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Volumn 22, Issue 1, 2011, Pages 17-25

Metabolomics in systems microbiology

Author keywords

[No Author keywords available]

Indexed keywords

CELL EXTRACTS; DATA TYPE; FLUX MEASUREMENTS; INTEGRATED METHOD; METABOLIC ACTIVITY; METABOLIC PATHWAYS; METABOLITE LEVEL; METABOLOMICS; MODEL ORGANISMS; REGULATORY INTERACTIONS; SUB-CELLULAR;

EID: 79551571018     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.copbio.2010.10.001     Document Type: Review
Times cited : (104)

References (51)
  • 1
    • 0035125986 scopus 로고    scopus 로고
    • In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
    • Edwards J.S., Ibarra R.U., Palsson B.O. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol 2001, 19:125-130. http://www.ncbi.nlm.nih.gov/pubmed/11175725.
    • (2001) Nat Biotechnol , vol.19 , pp. 125-130
    • Edwards, J.S.1    Ibarra, R.U.2    Palsson, B.O.3
  • 3
    • 68049100110 scopus 로고    scopus 로고
    • Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli
    • Bennett B.D., Kimball E.H., Gao M., Osterhout R., Van Dien S.J., Rabinowitz J.D. Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol 2009, 5:593-599. http://www.nature.com/doifinder/510.1038/nchembio.1186.
    • (2009) Nat Chem Biol , vol.5 , pp. 593-599
    • Bennett, B.D.1    Kimball, E.H.2    Gao, M.3    Osterhout, R.4    Van Dien, S.J.5    Rabinowitz, J.D.6
  • 4
    • 64649089947 scopus 로고    scopus 로고
    • Cross-platform comparison of methods for quantitative metabolomics of primary metabolism
    • Büscher J.M., Czernik D., Ewald J.C., Sauer U., Zamboni N. Cross-platform comparison of methods for quantitative metabolomics of primary metabolism. Anal Chem 2009, 81:2135-2143. http://www.ncbi.nlm.nih.gov/pubmed/19236023.
    • (2009) Anal Chem , vol.81 , pp. 2135-2143
    • Büscher, J.M.1    Czernik, D.2    Ewald, J.C.3    Sauer, U.4    Zamboni, N.5
  • 5
    • 38949209075 scopus 로고    scopus 로고
    • NMR-based metabolic profiling and metabonomic approaches to problems in molecular toxicology
    • Coen M., Holmes E., Lindon J.C., Nicholson J.K. NMR-based metabolic profiling and metabonomic approaches to problems in molecular toxicology. Chem Res Toxicol 2008, 21:9-27.
    • (2008) Chem Res Toxicol , vol.21 , pp. 9-27
    • Coen, M.1    Holmes, E.2    Lindon, J.C.3    Nicholson, J.K.4
  • 6
    • 41049100247 scopus 로고    scopus 로고
    • Extending the breadth of metabolite profiling by gas chromatography coupled to mass spectrometry
    • Fiehn O. Extending the breadth of metabolite profiling by gas chromatography coupled to mass spectrometry. Trends Anal Chem 2008, 27:261-269.
    • (2008) Trends Anal Chem , vol.27 , pp. 261-269
    • Fiehn, O.1
  • 8
    • 0030596516 scopus 로고    scopus 로고
    • Salmonella typhimurium apparently perceives external nitrogen limitation as internal glutamine limitation
    • Ikeda T.P., Shauger A.E., Kustu S. Salmonella typhimurium apparently perceives external nitrogen limitation as internal glutamine limitation. J Mol Biol 1996, 259:589-607. http://www.ncbi.nlm.nih.gov/pubmed/8683567.
    • (1996) J Mol Biol , vol.259 , pp. 589-607
    • Ikeda, T.P.1    Shauger, A.E.2    Kustu, S.3
  • 9
    • 1442326111 scopus 로고    scopus 로고
    • MIRACLE: mass isotopomer ratio analysis of U-13C-labeled extracts. A new method for accurate quantification of changes in concentrations of intracellular metabolites
    • Mashego M.R., Wu L., Van Dam J.C., Ras C., Vinke J.L., Van Winden W.A., Van Gulik W.M., Heijnen J.J. MIRACLE: mass isotopomer ratio analysis of U-13C-labeled extracts. A new method for accurate quantification of changes in concentrations of intracellular metabolites. Biotechnol Bioeng 2004, 85:620-628. http://doi.wiley.com/610.1002/bit.10907.
