ArticleThe Plant cell2013
Integration of genome-scale modeling and transcript profiling reveals metabolic pathways underlying light and temperature acclimation in Arabidopsis.
Article in The Plant cell, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Integration of metatranscriptomics data improves the predictive capacity of microbial community metabolic models.The ISME journal · 2025Article
- A diel multi-tissue genome-scale metabolic model of Vitis vinifera.PLoS computational biology · 2024Article
- Elucidating the impact ofFrontiers in plant science · 2023Article
- Multi-Omics Approaches and Resources for Systems-Level Gene Function Prediction in the Plant Kingdom.Plants (Basel, Switzerland) · 2022Review
- Exploring synergies between plant metabolic modelling and machine learning.Computational and structural biotechnology journal · 2022Review
- Transcriptome integrated metabolic modeling of carbon assimilation underlying storage root development in cassava.Scientific reports · 2021Article
- Environment-coupled models of leaf metabolism.Biochemical Society transactions · 2021Review
- Untargeted Metabolomics ofFrontiers in plant science · 2019Article
- A genome-scale metabolic model of potato late blight suggests a photosynthesis suppression mechanism.BMC genomics · 2018Article
- Different strategies of metabolic regulation in cyanobacteria: from transcriptional to biochemical control.Scientific reports · 2016Article
- Modeling Rice Metabolism: From Elucidating Environmental Effects on Cellular Phenotype to Guiding Crop Improvement.Frontiers in plant science · 2016Review
- Unraveling the Light-Specific Metabolic and Regulatory Signatures of Rice through Combined in Silico Modeling and Multiomics Analysis.Plant physiology · 2015Article
- Integrative Approaches to Enhance Understanding of Plant Metabolic Pathway Structure and Regulation.Plant physiology · 2015Article
- Inference and Prediction of Metabolic Network Fluxes.Plant physiology · 2015Article
- Integration of metabolomics data into metabolic networks.Frontiers in plant science · 2015Review
- Metabolomics, Standards, and Metabolic Modeling for Synthetic Biology in Plants.Frontiers in bioengineering and biotechnology · 2015Review
- Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm.Frontiers in plant science · 2015Article
- Plant metabolic modeling: achieving new insight into metabolism and metabolic engineering.The Plant cell · 2014Review
- Flux profiling of photosynthetic carbon metabolism in intact plants.Nature protocols · 2014Article
- Variability of metabolite levels is linked to differential metabolic pathways in Arabidopsis's responses to abiotic stresses.PLoS computational biology · 2014Article
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6 authors.
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Abstract
Understanding metabolic acclimation of plants to challenging environmental conditions is essential for dissecting the role of metabolic pathways in growth and survival. As stresses involve simultaneous physiological alterations across all levels of cellular organization, a comprehensive characterization of the role of metabolic pathways in acclimation necessitates integration of genome-scale models with high-throughput data. Here, we present an integrative optimization-based approach, which, by coupling a plant metabolic network model and transcriptomics data, can predict the metabolic pathways affected in a single, carefully controlled experiment. Moreover, we propose three optimization-based indices that characterize different aspects of metabolic pathway behavior in the context of the entire metabolic network. We demonstrate that the proposed approach and indices facilitate quantitative comparisons and characterization of the plant metabolic response under eight different light and/or temperature conditions. The predictions of the metabolic functions involved in metabolic acclimation of Arabidopsis thaliana to the changing conditions are in line with experimental evidence and result in a hypothesis about the role of homocysteine-to-Cys interconversion and Asn biosynthesis. The approach can also be used to reveal the role of particular metabolic pathways in other scenarios, while taking into consideration the entirety of characterized plant metabolism.
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