Loss-of-Function RUP-Variants Influence Ubiquitin-Proteasome System and Enhance Carotenoid and Folate Levels in Tomato

REPRESSOR OF UV-B PHOTOMORPHOGENESIS (RUP) negatively regulates UV- B signalling, yet its broader physiological roles in crop plants remain largely unexplored. We compared two tomato accessions bearing truncated RUP proteins— rup-1 and rup-2 ( rup- variants)—with the cultivar Arka Vikas (AV), which harbours the native RUP protein. Seedlings of rup -variants exhibited enhanced tolerance to supplemental UV-B light. Red ripe (RR) fruits of rup -variants showed significantly elevated carotenoid and folate levels compared to AV. Introgression of rup -variants into AV confirmed that the increased carotenoid accumulation is genetically linked to RUP truncation. Metabolomic profiling of rup -variants revealed a substantial shift in primary metabolic homeostasis, particularly at the breaker stage, marked by a pronounced reduction in sugars and amino acids. Proteomic analyses of rup - variants across ripening stages identified that a significant proportion of differentially expressed proteins belonged to chaperones and ubiquitin-proteasome system (UPS). Upregulation of four key enzymes in the carotenoid biosynthesis pathway likely contributed to increased lycopene content in rup -variants. Elevated folate levels in rup -variants were associated with the upregulation of folate biosynthesis and C1 metabolism enzymes. Despite widespread metabolic reprogramming in rup -variants, hormonal regulatory pathways remained largely unaltered. Our results suggest that RUP modulates metabolic pathways during fruit ripening, and its loss triggers metabolic reprogramming associated with elevated folate/carotenoid levels.