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General Information
Manuscript title Changes in substrate availability in Escherichia coli lead to rapid metabolite, flux and growth rate responses.
PubMed ID 23370343
Journal Metabolic Engineering
Year 2013
Authors Hilal Taymaz-Nikerel, Marjan De Mey, Gino Baart, Jo Maertens, Joseph J. Heijnen, Walter M. Van Gulik
Affiliations Department of Biotechnoloy, Delft University of Technology, Kluyver Center for Genomics of Industrial Fermentation Julianalaan 67, 2628 BC Delft, The Netherlands
Keywords Escherichia coli, intracellular metabolites, stimulus response
Full text article Nikerel_2013.pdf
Project name not specified


Experiment Description
Organism Escherichia coli
Strain K-12 MG1655
Data type time-series data of metabolites
Data units (µmol/gDW)
Execution date not specified


Experimental Details
Temperature (°C) 37.0
pH 7.0
Carbon source glucose,
Culture mode chemostat
Process condition aerobic
Dilution rate (h⁻¹) 0.1
Working volume (L) 4.0
Biomass concentration (g/L) 8.36 (Experiment 1) and 8.02 (Experiment 2)
Medium composition

The composition of the low Cl- minimal medium was, per liter: 1.25g(NH4)2SO4, 1.15g KH2PO4, 0.5g MgSO4.7H2O, 0.5g NaCl, 30g glucose.1H2O, 0.001 gthiamine–HCl, 2ml of trace elements solution and 0.2 ml silicone-based antifoaming agent (BDH,Poole,UK). The composition of the trace elements solution was described in Verduyn et al. [1].

-----------References-------------
[1] Verduyn, C., Postma, E., Scheffers, W.A., van Dijken, J.P., 1992. Effect of benzoic acid on metabolic fluxes in yeasts: a continuous-culture study on the regulation of respiration and alcoholic fermentation. Yeast 8 (7), 501–517

General protocol information Sampling method: differential method

Quenching procedure: not specified

Extraction technique: boiling ethanol

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

Methods description - Notes

Rapid substrate pulse experiments - Short-term rapid pulse experiments in the bioreactor and in the BioScope were carried out as described previously [1,2].
Rapid sampling for extra-/intracellular metabolites - the differential method [3] was applied to obtain the amou ...

-----------------References-----------------------
[1] De Mey,M., Taymaz-Nikerel,H., Baart,G., Waegeman,H., Maertens,J., Heijnen,J.J., van Gulik,W.M., 2010. Catching prompt metabolite dynamics in Escherichia coli with the BioScope at oxygen rich conditions. Metab. Eng. 12 (5), 477–487. http://doi.org/cdwz4c
[2] Taymaz-Nikerel, H.,vanGulik,W.M.,Heijnen,J.J., 2011. Escherichia coli responds with a rapid and large change in growth rate upon a shift from glucose-limited to glucose-excess conditions. Metab. Eng.13 (3), 307–318. http://doi.org/cwkdjz
[3] Taymaz-Nikerel, H., de Mey,M., Ras,C., tenPierick,A., Seifar,R.M., vanDam,J.C., Heijnen, J.J., vanGulik,W.M., 2009. Development and application of a differential method for reliable metabolome analysis in Escherichia coli. Anal. Biochem. 386 (1), 9–19. http://doi.org/bk5b8m
[4] Wu,L., Mashego,M.R., vanDam,J.C., Proell,A.M., Vinke,J.L., Ras,C., vanWinden,W.A., vanGulik,W.M., Heijnen,J.J., 2005. Quantitative analysis of the microbial metabolome by isotope dilution mass spectrometry using uniformly 13C labeled cell extracts as internal standards. Anal. Biochem. 336 (2), 164–171. http://doi.org/dp4h5k
[5] van Dam,J.C., Eman,M.R., Frank,J., Lange,H.C., vanDedem,G.W.K., Heijnen,S.J., 2002. Analysis of glycolytic intermediates in Saccharomyces cerevisiae using anion exchange chromatography and electrospray ionization with tandem mass spectrometric detection. Anal. Chim. Acta 460 (2), 209–218. http://doi.org/ck9bk6

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Submission and curation

Entered by: Administrator KiMoSysFirst name: Administrator
Affiliation: INESC-ID/IST
Homepage: http://kdbio.inesc-id.pt/kimosys
Interests: mathematical modeling, accessible data, use of data

Created: 2013-06-25 15:06:47 UTC

Updated: 2020-04-24 16:10:34 UTC

Version: 1

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

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