메뉴 건너뛰기




Volumn 15, Issue 1, 2004, Pages 58-63

High-throughput phenomics: Experimental methods for mapping fluxomes

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; CARBON NUCLEAR MAGNETIC RESONANCE; CELL LABELING; GENE MAPPING; GENOMICS; GLYCOLYSIS; HIGH THROUGHPUT SCREENING; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NUCLEAR MAGNETIC RESONANCE IMAGING; PRIORITY JOURNAL; REVIEW; STATISTICAL ANALYSIS;

EID: 1242306261     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.copbio.2003.11.001     Document Type: Review
Times cited : (209)

References (53)
  • 1
    • 0032977883 scopus 로고    scopus 로고
    • Lessons from metabolic engineering for functional genomics and drug discovery
    • Bailey J.E. Lessons from metabolic engineering for functional genomics and drug discovery. Nat Biotechnol. 17:1999;616-618.
    • (1999) Nat Biotechnol , vol.17 , pp. 616-618
    • Bailey, J.E.1
  • 2
    • 0041864127 scopus 로고    scopus 로고
    • In vivo measurement of fluxes through metabolic pathways: The missing link in functional genomics and pharmaceutical research
    • A seminal review on the relevance of in vivo flux measurements for functional genomics and pharmaceutical research with a focus on recent advances in MS for the analysis of higher organisms.
    • Hellerstein M.K. In vivo measurement of fluxes through metabolic pathways: the missing link in functional genomics and pharmaceutical research. Annu Rev Nutr. 23:2003;379-402 A seminal review on the relevance of in vivo flux measurements for functional genomics and pharmaceutical research with a focus on recent advances in MS for the analysis of higher organisms.
    • (2003) Annu Rev Nutr , vol.23 , pp. 379-402
    • Hellerstein, M.K.1
  • 3
    • 0032600888 scopus 로고    scopus 로고
    • Metabolic fluxes and metabolic engineering
    • Stephanopoulos G. Metabolic fluxes and metabolic engineering. Metab Eng. 1:1999;1-11.
    • (1999) Metab Eng , vol.1 , pp. 1-11
    • Stephanopoulos, G.1
  • 4
    • 0032753923 scopus 로고    scopus 로고
    • Metabolic flux ratio analysis of genetic and environmental modulations of Escherichia coli central carbon metabolism
    • Sauer U., Lasko D.R., Fiaux J., Hochuli M., Glaser R., Szyperski T., Wüthrich K., Bailey J.E. Metabolic flux ratio analysis of genetic and environmental modulations of Escherichia coli central carbon metabolism. J Bacteriol. 181:1999;6679-6688.
    • (1999) J Bacteriol , vol.181 , pp. 6679-6688
    • Sauer, U.1    Lasko, D.R.2    Fiaux, J.3    Hochuli, M.4    Glaser, R.5    Szyperski, T.6    Wüthrich, K.7    Bailey, J.E.8
  • 5
    • 0034741983 scopus 로고    scopus 로고
    • 13C metabolic flux analysis
    • 13C metabolic flux analysis Metab Eng. 3:2001;195-206.
    • (2001) Metab Eng , vol.3 , pp. 195-206
    • Wiechert, W.1
  • 6
    • 0031594984 scopus 로고    scopus 로고
    • 13C -NMR, MS and metabolic flux balancing in biotechnological research
    • 13C -NMR, MS and metabolic flux balancing in biotechnological research Q Rev Biophys. 31:1998;41-106.
    • (1998) Q Rev Biophys , vol.31 , pp. 41-106
    • Szyperski, T.1
  • 7
    • 0028108519 scopus 로고
    • Metabolic flux balancing: Basic concepts, scientific, and practical use
    • Varma A., Palsson B.O. Metabolic flux balancing: basic concepts, scientific, and practical use. Biol/Technol. 12:1994;994-998.
    • (1994) Biol/Technol , vol.12 , pp. 994-998
    • Varma, A.1    Palsson, B.O.2
  • 8
    • 0033987329 scopus 로고    scopus 로고
    • Metabolic network analysis. A powerful tool in metabolic engineering
    • Christensen B., Nielsen J. Metabolic network analysis. A powerful tool in metabolic engineering. Adv Biochem Eng Biotechnol. 66:2000;209-231.
    • (2000) Adv Biochem Eng Biotechnol , vol.66 , pp. 209-231
    • Christensen, B.1    Nielsen, J.2
  • 10
    • 0037422210 scopus 로고    scopus 로고
    • 13C -labeled acetate and glucose using GC-MS and powerful flux calculation method
    • 13C -labeled acetate and glucose using GC-MS and powerful flux calculation method J Biotechnol. 101:2003;101-117.
