DataEntryID 120
    General information
      Manuscript title: Metabolome, transcriptome and metabolic flux analysis of arabinose fermentation by engineered Saccharomyces cerevisiae
      PubMed ID: http://www.ncbi.nlm.nih.gov/pubmed/20816840
      Journal: Metabolic Engineering
      Year: 2010
      Authors: H. Wouter Wisselink, Chiara Cipollina, Bart Oud, BarbaraCrimi, Joseph J. Heijnen, Jack T. Pronk, Antonius J.A.van Maris
      Affiliations: Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands.
      Keywords: Saccharomyces cerevisiae, Evolutionary engineering, Arabinose, Transcriptomics, Metabolomics, Metabolic flux ana
      Full text article: https://www.kimosys.org/rails/active_storage/blobs/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBdVVFIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--f31a1f246642f96af680acd59ab79799c5b5dc75/Wisselink_2010.pdf
      Project name: not specified

    Experiment description
      Organism: Saccharomyces cerevisiae
      Strain: IMS0001 and IMS0002 
      Data type: metabolites at steady-state
      Data units: mmol/[gDW]
      Execution date: not specified

    Experimental details
      Temperature (°C): 30
      pH: 5.0
      Carbon source: glucose and arabinose
      Culture mode: chemostat
      Process condition: anaerobic
      Dilution rate (h⁻¹): 0.03
      Working volume: 1.0 L
      Biomass concentration (g/L): Biomass yield (g g−1) =  0.066±0.001 (IMS0001, Glucose), 0.072±0.003 (IMS0002, Glucose) and 0.075±0.001 (IMS0002, Arabinose) 
      Medium composition: Cultures were performed in MY supplemented with 0.01 g l−1 ergosterol and 0.42 g l−1 Tween 80 dissolved in ethanol, silicon antifoam, vitamin solution and trace elements [5], and 20 g l−1 glucose (MYG) or arabinose (MYA).
      General protocol information: Sampling Method: Sampling and sample preparation for analysis of intracellular metabolite concentrations was carried out as previously described in [1].; Quenching: 1 ml of broth was rapidly quenched in 5 ml of −40 °C 60% (vol/vol) aqueous methanol. After centrifugation (2000g, −20 °C, 5 min), the pellet was resuspended in 5 ml of −40 °C 60% (vol/vol) aqueous methanol and centrifuged again.; Extraction list: boiling ethanol; Analysis list: GC-MS, LC-ESI-MS;
      Methods description: All data were obtained by LC-MS/MS analysis ,except for GAP and DHAP which were measured by GC–MS [2].  Concentrations of G6P, F6P, T6P, G1P, F1,6BP, PYR, 2,3PG, PEP and the TCA cycle intermediates FUM, SUC, MAL, OXG and CIT in the cell extracts were analyzed by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) according to [3].  Intracellular concentrations of the PPP intermediates R5P, RBU5P, X5P, S7P, E4P, and RBU, GAP and DHAP were determined with a recently described GC-IDMS method [2].  Intracellular concentrations of adenine nucleotides (AMP, ADP and ATP) were quantified by LC-ESI-MS/MS [4].                                                                                                                                                                                                                                                                                                                                                                                                               ----------------------------------References--------------------------------------  
[1] M.R. Mashego, L. Wu, J.C. Van Dam, C. Ras, J.L. Vinke, W.A. van Winden, W.M. van Gulik, J.J. Heijnen. Biotechnol. Bioeng., 85 (2004), pp. 620-628. http://doi.org/chdxwz
[2] C. Cipollina, A. ten Pierick, A. Canelas, R.M. Seifar, A.J.A. van Maris, J.C. Van Dam, J.J. Heijnen. J. Chromatogr. B, 877 (2009), pp. 3231-3236. http://doi.org/dmxzd5
[3] J.C. Van Dam, M.R. Eman, J. Frank, H.C. Lange, G.W.K. van Dedem, J.J. Heijnen. Anal. Chim. Acta, 460 (2002), pp. 209-218. http://doi.org/ck9bk6
[4] R.M. Seifar, C. Ras, J.C. Van Dam, W.M. van Gulik, J.J. Heijnen, W.A. van Winden. Anal. Biochem., 388 (2009), pp. 213-219. http://doi.org/cpxjw9 
[5] C. Verduyn, E. Postma, W.A. Scheffers, J.P. van Dijken. Yeast, 8 (1992), pp. 501-517. http://doi.org/fgpqk3
      Data file: http://kimosys.org/repository/120/download?parameter=1252; 
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    Submission and curation
      Entered by: Administrator KiMoSys
      Created: 2018-08-27 21:00:50 UTC
      Updated: 2020-04-24 16:10:37 UTC
      Version: 2
      Status: (reviewed) 2018-08-27 21:05:37 UTC
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