Search Results (273)

Epithelial ovarian cancer (EOC) poses a challenge owing to its high rate of recurrence and drug resistance, resulting in a 5-year survival rate of 30% in advanced stages. To elucidate the molecular mechanisms underlying EOC recurrence, we analyzed transcriptome data from patients with EOC and identified elevated USP19, a deubiquitinating enzyme, as being elevated in patients without recurrence in our previous study. Single-cell RNA sequencing analysis revealed that increased USP19 expression in epithelial cells is associated with activation of apoptotic pathways, suggesting that USP19 may inhibit EOC recurrence through deubiquitination of its binding proteins. Using the protein–protein interaction database, we identified DnaJC7 as a binding partner of USP19 and confirmed their interaction experimentally. USP19-mediated deubiquitination of DnaJC7 increases its protein stability. Notably, upregulation of USP19 and DnaJC7 disrupted the interaction between p53 and MDM2, and knockdown of USP19 and DnaJC7 resulted in decreased p53 expression following cisplatin treatment. These findings highlight the therapeutic potential of enhancing the USP19-DnaJC7 axis to stabilize p53 and improve cisplatin efficacy. Promoting USP19-mediated deubiquitination by stabilizing DnaJC7 may offer a novel combination strategy to enhance the efficacy of cisplatin-based cancer therapy. Full article

The ubiquitin–proteasome system (UPS) is a highly conserved protein degradation pathway in eukaryotic cells. Through precisely controlled proteolysis of key regulatory proteins, the UPS plays a particularly critical role in plant sexual reproduction, where precise spatiotemporal regulation is essential. The UPS governs multiple aspects of plant sexual reproduction, including male and female gametophyte development, pollen–pistil interactions, double fertilization, and post-fertilization embryogenesis and endosperm development. Among UPS components, E3 ubiquitin ligases play a central role by mediating the spatiotemporal degradation of key proteins, while E2 conjugating enzymes and deubiquitinating enzymes also make essential contributions. Through cross-species and cross-stage comparisons, we find that the UPS exhibits conserved regulatory logic—including cell-cycle gating, spatial control of protein accumulation, and signal integration—while also having evolved lineage-specific functional diversification. In this review, we systematically synthesize UPS functions across the reproductive cycle and highlight persistent knowledge gaps, aiming to provide an integrated framework and a reference for future studies investigating the regulatory roles of the UPS in plant sexual reproduction. Full article

Ubiquitin-specific protease 7 (USP7/HAUSP) is one of the most studied deubiquitinating enzymes and plays a crucial role in regulating numerous cellular processes, making it a promising therapeutic target. In the nucleus, USP7 partially colocalizes with PML nuclear bodies (PML-NB)—multifunctional membraneless organelles involved in post-translational modifications and protein complexes assembly. The molecular basis and functional significance of this association remain uncharacterized. In this study, comparison of USP7 and PML interactomes revealed a significant overlap of 166 shared proteins. Functional enrichment analysis showed that USP7 and PML may operate within a common molecular context related to transcriptional regulation, chromatin remodeling, and DNA damage responses. Furthermore, these processes are also linked to cellular senescence and human aging (CellAge and GenAge databases). Focused analysis of overlaps between the USP7 interactome and core PML-NB proteins identified 61 proteins forming a dense “small-world” network. Most are prone to liquid–liquid phase separation, are intrinsically disordered, and serve as substrates for SUMOylation or ubiquitination. These findings not only expand our understanding of the molecular functions of USP7 but also highlight PML-NB as an important cellular context for investigating mechanisms associated with USP7 activity. Full article

Bax, a key member of the B-cell lymphoma 2 (Bcl-2) protein family, is essential for inducing mitochondrial apoptosis. In this study, we employed yeast two-hybrid screening to identify ubiquitin-specific protease 49 (USP49) as a binding partner of Bax. Subsequent immunoprecipitation and glutathione S-transferase (GST) pull-down assays confirmed their direct interaction. Functional assays showed that USP49 reduces Bax polyubiquitination at multiple lysine residues within ubiquitin, with the strongest effects observed on K11, K29, K33, and K63 linkages. In contrast, its effect on K48-linked ubiquitination was weak and insufficient to influence Bax protein stability, indicating that USP49 does not regulate Bax abundance through proteasomal degradation. Instead, RT-qPCR analysis revealed that USP49 overexpression significantly increased Bax mRNA levels, and this effect was maintained under apoptosis stimuli (UV, H₂O₂, and STS), indicating transcriptional regulation largely independent of stress-induced damage, whereas its effect was modest and not statistically significant under starurosporine treatment. Collectively, these findings demonstrate that USP49 regulates Bax primarily through K29/K33/K63-linked ubiquitination and transcriptional upregulation, highlighting its role as a stress-responsive modulator of apoptosis and a potential therapeutic target in cancer. Moreover, under DNA damage condition (UV), USP49 overexpression marked enhanced apoptosis. Full article

