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Open Access Highly Accessed Research article

Time-resolved metabolomics reveals metabolic modulation in rice foliage

Shigeru Sato1, Masanori Arita123, Tomoyoshi Soga14, Takaaki Nishioka15 and Masaru Tomita14*

Author Affiliations

1 Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan

2 Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo and PRESTO-JST, Kashiwa, Japan

3 Plant Science Center, Riken, Yokohama, Japan

4 Human Metabolome Technologies, Inc., Tsuruoka, Japan

5 Graduate School of Agriculture, Kyoto University, Kyoto, Japan

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BMC Systems Biology 2008, 2:51  doi:10.1186/1752-0509-2-51

Published: 18 June 2008



To elucidate the interaction of dynamics among modules that constitute biological systems, comprehensive datasets obtained from "omics" technologies have been used. In recent plant metabolomics approaches, the reconstruction of metabolic correlation networks has been attempted using statistical techniques. However, the results were unsatisfactory and effective data-mining techniques that apply appropriate comprehensive datasets are needed.


Using capillary electrophoresis mass spectrometry (CE-MS) and capillary electrophoresis diode-array detection (CE-DAD), we analyzed the dynamic changes in the level of 56 basic metabolites in plant foliage (Oryza sativa L. ssp. japonica) at hourly intervals over a 24-hr period. Unsupervised clustering of comprehensive metabolic profiles using Kohonen's self-organizing map (SOM) allowed classification of the biochemical pathways activated by the light and dark cycle. The carbon and nitrogen (C/N) metabolism in both periods was also visualized as a phenotypic linkage map that connects network modules on the basis of traditional metabolic pathways rather than pairwise correlations among metabolites. The regulatory networks of C/N assimilation/dissimilation at each time point were consistent with previous works on plant metabolism. In response to environmental stress, glutathione and spermidine fluctuated synchronously with their regulatory targets. Adenine nucleosides and nicotinamide coenzymes were regulated by phosphorylation and dephosphorylation. We also demonstrated that SOM analysis was applicable to the estimation of unidentifiable metabolites in metabolome analysis. Hierarchical clustering of a correlation coefficient matrix could help identify the bottleneck enzymes that regulate metabolic networks.


Our results showed that our SOM analysis with appropriate metabolic time-courses effectively revealed the synchronous dynamics among metabolic modules and elucidated the underlying biochemical functions. The application of discrimination of unidentified metabolites and the identification of bottleneck enzymatic steps even to non-targeted comprehensive analysis promise to facilitate an understanding of large-scale interactions among components in biological systems.