Metabolomics-based post-genome science in plants

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Integrated analysis of omics can provide the clues for identification of gene function and precise information about gene-to-metabolite and/or metabolite-to-metabolite networks. We ran the functional genomics project combining metabolome and transcriptome in Arabidopsis thaliana. Nutritional stress of nitrogen and sulfur resulted in global change of metabolome that could be correlated with the modulation of gene expression, indicating the presence of gene-to-metabolite networks, in particular, in glucosinolate biosynthesis. The comprehensive gene expression and metabolite profiles of anthocyanin overproducing Arabidopsis lines revealed the function of novel genes that are responsible for modification and storage of anthocyanins. The function of those genes was identified by analysis of the T-DNA insertion lines and recombinant proteins. By expanding this strategy, we used a transcriptome database publicly available for functional identification of unknown genes and networks. Upon these co-expression analyses, the models of co-expressed genes in particular metabolic pathways were constructed, leading to speculation of functions of those genes followed by confirmation with reverse genetics strategy. Extensive metabolic profiling of the knockout mutants of genes of interest was performed by a metabolome-analytical platform employing mass spectrometry. Detailed metabolite analysis of the mutants revealed the changes in metabolo-types, indicating the gene functions. This strategy of integrated analysis of metabolome and transcriptome is applicable to decipher the function of genes not only for a model plant A. thaliana but also for unexplored plants expected rich with a variety of phychemicals.