Metabolite-Centric Reporter Pathway and Tripartite Network Analysis of Arabidopsis Under Cold Stress

Abstract

The study of plant resistance to cold stress and the metabolic processes underlying its molecular mechanisms benefit crop improvement programs. Here we investigate the effects of cold stress on the metabolic pathways of Arabidopsis when directly inferred at system level from transcriptome data. A metabolite-centric reporter pathway analysis approach enabled the computation of metabolites associated with transcripts at four time points of cold treatment. Tripartite networks of gene-metabolite-pathway connectivity outlined the response of metabolites and pathways to cold stress. Our metabolome-independent analysis revealed stress-associated metabolites in pathway routes of the cold stress response, including amino acid, carbohydrate, lipid, hormone, energy, photosynthesis, and signaling pathways. Cold stress first triggered the mobilization of energy from glycolysis and ethanol degradation to enhance TCA cycle activity via acetyl-CoA. Interestingly, tripartite networks lacked power law behavior and scale free connectivity, favoring modularity. Network rewiring explicitly involved energetics, signal, carbon and redox metabolisms and membrane remodeling.

Research Progress on the Roles of Cytokinin in Plant Response to Stress

“…Cold stress exhibits a significant strain on energy production and biochemical demand [69]. Therefore, compared with low latitudes (relatively high-temperature area), Zoysia grass (Zoysia japonica) at high latitudes (relatively low-temperature area) displays higher frost resistance.…”

Reactive Oxygen Species and the Redox-Regulatory Network in Cold Stress Acclimation

“…APX activity also increased in cold-tolerant J. macrocarpa , whereas the APX activity decreased >6-fold in the cold-sensitive J. curcas [ 11 ]. The ascorbate-dependent water-water cycle is supported by stimulated ascorbate biosynthesis, strengthened glutathione homeostasis, enhanced sulphate reduction, and TRX pathway [ 41 ].…”

Systematic Multi-Omics Integration (MOI) Approach in Plant Systems Biology

“…Differential analysis has been applied to various plant and fruit studies ( Koç et al., 2018 ; Wang et al., 2018 ; Belouah et al., 2019 ) and can be divided into either non-targeted or targeted pathway studies. One recent example of the former (non-targeted pathway) approach is the development of differential equation for protein density during tomato ripening ( Belouah et al., 2019 ).…”

“…Such a model consistently predicts the effect of gene perturbation in improving lignin content and wood properties and hence will be of interest to the breeding program of this valuable tree species. Additionally, another mathematical analysis study in targeted pathways was performed on Arabidopsis acclimatized to cold stress ( Koç et al., 2018 ). Microarray (transcriptomics) data sets were obtained for four periods of cold conditions before the expression data was mapped to available metabolic pathways from AraCyc and KEGG.…”

“…Using Reporter Metabolic Centric Algorithm in Matlab, DEGs were linked to corresponding metabolites before metabolite and pathway scores (called reporter metabolite and reporter pathway, respectively) were calculated. Tripartite network model encompassing gene, metabolite and pathways were built which revealed stress modulated pathways related to carbon, redox, and signal metabolisms upon the cold treatment ( Koç et al., 2018 ). Furthermore, constraint-based modeling such as flux balance analysis (FBA), usually performed using COBRA (constraint-based reconstruction and analysis) toolbox in Matlab application ( Orth et al., 2010 ) has also been used in this mathematical modeling ( Table 2 ).…”