ArticlePlant physiology2014
Bottom-up Metabolic Reconstruction of Arabidopsis and Its Application to Determining the Metabolic Costs of Enzyme Production.
Article in Plant physiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers, 1 of them a synthesis that pooled it.
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Who cites it
69 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Systematic comparison of local approaches for isotopically nonstationary metabolic flux analysis.Frontiers in plant science · 2023Pooled it
- Metabolic modeling predicts synergistic growth benefits between arbuscular mycorrhizal fungi and theoretical N2-fixing rhizobia symbiosis in maize.Plant physiology · 2026Article
- Predictive Algal Systems Biology: Integrating Omics, Genome-Scale Metabolic Models, and Machine Learning.Bioengineering (Basel, Switzerland) · 2026Review
- A constraint-based framework for exploring the impact of multireaction dependencies on metabolic functions.NPJ systems biology and applications · 2025Article
- Evaluating plant growth-defense trade-offs by modeling the interaction between primary and secondary metabolism.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Selection on genome-wide gene expression plasticity of rice in wet and dry field environments.Molecular ecology · 2025Article
- Metabolic modeling identifies determinants of thermal growth responses in Arabidopsis thaliana.The New phytologist · 2025Article
- New insights in metabolism modelling to decipher plant-microbe interactions.The New phytologist · 2025Review
- Flux-sum coupling analysis of metabolic network models.PLoS computational biology · 2025Article
- Plant cold acclimation and its impact on sensitivity of carbohydrate metabolism.NPJ systems biology and applications · 2025Article
- A data-integrative modeling approach accurately characterizes the effects of mutations on Arabidopsis lipid metabolism.Plant physiology · 2025Article
- Metabolic modeling reveals distinct roles of sugars and carboxylic acids in stomatal opening as well as unexpected carbon fluxes.The Plant cell · 2024Article
- Evolution of aromatic amino acid metabolism in plants: a key driving force behind plant chemical diversity in aromatic natural products.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- PolyID: Artificial Intelligence for Discovering Performance-Advantaged and Sustainable Polymers.Macromolecules · 2023Article
- Growth in fluctuating light buffers plants against photorespiratory perturbations.Nature communications · 2023Article
- The effective deficiency of biochemical networks.Scientific reports · 2023Article
- Diversification of JAZ-MYC signaling function in immune metabolism.The New phytologist · 2023Article
- The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber.PLoS computational biology · 2023Article
- Maximizing multi-reaction dependencies provides more accurate and precise predictions of intracellular fluxes than the principle of parsimony.PLoS computational biology · 2023Article
- Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism.Nature communications · 2023Article
9 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Large-scale modeling of plant metabolism provides the possibility to compare and contrast different cellular and environmental scenarios with the ultimate aim of identifying the components underlying the respective plant behavior. The existing models of Arabidopsis (Arabidopsis thaliana) are top-down assembled, whereby the starting point is the annotated genome, in particular, the metabolic genes. Hence, dead-end metabolites and blocked reactions can arise that are subsequently addressed by using gap-filling algorithms in combination with species-unspecific genes. Here, we present a bottom-up-assembled, large-scale model that relies solely on Arabidopsis-specific annotations and results in the inclusion of only manually curated reactions. While the existing models are largely condition unspecific by employing a single biomass reaction, we provide three biomass compositions that pertain to realistic and frequently examined scenarios: carbon-limiting, nitrogen-limiting, and optimal growth conditions. The comparative analysis indicates that the proposed Arabidopsis core model exhibits comparable efficiency in carbon utilization and flexibility to the existing network alternatives. Moreover, the model is utilized to quantify the energy demand of amino acid and enzyme de novo synthesis in photoautotrophic growth conditions. Illustrated by the case of the most abundant protein in the world, Rubisco, we determine its synthesis cost in terms of ATP requirements. This, in turn, allows us to explore the tradeoff between protein synthesis and growth in Arabidopsis. Altogether, the model provides a solid basis for completely species-specific integration of high-throughput data, such as gene expression levels, and for condition-specific investigations of in silico metabolic engineering strategies.
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Registered trials
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