Genome-Wide Identification and Expression Analysis of the U-Box E3 Ubiquitin Ligase Gene Family Related to Monoterpene Indole Alkaloids Biosynthesis in Uncaria rhynchophylla

Plant U-box E3 ubiquitin ligases (PUBs) are involved in various biological processes in response to abiotic stress. Recent studies have shown that E3 ubiquitin ligases can regulate the production of important compounds in medicinal plants by targeted degradation of transcription factors. Abscisic acid (ABA), a plant stress response hormone, can cause changes in the content of the medically important monoterpene indole alkaloids (MIAs) in U. rhynchophylla. In this study, we explored the relationship between UrPUB gene expression and MIA content. ABA was applied to tissue-cultured seedlings of U. rhynchophylla, resulting in consistent changes in the content of four MIAs. Seventy-three UrPUB genes were identified and bioinformatically characterized from the genome sequence of U. rhynchophylla. The expression levels of transcription factors involved in regulating the biosynthesis pathway of MIAs and UrPUB genes with higher RNA transcript levels in the roots were determined. Co-expression association analysis revealed that UrPUB17, UrPUB40, UrPUB41, UrPUB44 and UrPUB55 negatively correlate with UrGATA8 and UrWRKY37 under ABA stimulation. Based solely on these correlation data, we hypothesize that these UrPUBs might regulate MIA biosynthesis via ubiquitination of UrGATA8 and UrWRKY37, but direct evidence (protein interaction, ubiquitination, degradation, or genetic manipulation) is lacking. This study identified the UrPUB gene family in the U. rhynchophylla genome and proposes this ubiquitination model as a testable hypothesis, not a demonstrated mechanism. These findings provide new insights into the biological function of the PUB family in response to ABA.