Metabolic flux analysis in eukaryotes

Current Opinion in Biotechnology

Volumn 21, Issue 1, 2010, Pages 63-69

  Niklas, Jens ^a   Schneider, Konstantin ^a   Heinzle, Elmar ^a  

^a SAARLAND UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CARBON SOURCE; CELLULAR METABOLISM; COMPARTMENTATION; EUKARYOTIC CELLS; IN-CELL; MAMMALIAN CELLS; MEDIA COMPOSITION; METABOLIC FLUX ANALYSIS; SYSTEMS BIOLOGY; TOXICOLOGICAL RESEARCH; WHOLE PLANTS;

ANIMAL CELL CULTURE; CELLS; FUNGI; MAMMALS; METABOLISM;

CELL CULTURE;

CARBON 13;

ANALYTIC METHOD; CELL COMPARTMENTALIZATION; CELL CULTURE; CELL METABOLISM; CYTOTOXICITY; EUKARYOTE; FUNGAL METABOLISM; ISOTOPE LABELING; MAMMAL CELL; MASS SPECTROMETRY; METABOLIC FLUX ANALYSIS; METABOLITE; METABOLOMICS; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PLANT METABOLISM; PRIORITY JOURNAL; REVIEW; STEADY STATE;

ALGORITHMS; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; METABOLIC CLEARANCE RATE; MODELS, BIOLOGICAL; PROTEOME; SIGNAL TRANSDUCTION;

EUKARYOTA; FUNGI; MAMMALIA;

EID: 77950628238     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.copbio.2010.01.011     Document Type: Review

References (47)

