The ubiquitin system

Systems biology of Haemonchus contortus - Advancing biotechnology for parasitic nematode control

Parasitic nematodes represent a substantial global burden, impacting animal health, agriculture and economies worldwide. Of these worms, Haemonchus contortus - a blood-feeding nematode of ruminants - is a major pathogen and a model for molecular and applied parasitology research. This review synthesises some key advances in understanding the molecular biology, genetic diversity and host-parasite interactions of H. contortus, highlighting its value for comparative studies with the free-living nematode Caenorhabditis elegans. Key themes include recent developments in genomic, transcriptomic and proteomic technologies and resources, which are illuminating critical molecular pathways, including the ubiquitination pathway, protease/protease inhibitor systems and the secretome of H. contortus. Some of these insights are providing a foundation for identifying essential genes and exploring their potential as targets for novel anthelmintics or vaccines, particularly in the face of widespread anthelmintic resistance. Advanced bioinformatic tools, such as machine learning (ML) algorithms and artificial intelligence (AI)-driven protein structure prediction, are enhancing annotation capabilities, facilitating and accelerating analyses of gene functions, and biological pathways and processes. This review also discusses the integration of these tools with cutting-edge single-cell sequencing and spatial transcriptomics to dissect host-parasite interactions at the cellular level. The discussion emphasises the importance of curated databases, improved culture systems and functional genomics platforms to translate molecular discoveries into practical outcomes, such as novel interventions. New research findings and resources not only advance research on H. contortus and related nematodes but may also pave the way for innovative solutions to the global challenges with anthelmintic resistance.

Nuclear pore complex protein RANBP2 and related SUMOylation in solid malignancies

The growing interest in post-translational protein modification, particularly in SUMOylation, is driven by its crucial role in cell cycle regulation. SUMOylation affects various cell cycle regulators, including oncogenes, suggesting its relevance in cancer. SUMO E3 ligases are pivotal in this process, exhibiting diverse functionalities through structural domains and subcellular localizations. A less-explored SUMO E3 ligase, RANBP2, a component of the vertebrate nuclear pore complex, emerges as a central player in cellular cycle processes, as well as in tumorigenesis. The current studies illuminate the importance of RANBP2 and underscore the need for more extensive studies to validate its clinical applicability in neoplastic interventions. Our review elucidates the significance of RANBP2 across various types of malignancies. Additionally, it delves into exploring RANBP2 as a prospective therapeutic target for cancer treatment, offering insights into the avenues that scholars should pursue in their subsequent research endeavors. Thus, further investigation into RANBP2's role in solid tumorigenesis is eagerly awaited.

Utilizing aptamers in targeted protein degradation strategies for disease therapy

Targeted protein degradation (TPD) has emerged as a promising therapeutic strategy, offering the potential to reduce disease-causing proteins that have traditionally been challenging to target using conventional small molecules. Despite significant advances made with TPD technologies, challenges such as high molecular weight, difficulties in identifying suitable ligands, suboptimal absorption, and metabolic instability remain unresolved. Recently, aptamers - single-stranded DNA or RNA oligonucleotides known for their high specificity and affinity for protein targets - have introduced novel opportunities to expand the scope of TPD, a strategy now referred to as aptamer-based TPD. This approach has demonstrated considerable promise in treating various diseases, such as cancer and ocular disorders. For example, an aptamer-proteolysis-targeting chimera (PROTAC) conjugate (APC) improved tumor targeting and reduced toxicity in a breast cancer model, and a vascular endothelial growth factor-degrading (VED)-lysosome-targeting chimera (LYTAC) molecule effectively inhibited abnormal vascular growth in vascular retinal diseases. These examples highlight the practical relevance and potential in advancing drug discovery efforts. In this review we provide a comprehensive overview of the latest advances in aptamer-based TPD strategies, including proteolysis-targeting and lysosome-targeting chimeras, emphasizing their applications, potential therapeutic benefits, as well as the challenges that must be overcome to fully harness their clinical potential. © 2025 The Pathological Society of Great Britain and Ireland.

CXXC5 is a ubiquitinated protein and is degraded by the ubiquitin-proteasome pathway

CXXC5, as a member of the zinc-finger CXXC family proteins, interacts with unmodified CpG dinucleotides to modulate the expression of genes involved in cellular proliferation, differentiation, and death in physiology and pathophysiology. Various signaling pathways, including mitogenic 17β-estradiol (E2), contribute to the expression and synthesis of CXXC5. However, how signaling pathways modulate protein levels of CXXC5 in cells is largely unknown. We previously reported that some key regulators, including retinoblastoma 1 and E74-like ETS transcription factor 1, of the G1 to S phase transitions are involved in the expression of CXXC5 in estrogen-responsive MCF-7 cells, derived from a breast adenocarcinoma. We, therefore, predict that the synthesis of CXXC5 is regulated in a cell cycle-dependent manner. We report here that although E2 in synchronized MCF-7 cells augments both transcription and synthesis of CXXC5 in the G1 phase, CXXC5 protein levels are primarily mediated by ubiquitination independently of cell cycle phases. Utilizing the bioUbiquitination approach, which is based on cellular biotinylation of ubiquitin, in HEK293FT cells derived from immortalized human embryonic kidney cells, followed by sequential immunoprecipitation coupled mass spectrometry analyses, we identified ubiquitinated lysine residues of CXXC5. We show in both MCF-7 and HEK293FT cells that the ubiquitinated lysine residues contribute to the degradation of CXXC5 through the ubiquitin-proteasome pathway.

