Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism

Lipids play fundamental roles in regulating agronomically important traits. Advances in plant lipid metabolism have until recently largely been based on reductionist approaches, although modulation of its components can have system-wide effects. However, existing models of plant lipid metabolism provide lumped representations, hindering detailed study of component modulation. Here, we present the Plant Lipid Module (PLM) which provides a mechanistic description of lipid metabolism in the Arabidopsis thaliana rosette. We demonstrate that the PLM can be readily integrated in models of A. thaliana Col-0 metabolism, yielding accurate predictions (83%) of single lethal knock-outs and 75% concordance between measured transcript and predicted flux changes under extended darkness. Genome-wide associations with fluxes obtained by integrating the PLM in diel condition- and accession-specific models identify up to 65 candidate genes modulating A. thaliana lipid metabolism. Using mutant lines, we validate up to 40% of the candidates, paving the way for identification of metabolic gene function based on models capturing natural variability in metabolism.

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Evaluating plant growth-defence trade-offs by modelling the interaction between primary and secondary metabolism

Zrimec,

Correa,

Zagorščak

et al. 2024

Preprint

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Plants respond to stress by redistributing resources from growth- to defence-related processes, often resulting in decreased yields. Understanding the molecular mechanisms behind these growth-defence trade-offs can enhance breeding strategies to help us design crop varieties with improved stress tolerance, yields and quality. To enable the investigation of growth-defence trade-offs in the context of metabolism in an essential tuber crop, potato, here we develop a large-scale compartmentalised genome-scale metabolic model, Potato-GEM. Apart from primary metabolism, the model is curated to include the full potato secondary metabolism spanning over 600 reactions that facilitate the biosynthesis of 182 distinct potato secondary metabolites. Using constraint-based modelling, we find that the activation of the largest amount of secondary (defence) pathways occurs at a decrease of the relative growth rate of potato leaf, due to the costs incurred by defence. To investigate if the model can pinpoint reactions underlying growth-defence trade-offs, we then perform and process transcriptomics experiments by exposing potato leaves to two biotic stress scenarios, a chewing herbivore and a viral pathogen. By constraining the model with the resulting transcriptomics data, we obtain a set of condition-specific models, which predict decrease in optimal growth rates under treatment, in line with experimental observations. Potato-GEM thus presents a highly useful resource to study and broaden our understanding of potato and general plant defence responses under stress conditions.

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Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism

Cited by 3 publications

References 81 publications

Biosynthesis of biomolecules from saffron as an industrial crop and their regulation, with emphasis on the chemistry, extraction methods, identification techniques, and potential applications in human health and food: A critical comprehensive review

Biosynthesis of biomolecules from saffron as an industrial crop and their regulation, with emphasis on the chemistry, extraction methods, identification techniques, and potential applications in human health and food: A critical comprehensive review

Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism

Evaluating plant growth-defence trade-offs by modelling the interaction between primary and secondary metabolism

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