Integrated modelling of whole-plant metabolism and growth

<p>Source-sink interactions describe the relationship between different plant organs and the division of labour in relation to source activity (resource uptake and assimilation) and sink activity (resource utilisation). Recently, multiscale growth models have been proposed as a tool to investi...

Full description

Bibliographic Details
Main Author: Konuntakiet, T
Format: Thesis
Language:English
Published: 2020
Subjects:
_version_ 1817931789832814592
author Konuntakiet, T
author_facet Konuntakiet, T
author_sort Konuntakiet, T
collection OXFORD
description <p>Source-sink interactions describe the relationship between different plant organs and the division of labour in relation to source activity (resource uptake and assimilation) and sink activity (resource utilisation). Recently, multiscale growth models have been proposed as a tool to investigate unresolved aspects of whole-plant level processes, including source-sink interactions. In particular, constraint-based modelling using stoichiometric biochemical models has been shown to generate accurate predictions of metabolic fluxes and fine-grained, quantitative descriptions of plant biochemistry. The aim of this work was to develop a computational framework that captures the interactions between different organs during plant growth and the metabolic activity of each organ.</p> <p>Two main modelling approaches are presented in this work. The first approach consists of stoichiometric metabolic models integrated into a previously established multiscale Arabidopsis growth model. However, exploration of the resulting model revealed that the model's structure was unable to account for the effects of non-carbon resources on growth, which led to poor predictions of growth rates.</p> <p>The second modelling approach was developed to overcome this issue. I generated a whole-plant stoichiometric network of tomato metabolism by connecting organ-specific models via a common metabolite pool. Vegetative growth simulations produced predictions for metabolic fluxes that were in good agreement with known biochemistry (e.g. phototrophism in leaves and heterotrophism in stems and roots) and accurate growth patterns. Relaxing model constraints for metabolite flow between organs revealed optimal patterns of resource partitioning and utilisation for improved growth, including leaf-based nitrate assimilation, increased amino acid transport in the phloem, threonine catabolism as a carbon-efficient route for acetyl-CoA production, and branch-chain amino acids as a respiratory substrate. Additionally, simulations of reproductive growth with altered biomass partitioning patterns between organs identified reduced stem growth as being highly beneficial for increasing fruit yield. As individual biochemical reactions are represented in the model, specific molecular targets for improving plant growth and crop yield were deduced from model predictions.</p> <p>Overall, the results presented in this work indicate that multiscale whole-plant models are useful tools for generating insight into plant biology. Future explorations using these models should be pursued.</p>
first_indexed 2024-03-06T18:24:06Z
format Thesis
id oxford-uuid:07561e1e-50c5-40d4-af94-f5a0d6fba6fe
institution University of Oxford
language English
last_indexed 2024-12-09T03:27:36Z
publishDate 2020
record_format dspace
spelling oxford-uuid:07561e1e-50c5-40d4-af94-f5a0d6fba6fe2024-12-01T10:31:39ZIntegrated modelling of whole-plant metabolism and growthThesishttp://purl.org/coar/resource_type/c_db06uuid:07561e1e-50c5-40d4-af94-f5a0d6fba6fePlant PhysiologyMetabolismPlant BiochemistryMetabolic ModellingSystems BiologyCrop EngineeringEnglishHyrax Deposit2020Konuntakiet, T<p>Source-sink interactions describe the relationship between different plant organs and the division of labour in relation to source activity (resource uptake and assimilation) and sink activity (resource utilisation). Recently, multiscale growth models have been proposed as a tool to investigate unresolved aspects of whole-plant level processes, including source-sink interactions. In particular, constraint-based modelling using stoichiometric biochemical models has been shown to generate accurate predictions of metabolic fluxes and fine-grained, quantitative descriptions of plant biochemistry. The aim of this work was to develop a computational framework that captures the interactions between different organs during plant growth and the metabolic activity of each organ.</p> <p>Two main modelling approaches are presented in this work. The first approach consists of stoichiometric metabolic models integrated into a previously established multiscale Arabidopsis growth model. However, exploration of the resulting model revealed that the model's structure was unable to account for the effects of non-carbon resources on growth, which led to poor predictions of growth rates.</p> <p>The second modelling approach was developed to overcome this issue. I generated a whole-plant stoichiometric network of tomato metabolism by connecting organ-specific models via a common metabolite pool. Vegetative growth simulations produced predictions for metabolic fluxes that were in good agreement with known biochemistry (e.g. phototrophism in leaves and heterotrophism in stems and roots) and accurate growth patterns. Relaxing model constraints for metabolite flow between organs revealed optimal patterns of resource partitioning and utilisation for improved growth, including leaf-based nitrate assimilation, increased amino acid transport in the phloem, threonine catabolism as a carbon-efficient route for acetyl-CoA production, and branch-chain amino acids as a respiratory substrate. Additionally, simulations of reproductive growth with altered biomass partitioning patterns between organs identified reduced stem growth as being highly beneficial for increasing fruit yield. As individual biochemical reactions are represented in the model, specific molecular targets for improving plant growth and crop yield were deduced from model predictions.</p> <p>Overall, the results presented in this work indicate that multiscale whole-plant models are useful tools for generating insight into plant biology. Future explorations using these models should be pursued.</p>
spellingShingle Plant Physiology
Metabolism
Plant Biochemistry
Metabolic Modelling
Systems Biology
Crop Engineering
Konuntakiet, T
Integrated modelling of whole-plant metabolism and growth
title Integrated modelling of whole-plant metabolism and growth
title_full Integrated modelling of whole-plant metabolism and growth
title_fullStr Integrated modelling of whole-plant metabolism and growth
title_full_unstemmed Integrated modelling of whole-plant metabolism and growth
title_short Integrated modelling of whole-plant metabolism and growth
title_sort integrated modelling of whole plant metabolism and growth
topic Plant Physiology
Metabolism
Plant Biochemistry
Metabolic Modelling
Systems Biology
Crop Engineering
work_keys_str_mv AT konuntakiett integratedmodellingofwholeplantmetabolismandgrowth