Targeting PD-1 post-translational modifications for improving cancer immunotherapy

Programmed cell death protein 1 (PD-1) is a critical immune checkpoint receptor that suppresses immune responses largely through its interaction with PD-L1. Tumors exploit this mechanism to evade immune surveillance, positioning immune checkpoint inhibitors targeting the PD-1/PD-L1 axis as groundbreaking advancements in cancer therapy. However, the overall effectiveness of these therapies is often constrained by an incomplete understanding of the underlying mechanisms. Recent research has uncovered the pivotal role of various post-translational modifications (PTMs) of PD-1, including ubiquitination, UFMylation, phosphorylation, palmitoylation, and glycosylation, in regulating its protein stability, localization, and protein-protein interactions. As much, dysregulation of these PTMs can drive PD-1-mediated immune evasion and contribute to therapeutic resistance. Notably, targeting PD-1 PTMs with small-molecule inhibitors or monoclonal antibodies (MAbs) has shown potential to bolster anti-tumor immunity in both pre-clinical mouse models and clinical trials. This review highlights recent findings on PD-1's PTMs and explores emerging therapeutic strategies aimed at modulating these modifications. By integrating these mechanistic insights, the development of combination cancer immunotherapies can be further rationally advanced, offering new avenues for more effective and durable treatments.

Protacs in cancer therapy: mechanisms, design, clinical trials, and future directions

Cancer develops as a result of changes in both genetic and epigenetic mechanisms, which lead to the activation of oncogenes and the suppression of tumor suppressor genes. Despite advancements in cancer treatments, the primary approach still involves a combination of chemotherapy, radiotherapy, and surgery, typically providing a median survival of approximately five years for patients. Unfortunately, these therapeutic interventions often bring about substantial side effects and toxicities, significantly impacting the overall quality of life for individuals undergoing treatment. Therefore, urgent need of research required which comes up with effective treatment of cancer. This review explores the transformative role of Proteolysis-Targeting Chimeras (PROTACs) in cancer therapy. PROTACs, an innovative drug development strategy, utilize the cell's protein degradation machinery to selectively eliminate disease-causing proteins. The review covers the historical background, mechanism of action, design, and structure of PROTACs, emphasizing their precision in targeting oncogenic proteins. The discussion extends to the challenges, nanotechnology applications, and ongoing clinical trials, showcasing promising results and clinical progress. The review concludes with insights into patents, future directions, and the potential impact of PROTACs in addressing dysregulated protein expression across various diseases. Overall, it provides a concise yet comprehensive overview for researchers, clinicians, and industry professionals involved in developing targeted therapies.

The E3 ubiquitin ligase SlATL2 suppresses tomato immunity by promoting SlCSN5a degradation during Pseudomonas syringae pv. tomato DC3000 infection

Plant immunity involves complex regulatory mechanisms that mediate the activation of defense responses against pathogens. Protein degradation via ubiquitination plays a crucial role in modulating these defenses, with E3 ubiquitin ligases functioning as central regulators. This study investigates the role of SlATL2, an ARABIDOPSIS TÓXICOS EN LEVADURA (ATL)-type E3 ubiquitin ligase localized in the plasma membrane, in the immune response of tomato plants against Pseudomonas syringae pv. tomato (Pst) DC3000. Our findings demonstrate that SlATL2 expression is induced upon Pst DC3000 infection and treatment with defense hormones salicylic acid and jasmonic acid. Functionally, SlATL2 negatively regulates immune responses, impairing resistance to Pst DC3000 and suppressing flg22-triggered immunity. In addition, SlATL2 limits pathogen-induced reactive oxygen species and callose accumulation by targeting the COP9 signalosome subunit 5a (SlCSN5a), a key positive regulator of tomato defense responses against Pst DC3000. This interaction, which occurs via the N-terminal residue of SlATL2, results in the ubiquitination and 26S proteasomal degradation of SlCSN5a, thereby suppressing SA-dependent expression of defense response genes associated and limiting reactive oxygen species production. This work sheds light on the molecular mechanism through which the E3 ubiquitin ligase SlATL2 attenuates tomato immune responses by targeting a COP9 signalosome subunit for degradation. These discoveries deepen our insights into the post-translational mechanisms governing plant immune responses and provide fresh opportunities to bolster crop resistance against bacterial pathogens.

