Decoding Isoprenoid Transcript–Metabolite Interactions in Carotenoid Tomato Fruit Mutants Uncovers Novel Metabolic Cross-Links

Carotenoids are an important class of natural compounds, essential for human nutrition, acting in plants as pigments and apocarotenoid precursors. Tomato is a key model for carotenoid metabolism, as genetic variation strongly affects carotenoid composition during fruit ripening. To date, most of the enzymes involved in carotenoid pathway were mainly characterized by linking gain- or loss-of-function phenotypes to their genetic basis (e.g., mutation in a single gene), with limited integration into pathway-wide analyses. Here we report an extensive biochemical and molecular characterization of a collection of tomato carotenoid mutants—apricot (at), yellow flesh (r), tangerine (t), Delta (Del) and Beta (B)—throughout three different stages of fruit ripening (mature green, breaker, red ripe). Using correlation-based integrative analyses, we integrated targeted isoprenoid metabolomics (carotenoids, chlorophylls, tocochromanols, quinones, abscisic acid) with gene expression profiling and correlation-based analyses. The pronounced, stage-dependent remodeling of the isoprenoid profiles exceeded the expected changes in substrates/products and was accompanied by significant transcriptional changes, largely independent of the position of the mutated step in the pathway. This integration highlighted metabolite/transcript regulatory links and the central role of lycopene cyclization in isoprenoid metabolism rewiring, thus improving our understanding of mechanisms controlling their accumulation during tomato fruit ripening.