Abstract
The metabolome comprises the complete set of metabolites, the non-genetically encoded substrates,intermediates, and products of metabolic pathways, associated to a cell. By representing integrativeinformation across multiple functional levels and by linking DNA encoded processes with the environment,the metabolome offers a window to map core attributes responsible for different phenotypes. Givenincreasing demand to quantitatively identify the metabolome and understand how trafficking of metabolitesthrough the metabolic network impact cellular behavior, metabolomics has emerged as an important complementarytechnology to the cell-wide measurements of mRNA, proteins, fluxes, and interactions (e.g. protein-DNA).Metabolomics is already a powerful tool in drug discovery and development and in metabolic engineering.While maintaining these strengths, the field promises to play a heightened role in systems biologyresearch, which is transforming the practice of medicine and our ability to engineer living organisms.
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References
Allen J, Davey HM, Broadhurst D, Heald JK, Rowland JJ, Oliver SG, Kell DB (2003) High-throughput classification of yeast mutants for functional genomics using metabolic footprinting. Nat Biotechnol 21:692–696
Bennett JW, Klich M (2003) Mycotoxins. Clin Microbiol Rev 16:497–516
Blank LM, Kuepfer L, Sauer U (2005) Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast. Genome Biol 6:R49
Catchpole GS, Beckmann M, Enot DP, Mondhe M, Zywicki B, Taylor J, Hardy N, Smith A, King RD, Kell DB, Fiehn O, Draper J (2005) Hierarchical metabolomics demonstrates substantial compositional similarity between genetically modified and conventional potato crops. Proc Natl Acad Sci USA 102:14458–14462
Çakir T, Patil KR, Onsan ZI, Ulgen KO, Kirdar B, Nielsen J (2006) Integration of metabolome data with metabolic networks reveals reporter reactions. Mol Sys Biol 2:0050 doi:10.1038/msb4100085
Food and Agriculture Organization (2004) Worldwide regulations for mycotoxins in food and feed in 2003. FAO Food Nutrition paper 81
Fiehn O (2001) Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks. Comp Funct Genomics 2:155–168
Fischer E, Sauer U (2005) Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism. Nat Genet 37:636–640
Frisvad JC, Filtenborg O (1983) Classification of terverticillate penicillia based on profiles of mycotoxins and other secondary metabolites. Appl Environ Microbiol 46:1301–1310
Gates SC, Sweeley CC (1978) Quantitative metabolic profiling based on gas chromatography. Clin Chem 24:1663–1673
Goodacre R, Vaidyanathan S, Dunn WB, Harrigan GG, Kell DB (2004) Metabolomics by numbers: acquiring and understanding global metabolite data. Trends Biotechnol 22:245–252
Grotkjaer T, Akesson M, Christensen B, Gombert AK, Nielsen J (2004) Impact of transamination reactions and protein turnover on labeling dynamics in C-13-labeling experiments. Biotechnol Bioeng 86:209–216
Hood L, Perlmutter RM (2004) The impact of systems approaches on biological problems in drug discovery. Nat Biotechnol 22:1215–1217
Horning EC, Horning MG (1971) Human metabolic profiles obtained by GC and GC/MS. J Chromatogr Sci 9:129–140
Jewett MC, Hofmann G, Nielsen J (2006) Fungal metabolite analysis in genomics and phenomics. Curr Opin Biotechnol 17:191–197
Kell DB (2004) Metabolomics and systems biology: making sense of the soup. Curr Opin Microbiol 7:296–307
Krska R, Welzig E, Berthiller F, Molinelli A, Mizaikoff B (2005) Advances in the analysis of mycotoxins and its quality assurance. Food Addit Contam 22:345–353
Logrieco A, Arrigan DW, Brengel-Pesce K, Siciliano P, Tothill I (2005) DNA arrays, electronic noses and tongues, biosensors and receptors for rapid detection of toxigenic fungi and mycotoxins: a review. Food Addit Contam 22:335–344