The RBR E3 ubiquitin ligase HOIL-1 can ubiquitinate diverse non-protein substrates in vitro

HOIL-1 is a RING-between-RING-family E3 ubiquitin ligase and a component of the linear ubiquitin chain assembly complex. Although most E3 ubiquitin ligases conjugate ubiquitin to protein lysine sidechains, HOIL-1 has also been reported to ubiquitinate hydroxyl groups in protein serine and threonine sidechains and glucosaccharides, such as glycogen and its building block maltose, in vitro. However, HOIL-1 substrate specificity is currently poorly defined. Here, we show that HOIL-1 is unable to ubiquitinate lysine but can efficiently ubiquitinate serine and a variety of model and physiologically relevant di- and monosaccharides in vitro. We identify a critical catalytic histidine residue, His510, in the flexible catalytic site of HOIL-1 that enables this O-linked ubiquitination and prohibits ubiquitin discharge onto lysine sidechains. We use HOIL-1's in vitro non-proteinaceous ubiquitination activity to produce preparative amounts of different ubiquitinated saccharides that can be used as tool compounds and standards in the rapidly emerging field of non-proteinaceous ubiquitination. Finally, we report an engineered, constitutively active HOIL-1 variant that simplifies in vitro generation of ubiquitinated saccharides.

Red blood cell proteomic profiling in mild and severe obstructive sleep apnea patients before and after positive airway pressure treatment

Obstructive Sleep Apnea (OSA) is characterized by recurrent-episodes of apneas/hypopneas during sleep, leading to recurrent intermittent-hypoxia and sleep fragmentation. Non-treated OSA can result in cardiometabolic diseases. In this study, we applied a shotgun-proteomics strategy to deeper investigate the red blood cell-(RBC) homeostasis regulation in the context of OSA-severity and their response to six months of positive airway pressure (PAP)-treatment. RBC-samples from patients with Mild/Severe-OSA before/after-PAP treatment and patients as simple-snoring controls were selected. The mass-spectrometry raw-data was analysed by MaxQuant for protein identification/quantification followed by statistical Linear Models-(LM) and Linear Mixed Models-(LMM) to investigate OSA-severity effect and interaction with PAP, respectively. The functional/biological network analysis were performed by DAVID-platform. The results indicated that key-enzymes of the Embden-Meyerhof-Parnas (EMP)-glycolysis and pentose phosphate pathway-(PPP) were differentially changed in Severe-OSA, suggesting that the O2-dependent metabolic flux through EMP and PPP maybe compromised in these cells due to severe intermittent hypoxia/reoxygenation-induced oxidative-stress events in these patients. The Rapoport-Luebering-glycolytic shunt showed a significant downregulation across OSA-severity maybe to increase hemoglobin-O2 affinity to adapt to O2 low availability in the lung, although EMP-glycolysis showed decreased only in Severe-OSA. Proteins of the immunoproteasome were upregulated in Severe-OSA maybe to respond to severe oxidative-stress. In Mild-OSA, proteins related to the ubiquitination/neddylation-(Ub/Ned)-dependent proteasome system were upregulated. After PAP, proteins of Glycolysis and Ub/Ned-dependent proteasome system showed reactivated in Severe-OSA. In Mild-OSA, PAP induced upregulation of immunoproteasome proteins, suggesting that this treatment may increase oxidative-stress in these patients. Once validated these proteins maybe candidate biomarkers for OSA or OSA-therapy response.

UBE2N modulates osteoclast differentiation via BTK-PLCγ2-Ca2+ signaling pathway to promote osteoporosis

Osteoporosis is a prevalent public health issue and the underlying mechanism is an imbalance in bone remodeling. Excessive bone resorption caused by upregulation of osteoclast activity is a key factor in the pathogenesis of osteoporosis. Studies have shown that RNA binding protein (RBP) may play an important role in mechanism of OP through interaction with RNA. It has been reported that ubiquitin conjugating enzyme 2 N (UBE2N), as an RBP, is highly expressed in the clinical samples of osteoporotic patients. However, the role and mechanism of action of UBE2N in the regulation of osteoclast differentiation remain unclear. The aim of this study is to evaluate the effects and mechanisms of UBE2N in promoting osteoclastogenesis. In this study, we demonstrated that UBE2N is notably elevated in patients with osteoporosis. Furthermore, our findings revealed that the interference of UBE2N significantly improves osteoporosis of mice, and impedes osteoclast differentiation and bone resorption both in vitro and in vivo. To investigate the molecular mechanisms by which UBE2N influences osteoclast differentiation and bone resorption, we employed RNA sequencing to investigate its downstream related molecules and established that UBE2N regulated the expression of bruton tyrosine kinase (BTK). More importantly, we found that UBE2N may affect osteoclast differentiation and bone resorption by enhancing the expression of the p-BTK gene, which activates the phospholipase Cγ2 (PLCγ2)-Ca2+ signaling pathway. Based on these findings, our study highlights the potential of UBE2N as a promising therapeutic target for osteoporosis.

Inhibition of UCH-L1 Enhances Immunotherapy Efficacy in Triple-Negative Breast Cancer by Stabilizing PD-L1

Recent research indicates that programmed death 1 (PD-1) and programmed death-ligand 1 (PD-L1) inhibitors show promise in treating triple-negative breast cancer (TNBC), but their efficacy is lower than anticipated, especially when used alone. Therefore, enhancing the anti-tumor immune response strategy for TNBC is crucial. Ubiquitin carboxy-terminal hydrolase L1 (UCH-L1), involved in tumor cell regulation and a potential therapeutic target, has an undefined role in TNBC immunotherapy. In this study, we explored the inverse correlation between UCH-L1 and PD-L1 in TNBC patient tissues. Through in vitro experiments, we found that UCH-L1 negatively regulates PD-L1 by stabilizing the E3 ubiquitin ligase ariadne-1 homolog (ARIH1), which promotes PD-L1 ubiquitination and degradation. Further analysis in Balb/c mice xenograft tumors showed that UCH-L1 correlates with GZMB+/CD8+ T cell infiltration in TNBC, suggesting potential synergistic effects when combining UCH-L1 inhibitors with PD-L1 antibodies. Overall, in TNBC, UCH-L1 stabilizes ARIH1, leading to low PD-L1 expression, which may explain the limited effectiveness of immunotherapy in TNBC patients. Our mouse experiments showed improved therapeutic effects when combining UCH-L1 inhibitors with PD-L1 antibodies. These findings offer a new avenue for immunotherapy in TNBC patients.

