Detail View - Data AccessID 89
General Information
Manuscript title | Transcriptional regulation is insufficient to explain substrate-induced flux changes in Bacillus subtilis. |
PubMed ID | 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 | 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 (L) | 0.03 |
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 |
Flux analysis method:
13C constrained MFA Platform: GC-MS |
Methods description - Notes | 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 ... 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---------------------------------------
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Related Data: AccessID 88 | AccessID 94 | AccessID 95
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Administrator KiMoSysFirst name: Administrator
Affiliation: INESC-ID/IST
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Created: 2015-05-12 15:24:47 UTC
Updated: 2020-04-24 16:10:35 UTC
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Status: (reviewed) 2015-05-12 15:46:59 UTC
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