1. Niittylae T., Chaudhuri B., Sauer U., Frommer W.B. Comparison of quantitative metabolite imaging tools and carbon-13 techniques for fluxomics. Methods Mol Biol 2009, 553:355-372.
2. Varma A., Palsson B.O. Metabolic flux balancing: basic concepts, scientific and practical use. Biotechnol 1994, 12:994-998.
3. Wiechert W. 13C metabolic flux analysis. Metab Eng 2001, 3:195-206.
4. Wiechert W., Mollney M., Isermann N., Wurzel M., de Graaf A.A. Bidirectional reaction steps in metabolic networks: III. Explicit solution and analysis of isotopomer labeling systems. Biotechnol Bioeng 1999, 66:69-85.
5. Antoniewicz M.R., Kelleher J.K., Stephanopoulos G. Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions. Metab Eng 2007, 9:68-86.
6. Dunn I.J., Heinzle E., Ingham J., Prenosil J.E. Biological Reaction Engineering 2000, Wiley-VCH.
7. Stephanopoulos G.N., Aristidou A.A., Nielsen J. Metabolic Engineering: Principles and Methodologies 1998, Academic Press.
8. Deshpande R., Yang T.H., Heinzle E. Towards a metabolic and isotopic steady state in CHO batch cultures for reliable isotope-based metabolic profiling. Biotechnol J 2009, 4:247-263.
9. Noh K., Wahl A., Wiechert W. Computational tools for isotopically instationary (13)C labeling experiments under metabolic steady state conditions. Metab Eng 2006, 8:554-577.
10. Noh K., Wiechert W. Experimental design principles for isotopically instationary 13C labeling experiments. Biotechnol Bioeng 2006, 94:234-251.
11. Hofmann U., Maier K., Niebel A., Vacun G., Reuss M., Mauch K. Identification of metabolic fluxes in hepatic cells from transient 13C-labeling experiments: Part I. Experimental observations. Biotechnol Bioeng 2008, 100:344-354.
12. Maier K., Hofmann U., Reuss M., Mauch K. Identification of metabolic fluxes in hepatic cells from transient 13C-labeling experiments: Part II. Flux estimation. Biotechnol Bioeng 2008, 100:355-370.
13. Bolten C.J., Kiefer P., Letisse F., Portais J.C., Wittmann C. Sampling for metabolome analysis of microorganisms. Anal Chem 2007, 79:3843-3849.
14. Zelle R.M., de Hulster E., van Winden W.A., de Waard P., Dijkema C., Winkler A.A., Geertman J.M., van Dijken J.P., Pronk J.T., van Maris A.J. Malic acid production by Saccharomyces cerevisiae: engineering of pyruvate carboxylation, oxaloacetate reduction, and malate export. Appl Environ Microbiol 2008, 74:2766-2777.
15. Kleijn R.J., Geertman J.M., Nfor B.K., Ras C., Schipper D., Pronk J.T., Heijnen J.J., van Maris A.J., van Winden W.A. Metabolic flux analysis of a glycerol-overproducing Saccharomyces cerevisiae strain based on GC-MS, LC-MS and NMR-derived C-labelling data. FEMS Yeast Res 2007, 7:216-231.
16. Frick O., Wittmann C. Characterization of the metabolic shift between oxidative and fermentative growth in Saccharomyces cerevisiae by comparative 13C flux analysis. Microb Cell Fact 2005, 4:30.
17. Velagapudi V.R., Wittmann C., Schneider K., Heinzle E. Metabolic flux screening of Saccharomyces cerevisiae single knockout strains on glucose and galactose supports elucidation of gene function. J Biotechnol 2007, 132:395-404.
18. Costenoble R., Muller D., Barl T., van Gulik W.M., van Winden W.A., Reuss M., Heijnen J.J. 13C-Labeled metabolic flux analysis of a fed-batch culture of elutriated Saccharomyces cerevisiae. FEMS Yeast Res 2007, 7:511-526.
19. Sola A., Jouhten P., Maaheimo H., Sanchez-Ferrando F., Szyperski T., Ferrer P. Metabolic flux profiling of Pichia pastoris grown on glycerol/methanol mixtures in chemostat cultures at low and high dilution rates. Microbiology 2007, 153:281-290.
20. Celik E., Calik P., Oliver S.G. Metabolic flux analysis for recombinant protein production by Pichia pastoris using dual carbon sources: effects of methanol feeding rate. Biotechnol Bioeng 2010, 105:317-329.
21. Gheshlaghi R., Scharer J.M., Moo-Young M., Douglas P.L. Metabolic flux analysis for optimizing the specific growth rate of recombinant Aspergillus niger. Bioproc Biosyst Eng 2007, 30:397-418.
22. Meijer S., Otero J., Olivares R., Andersen M.R., Olsson L., Nielsen J. Overexpression of isocitrate lyase-glyoxylate bypass influence on metabolism in Aspergillus niger. Metab Eng 2009, 11:107-116.
23. Melzer G., Dalpiaz A., Grote A., Kucklick M., Gocke Y., Jonas R., Dersch P., Franco-Lara E., Nortemann B., Hempel D.C. Metabolic flux analysis using stoichiometric models for Aspergillus niger: comparison under glucoamylase-producing and non-producing conditions. J Biotechnol 2007, 132:405-417.
24. Kleijn R.J., Liu F., van Winden W.A., van Gulik W.M., Ras C., Heijnen J.J. Cytosolic NADPH metabolism in penicillin-G producing and non-producing chemostat cultures of Penicillium chrysogenum. Metab Eng 2007, 9:112-123.
