DataEntryID 89 General information Manuscript title: Transcriptional regulation is insufficient to explain substrate-induced flux changes in Bacillus subtilis. PubMed ID: http://www.ncbi.nlm.nih.gov/pubmed/24281055 Journal: Molecular Systems Biology Year: 2013 Authors: Victor Chubukov, Markus Uhr, Ludovic Le Chat, Roelco J Kleijn, Matthieu Jules, Hannes Link, Stephane Aymerich, Joerg Stelling and Uwe Sauer Affiliations: Institute of Molecular System Biology, ETH Zurich, Zurich, Switzerland. Keywords: central carbon metabolism, metabolic flux, transcriptional regulation Full text article: https://kimosys.org/rails/active_storage/blobs/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBcXNFIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--5e169158772d2bb360474a5193d99878efaffc72/Chubukov_2013.pdf Project name: not specified Experiment description Organism: Bacillus subtilis Strain: BSB168 Data type: flux measurements Data units: mmol/g/h Execution date: not specified Experimental details Temperature (°C): 37.0 pH: — Carbon source: glucose, fructose, gluconate, succinate+glutamate, glycerol, malate, malate, malate+glucose, pyruvate Culture mode: batch Process condition: aerobic Dilution rate (h⁻¹): — Working volume: 0.03 L Biomass concentration (g/L): 3.0 g cells/OD600 Medium composition: M9 minimal medium (per liter): 8.5 g Na2HPO4·2H2O, 3 g KH2PO4, 1 g NH4Cl, 0.5 g NaCl. The following components were sterilized separately and then added (per liter of final medium): 1 ml 0.1 M CaCl2, 1 ml 1 M MgSO4, 1 ml 50 mM FeCl3 and 10 ml trace salts solution. The trace salts solution contained (per liter): 170 mg ZnCl2, 100 mg MnCl2·4H2O, 60.0 mg CoCl2·6H2O, 60.0 mg Na2MoO4·2H2O and 43.0 mg CuCl2·2H2O. Filter‐sterilized carbon sources were added separately to the medium, pH neutralized with 4 M NaOH where necessary. General protocol information: Type analysis list: 13C constrained MFA; Platform list: GC-MS; Methods description: Extracellular substrate and byproduct concentrations were measured by HPLC analysis using an Agilent 1100 series HPLC stack (Agilent Technologies, Waldbronn, Germany) in combination with an Aminex HPX‐87H polymer column (Bio‐Rad, Hercules, CA, USA). Sugars were detected with a refractive index detector and organic acids with an UV/Vis detector. Substrate or product yields were calculated by linear regression of external concentration against biomass, and specific rates were calculated as yield multiplied by the growth rate. At least five time points during the exponential growth phase were used for the regression analysis. Cell growth was monitored photometrically at 600 nm and cell dry weight was inferred from a predetermined conversion factor of 0.48 g cells/OD600 [1]. All measurement errors for physiological parameters are reported as the standard deviation of 2–3 biological replicates. Metabolic flux analysis Biomass sample processing and GC‐MS analysis to determine isotopomer fractions of proteinogenic amino acids was performed as previously described [2]. Stoichiometric network models were based on a core model containing the reactions of central carbon metabolism [3]. When unconstrained by labeling information, futile cycle fluxes were set to zero. The growth rate‐dependent biomass requirements of B. subtilis were previously established [4] and added to the network as unidirectional biomass precursor withdrawing reactions. Metabolic fluxes were derived using the whole isotopomer modeling approach [5]. The procedure uses the cumomer balances and cumomer to isotopomer mapping matrices [6] to calculate the isotopomer distributions of metabolites in a predefined 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 (The Mathworks Inc, Natick, MA, USA). --------------------------------------------References--------------------------------------- [1] Tännler S, Decasper S, Sauer U (2008). Microb Cell Fact 7: 19. http://doi.org/cjbk3x [2] Zamboni N, Fendt S‐M, Rühl M, Sauer U (2009). Nat Protoc 4: 878–892. http://doi.org/b8ck9w [3] Oh Y‐K, Palsson BO, Park SM, Schilling CH, Mahadevan R (2007). J Biol Chem 282: 28791–28799. http://doi.org/bvbtsq [4] Dauner M, Storni T, Sauer U (2001). J Bacteriol 183: 7308–7317. http://doi.org/cs9gqv [5] Van Winden WA, van Dam JC, Ras C, Kleijn RJ, Vinke JL, van Gulik WM, Heijnen JJ (2005). FEMS Yeast Res 5: 559–568. http://doi.org/cgg3tw [6] Wiechert W, Möllney M, Isermann N, Wurzel M, de Graaf AA (1999). Biotechnol Bioeng 66: 69–85. http://doi.org/ctxdtx Data file: http://kimosys.org/repository/89/download?parameter=1194; Alternative formats: no files uploaded Submission and curation Entered by: Administrator KiMoSys Created: 2015-05-12 15:24:47 UTC Updated: 2020-04-24 16:10:35 UTC Version: 0 Status: (reviewed) 2015-05-12 15:46:59 UTC Views: 231 Downloads: 72