Ubiquitin-specific protease 13 (USP13) is a deubiquitinating enzyme that stabilizes phosphatase and tensin homolog deleted on chromosome 10 (PTEN), a well-established tumor suppressor involved in PI3K/AKT signaling. This study aimed to evaluate the relationship between USP13 immunohistochemical staining intensity and clinicopathological factors associated with prostate cancer progression. USP13 staining was scored as grade 0 (negative), 1 (weak), 2 (moderate), or 3 (strong) in 242 prostate cancer tissues and 22 adjacent non-neoplastic control tissues. Higher USP13 grades were exhibited by adjacent non-neoplastic tissues than prostate carcinoma. In comparison, lower USP13 grades were observed in 88.6% of the neoplastic regions (p < 0.001). No differences in PSA level, Gleason’s score, disease stage, involvement of either the seminal vesicle or lymph nodes, surgical margin positivity, biochemical or clinical recurrence rates, or overall survival statistics were found. Cox proportional hazards modeling showed no significant association between USP13 expression and biochemical recurrence-free survival or overall survival. Kaplan–Meier analysis demonstrated no statistically significant differences in survival outcomes according to USP13 expression, although a descriptive trend was observed. USP13 immunohistochemical staining distinguished malignant prostate tissue from adjacent non-neoplastic tissue in tissue microarrays. However, USP13 expression was not independently associated with pathological aggressiveness or survival outcomes in this cohort. Full article

Deubiquitinases, or DUBs, have emerged as pivotal regulators of cellular homeostasis, coordinating the delicate balance between protein ubiquitination and deubiquitination. Their versatile roles span from controlling protein turnover to modulating signal transduction pathways, thereby influencing diverse cellular processes, including DNA damage repair, apoptosis, and immune responses. This review comprehensively explores the current understanding of DUBs, elucidating their structural diversity, catalytic mechanisms, physiological functions, and implications in human diseases. Moreover, we discuss the therapeutic potential of targeting DUBs in various pathological conditions, highlighting recent advancements and challenges in developing DUB-specific inhibitors. Full article

Ubiquitination is a reversible post-translational modification crucial for cellular homeostasis and protein degradation. It is orchestrated by a cascade of ubiquitin-activating enzymes (E1), conjugating enzymes (E2), and ligases (E3) that tag proteins with ubiquitin, and deubiquitinating enzymes (DUBs) that remove these tags. Through this tightly regulated ubiquitination/deubiquitination system, cells control protein turnover, localization, and activity, thereby governing processes ranging from cell cycle progression and DNA repair to immune and stress responses. Here, we review the structural and functional mechanisms of each class of enzymes in the ubiquitin–proteasome system, including E1, E2, E3, and DUBs, and highlight their roles in key signaling pathways and physiological processes. We further discuss how the dysregulation of these enzymes leads to diseases such as cancer, neurodegenerative disorders, and immune diseases, underlining the potential of targeting ubiquitination pathways for therapeutic intervention. Full article

Ubiquitin-specific peptidase 10 (USP10) deubiquitinates multiple signaling proteins in cancer cells. These USP10 substrates contain both tumor suppressors and oncogenic proteins, thus conferring both inhibitory and promoting effects of USP10 on tumorigenesis and progression. This review focuses on the dual roles of USP10 in various cancer types and addresses the association of aberrant USP10 expression with the development of various types of cancers, including hepatocellular carcinoma, lung cancer, breast cancer, prostate cancer, gastric cancer, and acute and chronic myelogenous leukemia. In addition, this review discusses the potential applications of USP10 inhibitors as targeted drugs for cancer therapy. Full article

Deubiquitinating enzymes (DUBs) play essential roles in diverse plant biological processes, yet the ovarian tumor proteases (OTUs), a major DUB subfamily, have not been systematically characterized in wheat, and their functions in grain development remain unclear. Here, we identified 49 OTU genes (TaOTUs) in the hexaploid wheat genome and classified them into four subfamilies based on phylogenetic relationships, with nomenclature assigned according to homology. TaOTU6-7B was highly expressed during early and mid-grain development and was responsive to gibberellin and jasmonic acid. Its expression differed significantly between large-grain wheat Pindong34 (PD34) and small-grain wheat MY11847 at 7 and 11 days after flowering. To elucidate its function, we used CRISPR/Cas9 to generate loss-of-function mutants by knocking out the three homoeologs (TaOTU6-7A, -7B, and -7D). These mutants exhibited significantly increased grain width and weight relative to wild type. Moreover, TaOTU6-7B directly interacted with TaUBC13, whose expression was markedly elevated in the TaOTU6 knockout background, suggesting that TaUBC13 may positively regulate wheat grain size. Collectively, this study establishes the TaOTU gene family in wheat, reveals TaOTU6 as a negative regulator of grain width and weight, and provides valuable genetic resources and a theoretical foundation for high-yield wheat breeding. Full article

