DataEntryID 106
    General information
      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: http://www.ncbi.nlm.nih.gov/pubmed/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: https://kimosys.org/rails/active_storage/blobs/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBc3dFIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--36bb70f21d6049a3e583fd97b10f2937bcef6c26/Yang2003.pdf
      Project name: not specified

    Experiment description
      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
      Temperature (°C): 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: 1.0 L
      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: Type analysis list: 13C constrained MFA; Platform list: NMR;
      Methods description: 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: http://kimosys.org/repository/106/download?parameter=1227; 
      Alternative formats: no files uploaded

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      Entered by: Administrator KiMoSys
      Created: 2018-07-21 16:52:41 UTC
      Updated: 2020-04-24 16:10:36 UTC
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