    • (2004) Biotechnol Bioeng , vol.85 , pp. 620-628
    • Mashego, M.R.1    Wu, L.2    Van Dam, J.C.3    Ras, C.4    Vinke, J.L.5    Van Winden, W.A.6    Van Gulik, W.M.7    Heijnen, J.J.8
  • 10
    • 34247123157 scopus 로고    scopus 로고
    • Cellular metabolomics of Escherichia coli
    • Rabinowitz J.D. Cellular metabolomics of Escherichia coli. Expert Rev Proteom 2007, 4:187-198.
    • (2007) Expert Rev Proteom , vol.4 , pp. 187-198
    • Rabinowitz, J.D.1
  • 11
    • 34548023950 scopus 로고    scopus 로고
    • Acidic acetonitrile for cellular metabolome extraction from Escherichia coli
    • Rabinowitz J.D., Kimball E. Acidic acetonitrile for cellular metabolome extraction from Escherichia coli. Anal Chem 2007, 79:6167-6173. http://www.ncbi.nlm.nih.gov/pubmed/17630720.
    • (2007) Anal Chem , vol.79 , pp. 6167-6173
    • Rabinowitz, J.D.1    Kimball, E.2
  • 13
    • 77952985821 scopus 로고    scopus 로고
    • Ultrahigh performance liquid chromatography-tandem mass spectrometry method for fast and robust quantification of anionic and aromatic metabolites
    • Buescher J.M., Moco S., Sauer U., Zamboni N. Ultrahigh performance liquid chromatography-tandem mass spectrometry method for fast and robust quantification of anionic and aromatic metabolites. Anal Chem 2010, 82:4403-4412. http://www.ncbi.nlm.nih.gov/pubmed/20433152.
    • (2010) Anal Chem , vol.82 , pp. 4403-4412
    • Buescher, J.M.1    Moco, S.2    Sauer, U.3    Zamboni, N.4
  • 14
    • 77951072181 scopus 로고    scopus 로고
    • Metabolomic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone orbitrap mass spectrometer
    • Lu W., Clasquin M.F., Melamud E., Amador-Noguez D., Caudy A.A., Rabinowitz J.D. Metabolomic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone orbitrap mass spectrometer. Anal Chem 2010, 82:3212-3221. http://pubs.acs.org/doi/abs/3210.1021/ac902837x.
    • (2010) Anal Chem , vol.82 , pp. 3212-3221
    • Lu, W.1    Clasquin, M.F.2    Melamud, E.3    Amador-Noguez, D.4    Caudy, A.A.5    Rabinowitz, J.D.6
  • 15
    • 33947503169 scopus 로고    scopus 로고
    • Simultaneous determination of multiple intracellular metabolites in glycolysis, pentose phosphate pathway and tricarboxylic acid cycle by liquid chromatography-mass spectrometry
    • Luo B., Groenke K., Takors R., Wandrey C., Oldiges M. Simultaneous determination of multiple intracellular metabolites in glycolysis, pentose phosphate pathway and tricarboxylic acid cycle by liquid chromatography-mass spectrometry. J Chromatogr A 2007, 1147:153-164. http://linkinghub.elsevier.com/retrieve/pii/S0021967307002907.
    • (2007) J Chromatogr A , vol.1147 , pp. 153-164
    • Luo, B.1    Groenke, K.2    Takors, R.3    Wandrey, C.4    Oldiges, M.5
  • 16
    • 0038699591 scopus 로고    scopus 로고
    • High-throughput classification of yeast mutants for functional genomics using metabolic footprinting
    • Allen J., Davey H.M., Broadhurst D., Heald J.K., Rowland J.J., Oliver S.G., Kell D.B. High-throughput classification of yeast mutants for functional genomics using metabolic footprinting. Nat Biotechnol 2003, 21:692-696. http://www.nature.com/doifinder/610.1038/nbt1823.
    • (2003) Nat Biotechnol , vol.21 , pp. 692-696
    • Allen, J.1    Davey, H.M.2    Broadhurst, D.3    Heald, J.K.4    Rowland, J.J.5    Oliver, S.G.6    Kell, D.B.7
  • 18
    • 77952883945 scopus 로고    scopus 로고
    • Systems biology of microbial metabolism
    • Heinemann M., Sauer U. Systems biology of microbial metabolism. Curr Opin Microbiol 2010, 13:337-343. http://linkinghub.elsevier.com/retrieve/pii/S1369527410000263.
