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General Information info

Manuscript title Metabolome, transcriptome and metabolic flux analysis of arabinose fermentation by engineered Saccharomyces cerevisiae
PubMed ID 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 Downloadarticle Wisselink_2010.pdf
Project name not specified

Experiment Description info

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

Experimental Details info

Temperature (0C) 30
pH 5.0
Carbon source glucose and arabinose
Culture mode chemostat
Process condition anaerobic
Dilution rate (h-1) 0.03
Working volume (L) 1.0
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 procedure: 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 technique: boiling ethanol

Sample analyzing method: GC-MS, LC-ESI-MS

Methods description - Notes

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.
[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.
[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.
[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.
[5] C. Verduyn, E. Postma, W.A. Scheffers, J.P. van Dijken. Yeast, 8 (1992), pp. 501-517.

Data file
Downloadmetabolites KIMODATAID120_v2.xlsx
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Submission and curation info

Entered by Administrator KiMoSysFirst name: Administrator
Affiliation: INESC-ID/IST
Interests: mathematical modeling, accessible data, use of data

Created 2018-08-27 21:00:50 UTC

Updated 2018-08-27 21:44:21 UTC

Version 2

Status (reviewed) 2018-08-27 21:05:37 UTC

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