1. Deciphering rice metabolic flux reprograming under salinity stress via in silico metabolic modeling
- Author
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Supachitra Chadchawan, Kwanjeera Wanichthanarak, Chuthamas Boonchai, Wichian Sangwongchai, Thammaporn Kojonna, and Maysaya Thitisaksakul
- Subjects
CINV, Cytosolic invertase ,MAPK, Mitogen-activated protein kinase ,GSSG, Glutathione disulfide ,gs, Stomatal conductance ,Metabolic network ,Biochemistry ,SOD, Superoxide dismutase ,MDH, Malate dehydrogenase ,0302 clinical medicine ,Salinity stress ,Structural Biology ,Metabolic flux analysis ,GAPDH, Glyceraldehyde-3-phosphate dehydrogenase ,GSH, Glutathione ,iMAT, Integrative Metabolic Analysis Tool ,0303 health sciences ,ADH, Arogenate dehydrogenase ,PFK, Phosphofructokinase ,E, Transpiration rate ,food and beverages ,ASA, Ascorbate ,TAT, Tyrosine aminotransferase ,Computer Science Applications ,GLYK, 3-Phosphoglycerate kinase ,Ci, Intercellular CO2 concentration ,030220 oncology & carcinogenesis ,Systems biology ,IPA, Indolepyruvate ,Biotechnology ,Research Article ,PGK, Phosphoglycerate kinase ,GC-TOF-MS, Gas chromatography time-of-flight mass spectrometry ,Cellular respiration ,GEM, Genome-scale metabolic model ,lcsh:Biotechnology ,CGS, Cystathionine γ-synthase ,Biophysics ,Biology ,Metabolic modeling ,03 medical and health sciences ,Multi-omics analysis ,Metabolomics ,lcsh:TP248.13-248.65 ,Genetics ,Pn, Net photosynthesis rate ,IAA, Indole-3-acetic acid ,PLS-DA, Partial-Least Squares Discriminant Analysis ,GMD, Golm Metabolome Database ,Transcriptomics ,030304 developmental biology ,Rice (Oryza sativa L.) ,Salinity ,Metabolic pathway ,3-PGA, 3-Phosphoglycerate ,Flux (metabolism) - Abstract
Highlights • Integrative GEMs can reveal the metabolic responses of rice to salinity stress. • Photosynthesis and hexose utilization were downregulated by salinity stress. • Photorespiration was enhanced and could contribute to redox homeostasis under salinity stress. • Flux predictions, metabolite levels and photosynthesis parameters were in good agreement., Rice is one of the most economically important commodities globally. However, rice plants are salt susceptible species in which high salinity can significantly constrain its productivity. Several physiological parameters in adaptation to salt stress have been observed, though changes in metabolic aspects remain to be elucidated. In this study, rice metabolic activities of salt-stressed flag leaf were systematically characterized. Transcriptomics and metabolomics data were combined to identify disturbed pathways, altered metabolites and metabolic hotspots within the rice metabolic network under salt stress condition. Besides, the feasible flux solutions in different context-specific metabolic networks were estimated and compared. Our findings highlighted metabolic reprogramming in primary metabolic pathways, cellular respiration, antioxidant biosynthetic pathways, and phytohormone biosynthetic pathways. Photosynthesis and hexose utilization were among the major disturbed pathways in the stressed flag leaf. Notably, the increased flux distribution of the photorespiratory pathway could contribute to cellular redox control. Predicted flux statuses in several pathways were consistent with the results from transcriptomics, end-point metabolomics, and physiological studies. Our study illustrated that the contextualized genome-scale model together with multi-omics analysis is a powerful approach to unravel the metabolic responses of rice to salinity stress.
- Published
- 2020