Charakana, C.; Gupta, S. K.; Sunkum, A.; Valluri, S.; Bagri, J.; Tyagi, K.; Kumar, R.; Salava, H.; Kilambi, H. V.; Sivapuram, V.; Sharma, R.; Sreelakshmi, Y.

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.