    • (2003) J Biotechnol , vol.101 , pp. 101-117
    • Zhao, J.1    Shimizu, K.2
  • 11
    • 0034115397 scopus 로고    scopus 로고
    • Quantitative determination of metabolic fluxes during coutilization of two carbon sources: Comparative analyses with Corynebacterium glutamicum during growth on acetate and/or glucose
    • Wendisch V.F., de Graaf A.A., Sahm H., Eikmanns B.J. Quantitative determination of metabolic fluxes during coutilization of two carbon sources: comparative analyses with Corynebacterium glutamicum during growth on acetate and/or glucose. J Bacteriol. 182:2000;3088-3096.
    • (2000) J Bacteriol , vol.182 , pp. 3088-3096
    • Wendisch, V.F.1    De Graaf, A.A.2    Sahm, H.3    Eikmanns, B.J.4
  • 15
    • 0141504947 scopus 로고    scopus 로고
    • Analysis of Escherichia coli anaplerotic metabolism and its regulation mechanisms from the metabolic responses to altered dilution rates and phosphoenolpyruvate carboxykinase knockout
    • Yang C., Hua Q., Baba T., Mori H., Shimizu K. Analysis of Escherichia coli anaplerotic metabolism and its regulation mechanisms from the metabolic responses to altered dilution rates and phosphoenolpyruvate carboxykinase knockout. Biotechnol Bioeng. 84:2003;129-144.
    • (2003) Biotechnol Bioeng , vol.84 , pp. 129-144
    • Yang, C.1    Hua, Q.2    Baba, T.3    Mori, H.4    Shimizu, K.5
  • 16
    • 0034680782 scopus 로고    scopus 로고
    • In vivo quantification of parallel and bidirectional fluxes in the anaplerosis of Corynebacterium glutamicum
    • Petersen S., de Graaf A.A., Eggeling L., Möllney M., Wiechert W., Sahm H. In vivo quantification of parallel and bidirectional fluxes in the anaplerosis of Corynebacterium glutamicum. J Biol Chem. 275:2000;35932-35941.
    • (2000) J Biol Chem , vol.275 , pp. 35932-35941
    • Petersen, S.1    De Graaf, A.A.2    Eggeling, L.3    Möllney, M.4    Wiechert, W.5    Sahm, H.6
  • 18
    • 0344443759 scopus 로고    scopus 로고
    • A novel metabolic cycle catalyzes glucose oxidation and anaplerosis in hungry Escherichia coli
    • By the identification of a previously unrecognized metabolic pathway for the seemingly well-characterized glucose metabolism in E. coli, this paper demonstrates the potential for scientific discoveries with flux analysis.
    • Fischer E., Sauer U. A novel metabolic cycle catalyzes glucose oxidation and anaplerosis in hungry Escherichia coli. J Biol Chem. 278:2003;46446-46451 By the identification of a previously unrecognized metabolic pathway for the seemingly well-characterized glucose metabolism in E. coli, this paper demonstrates the potential for scientific discoveries with flux analysis.
    • (2003) J Biol Chem , vol.278 , pp. 46446-46451
    • Fischer, E.1    Sauer, U.2
  • 19
    • 0035922027 scopus 로고    scopus 로고
    • Simple and robust method for estimation of the split ratio between the oxidative pentose phosphate pathways and the Embden-Meyerhof-Parnas pathway in microorganisms
    • Christensen B., Christiansen T., Gombert A.K., Nielsen J. Simple and robust method for estimation of the split ratio between the oxidative pentose phosphate pathways and the Embden-Meyerhof-Parnas pathway in microorganisms. Biotechnol Bioeng. 74:2001;517-523.
    • (2001) Biotechnol Bioeng , vol.74 , pp. 517-523
    • Christensen, B.1    Christiansen, T.2    Gombert, A.K.3    Nielsen, J.4
  • 20
    • 0029146299 scopus 로고
    • 13C -labeling of proteinogenic amino acids: An efficient analytical tool to investigate intermediary metabolism
    • 13C -labeling of proteinogenic amino acids: an efficient analytical tool to investigate intermediary metabolism Eur J Biochem. 232:1995;433-448.
