ReviewPlant physiology2019
Computational Approaches to Design and Test Plant Synthetic Metabolic Pathways.
Review in Plant physiology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Mitochondrial glutamine synthetase overexpression in tomato source leaves increases assimilate export and fruit yield.The Plant cell · 2026Article
- AI-driven multiscale virtual plant cell modeling: from molecular mechanisms to tissue functions.Planta · 2026Review
- Accurate prediction of flux distributions compatible with metabolite concentration effects in genome-scale metabolic networks.PLoS computational biology · 2026Article
- 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
- Metabolic modeling identifies determinants of thermal growth responses in Arabidopsis thaliana.The New phytologist · 2025Article
- Using supervised machine-learning approaches to understand abiotic stress tolerance and design resilient crops.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Flux-sum coupling analysis of metabolic network models.PLoS computational biology · 2025Article
- Harnessing the optimization of enzyme catalytic rates in engineering of metabolic phenotypes.PLoS computational biology · 2024Article
- Development and applications of metabolic models in plant multi-omics research.Frontiers in plant science · 2024Review
- Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism.Nature communications · 2023Article
- Toward mechanistic modeling and rational engineering of plant respiration.Plant physiology · 2023Article
- Integration of physiologically relevant photosynthetic energy flows into whole genome models of light-driven metabolism.The Plant journal : for cell and molecular biology · 2022Article
- Characterization of effects of genetic variants via genome-scale metabolic modelling.Cellular and molecular life sciences : CMLS · 2021Review
- A synthetic C4 shuttle via the β-hydroxyaspartate cycle in C3 plants.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Biological Parts for Plant Biodesign to Enhance Land-Based Carbon Dioxide Removal.Biodesign research · 2021Review
- SynPharm and the guide to pharmacology database: A toolset for conferring drug control on engineered proteins.Protein science : a publication of the Protein Society · 2021Article
- Review of Machine Learning Methods for the Prediction and Reconstruction of Metabolic Pathways.Frontiers in molecular biosciences · 2021Review
- Metabolic flux analysis of secondary metabolism in plants.Metabolic engineering communications · 2020Review
- Emerging Advanced Technologies to Mitigate the Impact of Climate Change in Africa.Plants (Basel, Switzerland) · 2020Review
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2 authors.
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Abstract
Successfully designed and implemented plant-specific synthetic metabolic pathways hold promise to increase crop yield and nutritional value. Advances in synthetic biology have already demonstrated the capacity to design artificial biological pathways whose behavior can be predicted and controlled in microbial systems. However, the transfer of these advances to model plants and crops faces the lack of characterization of plant cellular pathways and increased complexity due to compartmentalization and multicellularity. Modern computational developments provide the means to test the feasibility of plant synthetic metabolic pathways despite gaps in the accumulated knowledge of plant metabolism. Here, we provide a succinct systematic review of optimization-based and retrobiosynthesis approaches that can be used to design and in silico test synthetic metabolic pathways in large-scale plant context-specific metabolic models. In addition, by surveying the existing case studies, we highlight the challenges that these approaches face when applied to plants. Emphasis is placed on understanding the effect that metabolic designs can have on native metabolism, particularly with respect to metabolite concentrations and thermodynamics of biochemical reactions. In addition, we discuss the computational developments that may help to transform the identified challenges into opportunities for plant synthetic biology.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.