Model approaches to advance crassulacean acid metabolism system integration

Abstract

Summary This review summarises recent progress in understanding crassulacean acid metabolism (CAM) systems and the integration of internal and external stimuli to maximise water‐use efficiency. Complex CAM traits have been reduced to their minimum and captured as computational models, which can now be refined using recently available data from transgenic manipulations and large‐scale omics studies. We identify three key areas in which an appropriate choice of modelling tool could help capture relevant comparative molecular data to address the evolutionary drivers and plasticity of CAM. One focus is to identify the environmental and internal signals that drive inverse stomatal opening at night. Secondly, it is important to identify the regulatory processes required to orchestrate the diel pattern of carbon fluxes within mesophyll layers. Finally, the limitations imposed by contrasting succulent systems and associated hydraulic conductance components should be compared in the context of water‐use and evolutionary strategies. While network analysis of transcriptomic data can provide insights via co‐expression modules and hubs, alternative forms of computational modelling should be used iteratively to define the physiological significance of key components and informing targeted functional gene manipulation studies. We conclude that the resultant improvements of bottom‐up, mechanistic modelling systems can enhance progress towards capturing the physiological controls for phylogenetically diverse CAM systems in the face of the recent surge of information in this omics era.

Integrated analysis of DNA methylome and transcriptome reveals epigenetic regulation of CAM photosynthesis in pineapple

“…The benefits of this system are that CAM plants reduce water loss by closing stomata during the day and also have increased photosynthetic efficiency. The mechanism and evolution of CAM have been extensively investigated [6][7][8][9][10]. For instance, many genes putatively involved in the carbon fixation module of CAM in pineapple have been identified [6], and many of them are differentially regulated in different leaf tissues [11].…”

Integrated Analysis of DNA Methylome and Transcriptome Reveals Epigenetic Regulation of CAM Photosynthesis in Pineapple

“…We rst focused on differentially expressed genes across different diel time courses between green tip and white base. Approximately 12,191 DEGs were identi ed across different time stages, and the most differentially expressed genes were identi ed at 4am (8,623) and the least were at 10am (6,916) (Fig. 5a).…”

“…the day and also have increased photosynthetic e ciency. The mechanism and evolution of CAM have been extensively investigated [6][7][8][9][10]. For instance, many genes putatively involved in the carbon xation module of CAM in pineapple have been identi ed [6], and many of them are differentially regulated in different leaf tissues [11].…”

How to resolve the enigma of diurnal malate remobilisation from the vacuole in plants with crassulacean acid metabolism?

“…Driven by its growing eco‐agricultural importance, the field of CAM research is now advancing quickly and important technical breakthroughs in the past decade have allowed an unprecedented exploration of CAM genomes, transcriptomes, proteomes and metabolomes (Ming et al ., 2015; Yang et al ., 2017; Ceusters et al ., 2019; Abraham et al ., 2020). In combination with rapidly progressing computational modelling approaches (Shameer et al ., 2018; Chomthong & Griffiths, 2020) various new tools and genetic resources are now available to shed more light on diurnal malate metabolism in CAM plants. In this research review three important key questions are addressed: Q1: Does light‐dependent assimilation of CO 2 via RuBisCo dictate the rate of malate mobilisation?…”