Repository » Data AccessID 118

Detail View - Data AccessID 118

Backimage Back

General Information info

Manuscript title Metabolic and Transcriptional Response to Cofactor Perturbations in Escherichia coli.
PubMed ID 20299454
Journal Journal of Biological Chemistry
Year 2010
Authors Anders K. Holm, Lars M. Blank, Marco Oldiges, Andreas Schmid, Christian Solem, Peter R. Jensen and Goutham N. Vemuri
Affiliations Department of Systems Biology, Center for Systems Microbiology, Technical University of Denmark, 2800 Denmark
Keywords F1Fo ATPase, Glycolysis, Metabolic Regulation, Transcription Regulation, Tricarboxylic Acid (TCA) Cycle, Cofactor Perturbation, Escherichia coli, NADH Oxidase, Soluble ATPase, Systems Biology
Full text article Downloadarticle Holm_2010.pdf
Project name not specified

Experiment Description info

Organism Escherichia coli
Strain MG1655 and 2 over-expression strains (NOX, ATPase)
Data type flux measurements
Data units mmol/gdw h
Execution date not specified

Experimental Details info

Temperature (0C) 37
pH not specified
Carbon source glucose,
Culture mode batch
Process condition aerobic
Dilution rate (h-1)
Working volume (L) 0.1
Biomass concentration (g/L) Biomass yield from glucose (g dry cell weight/g glucose): WT = 0.43 ± 0.02, NOX = 0.29 ± 0.03 and ATPase = 0.22 ± 0.00
Medium composition

Defined MOPS medium [1] supplemented with 0.1% glucose and 200 μg/ml erythromycin. The flasks were agitated at 150 rpm to ensure aerobic conditions.

General protocol information Flux analysis method: flux ratio

Platform: GC-MS, LC-MS

Methods description - Notes

Biomass samples for determining the fluxes were centrifuged (5000 × g, 10 min at 4 °C) and harvested in 150 μl of 6 m HCl and hydrolyzed at 105 °C for 24 h before drying at 85 °C. The hydrolyzate was dissolved in 50 μl of dimethyl formamide and derivatized using 30 μl of N-methyl-N-(tert-butyldimethylsilyl)-trifluoroacetamide. The mixture was incubated at 85 °C with shaking at 550 rpm for 60 min (Orbital Shaker CSA, Thermo Scientific) before GC-MS analysis, using previously described protocols [2,3]. From the mass isotope distribution patterns of the proteinogenic amino acids, relative pathway contributions (metabolic flux ratios) were computed that were used as constraints to infer metabolic activity [2,3]. An aliquot of 5 ml of the culture from mid-exponential phase was quenched in hot phenol (80 °C) and subsequently frozen at −20 °C for measuring the concentration of intracellular metabolites. The samples were processed as described previously [4] and analyzed using LC-MS/MS for quantitative determination of central carbon metabolites and cofactors. The values were normalized with biomass concentrations at the time of sampling. --------------------------------------------References---------------------------------------
[1] Neidhardt F. C., Bloch P. L., Smith D. F. (1974) J. Bacteriol. 119, 736–747.
[2] Fischer E., Sauer U. (2003) Eur. J. Biochem. 270, 880–891. http://doi.org/dg3q64
[3] Fischer E., Zamboni N., Sauer U. (2004) Anal. Biochem. 325, 308–316. http://doi.org/c6kx35
[4] Luo B., Groenke K., Takors R., Wandrey C., Oldiges M. (2007) J. Chromatogr. A. 1147, 153–164. http://doi.org/cxdj7w

Data file
Downloadfluxes KIMODATAID118_v1.xlsx
Alternative format(s)
no file uploaded
Cite|Share

Organism


Related Data: AccessID 30 | AccessID 35 | AccessID 41 | AccessID 44 | AccessID 51 | AccessID 54 | AccessID 63 | AccessID 64 | AccessID 65 | AccessID 67 | AccessID 68 | AccessID 74 | AccessID 75 | AccessID 78 | AccessID 79 | AccessID 80 | AccessID 86 | AccessID 87 | AccessID 92 | AccessID 96 | AccessID 101 | AccessID 102 | AccessID 103 | AccessID 104 | AccessID 105 | AccessID 106 | AccessID 107 | AccessID 108 | AccessID 109 | AccessID 110 | AccessID 112 | AccessID 116 | AccessID 119 | AccessID 125 | AccessID 126


Submission and curation info

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 2018-08-24 18:15:24 UTC

Updated 2018-08-24 18:36:34 UTC

Version 1

Status (reviewed) 2018-08-24 18:15:40 UTC




Associated Models


Here we can find relevant models associated with Data EntryID 118:

Model
EntryID
Model name Category Model Type Data used for Access Json



Associate models to data

- Several models can be associated.

Add New Model



Backimage Back | Top