Emerging tools and methods to study cell signalling mediated by branched ubiquitin chains

Branched ubiquitin chains are complex molecular structures in which two or more ubiquitin moieties are attached to distinct lysine residues of a single ubiquitin molecule within a polyubiquitin chain. These bifurcated architectures significantly expand the signalling capacity of the ubiquitin system. Although branched chains constitute a substantial fraction of cellular polyubiquitin, their biological functions largely remain enigmatic due to their complex nature and the associated technical challenges of studying them. Recent technological innovations have enabled the identification of key molecular players and revealed essential roles for branched chains in diverse cellular processes. In this review, we discuss the bespoke strategies that have driven these discoveries, as well as the technologies needed to advance this rapidly evolving field.

Autophagy dysfunction and neurodegeneration: Where does it go wrong?

An infamous hallmark of neurodegenerative diseases is the accumulation of misfolded or unfolded proteins forming inclusions in the brain. The accumulation of these abnormal structures is a mysterious one, given that cells devote significant resources to integrate complementary pathways to ensure proteome integrity and proper protein folding. Aberrantly folded protein species are rapidly targeted for disposal by the ubiquitin-proteasome system (UPS), and even if this should fail, and the species accumulates, the cell can also rely on the lysosome-mediated degradation pathways of autophagy. Despite the many safeguards in place, failure to maintain protein homeostasis commonly occurs during, or preceding, the onset of disease. Over the last decade and a half, studies suggest that the failure of autophagy may explain the disruption in protein homeostasis observed in disease. In this review, we will examine how the highly complex cells of the brain can become vulnerable to failure of aggregate clearance at specific points during the processive pathway of autophagy, contributing to aggregate accumulation in brains with neurodegenerative disease.

The essential role of E3 ubiquitin ligases in the pathogenesis of neurodevelopmental and psychiatric disorders: Cul3, Cul4, Ube3a, and ZNRF1

The ubiquitin-proteasome system (UPS) is a crucial proteolytic pathway responsible for maintaining cellular homeostasis by degrading specific substrates and misfolded proteins. Protein ubiquitination, a key post-translational modification, is mediated by three enzymes: E1 (activating enzyme), E2 (conjugating enzyme), and E3 (ligase enzyme). Among these, E3 ligase genes have been linked to various neurological disorders, emphasizing the need to understand their molecular mechanisms. This paper reviews recent studies on the substrates of various E3 ubiquitin ligases including Cul3, Cul4, Ube3a, and ZNRF1, and explains how their dysfunction contributes to neuronal impairments and disease phenotypes. By deepening our understanding of these mechanisms, this review aims to facilitate the development of targeted therapies and guide future research into neurodegenerative and neurodevelopmental disorders.

STAT3-mediated upregulation of TRIM6 promotes hepatocellular carcinoma invasion through the DDX58-Snail1 axis

Hepatocellular carcinoma (HCC) is a highly aggressive malignancy with poor prognosis, driven by complex molecular mechanisms that remain inadequately understood. Among these, the ubiquitin-proteasome system plays a crucial role in regulating protein stability and function, with E3 ubiquitin ligases emerging as key players in cancer progression. Here, we identify Tripartite Motif-containing 6 (TRIM6), an E3 ubiquitin ligase, as a critical regulator of HCC metastasis. We demonstrate that TRIM6 is significantly upregulated in HCC tissues and correlates with poor overall survival. Mechanistically, we uncover that STAT3 directly regulates TRIM6 by binding to its promoter and enhancing its transcription. Functionally, TRIM6 promotes epithelial-mesenchymal transition (EMT) and cell invasion by upregulating the key EMT transcription factor Snail1. Importantly, we reveal that TRIM6 interacts with and ubiquitinates DDX58 (RIG-I), leading to its proteasomal degradation. The degradation of DDX58 by TRIM6 alleviates its inhibitory effects on Snail1, thereby facilitating EMT and enhancing the invasive potential of HCC cells. These findings establish the STAT3-TRIM6-DDX58-Snail1 axis as a pivotal pathway in HCC progression, offering novel insights into the molecular underpinnings of HCC metastasis and highlighting TRIM6 as a potential therapeutic target and prognostic biomarker in HCC.

