Computational Approaches to Design and Test Plant Synthetic Metabolic Pathways

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.

Designing Function-Specific Plant Systems for Sustainable Urban Development

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“…Despite the demonstrated potential, challenges including the inability to characterise plant cellular pathways, as well as complexity arising as a result of compartmentalization and multicellularity, present limitations to the technology. Increasing developments in modern computational capabilities is providing much needed solutions to these challenges by making available the means to test the feasibility of plant synthetic metabolic pathways, despite gaps in the accumulated knowledge of plant metabolism [62].…”

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“…Advances in plant synthetic biology could also expand these roles. [50][51][52] Examples include augmenting the native abilities of plants to perform specific functions (such as biotransformation of industrial toxins 53 or production of insect-repellant volatiles 41 ) by over-expressing key enzymes or by altering plant metabolomes (Fig. 4); developing new raw materials on-site that meet the needs of urban construction and consumption 54 ; locally producing natural plant-derived colorants for urban textile and food industries to replace toxic chemicals 55 ; and genetically engineering plants to use urban resources (water, nitrogen etc.)…”