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Practical Applications of Metabolomics in Plant Biology

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Plant Metabolomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 860))

Abstract

The technologies being developed for the large-scale, essentially unbiased analysis of the small molecules present in organic extracts made from plant materials are greatly changing our way of thinking about what is possible in plant biology. A range of different separation and detection techniques are being refined and expanded and their combination with advanced data management and data analysis approaches is already giving plant scientists far deeper insights into the complexity of plant metabolism and plant metabolic composition than was imaginable just a few years ago. This field of “metabolomics”, while still in its infancy, has nevertheless already been welcomed with open arms by the plant science community, partly because of these said advantages but also because of the broad potential applicability of the approaches in both fundamental and applied science. The diversity in application already ranges from understanding the considerable complexity of primary metabolic networks in Arabidopsis, to the changes which occur in the biochemical composition of foods occurring, for example, during the Pasteurization of tomato purée for long-term storage or the boiling of Basmati rice for direct consumption. The insights being gained are revealing valuable information on the strict control yet flexible nature of plant metabolic networks in many different systems. This volume aims to give a comprehensive overview of the approaches available for the performance of a “typical” plant metabolomics experiment, the choice of analytical techniques and to offer warnings on the potential pitfalls in experimental design and execution.

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References

  1. Hall, R. D. (2006) Plant metabolomics: from holistic hope, to hype, to hot topic. New Phytologist 169, 453–468.

    Article  PubMed  CAS  Google Scholar 

  2. Tohge, T. and Fernie, A. R. (2009) Web-based resources for mass-spectrometry-based metabolomics: A user’s guide. Phytochemistry 70, 450–456.

    Article  PubMed  CAS  Google Scholar 

  3. Saito, K., Dixon, R. A. and Willmitzer, L., eds. (2006) Plant Metabolomics. Biotechnology in Agriculture and Forestry, Vol. 57. T. Nagata, ed. Springer-Verlag: Berlin.

    Google Scholar 

  4. Bovy, A., Schijlen, E. and Hall, R. D. (2007) Metabolic engineering of flavonoids in tomato (Solanum lycopersicum): the potential for metabolomics. Metabolomics 3, 399–412.

    Article  CAS  Google Scholar 

  5. Biais, B., Allwood, J. W., Deborde, C., Xu, Y., Maucourt, M., Beauvoit, B., et al. (2009) H-1 NMR, GC-EI-TOFMS, and Data Set Correlation for Fruit Metabolomics: Application to Spatial Metabolite Analysis in Melon. Analytical Chemistry 81, 2884–2894.

    Article  PubMed  CAS  Google Scholar 

  6. Fait, A., Hanhineva, K., Beleggia, R., Dai, N., Rogachev, I., Nikiforova, V. J., et al. (2008) Reconfiguration of the achene and receptacle metabolic networks during strawberry fruit development. Plant Physiology 148, 730–750.

    Article  PubMed  CAS  Google Scholar 

  7. Hall, R. D., ed. (2011) Biology of Plant Metabolomics. Wiley-Blackwell, Oxford.

    Google Scholar 

  8. Beale, M. H. and Sussman, M. R. (2011) Metabolomics of Arabidopsis thaliana, in The Biology of Plant Metabolomics pp. 157–180 (R.D. Hall, ed.), Wiley-Blackwell.

    Google Scholar 

  9. Schauer, N., Zamir, D. and Fernie, A. R. (2005) Metabolic profiling of leaves and fruit of wild species tomato: a survey of the Solanum lycopersicum complex. J Expt Bot 56, 297–307.

    Article  CAS  Google Scholar 

  10. Bovy, A. G., Gomez-Roldan, V. and Hall, R. D. (2010) Strategies to optimize the ­flavonoid content of tomato fruit, in The Handbook of Polyphenols: Recent Advances in Polyphenol Research (C. Santos-Buelga, M.-T. Escribano-Bailon, and V. Lattanzio, eds.) pp. 138–162.

    Google Scholar 

  11. Ahuja, I., de Vos, C. H. R., Bones, A. and Hall, R. D. (2010) Plant molecular stress responses face climate change. Trends in Plant Science 15, 664–674.

    Google Scholar 

  12. Allwood, J. W., Ellis, D. I. and Goodacre, R. (2008) Metabolomic technologies and their application to the study of plants and plant-host interactions. Physiologia Plantarum 132, 117–135.

    PubMed  CAS  Google Scholar 

  13. Jansen, J. J., Allwood, J. W., Marsden-Edwards, E., van der Putten, W. H., Goodacre, R. and van Dam, N. M. (2009) Metabolomic analysis of the interaction between plants and herbivores. Metabolomics 5, 150–161.

    Article  CAS  Google Scholar 

  14. Capanoglu, E., Beekwilder, J., Boyacioglu, D., de Vos, C. H. R. and Hall, R. D. (2010) The effect of industrial food processing on potentially health-beneficial tomato antioxidants. Crit Rev Food Chem 50, 919–930.

    Google Scholar 

  15. Fernie, A. R. and Schauer, N. (2009) Metabolomics-assisted breeding: a viable option for crop improvement? Trends in Genetics 25, 39–48.

    Article  PubMed  CAS  Google Scholar 

  16. Goodacre, R., York, E. V., Heald, J. K. and Scott, I. M. (2003) Chemometric discrimination of unfractionated plant extracts analyzed by electrospray mass spectrometry. Phytochemistry 62, 859–863.

