ArticlePlant physiology2010
AraGEM, a genome-scale reconstruction of the primary metabolic network in Arabidopsis.
Article in Plant physiology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 151 papers.
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151 citing papers in PubMed.
- Overview of molecular mechanisms underlying stress responses; signaling pathways and secondary metabolite synthesis in plants.Plant molecular biology · 2026Review
- Engineering principles in plant metabolism: integrating control, mechanics, and transport under dynamic environments.Plant physiology · 2026Review
- Metabolic modeling predicts synergistic growth benefits between arbuscular mycorrhizal fungi and theoretical N2-fixing rhizobia symbiosis in maize.Plant physiology · 2026Article
- Enumeration of Autocatalytic Subsystems in Large Chemical Reaction Networks.Journal of chemical theory and computation · 2026Article
- Selecting methods for draft GEM generation in multicellular eukaryotes: a comparative analysis.BMC bioinformatics · 2026Article
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- A voyage of reprogrammable metabolic bioengineering reshapes plant defense: from editing tools to synthetic systems.Frontiers in plant science · 2026Review
- Moving from genome-scale to community-scale metabolic models for the human gut microbiome.Nature microbiology · 2025Review
- A Guide to Metabolic Network Modeling for Plant Biology.Plants (Basel, Switzerland) · 2025Review
- Multiscale Mathematical Modeling in Systems Biology: A Framework to Boost Plant Synthetic Biology.Plants (Basel, Switzerland) · 2025Review
- diel_models: a python package for systematic integration of day-night cycles into plant genome-scale metabolic models.Bioinformatics advances · 2025Article
- A diel multi-tissue genome-scale metabolic model of Vitis vinifera.PLoS computational biology · 2024Article
- Chloroplastic ascorbate modifies plant metabolism and may act as a metabolite signal regardless of oxidative stress.Plant physiology · 2024Article
- Design and construction of artificial metabolic pathways for the bioproduction of useful compounds.Plant biotechnology (Tokyo, Japan) · 2024Article
- A multi-organ maize metabolic model connects temperature stress with energy production and reducing power generation.iScience · 2023Article
- The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber.PLoS computational biology · 2023Article
- A Protocol for the Automatic Construction of Highly Curated Genome-Scale Models of Human Metabolism.Bioengineering (Basel, Switzerland) · 2023Article
- Accurate flux predictions using tissue-specific gene expression in plant metabolic modeling.Bioinformatics (Oxford, England) · 2023Article
- Toward mechanistic modeling and rational engineering of plant respiration.Plant physiology · 2023Article
- Review
91 more citing papers are in PubMed but not listed here.
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5 authors.
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Abstract
Genome-scale metabolic network models have been successfully used to describe metabolism in a variety of microbial organisms as well as specific mammalian cell types and organelles. This systems-based framework enables the exploration of global phenotypic effects of gene knockouts, gene insertion, and up-regulation of gene expression. We have developed a genome-scale metabolic network model (AraGEM) covering primary metabolism for a compartmentalized plant cell based on the Arabidopsis (Arabidopsis thaliana) genome. AraGEM is a comprehensive literature-based, genome-scale metabolic reconstruction that accounts for the functions of 1,419 unique open reading frames, 1,748 metabolites, 5,253 gene-enzyme reaction-association entries, and 1,567 unique reactions compartmentalized into the cytoplasm, mitochondrion, plastid, peroxisome, and vacuole. The curation process identified 75 essential reactions with respective enzyme associations not assigned to any particular gene in the Kyoto Encyclopedia of Genes and Genomes or AraCyc. With the addition of these reactions, AraGEM describes a functional primary metabolism of Arabidopsis. The reconstructed network was transformed into an in silico metabolic flux model of plant metabolism and validated through the simulation of plant metabolic functions inferred from the literature. Using efficient resource utilization as the optimality criterion, AraGEM predicted the classical photorespiratory cycle as well as known key differences between redox metabolism in photosynthetic and nonphotosynthetic plant cells. AraGEM is a viable framework for in silico functional analysis and can be used to derive new, nontrivial hypotheses for exploring plant metabolism.
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