    • (1995) Eur J Biochem , vol.232 , pp. 433-448
    • Szyperski, T.1
  • 22
    • 0037335931 scopus 로고    scopus 로고
    • Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism by GC-MS
    • Describes a novel methodology for the rapid diagnosis of intracellular flux responses based on metabolic flux ratios from GC-MS-derived mass distributions in proteinogenic amino acids. A first demonstration of the potential for high-throughput is given by the analysis of 68 E. coli shake flask cultures, by far the highest number of analyses reported in a single study to date. Moreover, the technical and biological robustness of the method was demonstrated by investigating the influence of key factors like culture conditions, harvest time, different isotopic tracers and known mutations.
    • Fischer E., Sauer U. Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism by GC-MS. Eur J Biochem. 270:2003;880-891 Describes a novel methodology for the rapid diagnosis of intracellular flux responses based on metabolic flux ratios from GC-MS-derived mass distributions in proteinogenic amino acids. A first demonstration of the potential for high-throughput is given by the analysis of 68 E. coli shake flask cultures, by far the highest number of analyses reported in a single study to date. Moreover, the technical and biological robustness of the method was demonstrated by investigating the influence of key factors like culture conditions, harvest time, different isotopic tracers and known mutations.
    • (2003) Eur J Biochem , vol.270 , pp. 880-891
    • Fischer, E.1    Sauer, U.2
  • 23
    • 0034847930 scopus 로고    scopus 로고
    • Metabolic flux analysis with a comprehensive isotopomer model in Bacillus subtilis
    • Dauner M., Bailey J.E., Sauer U. Metabolic flux analysis with a comprehensive isotopomer model in Bacillus subtilis. Biotechnol Bioeng. 76:2001;144-156.
    • (2001) Biotechnol Bioeng , vol.76 , pp. 144-156
    • Dauner, M.1    Bailey, J.E.2    Sauer, U.3
  • 27
    • 0642369576 scopus 로고    scopus 로고
    • 3 oxidase reduces TCA cycle fluxes in Bacillus subtilis
    • 13C -constrained flux analysis with physiological data from shake flask cultures and GC-MS-based metabolic flux ratios of proteinogenic amino acids. The principle with computation times of a few seconds is directly applicable to microscale cultures.
    • 13C -constrained flux analysis with physiological data from shake flask cultures and GC-MS-based metabolic flux ratios of proteinogenic amino acids. The principle with computation times of a few seconds is directly applicable to microscale cultures.
    • (2003) FEMS Microbiol Lett , vol.226 , pp. 121-126
    • Zamboni, N.1    Sauer, U.2
  • 28
    • 0036956758 scopus 로고    scopus 로고
    • Genealogy profiling through strain improvement by using metabolic network analysis: Metabolic flux genealogy of several generations of lysine-producing Corynebacteria
    • Iterative isotopomer balancing of GC-MS and MALDI-TOF MS data from only four secreted metabolites (alanine, valine, lysine and trehalose) was applied to shake flask cultures with few selected physiological data.
    • Wittmann C., Heinzle E. Genealogy profiling through strain improvement by using metabolic network analysis: metabolic flux genealogy of several generations of lysine-producing Corynebacteria. Appl Environ Microbiol. 68:2002;5843-5859 Iterative isotopomer balancing of GC-MS and MALDI-TOF MS data from only four secreted metabolites (alanine, valine, lysine and trehalose) was applied to shake flask cultures with few selected physiological data.
    • (2002) Appl Environ Microbiol , vol.68 , pp. 5843-5859
    • Wittmann, C.1    Heinzle, E.2
  • 29
    • 0042825675 scopus 로고    scopus 로고
    • Systematic quantification of complex metabolic flux networks using stable isotopes and mass spectrometry
    • Klapa M.I., Aon J.C., Stephanopoulos G. Systematic quantification of complex metabolic flux networks using stable isotopes and mass spectrometry. Eur J Biochem. 270:2003;3525-3542.
    • (2003) Eur J Biochem , vol.270 , pp. 3525-3542
    • Klapa, M.I.1    Aon, J.C.2    Stephanopoulos, G.3
  • 31
    • 1542265814 scopus 로고    scopus 로고
    • 13C -labeling experiments together with measurements of enzyme activities and intracellular metabolite concentrations
    • Epub ahead of print
    • 13C -labeling experiments together with measurements of enzyme activities and intracellular metabolite concentrations. Appl Microbiol Biotechnol 2003, Epub ahead of print DOI: 10.1007/s00253-003-1357-9 .
