Gene expression driving ethylene biosynthesis and signaling pathways in ripening tomato fruit: a kinetic modelling approach

Ethylene biosynthesis and signaling are pivotal pathways in various plant aging processes, including fruit ripening. Kinetic models can be used to better understand metabolic pathways, but modeling of the ethylene-related pathways is limited and the link between these pathways remains unsolved. A transcriptomics-based kinetic model was developed, consisting of ordinary differential equations describing ethylene biosynthesis and signaling pathways in tomato during fruit development and ripening, both on- and off-vine. This model was calibrated against a large volume of transcriptomic, proteomic, and metabolic data during on-vine fruit development and ripening of tomato fruit grown in winter and summer. The model was validated using data on off-vine ripening of mature green harvested fruit grown in the same seasons. The ethylene biosynthesis pathway under different conditions appeared to be largely driven by gene expression levels. The ethylene regulation of fruit ripening of a heat tolerant tomato grown in different seasons was organised similarly but with quantitative differences at the targeted omics levels. This is reflected by some of the same parameters with distinct values for summer and winter fruit. The current model approach is a first attempt to model the ethylene signaling pathway starting from gene expression, the various protein-protein interactions, including a link with ethylene production, internal ethylene levels, and ethylene binding to its receptors.