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Open AccessArticle

Drought Stress Responses in Context-Specific Genome-Scale Metabolic Models of Arabidopsis thaliana

1
RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
2
Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka 565-0871, Japan
3
Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
*
Author to whom correspondence should be addressed.
Metabolites 2020, 10(4), 159; https://doi.org/10.3390/metabo10040159
Received: 18 February 2020 / Revised: 26 March 2020 / Accepted: 16 April 2020 / Published: 18 April 2020
(This article belongs to the Special Issue Metabolomics-Driven Biotechnology)
Drought perturbs metabolism in plants and limits their growth. Because drought stress on crops affects their yields, understanding the complex adaptation mechanisms evolved by plants against drought will facilitate the development of drought-tolerant crops for agricultural use. In this study, we examined the metabolic pathways of Arabidopsis thaliana which respond to drought stress by omics-based in silico analyses. We proposed an analysis pipeline to understand metabolism under specific conditions based on a genome-scale metabolic model (GEM). Context-specific GEMs under drought and well-watered control conditions were reconstructed using transcriptome data and examined using metabolome data. The metabolic fluxes throughout the metabolic network were estimated by flux balance analysis using the context-specific GEMs. We used in silico methods to identify an important reaction contributing to biomass production and clarified metabolic reaction responses under drought stress by comparative analysis between drought and control conditions. This proposed pipeline can be applied in other studies to understand metabolic changes under specific conditions using Arabidopsis GEM or other available plant GEMs. View Full-Text
Keywords: Arabidopsis; drought; flux balance analysis; genome-scale metabolic model; metabolism; metabolome; transcriptome Arabidopsis; drought; flux balance analysis; genome-scale metabolic model; metabolism; metabolome; transcriptome
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MDPI and ACS Style

Siriwach, R.; Matsuda, F.; Yano, K.; Hirai, M.Y. Drought Stress Responses in Context-Specific Genome-Scale Metabolic Models of Arabidopsis thaliana. Metabolites 2020, 10, 159. https://doi.org/10.3390/metabo10040159

AMA Style

Siriwach R, Matsuda F, Yano K, Hirai MY. Drought Stress Responses in Context-Specific Genome-Scale Metabolic Models of Arabidopsis thaliana. Metabolites. 2020; 10(4):159. https://doi.org/10.3390/metabo10040159

Chicago/Turabian Style

Siriwach, Ratklao; Matsuda, Fumio; Yano, Kentaro; Hirai, Masami Y. 2020. "Drought Stress Responses in Context-Specific Genome-Scale Metabolic Models of Arabidopsis thaliana" Metabolites 10, no. 4: 159. https://doi.org/10.3390/metabo10040159

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