DataEntryID 116
    General information
      Manuscript title: Latent Pathway Activation and Increased Pathway Capacity Enable Escherichia coli Adaptation to Loss of Key Metabolic Enzymes.
      PubMed ID: http://www.ncbi.nlm.nih.gov/pubmed/16319065
      Journal: Journal of Biological Chemistry
      Year: 2006
      Authors: Stephen S. Fong, Annik Nanchen, Bernhard O. Palsson and Uwe Sauer
      Affiliations: Institute of Molecular Systems Biology, ETH Zurich, Zurich CH-8093, Switzerland
      Keywords: Escherichia coli, latent pathway activation
      Full text article: https://www.kimosys.org/rails/active_storage/blobs/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBdDBFIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--ec604072443d900fd195c2aec3533c2ca8072283/Fong_2006.pdf
      Project name: not specified

    Experiment description
      Organism: Escherichia coli
      Strain: MG1655 and (pgi, ppc, pta, tpi) mutants
      Data type: flux measurements
      Data units: mmol/gdw h
      Execution date: not specified

    Experimental details
      Temperature (°C): 37
      pH: not specified
      Carbon source: glucose
      Culture mode: batch
      Process condition: aerobic
      Dilution rate (h⁻¹): —
      Working volume: 0.03 L
      Biomass concentration (g/L): see spreadsheet
      Medium composition: M9 minimal medium supplemented with 2 g/liter of glucose in 500-ml Erlenmeyer flasks. M9 medium contained (per liter of deionized water) 0.8 g of NH4Cl, 0.5 g of NaCl, 7.5 g of Na2HPO4·2H2O, and 3.0 g of KH2PO4. The following components were sterilized separately and then added (per liter final volume of medium): 2 ml of 1 m MgSO4, 1 ml of 0.1 m CaCl2, 0.3 ml of 1 mm filter-sterilized thiamine HCl, and 10 ml of a trace element solution containing (per liter) 1 g of FeCl3·6H2O, 0.18 g of ZnSO4·7H2O, 0.12 g of CuCl2·2H2O, 0.12 g of MnSO4·H2O, and 0.18 g of CoCl2·6H2O. At the start of evolution, initial precultures of each mutant were grown overnight in LB medium before being transferred to minimal medium for adaptive evolution.
      General protocol information: Type analysis list: flux ratio, 13C constrained MFA; Platform list: GC-MS;
      Methods description: After 8 h of incubation at 37 °C and constant shaking, LB precultures were used to inoculate M9 medium precultures that were grown overnight for inoculation of cultures for physiological or 13C-labeling experiments. For 13C-labeling experiments, glucose was added either entirely as the 1-13C-labeled isotope isomer (>99%; Euriso-top, GIF-sur-Yvette, France) or as a mixture of 20% (w/w) U-13C (>98%; Isotech, Miamisburg, OH) and 80% (w/w) natural glucose. Cell growth was monitored by following the A600. Glucose and acetate concentrations were determined enzymatically using commercial kits (Beckman-Coulter (Zurich, Switzerland) or Dispolab (Dielsdorf, Switzerland)). Other organic acids in culture supernatants were detected by high pressure liquid chromatography analysis (PerkinElmer Life Sciences) at a wavelength of 210 nm, using a Supelcogel C8 column (4.6 × 250 mm) at 30 °C and a mobile phase of 2% (v/v) sulfuric acid at a flow rate of 0.3 ml/min.
The following physiological parameters were determined during the exponential growth phase as described previously [1]: maximum growth rate, biomass yield on glucose, specific glucose consumption rate, and specific byproduct production rates, using a predetermined correlation factor of 0.44 g of cellular dry weight per liter and A600 unit.
Metabolic Flux Ratio (METAFoR) Analysis by Gas Chromatography-Mass Spectrometry—Samples for gas chromatography-mass spectrometry analysis were prepared as described previously [2]. 13C-Constrained Net Flux Analysis—Intracellular net fluxes were estimated with a stoichiometric model that contained all major pathways of central carbon metabolism [3]. See more information in the original article.
-----------------------------------References---------------------------------
[1] Sauer, U., Lasko, D. R., Fiaux, J., Hochuli, M., Glaser, R., Szyperski, T., Wüthrich, K., and Bailey, J. E. (1999) J. Bacteriol. 181, 6679-6688.
[2] Fischer, E., and Sauer, U. (2003) Eur. J. Biochem. 270, 880-891. http://doi.org/dg3q64
[3]  Fischer, E., Zamboni, N., and Sauer, U. (2004) Anal. Biochem. 325, 308-316. http://doi.org/c6kx35                                                                           
      Data file: http://kimosys.org/repository/116/download?parameter=1244; 
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    Submission and curation
      Entered by: Administrator KiMoSys
      Created: 2018-08-22 22:25:31 UTC
      Updated: 2020-04-24 16:10:37 UTC
      Version: 2
      Status: (reviewed) 2018-08-22 22:25:40 UTC
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