Ubiquitin-specific proteases (USPs) constitute the largest and most diverse family of deubiquitinating enzymes (DUBs), playing a pivotal role in maintaining protein homeostasis through reversible post-translational modifications (PTMs). Renal fibrosis represents the final common pathway of various chronic kidney diseases (CKDs), ultimately leading to irreversible nephron loss and end-stage renal disease (ESRD). With CKD affecting over 10% of the global adult population, fibrosis imposes a substantial clinical and economic burden. Despite this, effective antifibrotic therapies remain clinically elusive. Emerging evidence highlights the critical involvement of USPs in the pathogenesis of renal fibrosis through the potentiation of pro-fibrotic signaling pathways, inflammation, oxidative stress, cell cycle arrest and cellular senescence, as well as some other pathways. This review comprehensively summarizes the current understanding of USPs in renal fibrosis, detailing their structural characteristics, molecular mechanisms, and specific regulatory roles. Furthermore, we discuss recent advances in developing small-molecule USP inhibitors, providing novel insights into targeting the ubiquitin–proteasome system as a promising therapeutic strategy for combating renal fibrosis. Full article

The SARS-CoV-2 papain-like protease (PL^pro) is an essential viral enzyme that promotes viral polyprotein processing while simultaneously suppressing the host innate immune response, which makes it a primary target for developing antiviral drugs. The present study employs a comprehensive approach integrating untargeted metabolomic profiling, in silico molecular docking and dynamics simulations, Molecular Mechanics Generalized Born Surface Area (MM-GBSA) energetic assessments, and biochemical enzyme assays. This integrated method aims to discover natural PL^pro inhibitors from two ethnomedicinal plants, Lippia javanica and Acorus calamus, which have long been utilized in African traditional medicine to treat respiratory diseases. Comprehensive metabolite profiling using untargeted Ultra-Performance Liquid Chromatography–Tandem Mass Spectrometry (UPLC-MS/MS) and Global Natural Products Social (GNPS) molecular networking revealed flavonoid glucuronides and phenylpropanoid derivatives as the major constituents in both plant species. In situ histochemical staining further offered spatial validation of phenolic- and lignin-associated tissues, supporting the phenolic-dominated molecular families detected by GNPS molecular networking. In silico evaluation of six selected compounds demonstrated spontaneous and thermodynamically favorable binding to PL^pro, with ΔG_bind values ranging from −5.63 to −6.43 kcal/mol. Catechin-7-glucoside emerged as the lead compound, establishing multiple hydrogen bond networks with Asp164, Gln269, Tyr264, and Asn267, supplemented by hydrophobic engagement with Pro247 and Pro248, and π-π stacking with the blocking loop 2 (BL2 loop). Molecular dynamics simulations confirmed the stability of the protein–ligand complexes. Biochemical enzyme assays confirmed concentration-dependent inhibition of PL^pro proteolytic and deubiquitinating activity by both crude plant extracts and isolated bioactive compounds. However, S-adenosyl-methionine showed comparatively high PL^pro proteolytic activity (IC₅₀ 5.872 µM) compared to catechin-7-glucoside, with an IC₅₀ of 7.493 µM, exhibiting efficacy similar to the reference inhibitor GRL0617. Both the extracts of L. javanica and A. calamus have shown significant inhibitory activity while maintaining cell viability in Human embryonic kidney 293T cell (HEK293T) culture models, indicating a favorable safety profile of the tested concentrations. Based on these results, catechin-based polyphenols and phenylpropanoid derivatives appear as promising lead compounds for the development of PL^pro inhibitors. To progress toward therapeutic use, further work is necessary in pharmacokinetics, structural optimization, and antiviral validation in cell models. Full article

