Abstract
The quantitative estimation of intracellular metabolite concentrations (metabolic profiling) is a prerequisite for a better understanding of biological processes and thus inevitable for the rational improvement of microbial production strains and process design. Since pool sizes of substrates regulate flux through different enzymes, the accurate determination of intracellular metabolite concentrations is necessary to understand in vivo reaction kinetics. Quantification of intracellular concentrations of glycolytic intermediates in Escherichia coli K12 was achieved by using a novel in situ rapid sampling and quenching procedure. A new extraction procedure using buffered hot water was established. By use of simultaneous multi-substrate feeding with various ratios of glucose, fructose and acetate during continuous cultivations several metabolic states were induced. Metabolic flux analysis and the newly developed metabolic profiling procedure were used to determine in vivo enzyme kinetics as exemplified for fructose 1,6-bisphosphate aldolase and citrate synthase.
Similar content being viewed by others
References
Babul J, Clifton D, Kretschmer M, Frankel DG (1993) Glucose metabolism in Escherichia coli and the effect of increased amount of aldolase. Biochemistry 32:4685–4692
Bergmeyer H (1985) Methods of enzymatic analysis, 3rd edn. Verlag Chemie, Weinheim
Bhattacharya M, Fuhrman L, Ingram A, Nickerson KW, Conway T (1995) Single-run separation and detection of multiple metabolic intermediates by anion-exchange high-performance liquid chromatography and application to cell pool extracts prepared from Escherichia coli. Anal Biochem 232:98–106
BRENDA (2007) The comprehensive enzyme information system. http://www.brenda.uni-koeln.de. Cited 3 Feb 2007
Buchholz A, Takors R, Wandrey C (2001) Quantification of intracellular metabolites in Escherichia coli K12 using liquid chromatographic-electrospray ionization tandem mass spectrometric techniques. Anal Biochem 295:129–137
Chassagnole C, Noisommit-Rizzi N, Schmid JW, Mauch K, Reuss M (2002) Dynamic modeling of the central carbon metabolism of Escherichia coli. Biotechnol Bioeng 79(1):53–73
Dunn WB, Bailey NJC, Johnson HE (2005) Measuring the metabolome: current analytical technologies. Analyst 130:606–625
Emmerling M, Bailey JE, Sauer U (1999) Glucose catabolism of Escherichia coli strains with increased activity and altered regulations of key glycolytic enzymes. Met Eng 1:117–127
Fuhrman LK, Wanken A, Nickerson KW, Conway T (1998) Rapid accumulation of intracellular 2-keto-3-deoxy-phosphogluconate in an Entner-Doudoroff aldolase mutant results in bacteriostasis. FEMS Microbiol Lett 159:261–266
Hans MA, Heinzle E, Wittmann C (2003) Free intracellular amino acid pools during autonomous oscillations in Saccharomyces cerevisiae. Biotechnol Bioeng 82(2):143–151
Hiller J, Franco-Lara E, Papaioannou V, Weuster-Botz D (2007) Fast sampling and quenching procedures for microbial metabolic profiling. Biotechnol Lett (submitted)
Holmes H (2001) Flux analysis: a basic tool of microbial physiology. Adv Microb Physiol 45:271–340
Kayser A, Weber J, Hecht V, Rinas U (2005) Metabolic flux analysis of Escherichia coli in glucose-limited continuous culture. I. Growth-rate-dependent metabolic efficiency at steady state. Microbiology 151:693–706
Maharjan RP, Ferenci T (2003) Global metabolite analysis: the influence of extraction methodology on metabolome profiles of Escherichia coli. Anal Biochem 313:145–154
Mashego MR, Wu L, van Dam JC, Ras C, Vinke JL, van Winden WA, van Gulik WM, Heijnen JJ (2004) Miracle: mass isotopomer ratio analysis of U-13C-labeled extracts. A new method for accurate quantification of changes in concentration of intracellular metabolites. Biotechnol Bioeng 85:620–628
Molgat GF, Donald LJ, Duckworth HW (1992) Chimeric allosteric citrate synthases: construction and properties of citrate synthases containing domains from two different enzymes. Arch Biochem Biophys 298:238–246
Oldiges M, Takors R (2005) Applying metabolic profiling techniques for stimulus-response experiments: chances and pitfalls. Adv Biochem Eng/Biotechnol 92:173–196
Peng L, Arauzo-Bravo MJ, Shimizu K (2004) Metabolic flux analysis for a ppc mutant Escherichia coli based on 13C-labelling experiments together with enzyme activity assays and intracellular metabolite measurements. FEMS Microbiol Lett 235:17–23
Pereira DS, Donald LJ, Hesfield DJ, Duckworth HW (1994) Active site mutants of Escherichia coli citrate synthase. Effects of mutations on catalytic and allosteric properties. J Biol Chem 269:412–417
Pramanik J, Keasling JD (1997) Stoichiometric model of Escherichia coli metabolism: incorporation of growth-rate dependent biomass composition and mechanistic energy requirements. Biotechnol Bioeng 56(4):399–421
Schäfer U, Takors R, Weuster-Botz D (1999) Automated sampling device for monitoring intracellular metabolite dynamics. Anal Biochem 270:88–96
Schaub J, Schiesling C, Reuss M, Dauner M (2006) Integrated sampling procedure for metabolome analysis. Biotechnol Prog 22:1434–1442
Stephanopoulos GN, Aristidou AA, Nielsen J (1998) Metabolic engineering. Principles and methodologies. Academic Press, San Diego
Tweeddale H, Notley-McRobb L, Ferenci T (1998) Effect of slow growth on metabolism of Escherichia coli, as revealed by global metabolite pool (“metabolome” analysis). J Bacteriol 180:5109–5116
van der Werf MJ, Jellema RH, Hankemeier T (2005) Microbial metabolomics: replacing trial-and-error by the unbiased selection and ranking of targets. J Ind Microbiol Biotechnol 32:234–252
Villas-Boas SG, Mats S, Åkesson M, Smedsgaard J, Nielsen J (2005) Mass spectrometry in metabolome analysis. Mass Spec Rev 24:613–646
Weuster-Botz D, de Graaf AA (1996) Reaction engineering methods to study intracellular metabolite concentrations. Adv Biochem Eng Biotech 54:75–108
Acknowledgements
We would like to thank Elisabeth Eckers for her substantial laboratory help in establishing the extraction procedure.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Hiller, J., Franco-Lara, E. & Weuster-Botz, D. Metabolic profiling of Escherichia coli cultivations: evaluation of extraction and metabolite analysis procedures. Biotechnol Lett 29, 1169–1178 (2007). https://doi.org/10.1007/s10529-007-9384-8
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10529-007-9384-8