    Article  PubMed  CAS  Google Scholar 

  17. Steward, D., Shepherd, L. V. T., Hall, R. D. and Fraser, P. D. (2011) Crops and tasty, nutritious food – how can metabolomics help? in The Biology of Plant Metabolomics (R.D. Hall, ed.), Wiley-Blackwell pp. 181–218.

    Google Scholar 

  18. Hall, R. D., Brouwer, I. D. and Fitzgerald, M. A. (2008) Plant metabolomics and its potential application for human nutrition. Physiologia Plantarum 132, 162–175.

    PubMed  CAS  Google Scholar 

  19. Graham, S. F., Amigues, E., Migaud, M. and Browne, R. A. (2009) Application of NMR based metabolomics for mapping metabolite variation in European wheat. Metabolomics 5, 302–306.

    Article  CAS  Google Scholar 

  20. Moco, S., Bino, R. J., Vorst, O., Verhoeven, H. A., de Groot, J., van Beek, T. A., et al. (2006) A liquid chromatography-mass spectrometry-based metabolome database for tomato. Plant Physiology 141, 1205–1218.

    Article  PubMed  CAS  Google Scholar 

  21. Moing, A., Aharoni, A., Biais, B., Rogachev, I., Meir, S., Brodsky, L., et al. (2011) Spatial and temporal metabolic profiling using multiple analytical platforms highlights the crosstalk between primary and secondary metabolites and mineral elements in melon fruit. New Phytologist 190, 683–696.

    Google Scholar 

  22. Jahangir, M., Kim, H. K., Choi, Y. H. and Verpoorte, R. (2009) Health-Affecting Compounds in Brassicaceae. Compr Rev Food & Sci Food Safety 8, 31–43.

    Article  CAS  Google Scholar 

  23. Lindinger, C., Pollien, P., de Vos, R. C. H., Tikunov, Y., Hageman, J. A., Lambot, C., et al. (2009) Identification of Ethyl Formate as a Quality Marker of the Fermented Off-note in Coffee by a Nontargeted Chemometric Approach. J Agric & Food Chem 57, 9972–9978.

    Article  CAS  Google Scholar 

  24. Beckmann, M., Enot, D. P., Overy, D. P. and Draper, J. (2007) Representation, comparison, and interpretation of metabolome fingerprint data for total composition analysis and quality trait investigation in potato cultivars. J Agric & Food Chem 55, 3444–3451.

    Article  CAS  Google Scholar 

  25. META-PHOR: Metabolomics for plants, health and outreach. (Accessed May 2010). Available at: http://www.meta-phor.eu/.

  26. AMDIS: The Automated Mass Spectral Deconvolution and Identification System. (Accessed May 2010). Available at: http://chemdata.nist.gov/mass-spc/amdis/.

  27. CAS: Chemical Abstracts Service. American Chemical Society. (Accessed May 2010). Available at: http://www.cas.org/.

  28. Fiehn, O., Robertson, D., Griffin, J., van der Werf, M., Nikolau, B., Morrison, N., et al. (2007) The metabolomics standards initiative (MSI). Metabolomics 3, 175–178.

    Article  CAS  Google Scholar 

  29. MSI: The Metabolomics Standards Initiative. Metabolomics Society. (Accessed May 2010). Available at: http://msi-workgroups.sourceforge.net/.

  30. NetCDF (network Common Data Form). Unidata. (Accessed May 2010). Available at: http://www.unidata.ucar.edu/software/netcdf/.

  31. NIST Scientific and Technical Databases. National Institute of Standards and Technology. (Accessed May 2010). Available at: http://www.nist.gov/srd/analy.htm.

  32. Oliver, S.G., Winston, M.K. and Kell, D.B. (1998) Systematic functional analysis of the yeast genome. Trends Biotech 16, 373–378.

    Article  CAS  Google Scholar 

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Acknowledgements

This work has been carried out under the auspices of the EU FPVI project META-PHOR—project number: FOOD-CT-2006-036220; (25). RDH acknowledges additional funding from the Centre for BioSystems Genomics (CBSG) and the Netherlands Metabolomics Centre (NMC), both part of the Netherlands Genomics Initiative (NGI). NWH acknowledges the support of Aberystwyth University.

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Authors and Affiliations

  1. Plant Research International, Wageningen, The Netherlands

    Robert D. Hall

  2. Centre for BioSystems Genomics, Wageningen, The Netherlands

    Robert D. Hall

  3. Netherlands Metabolomics Centre, Leiden, The Netherlands

    Robert D. Hall

  4. Department of Computer Science, Aberystwyth University, Aberystwyth, UK

    Nigel W. Hardy

Authors
  1. Robert D. Hall
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  2. Nigel W. Hardy
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Correspondence to Robert D. Hall .

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Editors and Affiliations

  1. , Dept. Computer Sciences, Aberystwyth University, King Street, Aberystwyth, SY23 3DB, United Kingdom

    Nigel W. Hardy

  2. Plant Research International, Wageningen, Netherlands

    Robert D. Hall

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Hall, R.D., Hardy, N.W. (2011). Practical Applications of Metabolomics in Plant Biology. In: Hardy, N., Hall, R. (eds) Plant Metabolomics. Methods in Molecular Biology, vol 860. Humana Press. https://doi.org/10.1007/978-1-61779-594-7_1

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  • DOI: https://doi.org/10.1007/978-1-61779-594-7_1

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-593-0

  • Online ISBN: 978-1-61779-594-7

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