Allosteric modulation of SERCA pumps in health and disease: structural dynamics, posttranslational modifications, and therapeutic potential

Sarco/endoplasmic reticulum (SR/ER) Ca2+-ATPase (SERCA) pumps are ubiquitous membrane proteins in all eukaryotic cells, playing a central role in maintaining intracellular calcium homeostasis by re-sequestering Ca2+ ions from the cytosol into the SR/ER at the expense of ATP hydrolysis. SERCA pumps are well-characterized components of the calcium transport machinery in the cell, playing a role in various physiological processes, including muscle contraction, energy metabolism, secretion exocytosis, gene expression, synaptic transmission, cell survival, and fertilization. Allosteric regulation of SERCA pumps plays a key role in health and disease, and modulation of the SERCA pumps has emerged as a therapeutic approach for the treatment of cardiovascular, muscular, metabolic, and neurodegenerative disorders. In this review, we provide a comprehensive overview of the structural dynamics underlying allosteric modulation of SERCA, focusing on the effects of endogenous regulatory proteins, Ca2+ ions, ATP, and small-molecule effectors on the dynamics and function of the pump. We also examine in detail the role of posttranslational modifications as allosteric modulators of SERCA function, focusing on the oxidative modifications S-glutathionylation, S-nitrosylation, tyrosine nitration, and carbonylation, and non-oxidative modifications that include SUMOylation, acetylation, O-GlcNAcylation, phosphorylation, and ubiquitination. Finally, we discuss the therapeutic potential and challenges of allosteric modulation of SERCA pumps, including the design of small-molecule effectors, microRNA-based interventions, and targeted strategies that modulate SERCA posttranslational regulation. Overall, this review aims to bridge the gap between the mechanisms underlying allosteric modulation of SERCA and the translation of basic science discoveries into effective therapies targeting SERCA pumps.

Ubiquitin proteasome system (UPS): a crucial determinant of the epigenetic landscape in cancer

The ubiquitin proteasome system (UPS), comprising of ubiquitinases, deubiquitinases and 26S proteasome plays a significant role in directly or indirectly regulating epigenetic players. DNA-templated processes like replication, repair and transcription require chromatin decondensation to allow access to specific DNA sequence. A thorough survey of literary articles in PubMed database revealed that the UPS functions as a key regulator, determining the precise state of open and closed chromatin by influencing histones and histone modifiers through proteolytic or non-proteolytic means. However, a comprehensive understanding of how specific UPS components affect particular epigenetic pathways in response to environmental cues remains underexplored. This axis holds substantial potential for deciphering mechanisms of tumorigenesis. Although our current knowledge is limited, it can still guide the development of novel therapeutic strategies that can potentially bridge the gap between cancer chemotherapeutics in bench and bedside.

Ubiquitin-conjugating enzyme E2S (UBE2S) as a prognostic biomarker and regulator of tumorigenesis in osteosarcoma

Ubiquitin-conjugating enzyme E2S (UBE2S) is a member of ubiquitin conjugating enzymes with unclear association with osteosarcoma (OS). This study aimed to assess UBE2S's predictive value in OS using data from TCGA and GEO databases. Kaplan-Meier survival analysis and ROC curves were used for prognostic evaluation, and a nomogram was developed for prognostic prediction. Potential biological functions, pathways, and correlations with tumor immune microenvironment, immunotherapy response, and drug sensitivity were analyzed. UBE2S overexpression was linked to poor prognosis, and the nomogram effectively predicted OS survival outcomes. UBE2S was found to impact tumorigenesis pathways, immune landscape, and treatment sensitivity in OS. Transcriptome sequencing, RT-qPCR, Western Blotting, and immunohistochemistry confirmed that UBE2S is abnormally overexpressed in OS. Additionally, a series of in vitro experiments showed that UBE2S knockdown reduced OS cell proliferation and migration while promoting apoptosis. In vivo experiments also confirmed that UBE2S knockdown could inhibit OS cell growth. In summary, our research demonstrates that UBE2S is a reliable prognostic factor for OS. Its abnormal overexpression enhances OS proliferation and migration, indicating its significance for future personalized treatment strategies in OS.

YY1 induced USP13 transcriptional activation drives the malignant progression of hepatocellular carcinoma by deubiquitinating WWP1

BACKGROUND

Hepatocellular carcinoma (HCC) is the sixth most prevalent cancer globally and the third leading cause of cancer-related mortality. Protein ubiquitination and deubiquitination play vital roles in human cancers. Ubiquitin-specific protease 13 (USP13) is a deubiquitinating enzyme (DUB) that is involved in many cellular processes. However, the mechanism by which USP13 regulates deubiquitination remains largely unknown.

METHODS

Clinical data were analyzed via online databases. USP13 expression in HCC cell lines and tissues was analyzed via western blotting and immunohistochemistry. A lentivirus was used to established stable USP13-knockdown and USP13-overexpression cells. Cell Counting Kit-8, colony formation, wound healing, Transwell, and sphere formation assays were used to detect the malignant behaviors of HCC cells in vitro. A subcutaneous mouse model was used to investigate the function of USP13 in vivo. Co-immunoprecipitation, chromatin immunoprecipitation and dual-luciferase reporter assays were conducted to explore the molecular regulation.

