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General Information info

Manuscript title Metabolic flux analysis of pykF gene knockout Escherichia coli based on 13C-labeling experiments together with measurements of enzyme activities and intracellular metabolite concentrations.
PubMed ID 12802531
Journal Appl Micriobiol Biotechnology
Year 2004
Authors Al Zaid Siddiquee K, Arauzo-Bravo MJ, Shimizu K.
Affiliations Department of Biochemical Engineering and Science, Kyushu Institute of Technology,Iizuka, 820–8502 Fukuoka, Japan
Keywords Dilution Ratem Intracellular Metabolite, Metabolic Flux Analysis, Oxidative Pentose Phosphate Pathway, Proteinogenic Amino Acid
Full text article no file uploaded
Project name not specified

Experiment Description info

Organism Escherichia coli
Strain BW25113 and pyk 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
Working volume (L) 0.5
Biomass concentration (g/L) see worksheet.
Medium composition

Minimal medium consisting of 5 g glucose per liter, 48 mM Na2HPO4,22mMKH2PO4, 10 mM NaCl, and40 mM (NH4)SO4, was used. For minimal medium, the following components were filter-sterilized separately and then added (per liter of final volume): 1 ml 1 M MgSO4, 1 ml 0.1 mM CaCl2, 1ml vitamin B1 (1 mg/l stock) and 10 ml trace element solution containing (per liter): 0.55 g CaCl2, 1 g FeCl3, 0.1 g 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 Flux analysis method: 13C constrained MFA

Platform: NMR, GC-MS

Methods description - Notes

The isotopomer balance systems were described using isotopomer mapping matrices [1] and solved through an iterative scheme, based on the approach of [1]. The isotopomers of the proteinogenic amino acids were used to generate NMR synthetic patterns. For the representation of the metabolic fluxes, the forward v and backward v fluxes associated with each bidirectional reaction step were transformed into a net v [2]. A non-linear mapping from exchange fluxes to exchange coefficients v exch[0,1] was made to overcome the numerical problems arising from very large parameters values [3]. Please see more details in the original publication. -----------------------------------References------------------------------
[1] Schmidt K, Carlsen M, Nielsen J, Villadsen J (1997). Biotechnol Bioeng 55:831–840.
[2] Schmidt K, Nielsen J, Villadsen J (1999). J Biotechnol 71:175–190. [3] Wiechert W, Siefke C, de Graff AA, Marx A (1997). Biotechnol Bioeng 55:118–135.

Data file
Downloadfluxes KIMODATAID107_v1.xlsx
Alternative format(s)
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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 2018-07-21 20:09:18 UTC

Updated 2018-07-21 20:18:48 UTC

Version 1

Status (reviewed) 2018-07-21 20:19:41 UTC

Associated Models

Here we can find relevant models associated with Data EntryID 107:

Model name Category Model Type Data used for Access Json
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":" (MATLAB)","used_for":"---\n- Model validation\n","year":2010} Administrator KiMoSys

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