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General Information
Manuscript title Glucose-methanol co-utilization in Pichia pastoris studied by metabolomics and instationary 13C flux analysis.
PubMed ID 23448228
Journal BMC Systems Biology
Year 2013
Authors Joel Jordà, Camilo Suarez, Marc Carnicer, Angela ten Pierick, Joseph J Heijnen, Walter van Gulik, Pau Ferrer, Joan Albiol and Aljoscha Wahl
Affiliations Department of Chemical Engineering, Escola d’Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, Cerdanyola del Vallès, Spain
Keywords Pichia pastoris, intracellular, extracellular, glucose, glucose:methanol
Full text article Jorda_2013.pdf
Project name not specified

Experiment Description
Organism Pichia pastoris
Strain X-33
Data type metabolites at steady-state
Data units (µmol/l) and (µmol/gDW)
Execution date not specified

Experimental Details
Temperature (°C) 25.0
pH 5.0
Carbon source glucose
Culture mode chemostat
Process condition aerobic
Dilution rate (h⁻¹) 0.09
Working volume (L) 1.0
Biomass concentration (g/L) 4.0
Medium composition

7.04 g/l Glucose monohydrate, 1.6 g/l Methanol, 0.915 g/l citric acid, 2 g/l (NH4)2 HPO4, 0.3 g/l MgSO4.7H2O, 1.4 g/l KH2PO4, 0.01 g/l CaCl2 · 2H2O, 0.5 ml/l trace salt solution, 0.3 ml/l biotin (0.2 g/l)

General protocol information Sampling method: One hour before the switch to the labelled feed using a dedicated rapid-sampling setup.

Quenching procedure: Approximately 1 g of broth were rapidly withdrawn and immediately mixed with 5 ml of precooled quenching solution at -40°C.

Extraction technique: boiling ethanol

Sample analyzing method: GC-MS, LC-MS, HPLC-UV/RI

Methods description - Notes

Sampling and measurement of metabolite concentrations - For quenching and extraction, the protocol recently described for P. pastoris growing on glucose [1] was used.
The metabolite extraction was performed with 75% (v/v) aqueous ethanol at 95 °C. Concentrations were m ...

[1] Carnicer M, Canelas AB, Pierick A, Zeng Z, Dam J, Albiol J, Ferrer P, Heijnen JJ, Gulik W: Development of quantitative metabolomics for Pichia pastoris. Metabolomics 2011, 8:284–298.
[2] Nöh K, Wahl A, Wiechert W: Computational tools for isotopically instationary 13C labeling experiments under metabolic steady state conditions. Metab Eng 2006, 8:554–577.
[3] Douma RD, de Jonge LP, Jonker CTH, Seifar RM, Heijnen JJ, van Gulik WM: Intracellular metabolite determination in the presence of extracellular abundance, Application to the penicillin biosynthesis pathway in Penicillium chrysogenum. Biotechnol Bioeng 2010, 107:105–115.

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Data file
KIMODATAID55_v0.xlsx Preview file
Alternative format(s)
KIMODATAID55_metab_intra_compound_SBtab.csv Preview
KIMODATAID55_metab_gluc-meth_compound_SBtab.csv Preview
KIMODATAID55_metab_extra_compound_SBtab.csv Preview
KIMODATAID55_cometab_gluc-meth_compound_SBtab.csv Preview
KIMODATAID55_aa_intra_compound_SBtab.csv Preview
KIMODATAID55_aa_gluc-meth_compound_SBtab.csv Preview
KIMODATAID55_aa_extra_compound_SBtab.csv Preview
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Submission and curation

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

Created: 2013-05-30 19:09:20 UTC

Updated: 2020-04-24 16:10:32 UTC

Version: 0

Status: (reviewed) 2013-12-06 17:17:38 UTC

Views: 185

Downloads: 28

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