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• W2101284429 endingPage "pp.01379.2015" @default.
• W2101284429 startingPage "pp.01379.2015" @default.
• W2101284429 abstract "Light quality is an important signaling component upon which plants orchestrate various morphological processes, including seed germination and seedling photomorphogenesis. However, it is still unclear how plants, especially food crops, sense various light qualities and modulate their cellular growth and other developmental processes. Therefore, in this work, we initially profiled the transcripts of a model crop, rice (Oryza sativa), under four different light treatments (blue, green, red, and white) as well as in the dark. Concurrently, we reconstructed a fully compartmentalized genome-scale metabolic model of rice cells, iOS2164, containing 2,164 unique genes, 2,283 reactions, and 1,999 metabolites. We then combined the model with transcriptome profiles to elucidate the light-specific transcriptional signatures of rice metabolism. Clearly, light signals mediated rice gene expressions, differentially regulating numerous metabolic pathways: photosynthesis and secondary metabolism were up-regulated in blue light, whereas reserve carbohydrates degradation was pronounced in the dark. The topological analysis of gene expression data with the rice genome-scale metabolic model further uncovered that phytohormones, such as abscisate, ethylene, gibberellin, and jasmonate, are the key biomarkers of light-mediated regulation, and subsequent analysis of the associated genes' promoter regions identified several light-specific transcription factors. Finally, the transcriptional control of rice metabolism by red and blue light signals was assessed by integrating the transcriptome and metabolome data with constraint-based modeling. The biological insights gained from this integrative systems biology approach offer several potential applications, such as improving the agronomic traits of food crops and designing light-specific synthetic gene circuits in microbial and mammalian systems." @default.
• W2101284429 created "2016-06-24" @default.
• W2101284429 creator A5007645247 @default.
• W2101284429 creator A5011206845 @default.
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• W2101284429 creator A5029580669 @default.
• W2101284429 creator A5076975897 @default.
• W2101284429 creator A5091055093 @default.
• W2101284429 date "2015-10-09" @default.
• W2101284429 modified "2023-10-16" @default.
• W2101284429 title "Unraveling the light-specific metabolic and regulatory signatures of rice through combined in silico modeling and multi-omics analysis" @default.
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• W2101284429 doi "https://doi.org/10.1104/pp.15.01379" @default.
• W2101284429 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/4677915" @default.
• W2101284429 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/26453433" @default.
• W2101284429 hasPublicationYear "2015" @default.
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