Carotenoids and apocarotenoids are widespread specialized metabolites, yet animals, including sponges, lack the ability to synthesize carotenoids de novo and must obtain them from dietary or microbial sources. The roles of carotenoid cleavage dioxygenases (CCDs) in marine animals remain largely unexplored. A CCD from the marine sponge Suberites domuncula (SdCDO) was evaluated for retinoid formation using a synthetic biology approach involving heterologous expression in Escherichia coli and tomato (Solanum lycopersicum), combined with metabolic, ultrastructural, and transcriptomic analyses. Unexpectedly, SdCDO did not produce retinoids. Instead, it cleaved lycopene and β-carotene to generate crocetin dialdehyde, the direct precursor of crocins. In tomato fruits, SdCDO expression triggered crocin accumulation, particularly in locular tissues, while reducing lycopene, lutein, and β-carotene levels. It also promoted the accumulation of upstream carotenoid intermediates, such as phytoene, phytofluene, and ζ-carotene. These metabolic changes resulted in orange fruit pigmentation and enhanced antioxidant capacity, along with altered chromoplast ultrastructure and broad downregulation of endogenous carotenoid biosynthetic genes. Overall, these findings reveal unexpected enzymatic plasticity in a sponge-derived CCD and demonstrate its ability to redirect plant carotenoid metabolism toward crocin biosynthesis. This work highlights the functional diversity of CCDs across kingdoms and their potential for synthetic biology and crop biofortification. © 2026 The Author(s). New Phytologist © 2026 New Phytologist Foundation.

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