Potential of metabolomics as a functional genomics tool

Raoul J. Bino, Robert D. Hall, Oliver Fiehn, Joachim Kopka, Kazuki Saito, John Draper, Basil J. Nikolau, Pedro Mendes, Ute Roessner-Tunali, Michael H. Beale, Richard N. Trethewey, B. Markus Lange (+2 others)
2004 Trends in Plant Science  
Metabolomics is developing as an important functional genomics tool; however, there is still room for technical improvements in both the large-scale determination of metabolites from complex plant tissues and the dissemination of metabolomics research data. For the continued maturation of metabolomics, the following three objectives need to be achieved: (i) improvement in the comprehensive coverage of the plant metabolome, (ii) facilitation of comparison of results between laboratories and
more » ... iments, and (iii) enhancement of the integration of metabolomic data with other functional genomic information. Because these challenges are widely recognized and endorsed, we propose community-based efforts to define common criteria and to initiate concerted actions directed towards the release of standard reference materials, construction of consolidated metabolite libraries, and development of metabolite-specific data-management systems. Metabolomics (comprehensive analysis in which all the metabolites of an organism are identified and quantified [1]) has emerged as a functional genomics methodology that contributes to our understanding of the complex molecular interactions in biological systems [2] . As such, metabolomics represents the logical progression from large-scale analysis of RNA and proteins at the systems level [3] . In recent years, several reviews have been published [1, [4] [5] [6] [7] [8] [9] describing the use of metabolomics in functional genomics research. Currently, metabolomics is being applied in many biological studies ranging from carbon-nitrogen interactions in plants [4] to the development of personal metabolomics as the next generation of nutritional assessment in humans [10] . Indeed, the biochemical response of an organism to a conditional perturbation can be characterized by its effect on the differential accumulation of individual metabolites [11] . A better understanding of the correlation between genes and the functional phenotype of an organism is the true goal of all functional genomics strategies. But, how far has metabolomics developed towards meeting this goal and how does it compare with other functional genomics approaches? In this opinion article, we briefly discuss the current status and suggest additional steps that are needed for further maturation and advancement of metabolomics as a productive, complementary functional genomics and systems biology tool. Current status Biological relevance For a holistic understanding of the biological behavior of a complex system, it is essential to follow, as unambiguously as possible, the response of an organism to a conditional perturbation at the transcriptome, proteome and metabolome levels [12, 13] . These three levels of expression profiling provide a complete picture of the RNAs, proteins and metabolites that enable one to: infer relevant associations between macromolecules; identify functional linkages between phenotypic expressions; and construct models that quantitatively describe the dynamics of the biological system. Broad phenotypic analyses are essential if we are to progress from prediction to experimental validation of gene function [4] .
doi:10.1016/j.tplants.2004.07.004 pmid:15337491 fatcat:e4fsk5rt4bcrpllsdbug7wfyju