    • (2010) Curr Opin Microbiol , vol.13 , pp. 337-343
    • Heinemann, M.1    Sauer, U.2
  • 19
    • 23044494653 scopus 로고    scopus 로고
    • Discovery metabolite profiling-forging functional connections between the proteome and metabolome
    • Saghatelian A., Cravatt B. Discovery metabolite profiling-forging functional connections between the proteome and metabolome. Life Sci 2005, 77:1759-1766. http://linkinghub.elsevier.com/retrieve/pii/S0024320505005072.
    • (2005) Life Sci , vol.77 , pp. 1759-1766
    • Saghatelian, A.1    Cravatt, B.2
  • 20
    • 32444446805 scopus 로고    scopus 로고
    • XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification
    • Smith C.A., Want E.J., O'Maille G., Abagyan R., Siuzdak G. XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem 2006, 78:779-787. http://pubs.acs.org/doi/abs/710.1021/ac051437y.
    • (2006) Anal Chem , vol.78 , pp. 779-787
    • Smith, C.A.1    Want, E.J.2    O'Maille, G.3    Abagyan, R.4    Siuzdak, G.5
  • 21
    • 66149122635 scopus 로고    scopus 로고
    • High-throughput quantitative metabolomics: workflow for cultivation, quenching, and analysis of yeast in a multiwell format
    • Ewald J.C., Heux Sp., Zamboni N. High-throughput quantitative metabolomics: workflow for cultivation, quenching, and analysis of yeast in a multiwell format. Anal Chem 2009, 81:3623-3629. http://pubs.acs.org/doi/abs/3610.1021/ac900002u.
    • (2009) Anal Chem , vol.81 , pp. 3623-3629
    • Ewald, J.C.1    Heux, S.2    Zamboni, N.3
  • 22
    • 77956511890 scopus 로고    scopus 로고
    • Systems-level metabolic flux profiling elucidates a complete, bifurcated TCA cycle in Clostridium acetobutylicum
    • Amador-Noguez D., Feng X.-J., Fan J., Roquet N., Rabitz H., Rabinowitz J.D. Systems-level metabolic flux profiling elucidates a complete, bifurcated TCA cycle in Clostridium acetobutylicum. J Bacteriol 2010.
    • (2010) J Bacteriol
    • Amador-Noguez, D.1    Feng, X.-J.2    Fan, J.3    Roquet, N.4    Rabitz, H.5    Rabinowitz, J.D.6
  • 24
    • 60649112635 scopus 로고    scopus 로고
    • Determination of ion structures in structurally related compounds using precursor ion fingerprinting
    • Sheldon M.T., Mistrik R., Croley T.R. Determination of ion structures in structurally related compounds using precursor ion fingerprinting. J Am Soc Mass Spectrom 2009, 20:370-376.
    • (2009) J Am Soc Mass Spectrom , vol.20 , pp. 370-376
    • Sheldon, M.T.1    Mistrik, R.2    Croley, T.R.3
  • 26
    • 77955969370 scopus 로고    scopus 로고
    • The Rut pathway for pyrimidine degradation: novel chemistry and toxicity problems
    • Kim K.-S., Pelton J.G., Inwood W.B., Andersen U., Kustu S., Wemmer D.E. The Rut pathway for pyrimidine degradation: novel chemistry and toxicity problems. J Bacteriol 2010, http://www.ncbi.nlm.nih.gov/pubmed/20400551.
    • (2010) J Bacteriol
    • Kim, K.-S.1    Pelton, J.G.2    Inwood, W.B.3    Andersen, U.4    Kustu, S.5    Wemmer, D.E.6
  • 27
    • 63849138401 scopus 로고    scopus 로고
    • Demonstration of the ethylmalonyl-CoA pathway by using 13C metabolomics
    • Peyraud R., Kiefer P., Christen P., Massou S., Portais J.C., Vorholt J.A. Demonstration of the ethylmalonyl-CoA pathway by using 13C metabolomics. Proc Natl Acad Sci 2009, 106:4846-4851. http://www.pnas.org/cgi/doi/4810.1073/pnas.0810932106.
