Metabolic flux analysis of Escherichia coli K12 grown on 13C-labeled acetate and glucose using GC-MS and powerful flux calculation method

Journal of Biotechnology

Volumn 101, Issue 2, 2003, Pages 101-117

  Zhao, Jiao ^a   Shimizu, Kazuyuki ^a,b  

^a KEIO UNIVERSITY   (Japan)

^b KYUSHU INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

Carbon source; Escherichia coli K12; Genetic algorithm; Levenberg Marquardt algorithm; Mass isotopomer analysis; Metabolic flux analysis

Indexed keywords

AMINO ACIDS; GENETIC ALGORITHMS; GLUCOSE; METABOLISM; PROTEINS;

METABOLIC FLUX;

ESCHERICHIA COLI;

ACETIC ACID; AMINO ACID; CARBON; CARBON 13; CITRIC ACID; GLUCOSE; ISOCITRATE DEHYDROGENASE; PENTOSE PHOSPHATE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE;

ALGORITHM; ARTICLE; BACTERIAL GROWTH; BACTERIAL METABOLISM; BIOCHEMISTRY; CALCULATION; CARBON SOURCE; CATALYSIS; CELL GROWTH; CITRIC ACID CYCLE; CONTROLLED STUDY; ESCHERICHIA COLI; GAS CHROMATOGRAPHY; GROWTH RATE; MASS SPECTROMETRY; METABOLIC REGULATION; NONHUMAN; PENTOSE PHOSPHATE CYCLE; PRIORITY JOURNAL; REGULATORY MECHANISM;

ACETATES; ALGORITHMS; CARBON; CARBON ISOTOPES; CELLS, CULTURED; COMPUTER SIMULATION; ENERGY METABOLISM; ESCHERICHIA COLI; GAS CHROMATOGRAPHY-MASS SPECTROMETRY; GLUCOSE; ISOTOPE LABELING; MODELS, BIOLOGICAL; MULTIENZYME COMPLEXES; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SPECIES SPECIFICITY;

ESCHERICHIA COLI;

EID: 0037422210     PISSN: 01681656     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-1656(02)00316-4     Document Type: Article

References (25)

1. 13C-labeled glucose. Biotechnol. Bioeng. 68:2000;652-659.
2. Dauner M., Storni T., Sauer U. Bacillus subtilis metabolism and energetics in carbon-limited and excess-carbon chemostat culture. J. Bacteriol. 183:2001;7308-7317.
3. Dauner M., Bailey J.E., Sauer U. Metabolic flux analysis with a comprehensive isotopomer model in Bacillus subtilis. Biotechnol. Bioeng. 76:2001;144-156.
4. Davis L. The Handbook of Genetic Algorithms. 1991;Van Nostrand Reinhold, New York.
5. Goel A., Ferrance J., Jeong J., Ataai M.M. Analysis of metabolic fluxes in batch and continuous cultures of Bacillus subtilis. Biotechnol. Bioeng. 42:1993;686-696.
6. Holms H. Flux analysis and control of the central metabolic pathways in Escherichia coli. FEMS Microbiol. Rev. 19:1996;85-116.
7. 13C-NMR: a simple yet comprehensive method for analysis of intermediary metabolism. TIBS. 16:1991;5-10.
8. Lin Y.Y., Cheng W.B., Wright C.E. Glucose metabolism in mammalian cells as determined by mass isotopomer analysis. Anal. Biochem. 209:1993;267-273.
9. Marx A., Graaf A.A., Wiechert W., Eggeling L., Sahm H. Determination of the fluxes in the central metabolism of Corynebacterium glutamicum by nuclear magnetic resonance spectroscopy combined with metabolite balancing. Biotechnol. Bioeng. 49:1996;111-129.
10. Neidhardt F.C., Ingraham J.L., Schaechter M. Physiology of the Bacterial Cell. A Molecular Approach. 1990;Sinauer Associate, Sunderland Inc., MA.
11. Michalewicz Z. Genetic Algorithm+Data Structure=Evolution Programs, AI Series. 1994;Springer, New York.
12. Monschau N., Stahmann K.-P., Sahm H., McNeil J.B., Bognar A.L. Identification of Saccharomyces cerevisiae GLY1 as a threonine aldolase: a key enzyme in glycine biosynthesis. FEMS Microbiol. Lett. 150:1997;55-60.
13. Moré J.J. The Levenberg-Marquardt algorithm: implementation and theory. Watson G.A. Numerical Analysis. 1977;Springer, New York.
14. Paul Lee W.-N. Mass isotopomer analysis: theoretical and practical consideration. Biol. Mass Spectrometry. 20:1991;451-458.
15. Paul Lee W.-N., Bergner E.A. Mass isotopomer pattern and precursor-product relationship. Biol. Mass Spectrometry. 21:1992;114-122.
16. 13C NMR evidence for pyruvate kinase flux attenuation underlying suppressed acid formation in Bacillus subtilis. Biotechnol. Prog. 16:2000;169-175.
17. Sauer U., Hatzimanikatis V., Hohmann H.P., Mannebegr M., Bailey J.E. Physiology and metabolic fluxes of wild-type and Riboflavin-producing Bacillus subtilis. Applied Environ. Microbiol. 62:1996;3687-3695.
18. Sauer U., Lasko D.R., Fiaux J., Hochuli M., Glaser R., Szyperski K.W., Bailey J.E. Metabolic flux ratio analysis of genetic and environmental modulations of Escherichia coli central carbon metabolism. J. Bacteriol. 181:1999;6679-6688.
19. Schmidt K., Nielsen J., Villadsen J. Modeling isotopomer distributions in metabolic networks using isotopomer mapping matrices. Biotechnol. Bioeng. 55:(6):1997;831-840.
20. Schmidt K., Nielsen J., Villadsen J. Quantitative analysis of metabolic fluxes in Escherichia coli, using two-dimensional NMR spectroscopy and complete isotopomer models. J. Biotechnol. 71:1999;175-190.
21. 13C coupling constraints on the isotopomer distribution in labeled biomass components. Metabolic Eng. 1:1999;166-179.
22. 13C-labeling of proteinogenic amino acids - an efficient analytical tool to investigate intermediary metabolism. Eur. J. Biochem. 232:1995;433-448.
23. 13C NMR isotope labeling experiments. Computer Applications in Biotechnology - CAB 6.
24. Wiechert W., Siefke C., Graaf A.A., Marx A. Biodirectional reaction steps in metabolic networks: II. Flux estimation and statistical analysis. Biotechnol. Bioeng. 55:1997;118-135.
25. Wittmann C., Heinzle E. Mass spectrometry for metabolic flux analysis. Biotechnol. Bioeng. 62:1999;739-750.