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Patterns of Metabolite Changes Identified from Large-Scale Gene Perturbations in Arabidopsis Using a Genome-Scale Metabolic Network
Plant Physiology
  • Taehyong Kim, Carnegie Institution for Science
  • Kate Dreher, Carnegie Institution for Science
  • Ricardo Nilo-Poyanco, Carnegie Institution for Science
  • Insuk Lee, Yonsei University
  • Oliver Fiehn, University of California, Davis
  • Bernd Markus Lange, Washington State University
  • Basil J Nikolau, Iowa State University
  • Lloyd Sumner, The Samuel Roberts Noble Foundation
  • Ruth Welti, Kansas State University
  • Eve S. Wurtele, Iowa State University
  • Seung Y. Rhee, Carnegie Institution for Science
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Metabolomics enables quantitative evaluation of metabolic changes caused by genetic or environmental perturbations. However, little is known about how perturbing a single gene changes the metabolic system as a whole and which network and functional properties are involved in this response. To answer this question, we investigated the metabolite profiles from 136 mutants with single gene perturbations of functionally diverse Arabidopsis (Arabidopsis thaliana) genes. Fewer than 10 metabolites were changed significantly relative to the wild type in most of the mutants, indicating that the metabolic network was robust to perturbations of single metabolic genes. These changed metabolites were closer to each other in a genome-scale metabolic network than expected by chance, supporting the notion that the genetic perturbations changed the network more locally than globally. Surprisingly, the changed metabolites were close to the perturbed reactions in only 30% of the mutants of the well-characterized genes. To determine the factors that contributed to the distance between the observed metabolic changes and the perturbation site in the network, we examined nine network and functional properties of the perturbed genes. Only the isozyme number affected the distance between the perturbed reactions and changed metabolites. This study revealed patterns of metabolic changes from large-scale gene perturbations and relationships between characteristics of the perturbed genes and metabolic changes.


This article is published as Kim, Taehyong, Kate Dreher, Ricardo Nilo-Poyanco, Insuk Lee, Oliver Fiehn, Bernd Markus Lange, Basil J. Nikolau et al. "Patterns of metabolite changes identified from large-scale gene perturbations in Arabidopsis using a genome-scale metabolic network." Plant physiology 167, no. 4 (2015): 1685-1698. doi: 10.1104/pp.114.252361. Copyright American Society of Plant Biologists. Posted with permission.

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American Society of Plant Biologists
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Taehyong Kim, Kate Dreher, Ricardo Nilo-Poyanco, Insuk Lee, et al.. "Patterns of Metabolite Changes Identified from Large-Scale Gene Perturbations in Arabidopsis Using a Genome-Scale Metabolic Network" Plant Physiology Vol. 167 Iss. 4 (2015) p. 1685 - 1698
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