Mashego MR, Jansen ML, Vinke JL, van Gulik WM, Heijnen JJ (2005) Changes in the metabolome of Saccharomyces cerevisiae associated with evolution in aerobic glucose-limited chemostats. FEMS Yeast Res 5:419–430
Nielsen J (2003) It is all about metabolic fluxes. J Bacteriol 185:7031–7035
Nielsen J, Oliver S (2005) The next wave in metabolome analysis. Trends Biotechnol 23:544–546
Oliver SG, Winson MK, Kell DB, Baganz F (1998) Systematic functional analysis of the yeast genome. Trends Biotechnol 16:373–378
Patil KR, Nielsen J (2005) Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc Natl Acad Sci USA 102:2685–2689
Panagiotou G, Villas-Boas SG, Christakopoulos P, Nielsen J, Olsson L (2005) Intracellular metabolite profiling of Fusarium oxysporum converting glucose to ethanol. J Biotechnol 115:425–434
Raamsdonk LM, Teusink B, Broadhurst D, Zhang N, Hayes A, Walsh MC, Berden JA, Brindle KM, Kell DB, Rowland JJ, Westerhoff HV, van Dam K, Oliver SG (2001) A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nat Biotechnol 19:45–50
Roessner U, Wagner C, Kopka J, Trethewey RN, Willmitzer L (2000) Technical advance: simultaneous analysis of metabolites in potato tuber by gas chromatography-mass spectrometry. Plant J 23:131–142
Sauer U (2006) Metabolic networks in motion: 13C-based flux analysis. Mol Syst Biol 2:0062 doi:10.1038/msb4100109
Soga T, Ohashi Y, Ueno Y, Naraoka H, Tomita M, Nishioka T (2003) Quantitative metabolome analysis using capillary electrophoresis mass spectrometry. J Proteome Res 2:488–494
Stephanopoulos G, Alper H, Moxley J (2004) Exploiting biological complexity for strain improvement through systems biology. Nat Biotechnol 22:1261–1267
Trethewey RN (2001) Gene discovery via metabolic profiling. Curr Opin Biotechnol 12:135–138
van Winden WA, van Dam JC, Ras C, Kleijn RJ, Vinke JL, van Gulik WM, Heijnen JJ (2005) Metabolic-flux analysis of Saccharomyces cerevisiae CEN.PK113–7D based on mass isotopomer measurements of (13)C-labeled primary metabolites. FEMS Yeast Res 5:559–568
Villas-Boas SG, Mas S, Akesson M, Smedsgaard J, Nielsen J (2005a) Mass spectrometry in metabolome analysis. Mass Spectrom Rev 24:613–646
Villas-Boas SG, Moxley JF, Akesson M, Stephanopoulos G, Nielsen J (2005b) High-throughput metabolic state analysis: the missing link in integrated functional genomics of yeasts. Biochem J 388:669–677
Villas-Boas SG, Rasmussen S, Lane GA (2005c) Metabolomics or metabolite profiles? Trends Biotechnol 23:385–386
Wang QZ, Wu CY, Chen T, Chen X, Zhao XM (2006) Integrating metabolomics into a systems biology framework to exploit metabolic complexity: strategies and applications in microorganisms. Appl Microbiol Biotechnol 70:151–161
Weckwerth W, Loureiro ME, Wenzel K, Fiehn O (2004) Differential metabolic networks unravel the effects of silent plant phenotypes. Proc Natl Acad Sci USA 101:7809–7814
Weston AD, Hood L (2004) Systems biology, proteomics, and the future of health care: toward predictive, preventative, and personalized medicine. J Proteome Res 3:179–196
Wittmann C, Hans M, van Winden WA, Ras C, Heijnen JJ (2005) Dynamics of intracellular metabolites of glycolysis and TCA cycle during cell-cycle-related oscillation in Saccharomyces cerevisiae. Biotechnol Bioeng 89:839–847
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Nielsen, J., Jewett, M.C. (2007). The role of metabolomics in systems biology. In: Nielsen, J., Jewett, M.C. (eds) Metabolomics. Topics in Current Genetics, vol 18. Springer, Berlin, Heidelberg. https://doi.org/10.1007/4735_2007_0228
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DOI: https://doi.org/10.1007/4735_2007_0228
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