ArticleBMC bioinformatics2019
A mass and charge balanced metabolic model of Setaria viridis revealed mechanisms of proton balancing in C4 plants.
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 38 citations in OpenAlex.
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- Fermi calculations enable quick downselection of target genes and process optimization in photosynthetic systems.Plant physiology · 2025Review
- In silico encounters: harnessing metabolic modelling to understand plant-microbe interactions.FEMS microbiology reviews · 2025Review
- A diel multi-tissue genome-scale metabolic model of Vitis vinifera.PLoS computational biology · 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
- Toward mechanistic modeling and rational engineering of plant respiration.Plant physiology · 2023Article
- Spatial resolution of an integrated CScience advances · 2022Article
- A multi-organ metabolic model of tomato predicts plant responses to nutritional and genetic perturbations.Plant physiology · 2022Article
- Compartmentalization of metabolism between cell types in multicellular organisms: a computational perspective.Current opinion in systems biology · 2022Article
- Multi-omics intervention inFrontiers in plant science · 2022Review
- Exploring synergies between plant metabolic modelling and machine learning.Computational and structural biotechnology journal · 2022Review
- Characterization of effects of genetic variants via genome-scale metabolic modelling.Cellular and molecular life sciences : CMLS · 2021Review
- Advances in flux balance analysis by integrating machine learning and mechanism-based models.Computational and structural biotechnology journal · 2021Review
- Multi-tissue to whole plant metabolic modelling.Cellular and molecular life sciences : CMLS · 2020Review
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2 authors at 1 institution in 1 country.
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Abstract
backgroundC4 photosynthesis is a key domain of plant research with outcomes ranging from crop quality improvement, biofuel production and efficient use of water and nutrients. A metabolic network model of C4 "lab organism" Setaria viridis with extensive gene-reaction associations can accelerate target identification for desired metabolic manipulations and thereafter in vivo validation. Moreover, metabolic reconstructions have also been shown to be a significant tool to investigate fundamental metabolic traits.
resultsA mass and charge balance genome-scale metabolic model of Setaria viridis was constructed, which was tested to be able to produce all major biomass components in phototrophic and heterotrophic conditions. Our model predicted an important role of the utilization of NH[Formula: see text] and NO[Formula: see text] ratio in balancing charges in plants. A multi-tissue extension of the model representing C4 photosynthesis was able to utilize NADP-ME subtype of C4 carbon fixation for the production of lignocellulosic biomass in stem, providing a tool for identifying gene associations for cellulose, hemi-cellulose and lignin biosynthesis that could be potential target for improved lignocellulosic biomass production. Besides metabolic engineering, our modeling results uncovered a previously unrecognized role of the 3-PGA/triosephosphate shuttle in proton balancing.
conclusionsA mass and charge balance model of Setaria viridis, a model C4 plant, provides the possibility of system-level investigation to identify metabolic characteristics based on stoichiometric constraints. This study demonstrated the use of metabolic modeling in identifying genes associated with the synthesis of particular biomass components, and elucidating new role of previously known metabolic processes.
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