ArticlePloS one2016
Multiscale Metabolic Modeling of C4 Plants: Connecting Nonlinear Genome-Scale Models to Leaf-Scale Metabolism in Developing Maize Leaves.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- New insights in metabolism modelling to decipher plant-microbe interactions.The New phytologist · 2025Review
- A Guide to Metabolic Network Modeling for Plant Biology.Plants (Basel, Switzerland) · 2025Review
- 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
- Development and applications of metabolic models in plant multi-omics research.Frontiers in plant science · 2024Review
- Elucidating the impact ofFrontiers in plant science · 2023Article
- Metabolic modelling revealed source-sink interactions between four segments ofJournal of biosciences · 2023Article
- Flavonoid deficiency disrupts redox homeostasis and terpenoid biosynthesis in glandular trichomes of tomato.Plant physiology · 2022Article
- Exploring synergies between plant metabolic modelling and machine learning.Computational and structural biotechnology journal · 2022Review
- Elucidation of Triacylglycerol Overproduction in the CFrontiers in plant science · 2022Article
- The utility of metabolomics as a tool to inform maize biology.Plant communications · 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
- Plant science decadal vision 2020-2030: Reimagining the potential of plants for a healthy and sustainable future.Plant direct · 2020Article
- Systematic Multi-Omics Integration (MOI) Approach in Plant Systems Biology.Frontiers in plant science · 2020Review
- A mass and charge balanced metabolic model of Setaria viridis revealed mechanisms of proton balancing in C4 plants.BMC bioinformatics · 2019Article
- Computational Approaches to Design and Test Plant Synthetic Metabolic Pathways.Plant physiology · 2019Review
- Mathematical models of lignin biosynthesis.Biotechnology for biofuels · 2018Article
- A robust and efficient method for estimating enzyme complex abundance and metabolic flux from expression data.Computational biology and chemistry · 2015Article
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2 authors.
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Abstract
C4 plants, such as maize, concentrate carbon dioxide in a specialized compartment surrounding the veins of their leaves to improve the efficiency of carbon dioxide assimilation. Nonlinear relationships between carbon dioxide and oxygen levels and reaction rates are key to their physiology but cannot be handled with standard techniques of constraint-based metabolic modeling. We demonstrate that incorporating these relationships as constraints on reaction rates and solving the resulting nonlinear optimization problem yields realistic predictions of the response of C4 systems to environmental and biochemical perturbations. Using a new genome-scale reconstruction of maize metabolism, we build an 18000-reaction, nonlinearly constrained model describing mesophyll and bundle sheath cells in 15 segments of the developing maize leaf, interacting via metabolite exchange, and use RNA-seq and enzyme activity measurements to predict spatial variation in metabolic state by a novel method that optimizes correlation between fluxes and expression data. Though such correlations are known to be weak in general, we suggest that developmental gradients may be particularly suited to the inference of metabolic fluxes from expression data, and we demonstrate that our method predicts fluxes that achieve high correlation with the data, successfully capture the experimentally observed base-to-tip transition between carbon-importing tissue and carbon-exporting tissue, and include a nonzero growth rate, in contrast to prior results from similar methods in other systems.
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