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

Abstract

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.

Integrating proteomic data with metabolic modelling provides insight into key pathways ofBordetella pertussisbiofilms

“…As it is, the model in this study would have taken an average of overall expression and there may have been important differences between the layers of biofilm that could improve our understanding of the overall biofilm process. Additionally, it would be interesting to create temporal metabolic models to identify the changes that occur throughout biofilm development (80).…”

Guided extraction of genome-scale metabolic models for the integration and analysis of omics data

“…The normalised version of this score shows how well each gene in the expression data agrees with a particular metabolic function. GIMME has been successfully used in studies such as [41] aimed at understanding the impact of drought stress on Arabidopsis thaliana .…”

Transcriptome integrated metabolic modeling of carbon assimilation underlying storage root development in cassava

“…Among them, GIMME (Gene Inactivity Moderated by Metabolism and Expression) pre-defines inactive reactions based on a low-level of enzymatic gene expression under a set threshold and then minimizes fluxes through these reactions. The method incorporates gene expression to constrain the CBM model as demonstrated for E. coli 23 and in Arabidopsis leaves under drought stress 24 . To avoid the bias of threshold setting, E-Flux was proposed to directly constrain predicted fluxes to the measured level of gene expression.…”

“…Although gene expression data do not directly relate to fluxes because of post-transcriptional and translational modifications, they can confine the viable flux space to reflect the biological behavior better than the generic CBM model 26 . To date, very few studies have incorporated transcriptome data into CBM models of plants 24 , 26 , 29 , 30 , especially plant storage organs.…”