    • (2009) Proc Natl Acad Sci , vol.106 , pp. 4846-4851
    • Peyraud, R.1    Kiefer, P.2    Christen, P.3    Massou, S.4    Portais, J.C.5    Vorholt, J.A.6
  • 29
    • 15744405123 scopus 로고    scopus 로고
    • PII signal transduction proteins: sensors of ?-ketoglutarate that regulate nitrogen metabolism
    • Ninfa A., Jiang P. PII signal transduction proteins: sensors of ?-ketoglutarate that regulate nitrogen metabolism. Curr Opin Microbiol 2005, 8:168-173.
    • (2005) Curr Opin Microbiol , vol.8 , pp. 168-173
    • Ninfa, A.1    Jiang, P.2
  • 30
    • 0242276682 scopus 로고    scopus 로고
    • Nitrogen assimilation and global regulation in Escherichia coli
    • Reitzer L. Nitrogen assimilation and global regulation in Escherichia coli. Annu Rev Microbiol 2003, 57:155-176.
    • (2003) Annu Rev Microbiol , vol.57 , pp. 155-176
    • Reitzer, L.1
  • 33
    • 33646586048 scopus 로고    scopus 로고
    • Short-term metabolome dynamics and carbon, electron, and ATP balances in chemostat-grown Saccharomyces cerevisiae CEN. PK 113-7D following a glucose pulse
    • Wu L., van Dam J., Schipper D., Kresnowati M.T.A.P., Proell A.M., Ras C., van Winden W.A., van Gulik W.M., Heijnen J.J. Short-term metabolome dynamics and carbon, electron, and ATP balances in chemostat-grown Saccharomyces cerevisiae CEN. PK 113-7D following a glucose pulse. Appl Environ Microbiol 2006, 72:3566-3577. http://aem.asm.org/cgi/doi/3510.1128/AEM.3572.3565.3566-3577.2006.
    • (2006) Appl Environ Microbiol , vol.72 , pp. 3566-3577
    • Wu, L.1    van Dam, J.2    Schipper, D.3    Kresnowati, M.T.A.P.4    Proell, A.M.5    Ras, C.6    van Winden, W.A.7    van Gulik, W.M.8    Heijnen, J.J.9
  • 35
    • 77951125481 scopus 로고    scopus 로고
    • Tradeoff between enzyme and metabolite efficiency maintains metabolic homeostasis upon perturbations in enzyme capacity
    • Fendt S.-M., Buescher J.M., Rudroff F., Picotti P., Zamboni N., Sauer U. Tradeoff between enzyme and metabolite efficiency maintains metabolic homeostasis upon perturbations in enzyme capacity. Mol Syst Biol 2010, 6. http://www.nature.com/doifinder/10.1038/msb.2010.11.
    • (2010) Mol Syst Biol , pp. 6
    • Fendt, S.-M.1    Buescher, J.M.2    Rudroff, F.3    Picotti, P.4    Zamboni, N.5    Sauer, U.6
  • 36
    • 0004277661 scopus 로고    scopus 로고
    • Portland Press, London/Miami/Brookfield, VT, (Distributed by Ashgate Pub. Co. in North America)
    • Fell D. Understanding the Control of Metabolism 1997, Portland Press, London/Miami/Brookfield, VT, (Distributed by Ashgate Pub. Co. in North America). edn 1.
    • (1997) Understanding the Control of Metabolism
    • Fell, D.1
  • 38
    • 33845870439 scopus 로고    scopus 로고
    • Conservation of the metabolomic response to starvation across two divergent microbes
    • Brauer M.J., Yuan J., Bennett B.D., Lu W., Kimball E., Botstein D., Rabinowitz J.D. Conservation of the metabolomic response to starvation across two divergent microbes. Proc Natl Acad Sci 2006, 103:19302-19307. http://www.pnas.org/cgi/doi/19310.11073/pnas.0609508103.
    • (2006) Proc Natl Acad Sci , vol.103 , pp. 19302-19307
    • Brauer, M.J.1    Yuan, J.2    Bennett, B.D.3    Lu, W.4    Kimball, E.5    Botstein, D.6    Rabinowitz, J.D.7
  • 39
    • 70349306551 scopus 로고    scopus 로고
    • Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism
    • Nakahigashi K., Toya Y., Ishii N., Soga T., Hasegawa M., Watanabe H., Takai Y., Honma M., Mori H., Tomita M. Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism. Mol Syst Biol 2009, 5. http://www.nature.com/doifinder/10.1038/msb.2009.65.
