimates. In addition, the calculation of the flux distribution in the pck deletion mutant was performed without any constraint on the flux through PEP carboxykinase.
---------------------------------------------References--------------------------------------------
[1] Sauer U, Lasko DR, Fiaux J, Hochuli M, Glaser R, Szyperski T, Wuthrich K, Bailey JE. 1999. J Bacteriol 181:6679–6688.

Data file
Downloadfluxes KIMODATAID106_v1.xlsx
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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 2018-07-21 16:52:41 UTC

Updated 2018-07-31 09:18:03 UTC

Version 1

Status (reviewed) 2018-07-21 16:56:08 UTC




Associated Models


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EntryID
Model name Category Model Type Data used for Access Json
16
Authors: Tuty AA Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden and Kazuyuki Shimizu

Original paper: Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.

glycolysis Escherichia coli model Metabolism ordinary differential equations Model validation Visto4 {"affiliation":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan","article_file_name":null,"authors":"Tuty AA Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden and Kazuyuki Shimizu","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":"","control":"2018-07-21T20:34:09Z","dilution_rate":"\u2014","id":16,"journal":"Microbial Cell Factories","keywords":"Escherichia coli, single-gene knockouts, main central metabolism and TCA","main_organism":"Escherichia coli","manuscript_title":"Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.","model_name":"glycolysis Escherichia coli model","model_type":"ordinary differential equations","organism_id":38,"project_name":"","pubmed_id":"21092096","review_journal_id":null,"sbml_file_name":"Kadir_2010.pdf","software":"http://www.matlab.com (MATLAB)","used_for":"---\n- Model validation\n","year":2010} Administrator KiMoSys



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