Genome-wide identification of the UBC protein family in grapevine and preliminary functional characterization during berry ripening.

Ubiquitin-conjugating enzymes (UBCs) serve as core components of the ubiquitin-proteasome pathway and extensively participate in plant development and stress responses. However, the regulatory mechanism of grape (Vitis vinifera L.) UBC family genes underlying berry ripening remains unclear. Genome‑wide screening identified 44 VviUBC members within the grape UBC gene family. Systematic characterization of physicochemical features, conserved motifs, gene structures, chromosomal locations, cis‑regulatory elements and evolutionary expansion uncovered whole‑genome duplication as the major driving force for VviUBC family expansion. The abundant light-, hormone- and stress-responsive cis-elements in promoters further suggest the involvement of UBC family genes in light signaling, hormonal modulation and stress adaptation. Transcriptome profiling of berries from 'Kyoho' and its early-ripening bud mutant 'Fengzao' throughout fruit development was performed to screen differentially expressed VviUBC members. Further expression profiling pinpointed VviUBC25 as the hub gene closely linked to early ripening, which exhibited specific significant upregulation at E-L34 (the onset of berry‑softening) only in 'Fengzao'. Genes encoding proteins that potentially interact with VviUBC25 were screened via WGCNA and intra-module correlation analysis, among which VviMYB APL was identified. Subcellular localization assays verified that VviUBC25 is localized to the nucleus. Yeast two-hybrid and luciferase complementation imaging assays further confirmed the direct physical interaction between VviUBC25 and VviMYB APL. Transient overexpression in grape berries further showed that VviUBC25 overexpression was associated with reduced VviMYB APL transcript levels. This study systematically describes the grape UBC family and identifies a putative regulatory link whereby VviUBC25 may modulate grape berry ripening via the ubiquitination of VviMYB APL.