    • (2003) Appl Microbiol Biotechnol
    • Al Zaid Siddiquee, K.1    Arauzo-Bravo, M.J.2    Shimizu, K.3
  • 32
    • 0037470940 scopus 로고    scopus 로고
    • Analysis of metabolic and physiological responses to gnd knockout in Escherichia coli by using C-13 tracer experiment and enzyme activity measurements
    • Jiao Z., Baba T., Mori H., Shimizu K. Analysis of metabolic and physiological responses to gnd knockout in Escherichia coli by using C-13 tracer experiment and enzyme activity measurements. FEMS Microbiol Lett. 220:2003;295-301.
    • (2003) FEMS Microbiol Lett , vol.220 , pp. 295-301
    • Jiao, Z.1    Baba, T.2    Mori, H.3    Shimizu, K.4
  • 33
    • 0036365460 scopus 로고    scopus 로고
    • Metabolic flux analysis using mass spectroscopy
    • Wittmann C. Metabolic flux analysis using mass spectroscopy. Adv Biochem Eng Biotechnol. 74:2002;39-64.
    • (2002) Adv Biochem Eng Biotechnol , vol.74 , pp. 39-64
    • Wittmann, C.1
  • 34
    • 0037388423 scopus 로고    scopus 로고
    • Ion-trap mass spectrometry using in combination with gas chromatography for high-resolution metabolic flux determination
    • Klapa M.I., Aon J.C., Stephanopoulos G. Ion-trap mass spectrometry using in combination with gas chromatography for high-resolution metabolic flux determination. Biotechniques. 34:2003;832-836.
    • (2003) Biotechniques , vol.34 , pp. 832-836
    • Klapa, M.I.1    Aon, J.C.2    Stephanopoulos, G.3
  • 35
    • 0035002653 scopus 로고    scopus 로고
    • Application of MALDI-TOF MS to lysine-producing Corynebacterium glutamicum
    • This paper describes the first application of MALDI-TOF MS for metabolic flux analysis, thereby marking a breakthrough in analytical sensitivity and sample processing for high-throughput analyses.
    • Wittmann C., Heinzle E. Application of MALDI-TOF MS to lysine-producing Corynebacterium glutamicum. Eur J Biochem. 268:2001;2441-2455 This paper describes the first application of MALDI-TOF MS for metabolic flux analysis, thereby marking a breakthrough in analytical sensitivity and sample processing for high-throughput analyses.
    • (2001) Eur J Biochem , vol.268 , pp. 2441-2455
    • Wittmann, C.1    Heinzle, E.2
  • 37
    • 0036746724 scopus 로고    scopus 로고
    • Derivatization of small biomolecules for optimized matrix-assisted laser desorption/ionization mass spectometry
    • Describes methods that significantly widen the applicability of MALDI MS for the measurement of different classes of low molecular mass compounds. The compounds are potentially useful for flux analysis as physiological data or as analytes for mass isotopomer detection.
    • Tholey A., Wittmann C., Kang M.-J., Bungert D., Hollemeyer K., Heinzle E. Derivatization of small biomolecules for optimized matrix-assisted laser desorption/ionization mass spectometry. J Mass Spectrom. 37:2002;963-973 Describes methods that significantly widen the applicability of MALDI MS for the measurement of different classes of low molecular mass compounds. The compounds are potentially useful for flux analysis as physiological data or as analytes for mass isotopomer detection.
    • (2002) J Mass Spectrom , vol.37 , pp. 963-973
    • Tholey, A.1    Wittmann, C.2    Kang, M.-J.3    Bungert, D.4    Hollemeyer, K.5    Heinzle, E.6
  • 39
    • 0036819064 scopus 로고    scopus 로고
    • Changes of pentose phosphate pathway flux in vivo in Corynebacterium glutamicum during leucine-limited batch cultivation as determined from intracellular metabolite concentration measurements
    • Moritz B., Striegel K., de Graaf A.A., Sahm H. Changes of pentose phosphate pathway flux in vivo in Corynebacterium glutamicum during leucine-limited batch cultivation as determined from intracellular metabolite concentration measurements. Metab Eng. 4:2002;295-305.
    • (2002) Metab Eng , vol.4 , pp. 295-305
    • Moritz, B.1    Striegel, K.2    De Graaf, A.A.3    Sahm, H.4
  • 40
    • 85030896096 scopus 로고    scopus 로고
    • 13C flux analysis: Mass isotope correction, data consistency checking and precursor relationships
    • in press
    • 13C flux analysis: mass isotope correction, data consistency checking and precursor relationships. Biotechnol Bioeng, in press.
    • Biotechnol Bioeng
    • Wahl, A.1    Dauner, M.2    Wiechert, W.3
  • 41
    • 0343267841 scopus 로고    scopus 로고
    • Bidirectional reaction steps in metabolic networks: III. Explicit solution and analysis of isotopomer labeling systems
    • Wiechert W., Möllney 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. 66:1999;69-85.
