- Molecular basis for the production of cyclic peptides by plant asparaginyl endopeptidases
- Gene-guided discovery and engineering of branched cyclic peptides in plants
- Enzyme Fusion Removes Competition for Geranylgeranyl Diphosphate in Carotenogenesis
- Neopinone isomerase is involved in codeine and morphine biosynthesis in opium poppy
- Computational Approaches to Design and Test Plant Synthetic Metabolic Pathways
- Changing Form and Function through Carotenoids and Synthetic Biology
- Unleashing the Synthetic Power of Plant Oxygenases: From Mechanism to Application
- Parts-Prospecting for a High-Efficiency Thiamin Thiazole Biosynthesis Pathway
- Engineering of plastids to optimize the production of high-value metabolites and proteins
- Computational approaches to design and test plant synthetic metabolic pathways
- Improving the efficiency of photosynthetic carbon reactions
- Engineering of metabolic pathways using synthetic enzyme complexes
- Synthetic metabolic pathways for photobiological conversion of CO2 into hydrocarbon fuel
- Molecular Plant: Special Issue on Plant Metabolism and Synthetic Biology (2014)
Computational Approaches to Design and Test Plant Synthetic Metabolic Pathways
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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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