    • (2009) Mol Syst Biol , pp. 5
    • Nakahigashi, K.1    Toya, Y.2    Ishii, N.3    Soga, T.4    Hasegawa, M.5    Watanabe, H.6    Takai, Y.7    Honma, M.8    Mori, H.9    Tomita, M.10
  • 40
    • 34247612307 scopus 로고    scopus 로고
    • Multiple high-throughput analyses monitor the response of E. coli to perturbations
    • Ishii N., Nakahigashi K., Baba T., Robert M., Soga T., Kanai A., Hirasawa T., Naba M., Hirai K., Hoque A., et al. Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science 2007, 316:593-597. http://www.sciencemag.org/cgi/doi/510.1126/science.1132067.
    • (2007) Science , vol.316 , pp. 593-597
    • Ishii, N.1    Nakahigashi, K.2    Baba, T.3    Robert, M.4    Soga, T.5    Kanai, A.6    Hirasawa, T.7    Naba, M.8    Hirai, K.9    Hoque, A.10
  • 42
    • 75649152860 scopus 로고    scopus 로고
    • Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations
    • Boer V.M., Crutchfield C.A., Bradley P.H., Botstein D., Rabinowitz J.D. Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations. Mol Biol Cell 2009, 21:198-211. http://www.molbiolcell.org/cgi/doi/110.1091/mbc.E1009-1007-0597.
    • (2009) Mol Biol Cell , vol.21 , pp. 198-211
    • Boer, V.M.1    Crutchfield, C.A.2    Bradley, P.H.3    Botstein, D.4    Rabinowitz, J.D.5
  • 43
    • 77954197778 scopus 로고    scopus 로고
    • Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model
    • Yizhak K., Benyamini T., Liebermeister W., Ruppin E., Shlomi T. Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model. Bioinformatics 2010, 26:i255-i260. http://www.bioinformatics.oxfordjournals.org/cgi/doi/210.1093/bioinformatics/btq1183.
    • (2010) Bioinformatics , vol.26
    • Yizhak, K.1    Benyamini, T.2    Liebermeister, W.3    Ruppin, E.4    Shlomi, T.5
  • 45
    • 0037162304 scopus 로고    scopus 로고
    • Visualization of maltose uptake in living yeast cells by fluorescent nanosensors
    • Fehr M., Frommer W.B., Lalonde S. Visualization of maltose uptake in living yeast cells by fluorescent nanosensors. Proc Natl Acad Sci U S A 2002, 99:9846-9851.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 9846-9851
    • Fehr, M.1    Frommer, W.B.2    Lalonde, S.3
  • 47
    • 67849090833 scopus 로고    scopus 로고
    • Identification of an overabundant cholesterol precursor in hepatitis B virus replicating cells by untargeted lipid metabolite profiling
    • Rodgers M.A., Saghatelian A., Yang P.L. Identification of an overabundant cholesterol precursor in hepatitis B virus replicating cells by untargeted lipid metabolite profiling. J Am Chem Soc 2009, 131:5030-5031. http://pubs.acs.org/doi/abs/5010.1021/ja809949r.
    • (2009) J Am Chem Soc , vol.131 , pp. 5030-5031
    • Rodgers, M.A.1    Saghatelian, A.2    Yang, P.L.3
  • 48
    • 46749146517 scopus 로고    scopus 로고
    • Metabolomic analysis of the cerebrospinal fluid reveals changes in phospholipase expression in the CNS of SIV-infected macaques
    • Wikoff W.R., Pendyala G., Siuzdak G., Fox H.S. Metabolomic analysis of the cerebrospinal fluid reveals changes in phospholipase expression in the CNS of SIV-infected macaques. J Clin Investig 2008, 118.
    • (2008) J Clin Investig , pp. 118
    • Wikoff, W.R.1    Pendyala, G.2    Siuzdak, G.3    Fox, H.S.4
  • 50
    • 70350125099 scopus 로고    scopus 로고
    • Human gut microbiome adopts an alternative state following small bowel transplantation
    • Hartman A.L., Lough D.M., Barupal D.K., Fiehn O., Fishbein T., Zasloff M., Eisen J.A. Human gut microbiome adopts an alternative state following small bowel transplantation. Proc Natl Acad Sci 2009, 106:17187-17192. http://www.pnas.org/cgi/doi/17110.11073/pnas.0904847106.
    • (2009) Proc Natl Acad Sci , vol.106 , pp. 17187-17192
    • Hartman, A.L.1    Lough, D.M.2    Barupal, D.K.3    Fiehn, O.4    Fishbein, T.5    Zasloff, M.6    Eisen, J.A.7


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