| Literature DB >> 33492365 |
Abstract
The plant leaf is the main site of photosynthesis. This process converts light energy and inorganic nutrients into chemical energy and organic building blocks for the biosynthesis and maintenance of cellular components and to support the growth of the rest of the plant. The leaf is also the site of gas-water exchange and due to its large surface, it is particularly vulnerable to pathogen attacks. Therefore, the leaf's performance and metabolic modes are inherently determined by its interaction with the environment. Mathematical models of plant metabolism have been successfully applied to study various aspects of photosynthesis, carbon and nitrogen assimilation and metabolism, aided suggesting metabolic intervention strategies for optimized leaf performance, and gave us insights into evolutionary drivers of plant metabolism in various environments. With the increasing pressure to improve agricultural performance in current and future climates, these models have become important tools to improve our understanding of plant-environment interactions and to propel plant breeders efforts. This overview article reviews applications of large-scale metabolic models of leaf metabolism to study plant-environment interactions by means of flux-balance analysis. The presented studies are organized in two ways - by the way the environment interactions are modelled - via external constraints or data-integration and by the studied environmental interactions - abiotic or biotic.Entities:
Keywords: flux-balance analysis; leaf metabolism; plant-environment interactions
Mesh:
Substances:
Year: 2021 PMID: 33492365 PMCID: PMC7925006 DOI: 10.1042/BST20200059
Source DB: PubMed Journal: Biochem Soc Trans ISSN: 0300-5127 Impact factor: 5.407
Figure 1.Schematic representation of flux-balance modelling.
The top part illustrates the metabolic system under consideration. (Left) External constraints, such as exchange and uptake rates and biochemical properties constrain the allowed metabolic fluxes. (Middle) The metabolic network coverts input compounds and generates a metabolic output via a series of biochemical reactions. (Right) This metabolic output can be measured as e.g. growth rate, biomass composition or flux patterns. The bottom part illustrates the mathematical representation of the metabolic system under consideration. (Left) External constraints as well as experimental data can serve to constrain the lower and upper flux bounds (vmin ≥ v ≥ vmax). (Middle) The metabolic network and fluxes are represented as a stoichiometric matrix, S and the metabolic flux vector, v, respectively. The (usually) linear optimization problem optimizes the biological objective, e.g. growth or phloem output, in a metabolic steady-state (S × v = 0). (Right) Result of this optimization is a set of flux distributions captured in v. These optimal solutions can then be subjected to further analysis.
Figure 2.Representation of environment-coupled models of leaf metabolism.
(Left) Abiotic as well as biotic interactions between a plant leaf and the environment have been modelled using flux-balance analysis. (Middle) These interactions can occur at various sites of the leaf, e.g. light uptake through photosynthesis in the chloroplasts or gas-exchange through the stomata (marked A to H and listed on the right). (Right) Studies investigating abiotic constraints can be further classified based on environment-specific exchange constraints, such as light intensity or nutrient availability, data-integrative approaches, such as temporal response or accession specific outputs, or combinations of both. Data-integrative approaches have also been used to model biotic interactions.
Environment-coupled flux-balance models of leaf metabolism
| Author and year | Species | Biological question | Modelling approach |
|---|---|---|---|
| Poolman et al. [ | Rice, | Response to different light intensities | Different light constraints |
| Simons et al. [ | Maize, | Response to different nitrogen levels and sources | Condition-specific biomass compositions |
| Shaw and Cheung [ | Resource partitioning in whole-plant model | Dynamic FBA and different nutrient availability | |
| Lakshmanan et al. [ | Rice, Tomato, Generic CAM model | Response to different CO2 levels | Constraints on rubisco's |
| Mallmann et al. [ | Response to different CO2 levels | Flux-balance model coupled to a kinetic model of photosynthesis | |
| Blätke and Brautigam [ | Generic C4 model | Evolutionary drivers of C4 photosynthesis | CCM-dependent rubisco population, cell type-specific light availability |
| Töpfer et al. [ | Generic C3 — CAM model | Water-saving flux modes in a C3 leaf | 24 hour diel resolution, flux-balance model coupled to a biophysical model of gas–water exchange |
| Töpfer et al. [ | Response to changes in light and temperature | Transcript and metabolomics data integration | |
| Lakshmanan et al. [ | Rice | Response to changes in light | Transcriptomics data integration |
| Liu et al. [ | Response to low and elevated CO2 | Transcriptomics data integration | |
| Bogart and Myers [ | Maize | Source to sink transition along the leaf | Transcriptomics data integration, non-linear constraints |
| Nägele and Weckwert [ | Metabolite compartmentation in different accessions exposed to low temperature | Metabolomics data integration | |
| Sajitz-Hermstein et al. [ | High to low CO2 acclimation in wild type and photorespiratory mutants | Metabolomics data integration | |
| Botero et al. [ | Potato | Effect of pathogen attack on photosynthetic activity | Transcriptomics data integration |
| Rodenburg et al. [ | Tomato | Nutrient exchange between host leaf and pathogen | Transcriptomics data integration |
Overview of studies which analyze plant–environment interactions by coupling mathematical models of leaf metabolism to the environment. The presented approaches are organized by abiotic and biotic interactions and by the applied modelling approach — environmental constraint-driven and data-integrative.