RESULTS

USP13 was upregulated in HCC cell lines and tissues, which predicted a poor prognosis in patients with HCC. Functional experiments in which USP13 was overexpressed or depleted revealed the oncogenic role of USP13 in driving HCC progression both in vitro and in vivo. Mechanistically, WW domain-containing ubiquitin E3 ligase 1 (WWP1) was identified as a binding protein of USP13. Furthermore, USP13 can interact with WWP1 and then remove the K29- and K48-linked polyubiquitination chains from WWP1 to stabilize the WWP1 protein via the ubiquitin-proteasome pathway. Moreover, Yin Yang 1 (YY1) was explored as a new transcription factor of USP13, and YY1 could also upregulate WWP1 expression through USP13. Moreover, YY1 and WWP1 were shown to participate in the oncogenic role of USP13.

CONCLUSIONS

Our findings revealed the functional YY1/USP13/WWP1 signaling axis in HCC, identifying a promising therapeutic target for anti-HCC treatment.

Hsa_circ_0000479 promotes gastric cancer progression by inhibiting BTRC-mediated ubiquitination of G3BP1

An increasing number of studies have shown that circular RNAs (circRNAs) are key regulators of cancer development and progression. RNA-binding proteins (RBPs) play critical roles in the regulation of biological activities, such as RNA synthesis, selective splicing, modification, translocation, and translation; therefore, research on the interactions of circRNAs with RBPs is key to identifying potential targets for cancer treatment. However, the biological roles and mechanisms of circRNAs in gastric cancer (GC) remain largely unknown. We identified differentially expressed circRNAs in GC by analysing Gene Expression Omnibus (GEO) datasets. Concurrently, in vitro functional assays and in vivo animal studies were performed to explore the biological role of circRNAs in GC. We performed western blotting (WB) of labelled proteins, salvage assays, mass spectrometry (MS), and RNA sequencing to investigate the mechanism of circRNAs in GC to explore their effects on GC cell proliferation and metastasis and to validate their potential value as therapeutic targets. Upregulated expression of cyclic RNA EPSTI1 (circEPSTI1; hsa_circ_0000479) was found in GC tissues and was associated with a poor clinical prognosis. hsa_circ_0000479 promotes the proliferation and migration of GC cells in vitro and in vivo. Notably, hsa_circ_0000479 interacts with Ras-GTPase-activated protein-binding protein 1 (G3BP1) in GC cells and inhibits the degradation of G3BP1 via the ubiquitin‒proteasome pathway, whereas hsa_circ_0000479 blocks the binding of G3BP1 to the E3 ligase BTRC. Mechanistic studies suggest that hsa_circ_0000479 promotes GC progression by competitively inhibiting the G3BP1 ubiquitination-mediated degradation facilitated by BTRC. Our results reveal the molecular mechanism by which hsa_circ_0000479 promotes GC progression through BTRC-mediated competitive binding to G3BP1 to inhibit its ubiquitination-mediated degradation, which provides a new theoretical basis for the targeted treatment of GC and elucidates the potential of hsa_circ_0000479-G3BP1-BTRC as a therapeutic target in GC. These findings provide a new direction for the treatment of patients with GC.

Convergent Assembly of Homo- and Heterotypic Ubiquitin Chains from Functionalized, Expressed Monomers via Thiol-Ene Chemistry

Nature constructs ubiquitin tags with high spatiotemporal precision to execute defined functions that critically rely on the exact molecular composition of the ubiquitin chain. Deciphering the complex ubiquitin code is of paramount interest in biology and requires flexible access to homogeneous ubiquitin tags. As enzymatic approaches suffer from inherent drawbacks such as hardly controllable chain length or connectivity and substrate-specificity, we apply a combination of expression and chemical tools to assemble ubiquitin chains. Our strategy includes expression of ubiquitin-intein fusion constructs to obtain large quantities of defined ubiquitin monomers with C-terminal modifications such as hydrazides and propargylamides. Linkages between ubiquitins are generated via photoinitiated thiol-ene click (TEC) chemistry, resulting in a nearly native isopeptide bond. We demonstrate the generation of homo- and heterotypic ubiquitin oligomers with K27, 29, 48, and 63 linkages up to a K48-linked tetramer. The presented toolbox allows selective installation of ubiquitin on target peptides and proteins with reactive cysteine residues as demonstrated for segments of the microtubule-associated protein tau. Such segments can be implemented into protein semisyntheses as shown here for ubiquitylated full-length Tau4. The presented work combines minimal synthetic effort with high fidelity linkage chemistry, paving the way toward homogeneously ubiquitylated proteins.

The role of deubiquitinases in cardiovascular diseases: mechanisms and therapeutic implications

Cardiovascular diseases (CVDs) have become the leading cause of death globally, surpassing infectious diseases and other chronic illnesses. The incidence and mortality rates of CVDs are rising worldwide, posing a key challenge in public health. The ubiquitination system is a vast and complex. It is an important post-translational modification that plays a crucial role in various cellular processes. Deubiquitination is catalyzed by deubiquitinases (DUBs), which remove ubiquitin (Ub) from ubiquitinated proteins, thereby reversing the ubiquitination process. DUBs play an important role in many biological processes, such as DNA repair, cell metabolism, differentiation, epigenetic regulation, and protein stability control. They also participate in the regulation of many signaling pathways associated with the development and progression of CVDs. In this review, we primarily focus on the role of DUBs in various key pathological mechanisms of atherosclerosis (AS), such as foam cell formation, vascular remodeling (VR), endothelial-to-mesenchymal transition (End-MT), and clonal hematopoiesis (CH). In the heart, we summarize the involvement of DUBs in diseases and pathological processes, including heart failure (HF), myocardial infarction (MI), myocardial hypertrophy (MH) and ischemia/reperfusion (I/R) injury. Additionally, we also explore the diabetic cardiomyopathy (DCM) and the use of doxorubicin-induced cardiotoxicity in clinical settings. A comprehensive understanding of deubiquitination may provide new insights for the treatment and drug design of CVDs.

