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

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.

doi:10.1101/2025.04.17.649262

bioRxiv · 10.1101/2025.04.17.649262

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

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.

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Abstract

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.

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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.. 2025-04-22. Loss-of-Function RUP-Variants Influence Ubiquitin-Proteasome System and Enhance Carotenoid and Folate Levels in Tomato. https://doi.org/10.1101/2025.04.17.649262

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