Repository » Data AccessID 112

Detail View - Data AccessID 112

Backimage Back

General Information info

Manuscript title Analysis of Escherichia coli Anaplerotic Metabolism and Its Regulation Mechanisms From the Metabolic Responses to Altered Dilution Rates and Phosphoenolpyruvate Carboxykinase Knockout.
PubMed ID 12966569
Journal Biotechnology and Bioengineering
Year 2003
Authors Yang C, Hua Q, Baba T, Mori H, Shimizu K
Affiliations Metabolome Unit, Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan.
Keywords Escherichia coli; metabolic flux; 13C labeling; anaplerotic reaction; phosphoenolpyruvate carboxykinase; in vivo regulation
Full text article Downloadarticle Yang2003.pdf
Project name not specified

Experiment Description info

Organism Escherichia coli
Strain W3110 and pck mutant
Data type metabolites at steady-state
Data units mM
Execution date not specified

Experimental Details info

Temperature (0C) 37
pH 7.0
Carbon source glucose,
Culture mode chemostat
Process condition aerobic
Dilution rate (h-1) 0.1, 0.32, 0.55 (WT ) and 0.1 (pck)
Working volume (L) 1.0
Biomass concentration (g/L) Yield glu,X (g/g) = 0.40 ± 0.02 (D = 0.1h-1), 0.44 ± 0.02 (D = 0.32h-1) and 0.48 ± 0.03 (D = 0.55h-1) for WT; 0.46 ± 0.02 (D = 0.1h-1) for pck
Medium composition

Medium containing (per liter): 5.0 g of glucose, 1.0 g of NH4Cl, 2.7 g of (NH4)2SO4,6.8gofNa2HPO4,3.0gofKH2PO4, 0.6 g of NaCl, 0.2 g ofMgSO4 7H2O, 1.0 µg of thiamine HCl, 2.0 µL of polypropylene glycol 2000 as an antiform agent, and 10 mL of trace element solution [6].

General protocol information Sampling method: not described

Quenching procedure: To rapidly quench the cell metabolism, 5 mL of culture suspension was cooled to 0°C in a −50°C methanol bath within 15–20 s. Cells were separated from the culture medium by centrifugation, and resuspended in cold 100% methanol immediately.

Extraction technique: chloroform

Sample analyzing method: enzymatic

Methods description - Notes

To rapidly quench the cell metabolism, 5 mL of culture suspension was cooled to 0°C in a −50°C methanol bath within 15–20 s. Cells were separated from the culture medium by centrifugation, and resuspended in cold 100% methanol immediately. Intracellular metabolites were extracted by addition of cold chloroform at neutral pH based on the method of de Koning and van Dam [1]. This extraction method ensured minimal degradation of labile metabolites. After extraction, the aqueous phase was carefully collected, dried, and resuspended in MiliQ water. Shortly before the determination of metabolite concentrations, the cell extracts were filtered through a 0.2 m-poresize filter to remove possible small precipitates. The samples were stored for up to 5 days at −20°C for further analysis. The unstable metabolites (e.g., acetyl-CoA and oxaloacetate) were determined within 6 h after the extracts were obtained. Enzymatic determinations of the intracellular metabolites were performed on a microplate spectrofluorometer (SPECTRAmax GEMINI XS), following the changes in NAD(P)H fluorescence at the 355, 460-nm wavelength pair. The volume of the assay mixture was 200 L. The concentrations of fructose 1,6-bisphosphate, 3-phosphoglycerate, PEP, pyruvate, acetyl-CoA, isocitrate, L-malate, -ketoglutarate, oxaloacetate, L-aspartate, and adenine nucleotide (ATP and ADP) in the extracts were measured according to published protocols [2, 3, 4] with some modifications (such as the reduction of analytical volume). The value of the specific cell volume used for calculation of the intracellular concentrations was 1.77 L mgDW−1 [5]. All the intracellular concentrations were presented as the average of at least three measurements, with the corresponding standard deviation. ----------------------------------References--------------------------------------
[1] de Koning W, van Dam K. 1992. Anal Biochem 204:118–123.
[2] Bergmeyer HU. 1984. Methods of enzymatic analysis, 3rd edition, Vol. 6. Weinheim, Germany: VCH.
[3] Bergmeyer HU. 1985. Methods of enzymatic analysis, 3rd edition, Vol. 7. Weinheim, Germany: VCH.
[4] Williamson JR, Corkey BE. 1969. Methods in enzymology, Vol. 13. New York: Academic Press. p 434–513.
[5] Chassagnole C, Noisommit-Rizzi N, Schmid JW, Mauch K, Reuss M. 2002. Biotechnol Bioeng 79:53–73.
[6] Sauer U, Lasko DR, Fiaux J, Hochuli M, Glaser R, Szyperski T, Wuthrich K, Bailey JE. 1999. J Bacteriol 181:6679–6688.

Data file
Downloadmetabolites KIMODATAID112_v0.xlsx
Alternative format(s)
no file uploaded


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 116 | AccessID 118 | AccessID 119 | AccessID 125 | AccessID 126

Submission and curation info

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

Created 2018-07-31 15:50:28 UTC

Updated 2018-07-31 15:50:28 UTC

Version 0

Status (reviewed) 2018-07-31 15:51:08 UTC

Associated Models

Here we can find relevant models associated with Data EntryID 112:

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