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General Information info

Manuscript title Metabolic regulation analysis of wild-type and arcA mutant Escherichia coli under nitrate conditions using different levels of omics data.
PubMed ID 22790675
Journal Molecular BioSystems
Year 2012
Authors Yoshihiro Toya, Kenji Nakahigashi, Masaru Tomita and Kazuyuki Shimizu
Affiliations Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan
Keywords Escherichia coli, metabolic flux distributions
Full text article no file uploaded
Project name not specified

Experiment Description info

Organism Escherichia coli
Strain BW25113 and arcA mutant
Data type flux measurements
Data units (mmol/gDW.h)
Execution date not specified

Experimental Details info

Temperature (0C) 37.0
pH 7.0
Carbon source glucose,
Culture mode chemostat
Process condition aerobic and anaerobic
Dilution rate (h-1) 0.2
Working volume (L) 1.0
Biomass concentration (g/L) not specified
Medium composition

Synthetic medium for batch and continuous: 48 mM Na2HPO4, 22 mM KH2PO4, 10 mM NaCl, 45 mM (NH4)2SO4, 4 g/L glucose was supplemented with 1 mM MgSO4, 1 mg mL 1 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. In addition, 40 mM of potassium nitrate was added to the medium for the cultures under nitrate conditions.

General protocol information Flux analysis method: 13C constrained MFA

Platform: MALDI-TOF

Methods description - Notes

13C-Metabolic flux analysis - The stoichiometric reaction model for glycolysis, the pentose phosphate (PP) pathway, the TCA cycle, the glyoxylate shunt and the anaplerotic reaction was constructed for the flux analysis.
The fluxes for biosynthesis were calculated based on the specific growth rate and the precursor requirements for biomass production [1]. The flux distributions were optimized by the labeling pattern computed from assumed fluxes as the best fits to the measured labeling pattern of the metabolites [2]. A genetic algorithm was combined with a sequential quadratic programming method to perform this optimization. The mass isotopomer distributions of intermediates such as FDP, DHAP, 3PG, PEP, Ru5P, R5P, CIT, and MAL were used to compute the fluxes. These mass isotopomers were quantitated using Analyst QS software (Applied Biosystems), and appropriate corrections were made for natural isotope abundances [3]. A statistical analysis was employed to evaluate the sensitivity of the flux estimations for inaccuracies in measurement. Furthermore, 20 simulated measurement data sets were generated through the addition of artificial noise. Flux estimations were independently performed using these generated data sets to calculate the 99% confidence intervals for the fluxes. All calculations were performed using MATLAB R2010a with the Global Optimization Toolbox 3.0 software (Mathworks).

----------------References-----------------
[1] M. Li, P. Y. Ho, S. Yao and K. Shimizu, J. Biotechnol., 2006, 122, 254–266. http://doi.org/cr7qpd
[2] Y. Toya, N. Ishii, K. Nakahigashi, T. Hirasawa, T. Soga, M. Tomita and K. Shimizu, Biotechnol Prog, 2010, 26, 975–992. http://doi.org/b7nbgf
[3] W. A. van Winden, C. Wittmann, E. Heinzle and J. J. Heijnen, Biotechnol. Bioeng., 2002, 80, 477–479. http://doi.org/dp966z

Data file
Downloadfluxes KIMODATAID80_v0.xlsx
Alternative format(s)
KIMODATAID80_wt_nitrate.txt
KIMODATAID80_wt_anaerobic.txt
KIMODATAID80_wt_aerobic.txt
KIMODATAID80_arcA_nitrate.txt
KIMODATAID80_wt_nitrate_reaction_SBtab.csv
KIMODATAID80_wt_anaerobic_reaction_SBtab.csv
KIMODATAID80_wt_aerobic_reaction_SBtab.csv
KIMODATAID80_arcA_nitrate_reaction_SBtab.csv
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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 2013-07-08 15:29:28 UTC

Updated 2014-06-13 22:18:40 UTC

Version 0

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




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