DataEntryID 125 General information Manuscript title: Pseudo-transition Analysis Identifies the Key Regulators of Dynamic Metabolic Adaptations from Steady-State Data. PubMed ID: http://www.ncbi.nlm.nih.gov/pubmed/27136056 Journal: Cell Systems Year: 2015 Authors: Luca Gerosa, Bart R.B. Haverkorn van Rijsewijk, Dimitris Christodoulou, Karl Kochanowski, Thomas S.B. Schmidt, Elad Noor, Uwe Sauer Affiliations: Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland; Systems Biology Graduate School, Zurich 8057, Switzerland. Keywords: computational biology; metabolism; metabolomics; regulation network; transcription factor Full text article: https://kimosys.org/rails/active_storage/blobs/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBdThFIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--af32fee2d6ba853b4d108f7ca58f28e95b68ab1c/Gerosa_2015.pdf Project name: not specified Experiment description Organism: Escherichia coli Strain: BW25113 Data type: flux measurements Data units: mmol/gh Execution date: not specified Experimental details Temperature (°C): 37 pH: not specified Carbon source: acetate, fructose, galactose, glucose, glycerol, gluconate, pyruvate, succinate Culture mode: batch Process condition: aerobic Dilution rate (h⁻¹): — Working volume: 0.0035 L Biomass concentration (g/L): see worksheet Medium composition: LB cultures were used to inoculate M9 medium precultures with the indicated carbon sources for overnight cultivation. General protocol information: Type analysis list: 13C constrained MFA; Platform list: LC-MS; Methods description: Metabolic flux analysis For steady state analyses, separate 13C-labeling experiments were performed with a mixture of 20% (wt/wt) [U-13C] labeled isotopologue (>99%; Cambridge Isotope Laboratories, Andover, MA) and 80% (wt/wt) of natural abundance carbon sources. Separate 13C-labeling experiments were performed with 100% [1-13C]galactose, [1-13C]glucose, [1-13C]gluconate and [1-13C]fructose (>99%; Cambridge Isotope Laboratories, Andover, MA) and [1,3-13C]glycerol (>99%; CortecNet Voisins-Le-Bretonneux, France). Aliquots of fractionally 13C-labelled biomass were prepared from exponentially growing cultures and analyzed by gas chromatography mass spectrometry (GC-MS) [1]. Estimation of absolute fluxes was done by whole isotopologue balancing [2,3], using cumomer balances and cumomer to isotopologue mapping matrices [4] to calculate isotopologue partitioning of metabolites in a pre-defined stoichiometric network model for a given flux set. The flux set giving the best correspondence between measured and simulated 13C-label partitioning and physiology measurements of growth and extracellular fluxes was determined by non-linear optimization and selected as the final flux distribution. Standard deviations for metabolic fluxes were estimated through Monte Carlo simulations by re-estimating fluxes after adding Gaussian noise to the measured 13C-labeling data [5]. --------------------------------------------References--------------------------------------- [1] Zamboni, N., Fendt, S.-M., Rühl, M., and Sauer, U. (2009). Nat. Protoc. 4, 878–892. http://doi.org/b8ck9w [2] Kleijn, R.J., van Winden, W.A., van Gulik, W.M., and Heijnen, J.J. (2005). FEBS J. 272, 4970–4982. http://doi.org/bxpccx [3] Van Winden, W.A., van Dam, J.C., Ras, C., Kleijn, R.J., Vinke, J.L., van Gulik, W.M., and Heijnen, J.J. (2005). FEMS Yeast Res. 5, 559–568. http://doi.org/cgg3tw [4] Wiechert, W., Möllney, M., Isermann, N., Wurzel, M., and de Graaf, A.A. (1999). Biotechnol. Bioeng. 66, 69–85. [5] Schmidt, K., Nielsen, J., and Villadsen, J. (1999). J. Biotechnol. 71, 175–189. http://doi.org/bjxbj5 Data file: http://kimosys.org/repository/125/download?parameter=1262; Alternative formats: no files uploaded Submission and curation Entered by: Administrator KiMoSys Created: 2018-09-25 22:32:33 UTC Updated: 2020-04-24 16:10:37 UTC Version: 2 Status: (reviewed) 2018-09-25 22:33:52 UTC Views: 176 Downloads: 50