Regulation of N-degron recognin-mediated autophagy by the SARS-CoV-2 PLpro ubiquitin deconjugase

Viral proteases play critical roles in the host cell and immune remodeling that allows virus production. The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) papain-like protease (PLpro) encoded in the large nonstructural protein 3 (Nsp3) also possesses isopeptidase activity with specificity for ubiquitin and ISG15 conjugates. Here, we interrogated the cellular interactome of the SARS-CoV-2 PLpro catalytic domain to gain insight into the putative substrates and cellular functions affected by the viral deubiquitinase. PLpro was detected in protein complexes that control multiple ubiquitin and ubiquitin-like (UbL) regulated signaling and effector pathways. By restricting the analysis to cytosolic and membrane-associated ubiquitin ligases, we found that PLpro interacts with N-recognin ubiquitin ligases and preferentially rescues type I N-degron substrates from proteasomal degradation. PLpro stabilized N-degron carrying HSPA5/BiP/GRP78, which is arginylated in the cytosol upon release from the endoplasmic reticulum (ER) during ER stress, and enhanced the Arg-HSPA5-driven oligomerization of the N-recognin SQSTM1/p62 that serves as a platform for phagophore assembly. However, while in addition to Arg-HSPA5 and SQSTM1/p62, ATG9A, WIPI2, and BECN1/Beclin 1 were detected in PLpro immunoprecipitates, other components of the autophagosome biogenesis machinery, such as the ATG12-ATG5-ATG16L1 complex and MAP1LC3/LC3 were absent, which correlated with proteolytic inactivation of ULK1, impaired production of lipidated LC3-II, and inhibition of reticulophagy. The findings highlight a novel mechanism by which, through the reprogramming of autophagy, the PLpro deubiquitinase may contribute to the remodeling of intracellular membranes in coronavirus-infected cells.

Structural Dynamics, Evolutionary Significance, and Functions of Really Interesting New Gene Proteins in Ubiquitination and Plant Stress: A Review

Abiotic stress causes major crop losses worldwide. Plants have evolved complex intricate signaling network involving transcriptional regulators and posttranslational modifications (PTMs). Ubiquitination-a key PTM-regulates protein degradation through the ubiquitin-proteasome system (UPS). The UPS plays a pivotal role in detecting and modulating plant responses to environmental fluctuations. The E3 ligase family in plants is extensive, offering high substrate specificity and playing a vital role in signaling and protein turnover. Really Interesting New Gene (RING) proteins primarily function as E3 ubiquitin ligases, their functional diversity facilitates the transfer of ubiquitin molecules to specific target proteins. Plants possess abscisic acid (ABA)-dependent and ABA-independent stress-signaling pathways. RING-type E3 ligases regulate ABA signaling either negatively or positively in response to stress by regulating protein degradation, modulating transcription factors, ABA biosynthesis, and degradation. This dynamic interaction between ABA and E3 ligase proteins helps plants to adapt to environmental stress. Negative regulators, such as AIP2 and OsDSG1, target ABI3 for degradation. Keep on going (KEG) ubiquitinates ABI5, ABF1, and ABF3, though KEG itself is subject to feedback regulation by ABA levels, leading to its degradation. Positive regulators include SDIR1, OsSDIR1, AIRP1, RHA2b/RHA2a, and XERICO, along with its maize orthologs ZmXerico1 and ZmXerico2. Additionally, SINAT5 and BOI regulate auxin and gibberellin signaling, integrating hormonal responses to stress. The functional diversity of RING-type E3 ligases offers promising targets for genetic engineering to enhance crop resilience under adverse environmental conditions. Understanding these molecular mechanisms could lead to the development of climate-resilient crops, crucial for sustaining global food security.

Protein post-translational modifications (PTMS) unlocking resilience to abiotic stress in horticultural crops: A review

Horticultural crops are extensively cultivated throughout the world as crucial economical crops, encompassing fruits, vegetables, ornamentals, medicinal and beverage plants, for purposes such as food supply, special nutrition provision, medical application or aesthetic enjoyment. However, abiotic stress triggered by extreme climate change, such as excessive salt and prolonged drought, directly leads to the decline of nutritional quality of horticultural crops, contributing to the shortage of high-quality fruits. Post-translational modifications of proteins, such as phosphorylation and ubiquitination, can alter protein characteristics by adding specific groups to amino acids, which in turn impacts protein stability to regulate plant growth and development as well as environmental stress. Consequently, the revelation of the molecular mechanism of horticultural crops response to abiotic stress at post-translational modification level (PTMs) has always attracted a lot of scholars, as it is crucial for the development and breeding of climate-resilient apple varieties. At PTMs level, this review focuses on summarizing research advancements in horticultural crops responses to environmental stress, including drought, salt, cold, high temperature and iron (Fe) deficiency, with emphasis on sucrose non-fermentative 1 (SNF1) associated protein kinases (SnRKs) and mitogen-activated protein kinase (MAPK) cascade mediated phosphorylation, E3 ubiquitin ligases and BTB/TAZ subfamily BT2 mediated ubiquitination, SIZ1 SUMO E3 ligase mediated sumoylation, Nitric oxide (NO) mediated S-nitrosylation, and other forms of PTMs including protein glycosylation and lysine acetylation. In conclusion, this review adopts protein modification as an entry point to illuminate the mechanism of key genes regulating abiotic stress at PTMs level, providing a foundation for the cultivation of horticultural crops with superior resistance.

