ArticlePlant physiology2015
Unraveling the Light-Specific Metabolic and Regulatory Signatures of Rice through Combined in Silico Modeling and Multiomics Analysis.
Article in Plant physiology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 74 citations in OpenAlex.
- Integrated transcriptomic and metabolomic analyses reveal light-quality-dependent regulation of specialized metabolism in Pseudostellaria heterophylla.BMC genomics · 2026Article
- Transcriptome enhanced rice grain metabolic model identifies histidine level as a marker for grain chalkiness.Scientific reports · 2025Article
- A Guide to Metabolic Network Modeling for Plant Biology.Plants (Basel, Switzerland) · 2025Review
- A new conceptual model for seed germination and seedling tillering of winter wheat in the field.Royal Society open science · 2025Article
- A diel multi-tissue genome-scale metabolic model of Vitis vinifera.PLoS computational biology · 2024Article
- Systems biology of plant metabolic interactions.Journal of biosciences · 2024Review
- Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism.Nature communications · 2023Article
- The Role of Blue and Red Light in the Orchestration of Secondary Metabolites, Nutrient Transport and Plant Quality.Plants (Basel, Switzerland) · 2023Review
- Review
- Elucidating the impact ofFrontiers in plant science · 2023Article
- Light Intensity- and Spectrum-Dependent Redox Regulation of Plant Metabolism.Antioxidants (Basel, Switzerland) · 2022Review
- Between Light and Shading: Morphological, Biochemical, and Metabolomics Insights Into the Influence of Blue Photoselective Shading on Vegetable Seedlings.Frontiers in plant science · 2022Article
- Exploring synergies between plant metabolic modelling and machine learning.Computational and structural biotechnology journal · 2022Review
- Transcriptomic analyses of cacao flavonoids produced in photobioreactors.BMC genomics · 2021Article
- Systems biology for crop improvement.The plant genome · 2021Review
- Characterization of effects of genetic variants via genome-scale metabolic modelling.Cellular and molecular life sciences : CMLS · 2021Review
- Environment-coupled models of leaf metabolism.Biochemical Society transactions · 2021Review
- Toward Multiplexed Optogenetic Circuits.Frontiers in bioengineering and biotechnology · 2021Review
- Exploration of the Effects of Different Blue LED Light Intensities on Flavonoid and Lipid Metabolism in Tea Plants via Transcriptomics and Metabolomics.International journal of molecular sciences · 2020Article
- Red and blue light differentially impact retrograde signalling and photoprotection in rice.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Article
Corrections and comments
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Authors and funding
6 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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