Dysregulation of the deubiquitinating enzyme Ubiquitin-specific peptidase 14 (USP14) is implicated in several neurodegenerative diseases, and IU1, an allosteric inhibitor, has shown neuroprotective effects by reducing protein aggregate toxicity. This study aimed to develop new IU1 analogues and evaluate their ability to mitigate amyloid-β (Aβ) accumulation and toxicity in Alzheimer’s disease (AD) cell and Caenorhabditis elegans worm models. IU1 and 71 newly designed analogues identified using the AtomNet^® virtual screening platform were assessed in an amyloid precursor protein-C terminal fragment/amyloid-β (APP-C99/Aβ)-producing AD cell model using a high-throughput toxicity assay. Lead compounds were further evaluated for their effects on neurodegeneration, behaviour, and survival. IU1 reduced Aβ-mediated toxicity and neurodegeneration in cell and worm models. Of the 71 analogues predicted to bind ubiquitin-specific peptidase 14 (USP14), two compounds, AA10 and AA51, showed >50% rescue of Aβ-induced toxicity and robust enhancement of autophagy and proteasome activity. In Caenorhabditis elegans, both compounds alleviated glutamatergic neuron loss and rescued behavioural impairments. IU1 and analogues exhibit protective effects against Aβ toxicity in AD models. Analogues AA10 and AA51 showed greater potency than IU1 and effectively enhanced proteostasis pathways. These findings support USP14 as a promising therapeutic target and provide a basis for the development of improved IU1-derived compounds for AD and related disorders. Full article

Ubiquitination dynamically regulates critical cellular processes, including cell cycle progression, apoptosis, DNA repair, and chromatin remodeling. Deubiquitinating enzymes (DUBs) negatively regulate protein ubiquitination and are equally important for protein regulation in diverse biological processes. Spermatogenesis is a highly regulated process involving spermatogonia self-renewal and differentiation, ensuring continuous sperm production. Using a loss-of-function mouse model, several DUBs have been shown to be involved in spermatogenesis. In addition, specific genetic variants in the DUB genes have been associated with spermatogenic failure and male infertility. These studies provide strong evidence that DUBs are necessary for normal spermatogenesis and may influence male fertility. However, the exact mechanism by which these DUBs regulate spermatogenesis is still under investigation. The aim of this review is to highlight recent advances in the regulatory roles of DUBs in mammalian spermatogenesis and provide insight into the molecular mechanisms underlying their potential actions. An in-depth understanding of DUB-mediated regulation of spermatogenesis will provide a scientific rationale for the discovery and development of novel DUB-targeted therapeutic strategies for male infertility. Full article

(1) Background: The naked mole-rat (Heterocephalus glaber) survives hypoxia–reoxygenation stresses by utilizing metabolic rate depression, achieved in part by downregulating nonessential genes and processes to conserve endogenous cellular resources and prevent buildup of toxic waste byproducts. Tight molecular control of protein degradation (specifically the ubiquitin–proteasome system) is a potent regulatory tool for maintaining muscle integrity during hypoxia, but how this system is regulated in the heart of hypoxia-tolerant species is poorly understood. (2) Methods: The protein expression levels of cullin-RING E3 ligases (specifically CRL4 architecture), deubiquitinating enzymes, and proteasomal activity were assayed in cardiac tissues from H. glaber exposed to 24 h of normoxia or hypoxia in vivo. (3) Results: Overall, the protein expression of E3 ligases decreased, whereas expression of deubiquitinating enzymes increased during hypoxia, all of which play roles in themes of oxidative stress, heightened DNA damage repair, and the HIF-1-VHL-NFκB axis. Proteasomal activity was elevated during hypoxia, which conceivably links to the oxidative stress theory of aging and longevity of H. glaber. (4) Conclusions: Taken together, our results expand current research into protein degradation and extreme environmental stress responses, with a specific focus on cardiac mechanisms related to oxidative stress resistance along the hypoxia-longevity axis. Full article

Atrial fibrillation (AF) is the most common sustained arrhythmia, and its initiation and progression involve multiple mechanisms, including electrical remodeling, structural remodeling, inflammatory responses, and oxidative stress. In recent years, the ubiquitin–proteasome system (UPS), a central pathway for maintaining intracellular protein homeostasis, has attracted increasing attention in the pathogenesis of AF. By regulating the degradation and expression of ion channel proteins, Ca²⁺-handling molecules, and pro-fibrotic signaling factors, the UPS plays a pivotal role in key pathological processes such as electrical and structural remodeling. Several E3 ubiquitin ligases (e.g., NEDD4-1/2, MuRF1, WWP1/2, TRAF6), deubiquitinating enzymes (e.g., JOSD2), and immunoproteasome subunits (e.g., β5i) have been shown to exert critical regulatory effects on atrial electrophysiological disturbances, interstitial remodeling, and inflammation. This review provides a comprehensive summary of the regulatory mechanisms of the UPS in AF-associated pathological processes, outlines potential therapeutic targets, and highlights current intervention strategies, including proteasome inhibitors, selective E3 ligase modulators, and natural compounds. Moreover, we discuss the latest advances and future perspectives regarding the application of UPS-based interventions in AF, aiming to provide theoretical foundations and research insights for the mechanistic exploration and innovative therapeutic development of AF. Full article