Patterns of metabolite changes identified from large-scale gene perturbations in arabidopsis using a genome-scale metabolic network

Taehyong Kim, Kate Dreher, Ricardo Nilo-Poyanco, Insuk Lee, Oliver Fiehn, Bernd Markus Lange, Basil J. Nikolau, Lloyd Sumner, Ruth Welti, Eve S. Wurtele, Seung Y. Rhee

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

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

Original languageEnglish (US)
Pages (from-to)1685-1698
Number of pages14
JournalPlant Physiology
Volume167
Issue number4
DOIs
StatePublished - Apr 1 2015

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Metabolic Networks and Pathways
Arabidopsis
Genome
metabolites
genome
Genes
genes
mutants
functional properties
Metabolomics
metabolomics
Isoenzymes
isozymes
Arabidopsis thaliana

ASJC Scopus subject areas

  • Plant Science
  • Genetics
  • Physiology

Cite this

Patterns of metabolite changes identified from large-scale gene perturbations in arabidopsis using a genome-scale metabolic network. / Kim, Taehyong; Dreher, Kate; Nilo-Poyanco, Ricardo; Lee, Insuk; Fiehn, Oliver; Lange, Bernd Markus; Nikolau, Basil J.; Sumner, Lloyd; Welti, Ruth; Wurtele, Eve S.; Rhee, Seung Y.

In: Plant Physiology, Vol. 167, No. 4, 01.04.2015, p. 1685-1698.

Research output: Contribution to journalArticle

Kim, T, Dreher, K, Nilo-Poyanco, R, Lee, I, Fiehn, O, Lange, BM, Nikolau, BJ, Sumner, L, Welti, R, Wurtele, ES & Rhee, SY 2015, 'Patterns of metabolite changes identified from large-scale gene perturbations in arabidopsis using a genome-scale metabolic network', Plant Physiology, vol. 167, no. 4, pp. 1685-1698. https://doi.org/10.1104/pp.114.252361
Kim, Taehyong ; Dreher, Kate ; Nilo-Poyanco, Ricardo ; Lee, Insuk ; Fiehn, Oliver ; Lange, Bernd Markus ; Nikolau, Basil J. ; Sumner, Lloyd ; Welti, Ruth ; Wurtele, Eve S. ; Rhee, Seung Y. / Patterns of metabolite changes identified from large-scale gene perturbations in arabidopsis using a genome-scale metabolic network. In: Plant Physiology. 2015 ; Vol. 167, No. 4. pp. 1685-1698.
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