A transcriptomics-based kinetic model for enzyme-induced pectin degradation in apple (Malus × domestica) fruit

Modifications of cell wall pectin during apple softening involve the concerted action of several enzymes. A mathematical model was developed to describe the action of cell wall hydrolases resulting in specific modifications in cell wall pectin polysaccharides during softening of 'Jonagold' apple. A conceptual model of enzyme-induced pectin breakdown was formulated based on current knowledge. Activities of different cell wall enzymes were considered to be directly correlated to the expression levels of the respective genes. The first pectin modification to occur was assumed to be cleavage of side chain neutral sugars from the polymer backbone, by the action of side chain debranching enzymes, beta-galactosidase and alpha-l-arabinofuranosidase. It was considered that this increases cell wall porosity, facilitating the action of pectin methyl esterase, which de-methylates pectin polysaccharides, providing a substrate for polygalacturonase. Polygalacturonase degrades the de-methylated pectin chain, producing smaller pectin fragments which are easily solubilised in water. Coupled differential equations were written based on these reactions. The model was calibrated using data on expression of cell wall-related genes, activities of enzymes encoded by these genes, and the associated modifications in pectin polysaccharides during softening in 'Jonagold' apples stored at 1 °C under regular atmosphere or controlled atmosphere. The model could explain 79% of the variation in the data. Using the model, in silico investigations on the impact of downregulation of different key cell wall-related genes on softening were carried out, and the results were compared successfully with currently available literature data.