    • (1999) Biotechnol Bioeng , vol.66 , pp. 69-85
    • Wiechert, W.1    Möllney, M.2    Isermann, N.3    Wurzel, M.4    De Graaf, A.A.5
  • 42
    • 0035817410 scopus 로고    scopus 로고
    • Using isotopomer path tracing to quantify metabolic fluxes in pathway models containing reversible reactions
    • Forbes N., Clark D.P., Blanch H.W. Using isotopomer path tracing to quantify metabolic fluxes in pathway models containing reversible reactions. Biotechnol Bioeng. 74:2001;196-211.
    • (2001) Biotechnol Bioeng , vol.74 , pp. 196-211
    • Forbes, N.1    Clark, D.P.2    Blanch, H.W.3
  • 43
    • 0141763770 scopus 로고    scopus 로고
    • An improved method for statistical analysis of metabolic flux analysis using isotopomer mapping matrices with analytical expression
    • Arauzo-Bravo M.J., Shimizu K. An improved method for statistical analysis of metabolic flux analysis using isotopomer mapping matrices with analytical expression. J Biotechnol. 105:2003;117-133.
    • (2003) J Biotechnol , vol.105 , pp. 117-133
    • Arauzo-Bravo, M.J.1    Shimizu, K.2
  • 44
    • 85030894446 scopus 로고    scopus 로고
    • Metabolic network analysis of lysine producing Corynebacterium glutamicum at a miniaturized scale
    • in press.
    • Wittmann C, Kim HM, Heinzle E: Metabolic network analysis of lysine producing Corynebacterium glutamicum at a miniaturized scale. Biotechnol Bioeng, in press.
    • Biotechnol Bioeng
    • Wittmann, C.1    Kim, H.M.2    Heinzle, E.3
  • 46
    • 0035916866 scopus 로고    scopus 로고
    • MALDI-TOF MS for quantification of substrates and products in cultivations of Corynebacterium glutamicum
    • Wittmann C., Heinzle E. MALDI-TOF MS for quantification of substrates and products in cultivations of Corynebacterium glutamicum. Biotechnol Bioeng. 72:2001;642-647.
    • (2001) Biotechnol Bioeng , vol.72 , pp. 642-647
    • Wittmann, C.1    Heinzle, E.2
  • 47
    • 0343673773 scopus 로고    scopus 로고
    • Methods for intense aeration, growth, storage, and replication of bacterial strains in microtiter plates
    • Duetz W.A., Rüedi L., Hermann R., O'Connor K., Büchs J., Witholt B. Methods for intense aeration, growth, storage, and replication of bacterial strains in microtiter plates. Appl Environ Microbiol. 66:2000;2641-2646.
    • (2000) Appl Environ Microbiol , vol.66 , pp. 2641-2646
    • Duetz, W.A.1    Rüedi, L.2    Hermann, R.3    O'Connor, K.4    Büchs, J.5    Witholt, B.6
  • 48
    • 0242501473 scopus 로고    scopus 로고
    • Integrated optical sensing of dissolved oxygen in microtiter plates: A novel tool for microbial cultivation
    • John G.T., Klimant I., Wittmann C., Heinzle E. Integrated optical sensing of dissolved oxygen in microtiter plates: a novel tool for microbial cultivation. Biotechnol Bioeng. 81:2003;829-836.
    • (2003) Biotechnol Bioeng , vol.81 , pp. 829-836
    • John, G.T.1    Klimant, I.2    Wittmann, C.3    Heinzle, E.4
  • 49
    • 0037438569 scopus 로고    scopus 로고
    • Automated screening in environmental arrays allows analysis of quantitative phenotypic profiles in Saccharomyces cerevisiae
    • Warringer J., Blomberg A. Automated screening in environmental arrays allows analysis of quantitative phenotypic profiles in Saccharomyces cerevisiae. Yeast. 20:2003;53-67.
    • (2003) Yeast , vol.20 , pp. 53-67
    • Warringer, J.1    Blomberg, A.2
  • 50
    • 0037274223 scopus 로고    scopus 로고
    • Metabolic screening of mammalian cell cultures using well-plates
    • Balcarcel R.R., Clark L.M. Metabolic screening of mammalian cell cultures using well-plates. Biotechnol Prog. 19:2003;98-108.
    • (2003) Biotechnol Prog , vol.19 , pp. 98-108
    • Balcarcel, R.R.1    Clark, L.M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.