Search Results (5)

Deubiquitination plays a pivotal role in regulating plant responses to abiotic stress, growth, and development. Among the deubiquitinase (DUB) families, ubiquitin-specific proteases (UBPs) constitute the largest group. Despite this, limited research has been conducted on the functional characteristics of the UBP gene family in soybean (Glycine max). In this study, we identified 52 UBP gene family members in soybean, all of which harbored UCH (ubiquitin C-terminal hydrolase) domains with short yet evolutionarily conserved Cys-box and His-box. These genes were phylogenetically classified into 14 distinct groups; GmUBP genes within the same group shared analogous patterns of conserved domains and motifs. Moreover, a synteny analysis reveals that the GmUBP family has undergone extensive gene duplication events and shares a close evolutionary relationship with Arabidopsis thaliana. We conducted a focused analysis on GmUBP7, which is a gene exhibiting high expression levels in soybean seeds. Intriguingly, this gene exhibited several haplotypes in natural soybean varieties, with significant differences being observed in relation to seed traits, such as 100-seed weight, total fatty acid content, and protein content among different haplotypes. Collectively, the findings from this study provide a foundation for the functional characterization of GmUBP genes, offering new insights into the regulatory network underlying seed development in soybean. Full article

The Alternaria alternata tangerine pathotype causes Alternaria brown spot, a devastating disease of susceptible tangerine varieties and their hybrids. Alternaria citri toxin (ACT) is the primary virulence factor, but the regulatory mechanisms governing ACT synthesis remain unclear. Deubiquitinating enzymes maintain ubiquitination homeostasis and regulate fungal pathogenicity, yet their role in A. alternata remains unexplored. We characterized 13 ubiquitin-specific protease (UBP) family members in A. alternata tangerine pathotype. Six UBP genes (Aaubp2, Aaubp3, Aaubp4, Aaubp6, Aaubp14, and Aaubp15) regulated mycelial growth. Aaubp14 deletion abolished sporulation, while mutations of Aaubp3, Aaubp4, Aaubp6, Aaubp8, and Aaubp15 altered conidial morphology. qRT-PCR demonstrated distinct host-induced expression patterns among Aaubp genes. Pathogenicity tests showed that ΔAaubp6, ΔAaubp14, and ΔAaubp15 mutants failed to produce lesions on Citrus reticulata cv. Hongjv leaves. Moreover, Aaubp14 deletion significantly suppressed ACT biosynthesis gene expression and blocked ACT production. Comparative proteomics showed Aaubp14 regulates ACT biosynthesis by modulating protein ubiquitination in metabolic pathways and controls pathogenicity via a complex network. Our findings elucidate Aaubp gene function in development and pathogenicity, particularly the Aaubp14-mediated regulation mechanism, providing insights into ubiquitination-mediated pathogenicity in phytopathogenic fungi. Full article

The ubiquitin-specific protease (UBP) family constitutes the largest group within the deubiquitinating enzymes (DUBs) and plays a crucial role in regulating the cell cycle, growth, and developmental processes in living organisms. By utilizing genomic and transcriptomic databases, we employed bioinformatics tools to identify UBP family members within pepper genomes and to analyze the expression profiles of CaUBP genes under various abiotic stresses, as well as in different tissues and organs. Our findings revealed the presence of 40 CaUBPs in peppers, exhibiting significant variation in their physicochemical properties. Subcellular localization studies indicated that all CaUBPs are localized in the nucleus. Phylogenetic analysis categorized the 40 CaUBPs into 11 distinct subfamilies (G1–G11), with the largest subfamily comprising seven members. Members within the same subfamily displayed similar domain and motif structures. The promoter regions of CaUBP genes were found to be enriched with elements responsive to light, stress, and hormones. Syntenic analysis revealed that 12 CaUBPs were mapped to the Arabidopsis thaliana genome, suggesting potential functional conservation. Additionally, tandem duplications were observed in the alignment of two sets of genes within the pepper genome. CaUBPs were implicated in the stress response and organ growth, with CaUBP17/34/35 showing significant changes in expression under heat stress. While most genes were not expressed in leaves, the expression of several genes (CaUBP3/17/27/32/35/38) in flowers was significantly altered. This study establishes a foundation for further exploration of the roles of CaUBPs in pepper growth, development, and stress response mechanisms. Full article

The ubiquitin-specific protease (UBP) family represents a type of deubiquitinase (DUB) that plays a significant role in plant abiotic stress responses, growth, and development. Although UBP genes have been characterized in many species, a genome-wide systematic analysis and the potential functions under abiotic stresses have not yet been reported in rice (Oryza sativa L.). In this study, we identified 21 UBP gene family members in the genome of rice, all of which had UCH domains containing short but highly conserved Cys-box and His-box. The DUF4220 and DUF594 domains, which are found in monocotyledonous plants, were unique. Phylogenetic analysis suggested that OsUBP7 and OsUBP12 genes had the closest genetic relationships with AtUBP12 and AtUBP13, implying that OsUBP7 and OsUBP12 might have similar biological functions to AtUBP12 and AtUBP13. Synteny analysis revealed that OsUBP genes were expanded through segmental duplication under purifying selection. Meanwhile, they had closer evolutionary relationships with monocotyledonous plants. Additionally, all OsUBP genes had an ABRE cis-element, which was related to abscisic acid (ABA) stress hormone response. Protein interaction analysis suggested that OsUBP22 might modulate gene regulation through OsGCN5- and OsADA2-mediated chromatin modification, and OsUBP10 might regulate salt stress through modulating OsDNA2_4 stability. Specifically, the expression profiles and the transcriptional levels of 11 representative OsUBPs suggested the potential important functions of OsUBP9 and OsUBP17 under drought and cold stresses. Taken together, our study provided a systematic analysis of OsUBPs and preliminarily explored their potential roles under abiotic stresses. Our results lay a foundation for further research on the functions of the OsUBP gene family under abiotic stresses. Full article

The largest group of deubiquitinases—ubiquitin-specific proteases (UBPs)—perform extensive and significant roles in plants, including the regulation of development and stress responses. A comprehensive analysis of UBP genes has been performed in Arabidopsis thaliana, but no systematic study has been conducted in moso bamboo (Phyllostachys edulis). In this study, the genome-wide identification, classification, gene, protein, promoter region characterization, divergence time, and expression pattern analyses of the UBPs in moso bamboo were conducted. In total, 48 putative UBP genes were identified in moso bamboo, which were divided into 14 distinct subfamilies in accordance with a comparative phylogenetic analysis using 132 full-length protein sequences, including 48, 27, 25, and 32 sequences from moso bamboo, A. thaliana, rice (Oryza sativa), and purple false brome (Brachypodium distachyon), respectively. Analyses of the evolutionary patterns and divergence levels revealed that the PeUBP genes experienced a duplication event approximately 15 million years ago and that the divergence between PeUBP and OsUBP occurred approximately 27 million years ago. Additionally, several PeUBP members were significantly upregulated under abscisic acid, methyl jasmonate, and salicylic acid treatments, indicating their potential roles in abiotic stress responses in plants. Full article