Plant Metabolomics : the missiong link in functional genomics strategies

R.D. Hall, M. Beale, O. Fiehn, N. Hardy, L. Summer, R. Bino

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    190 Citations (Scopus)


    After the establishment of technologies for high-throughput DNA sequencing (genomics), gene expression analysis (transcriptomics), and protein analysis (proteomics), the remaining functional genomics challenge is that of metabolomics. Metabolomics is the term coined for essentially comprehensive, nonbiased, high-throughput analyses of complex metabolite mixtures typical of plant extracts. This potentially holistic approach to metabolome analysis is driven primarily by recent advances in mass spectrometry (MS) technology and by the goals of functional genomics research. Achieving the broadest overview of metabolic composition is very complex and entails establishing a multifaceted, fully integrated strategy for optimal sample extraction, metabolite separation/detection/identification, automated data gathering/handling/analysis, and, ultimately, quantification. Both analytical and computational developments are essential to achieve this goal. The First International Congress on Plant Metabolomics was held in Wageningen, The Netherlands, in April 2002, with the primary goal of bringing together those players who are already active in this field and those who soon plan to be. In so doing, opportunities are created for collaboration, overlap can be avoided, and joint strategies can be determined to meet the metabolomics challenge. Indexed abstracts from the oral and poster presentations at the meeting are now accessible at www., and this site will continue to be used as an aid to information exchange and enhanced collaboration. Although microbes may prove to be the richest overall source of metabolites, plants are the source of the most complex individual mixtures. Mariet van der Werf (TNO-Food, Zeist, The Netherlands) reported that it has been predicted that bacterial genomes already sequenced can support the biosynthesis of just a few hundred metabolites (e.g., 580 for Bacillus subtilis and 800 for Escherichia coli), but for individual plants, this value is likely to be in the tens of thousands. This metabolic richness comes not just from the number of genes present (20,000 to 50,000) but also from multiple substrate specificities for many enzymes (Aharoni et al., 2000), subcellular compartmentation, and the occurrence of nonenzymic reactions. Approximately 50,000 different compounds have been elucidated in plants (De Luca and St. Pierre, 2000), and it is predicted that the final figure for the plant kingdom will approach or even exceed 200,000 (Pichersky and Gang, 2000; Fiehn, 2001, 2002). Thus, metabolomics represents a considerable challenge for plant scientists. Metabolomics research will prove an invaluable tool for generating information of use in many fields. For functional genomics strategies, potentially fast-track methods exploiting metabolomics analyses of tagged lines or known mutants are likely to prove invaluable (Motoko Awazuhara, Chiba University, Japan [Arabidopsis]; Andy Pereira, Plant Research International, Wageningen, The Netherlands; and Jon Lightner, Exelixis Plant Sciences, Portland, OR [Arabidopsis and tomato]). Metabolomics information not only will assist in the establishment of a deeper understanding of the complex interactive nature of plant metabolic networks and their responses to environmental and genetic change but also will provide unique insights into the fundamental nature of plant phenotypes in relation to development, physiology, tissue identity, resistance, biodiversity, etc. Some key conference presentations are described below. This report is organized according to categories representing the fields of greatest importance to the successful establishment of plant metabolomics as a technology complementary to those for gene expression and protein profiling already in existence.
    Original languageEnglish
    Pages (from-to)1437-1441
    JournalThe Plant Cell
    Publication statusPublished - 2002

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