Biology subjects

Cheung, C. Y. M.

Publications and source records attributed to Cheung, C. Y. M..

5 recordsLinked to original sources

bioRxiv2022

An Investigation of the Effects of Nitrate vs. Ammonium on Plants Using Metabolic Modeling

As metabolism is a very complex process, it is essential to use computational modeling to better understand the changes in metabolism at a systems level. In this paper, we used a computational model that simulates the metabolism of mature plants to test how the use of nitrate and ammonium as nitrogen sources affects plant metabolism. Our model predicted and showed the possible changes in metabolism in different plant tissues in response to the use of different nitrogen sources. Our methodology produces predictions of metabolic fluxes in plants and improves our understanding of how plants react to changes in conditions. This research can potentially give insights into how we can improve crop yield by identifying metabolic processes that are important in plant growth and in the adaptation to different nitrogen sources. In future research work, we can apply the existing model to explore the effects of different nutrient availability under different conditions (e.g. well-watered vs drought) to optimize nutrient availability under particular environmental conditions. Experimental researchers, plant breeders, and farmers can use the knowledge gained from the modeling work to further our understanding of plant metabolism and apply the knowledge to improve plant growth in the lab and the field.

plant biology↗

bioRxiv2021

Spatial resolution of an integrated C4+CAM photosynthetic metabolism

C4 and CAM photosynthesis have repeatedly evolved in plants over the past 30 million years. Because both repurpose the same set of enzymes but differ in their spatial and temporal deployment, they have long been considered as distinct and incompatible adaptations. Remarkably, Portulaca contains multiple C4 species that perform CAM when droughted. Spatially explicit analyses of gene expression reveal that C4 and CAM systems are completely integrated in P. oleracea, with CAM and C4 carbon fixation occurring in the same cells and CAM-generated metabolites likely incorporated directly into the C4 cycle. Flux balance analysis corroborates the gene expression and predicts an integrated C4+CAM system under drought. This first spatially explicit description of a C4+CAM photosynthetic metabolism presents a new blueprint for crop improvement.

plant biology↗

bioRxiv2020

Constraint-based modelling revealed changes in metabolic flux modes associated with the Kok effect

Constraint-based modelling was applied to provide a mechanistic understanding of the possible metabolic origins of the Kok effect - the change in quantum yield of net photosynthesis at low light intensity. The well-known change in quantum yield near the light-compensation point (LCP) was predicted as an emergent behaviour from a purely stoichiometric model. From our modelling results, we discovered another subtle change in quantum yield at a light intensity lower than the LCP. Our model predicted a series of changes in metabolic flux modes in central carbon metabolism associated with the changes in quantum yields. We demonstrated that the Kok effect can be explained by changes in metabolic flux modes between catabolism and photorespiration. Changes in RuBisCO carboxylation to oxygenation ratio resulted in a change in quantum yield at light intensities above the LCP, but not below the LCP, indicating the role of photorespiration in producing the Kok effect. Cellular energy demand was predicted to have no impact on the quantum yield. Our model showed that the Kok method vastly overestimates day respiration - the CO2 released by non-photorespiratory processes in illuminated leaves. The theoretical maximum quantum yield at low light intensity was higher than typical measured values, suggesting that leaf metabolism at low light may not be regulated to optimise for energetic efficiency. Our model predictions gave insights into the set of energetically optimal changes in flux modes in low light as light intensity increases from darkness. One sentence summaryThe Kok effect can be explained by the changes in flux modes between catabolism and photorespiration.

plant biology↗

bioRxiv2020

A multi-phase flux balance model reveals flexibility of guard cell central carbon metabolism

Experimental research in guard cell metabolism has revealed the roles of the accumulation of various metabolites in guard cell function, but a comprehensive understanding of their metabolism over the diel cycle is still incomplete, given the limitations of current experimental methods. In this study, we constructed a four-phase flux balance model of guard cell metabolism to investigate the changes in guard cell metabolism over the diel cycle, including the day and night and stomata opening and closing. Our model demonstrated the metabolic flexibility in guard cells, showing that multiple metabolic processes can contribute to the synthesis and metabolism of malate and sucrose as osmolytes during stomatal opening and closing. We showed that guard cells can adapt to varying light availability and sucrose uptake from the apoplast during the day by operating in a mixotrophic mode with a switch between sucrose synthesis via the Calvin-Benson cycle and sucrose degradation via the oxidative pentose phosphate pathway. During stomatal opening, our model predicted an alternative flux mode of the Calvin-Benson cycle with all dephosphorylating steps diverted to diphosphate--fructose-6-phosphate 1-phosphotransferase to produce PPi, which is used to pump protons across the tonoplast for the accumulation of osmolytes. An analysis of the energetics of the use of different osmolytes in guard cells showed that malate and Cl- are similarly efficient as the counterion of K+ during stomatal opening. Significance statementThis work presents the first four-phase metabolic model for predicting guard cell metabolism over the diel cycle, which predicted an alternative flux model of the Calvin-Benson cycle that maximises the production of PPi during stomatal opening. While multiple metabolic processes were shown be important in synthesising and metabolising osmolytes in guard cells of different experimental systems, our model demonstrated that these processes can operate simultaneously and at different rates depending on conditions.

plant biology↗

bioRxiv2019

Metabolic modelling of CAM cycling, CAM idling and the C3-CAM continuum

The evolution of Crassulacean acid metabolism (CAM) is thought to be along a C3-CAM continuum including multiple variations of CAM such as CAM cycling and CAM idling. Here, we applied large-scale constraint-based modelling to investigate the metabolism and energetics of plants operating in C3, CAM, CAM cycling and CAM idling. Our modelling results suggested that CAM cycling and CAM idling could be potential evolutionary intermediates in CAM evolution by establishing a starch/sugar-malate cycle. Our model analysis showed that by varying CO2 exchange during the light period, as a proxy of stomatal conductance, there exists a C3-CAM continuum with gradual metabolic changes, supporting the notion that evolution of CAM from C3 could occur solely through incremental changes in metabolic fluxes. Along the C3-CAM continuum, our model predicted changes in metabolic fluxes not only through the starch/sugar-malate cycle that is involved in CAM photosynthetic CO2 fixation but also other metabolic processes including the mitochondrial electron transport chain and the tricarboxylate acid cycle at night. These predictions could guide engineering efforts in introducing CAM into C3 crops for improved water use efficiency.

biochemistry↗