25. Zhao Z., Kuijvenhoven K., Ras C., van Gulik W.M., Heijnen J.J., Verheijen P.J., van Winden W.A. Isotopic non-stationary 13C gluconate tracer method for accurate determination of the pentose phosphate pathway split-ratio in Penicillium chrysogenum. Metab Eng 2008, 10:178-186.
26. Niklas J., Noor F., Heinzle E. Effects of drugs in subtoxic concentrations on the metabolic fluxes in human hepatoma cell line Hep G2. Toxicol Appl Pharmacol 2009, 240:327-336.
27. Sidorenko Y., Wahl A., Dauner M., Genzel Y., Reichl U. Comparison of metabolic flux distributions for MDCK cell growth in glutamine- and pyruvate-containing media. Biotechnol Prog 2008, 24:311-320.
28. Llaneras F., Pico J. A procedure for the estimation over time of metabolic fluxes in scenarios where measurements are uncertain and/or insufficient. BMC Bioinform 2007, 8:421.
29. Niklas J, Schräder E, Noll T, Sandig V, Heinzle E: Time resolved 13C supported metabolic flux analysis characterizes growth phases of the new human cell line Age1.hn, 2009, submitted for publication.
30. Metallo C.M., Walther J.L., Stephanopoulos G. Evaluation of (13)C isotopic tracers for metabolic flux analysis in mammalian cells. J Biotechnol 2009.
31. Bonarius H.P., Ozemre A., Timmerarends B., Skrabal P., Tramper J., Schmid G., Heinzle E. Metabolic-flux analysis of continuously cultured hybridoma cells using (13)CO(2) mass spectrometry in combination with (13)C-lactate nuclear magnetic resonance spectroscopy and metabolite balancing. Biotechnol Bioeng 2001, 74:528-538.
32. Quek L.E., Dietmair S., Kromer J.O., Nielsen L.K. Metabolic flux analysis in mammalian cell culture. Metab Eng 2009, 10.1016/ j.ymben.2009.09.002.
33. Wahl A., Sidorenko Y., Dauner M., Genzel Y., Reichl U. Metabolic flux model for an anchorage-dependent MDCK cell line: characteristic growth phases and minimum substrate consumption flux distribution. Biotechnol Bioeng 2008, 101:135-152.
34. Santos S.S., Leite S.B., Sonnewald U., Carrondo M.J., Alves P.M. Stirred vessel cultures of rat brain cells aggregates: characterization of major metabolic pathways and cell population dynamics. J Neurosci Res 2007, 85:3386-3397.
35. Maier K., Hofmann U., Bauer A., Niebel A., Vacun G., Reuss M., Mauch K. Quantification of statin effects on hepatic cholesterol synthesis by transient (13)C-flux analysis. Metab Eng 2009, 11:292-309.
36. Balcarcel R.R., Clark L.M. Metabolic screening of mammalian cell cultures using well-plates. Biotechnol Prog 2003, 19:98-108.
37. Ratcliffe R.G., Shachar-Hill Y. Measuring multiple fluxes through plant metabolic networks. Plant J 2006, 45:490-511.
38. Allen D.K., Libourel I.G., Shachar-Hill Y. Metabolic flux analysis in plants: coping with complexity. Plant Cell Environ 2009, 32:1241-1257.
39. Kruger N.J., Huddleston J.E., Le Lay P., Brown N.D., Ratcliffe R.G. Network flux analysis: Impact of C-13-substrates on metabolism in Arabidopsis thaliana cell suspension cultures. Phytochemistry 2007, 68:2176-2188.
40. Graham J.W., Williams T.C., Morgan M., Fernie A.R., Ratcliffe R.G., Sweetlove L.J. Glycolytic enzymes associate dynamically with mitochondria in response to respiratory demand and support substrate channeling. Plant Cell 2007, 19:3723-3738.
41. Heinzle E., Matsuda F., Miyagawa H., Wakasa K., Nishioka T. Estimation of metabolic fluxes, expression levels and metabolite dynamics of a secondary metabolic pathway in potato using label pulse-feeding experiments combined with kinetic network modelling and simulation. Plant J 2007, 50:176-187.
42. Matsuda F., Morino K., Ano R., Kuzawa M., Wakasa K., Miyagawa H. Metabolic flux analysis of the phenylpropanoid pathway in elicitor-treated potato tuber tissue. Plant Cell Physiol 2005, 46:454-466.
43. Baxter C.J., Liu J.L., Fernie A.R., Sweetlove L.J. Determination of metabolic fluxes in a non-steady-state system. Phytochemistry 2007, 68:2313-2319.
44. Williams T.C., Miguet L., Masakapalli S.K., Kruger N.J., Sweetlove L.J., Ratcliffe R.G. Metabolic network fluxes in heterotrophic Arabidopsis cells: stability of the flux distribution under different oxygenation conditions. Plant Physiol 2008, 148:704-718.
45. Allen D.K., Shachar-Hill Y., Ohlrogge J.B. Compartment-specific labeling information in 13C metabolic flux analysis of plants. Phytochemistry 2007, 68:2197-2210.
46. Lehmeier C.A., Lattanzi F.A., Schaufele R., Wild M., Schnyder H. Root and shoot respiration of perennial ryegrass are supplied by the same substrate pools: assessment by dynamic 13C labeling and compartmental analysis of tracer kinetics. Plant Physiol 2008, 148:1148-1158.
47. Troufflard S., Roscher A., Thomasset B., Barbotin J.N., Rawsthorne S., Portais J.C. In vivo 13C NMR determines metabolic fluxes and steady state in linseed embryos. Phytochemistry 2007, 68:2341-2350.