Metabolite Profiling in Plants

Richard N Trethewey, metanomics GmbH, Berlin, Germany

Published online: April 2007

DOI: 10.1002/9780470015902.a0020105

Advances in analytical chemistry, computation and biotechnology have led to the recent development of methodologies for broad metabolite profiling. The study of plant metabolism has been one of the first beneficiaries of these technologies and applications have focused on plant metabolite engineering, functional genomics and physiology. In the future, the greatest value will be generated from metabolite profiling technology in applications that integrate plant sciences with nutrition and human health.

Keywords: metabolite profiling; metabolomics; metabolism; functional genomics; mass spectrometry

Figure 1. With current technologies there is a trade-off between the number of metabolites that can be measured and the quality of measurement. The term data quality is used to mean the accuracy, sensitivity and specificity of the measurement. Highest quality is achieved with dedicated single assays of individual metabolites. Targeted metabolite profiling methods provide data of reasonable quality on a subset of compounds with similar chemical properties, but are limited in their scope. Broad metabolite profiling provides data on many hundreds of different metabolites but the quality of the individual metabolite measurements can vary substantially. Finally, metabolite fingerprinting methods provide data derived from tens or hundreds of metabolites allowing samples to be classified, however, quantitative data on individual metabolites is not derived and therefore the data quality is very low. Currently, only a fraction of the metabolome can be assessed with any one approach.
Figure 2. Example of a typical total ion GC-MS chromatogram from a plant extract using the methods described by Sauter et al. Capillary gas chromatography leads to the resolution of many hundreds of individual peaks which correspond to known and unknown metabolites. The identity of each peak is determined and monitored through the mass spectrometry fingerprints generated for each of the peaks. Example mass spectrums are shown for the peaks at 8.05 and 20.00 min.
Figure 3. Image of a large GC-MS metabolite profiling facillity at the company metanomics. Due to the robust and stable performance of the mature GC-MS technology it is possible to run high throughput operations with many hundreds of samples processed per day.
Figure 4. Example Arabidopsis chromatogram from the new innovative GC/GC-MS technology. A total ion chromatogram analagous to that shown in figure 2 is visible at the back of the diagram and represents the first dimension of GC separation. The peaks that are formed in the orthagonal direction towards the front of the image represent the results of the second GC separation. The heights of these peaks represent the relative ion abundances for each analyte. Underlying these peaks, but not shown, are the unique mass spectra that allow precise determination and monitoring of metabolite identity.
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 Further Reading
    Fernie AR, Trethewey RN, Krotzky AJ and Willmitzer L (2004) Metabolite profiling: from diagnostics to systems biology. Nature Reviews Molecular Cell Biology 5: 763–769.
    Fernie AR, Willmitzer L and Trethewey RN (2002) Sucrose to starch: a transition in molecular plant physiology. Trends in Plant Science 7: 35–41
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    German JB, Watkins SM and Fay LB (2005) Metabolomics in practice: emerging knowledge to guide future dietetic advice toward individualized health. Journal of the American Dietetic Association 105: 1425–1432.
    Hall RD (2006) Plant metabolomics: from holistic hope, to hype, to hot topic. New Phytologist 169: 453–468.
    Krishnan P, Kruger NJ and Ratcliffe RG (2005) Metabolite fingerprinting and profiling in plants using NMR. Journal of Experimental Botany 56: 255–265.
    Oksman-Caldentey KM and Saito K (2005) Integrating genomics and metabolomics for engineering plant metabolic pathways. Current Opinion in Biotechnology 16: 174–179.
    Stitt M and Fernie AR (2003) From measurements of metabolites to metabolomics: an ‘on the fly’ perspective illustrated by recent studies of carbon-nitrogen interactions. Current Opinion in Biotechnology 14: 136–144.
    Sumner LW, Mendes P and Dixon RA (2003) Plant metabolomics: large-scale phytochemistry in the functional genomics era. Phytochemistry 62: 817–836.
    Sweetlove LJ and Fernie AR (2005) Regulation of metabolic networks: understanding metabolic complexity in the systems biology era. New Phytologist 168: 9–24.

Related Sub-Topics:

Plant Biotechnology | Plant Genetics and Molecular Biology | Plant Stress Physiology
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Article Title: Metabolite Profiling in Plants
 
How to Cite close
Trethewey, Richard N(Apr 2007) Metabolite Profiling in Plants. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0020105]