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Time-resolved metabolomics reveals metabolic modulation in rice foliage

BACKGROUND: 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...

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Autores principales: Sato, Shigeru, Arita, Masanori, Soga, Tomoyoshi, Nishioka, Takaaki, Tomita, Masaru
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2442833/
https://www.ncbi.nlm.nih.gov/pubmed/18564421
http://dx.doi.org/10.1186/1752-0509-2-51
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author Sato, Shigeru
Arita, Masanori
Soga, Tomoyoshi
Nishioka, Takaaki
Tomita, Masaru
author_facet Sato, Shigeru
Arita, Masanori
Soga, Tomoyoshi
Nishioka, Takaaki
Tomita, Masaru
author_sort Sato, Shigeru
collection PubMed
description BACKGROUND: 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. RESULTS: 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. CONCLUSION: 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.
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spelling pubmed-24428332008-07-03 Time-resolved metabolomics reveals metabolic modulation in rice foliage Sato, Shigeru Arita, Masanori Soga, Tomoyoshi Nishioka, Takaaki Tomita, Masaru BMC Syst Biol Research Article BACKGROUND: 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. RESULTS: 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. CONCLUSION: 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. BioMed Central 2008-06-18 /pmc/articles/PMC2442833/ /pubmed/18564421 http://dx.doi.org/10.1186/1752-0509-2-51 Text en Copyright © 2008 Sato et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Sato, Shigeru
Arita, Masanori
Soga, Tomoyoshi
Nishioka, Takaaki
Tomita, Masaru
Time-resolved metabolomics reveals metabolic modulation in rice foliage
title Time-resolved metabolomics reveals metabolic modulation in rice foliage
title_full Time-resolved metabolomics reveals metabolic modulation in rice foliage
title_fullStr Time-resolved metabolomics reveals metabolic modulation in rice foliage
title_full_unstemmed Time-resolved metabolomics reveals metabolic modulation in rice foliage
title_short Time-resolved metabolomics reveals metabolic modulation in rice foliage
title_sort time-resolved metabolomics reveals metabolic modulation in rice foliage
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2442833/
https://www.ncbi.nlm.nih.gov/pubmed/18564421
http://dx.doi.org/10.1186/1752-0509-2-51
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AT nishiokatakaaki timeresolvedmetabolomicsrevealsmetabolicmodulationinricefoliage
AT tomitamasaru timeresolvedmetabolomicsrevealsmetabolicmodulationinricefoliage