DataEntryID 95
    General information
      Manuscript title: Metabolic Fluxes during Strong Carbon Catabolite Repression by Malate in Bacillus subtilis.
      PubMed ID: http://www.ncbi.nlm.nih.gov/pubmed/19917605
      Journal: The Journal of Biological Chemistry
      Year: 2010
      Authors: Roelco J. Kleijn, Joerg M. Buescher, Ludovic Le Chat, Matthieu Jules, Stephane Aymerich and Uwe Sauer
      Affiliations: Institute of Molecular System Biology, ETH Zurich, CH-8093 Zurich, Switzerland
      Keywords: Metabolism, Metabolism/Gluconeogenesis, Metabolism/Intermediary, Metabolism/Regulation, Metabolism/Tricarboxylic Acid Cycle, Methods/Mass Spectrometry, flux analysis, metabolomics
      Full text article: https://kimosys.org/rails/active_storage/blobs/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBcllFIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--dd15f25a2a583bdd518482578b3cc133238f8d68/Kleijn_2010.pdf
      Project name: not specified

    Experiment description
      Organism: Bacillus subtilis
      Strain: Wild-type BSB168 trp+
      Data type: flux measurements
      Data units: not specified
      Execution date: not specified

    Experimental details
      Temperature (°C): 37
      pH: not specified
      Carbon source: glucose, glucose + malate, malate
      Culture mode: batch
      Process condition: aerobic
      Dilution rate (h⁻¹): -
      Working volume: 0.03 L
      Biomass concentration (g/L): dry weight was inferred from a predetermined conversion factor of 0.48 g of cells/A600
      Medium composition: M9 minimal medium (per liter):  8.5 g of Na2HPO4.2H20, 3 g of KH2PO4, 1 g of NH4Cl, 0.5 g of NaCl. The following components were sterilized separately and then added (per liter of final medium): 1 ml of 0.1 m CaCl2.2H2O, 1 ml of 1 m MgSO4.7H2O, 1 ml of 50 mm FeCl3.6H2O, and 10 ml of trace salt solution. The trace salts solution contained (per liter): 170 mg of ZnCl2, 100 mg of MnCl2.4H2O, 60.0 mg of CoCl2.6H2O, 60.0 mg of Na2MoO4.2H2O, and 43.0 mg CuCl2.2H2O. When preparing the medium, the base salts were added first followed by CalCl2, MgSO4, FeCl3, and finally the trace elements.
      General protocol information: Type analysis list: 13C constrained MFA; Platform list: GC-MS;
      Methods description: Physiological Parameters: Extracellular substrate and byproduct concentrations were measured by HPLC analysis using an Agilent 1100 series HPLC stack in combination with an Aminex HPX-87H polymer column (Bio-Rad). Sugars were detected with a refractive index detector, and organic acids were detected with a UV-visible detector. Specific rates were calculated by regression analysis for at least five time points during the exponential growth phase as described previously [1]. Cell growth was monitored photometrically at 600 nm, and cell dry weight was inferred from a predetermined conversion factor of 0.48 g of cells/A600 [2]. All physiological parameters were determined during the exponential growth phase, typically ranging from 0.10 to 1.5 A600.                                                                                                                                                                                       Metabolic Flux Analysis: Metabolic fluxes were derived using whole isotopologue analysis [3,4]. In short, the procedure uses the cumomer balances and cumomer to isotopologue mapping matrices introduced by Wiechert et al. [5] to calculate the isotopologue distributions of metabolites in a pre-defined stoichiometric network model for a given flux-set. The flux-set that gives the best correspondence between the measured and simulated 13C-label distribution is determined by non-linear optimization and denoted as the optimal flux-fit. All calculations were performed in Matlab 7.6.0.         
                                                                                                                                                                                                                                                                                                                                                                                                                                    ----------------------------------------------References-------------------------------------------      
[1]  Sauer U., Lasko D. R., Fiaux J., Hochuli M., Glaser R., Szyperski T., Wüthrich K., Bailey J. E. (1999) J. Bacteriol. 181, 6679–6688.                                                                                                                                                                                                                                                     [2]  Tännler S., Decasper S., Sauer U. (2008) Microb. Cell Fact. 7, 19. http://doi.org/cjbk3x                                                                                                                                                                                                                             [3]  van Winden W. A., van Dam J. C., Ras C., Kleijn R. J., Vinke J. L., van Gulik W. M., Heijnen J. J. (2005) FEMS Yeast Res. 5, 559–568. http://doi.org/cgg3tw                                                                                                                                                                                                                         [4]  Kleijn R. J., van Winden W. A., van Gulik W. M., Heijnen J. J. (2005) FEBS J. 272, 4970–4982. http://doi.org/bxpccx                                                                                                                                                                                                                                                                                                                                                [5]  Wiechert W, Möllney M, Isermann N, Wurzel M, de Graaf AA (1999). Biotechnol Bioeng 66: 69–85.
      Data file: http://kimosys.org/repository/95/download?parameter=1205; 
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      Entered by: Administrator KiMoSys
      Created: 2018-07-11 22:06:12 UTC
      Updated: 2020-04-24 16:10:35 UTC
      Version: 4
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