Distinct Stress Regulators in the CRL Family: Emerging Roles of F-Box Proteins: Cullin-RING Ligases and Stress-Sensing

Cullin-RING ligases (CRLs) are central regulators of environmental and cellular stress responses, orchestrating diverse processes through the ubiquitination of substrate proteins. As modular complexes, CRLs employ substrate-specific adaptors to target proteins for degradation and other ubiquitin-mediated processes, enabling dynamic adaptation to environmental cues. Recent advances have highlighted the largest CRL subfamily SCF (Skp1-cullin-F-box) in environmental sensing, a role historically underappreciated for SCF ubiquitin ligases. Notably, emerging evidence suggests that the F-box domain, a 50-amino acid motif traditionally recognized for mediating protein-protein interactions, can act as a direct environmental sensor due to its ability to bind heavy metals. Despite these advances, the roles of many CRL components in environmental sensing remain poorly understood. This review provides an overview of CRLs in stress response regulation and emphasizes the emerging functions of F-box proteins in environmental adaptation.

The Role of Ubiquitination on Macrophages in Cardiovascular Diseases and Targeted Treatment

Cardiovascular disease (CVD) is a leading cause of morbidity and mortality worldwide, with macrophage dysfunction playing a central role in its pathogenesis. Ubiquitination, a critical post-translational modification, regulates diverse macrophage functions, including lipoprotein metabolism, inflammation, oxidative stress, mitophagy, autophagy, efferocytosis, and programmed cell death (pyroptosis, necroptosis, ferroptosis, and apoptosis). This review highlights the regulatory roles of ubiquitination in macrophage-driven CVD progression, focusing on its effects on cholesterol metabolism, inflammation, activation, polarization, and the survival of macrophages. Targeting ubiquitination pathways has therapeutic potential by enhancing macrophage autophagy, reducing inflammation, and improving plaque stability. However, challenges, such as off-target effects, ubiquitination crosstalk, and macrophage heterogeneity, must be addressed. By integrating advances in ubiquitination biology, therapeutic strategies can be developed to mitigate CVD and other macrophage-driven inflammatory diseases. This review underscores the potential of ubiquitination-targeting therapies for mitigating CVD and highlights the key areas for further investigation.

Natural products that target p53 for cancer therapy

Wild-type p53 acts as a tumor suppressor, but p53 is frequently mutated and inactivated in tumor cells, promoting cancer progression, invasion, and metastasis. Thus, compounds that reactivate p53 may be leveraged for cancer treatment, and the development of drugs targeting p53 reactivation is actively progressing. Notably, natural products exhibit diverse structures and biological activities and are used as therapeutic agents for various diseases worldwide. This review discusses the natural products that inhibit p53 degradation through p53-Mdm2 interaction, promote p53 reactivation by inducing conformational changes, and exhibit p53-dependent growth inhibition.

Targeted protein degradation for cancer therapy

Targeted protein degradation (TPD) aims at reprogramming the target specificity of the ubiquitin-proteasome system, the major cellular protein disposal machinery, to induce selective ubiquitination and degradation of therapeutically relevant proteins. Since its conception over 20 years ago, TPD has gained a lot of attention mainly due to improvements in the design of bifunctional proteolysis targeting chimeras (PROTACs) and understanding the mechanisms underlying molecular glue degraders. Today, PROTACs are on the verge of a first clinical approval and recent structural and mechanistic insights combined with technological leaps promise to unlock the rational design of protein degraders, following the lead of lenalidomide and related clinically approved analogues. At the same time, the TPD universe is expanding at a record speed with the discovery of novel modalities beyond molecular glue degraders and PROTACs. Here we review the recent progress in the field, focusing on newly discovered degrader modalities, the current state of clinical degrader candidates for cancer therapy and upcoming design approaches.

Thioether-mediated protein ubiquitination in constructing affinity- and activity-based ubiquitinated protein probes

Protein ubiquitination, a critical regulatory mechanism and post-translational modification in eukaryotic cells, involves the formation of an isopeptide bond between ubiquitin (Ub) and targeted proteins. Despite extensive investigation into the roles played by protein ubiquitination in various cellular processes, many questions remain to be answered. A major challenge in the biochemical and biophysical characterization of protein ubiquitination, along with its associated pathways and protein players, lies in the generation of ubiquitinated proteins, either in mono- or poly-ubiquitinated forms. Enzymatic and chemical strategies have been reported to address this challenge; however, there are still unmet needs for the facile generation of ubiquitinated proteins in the quantity and homogeneity required to precisely decipher the role of various protein-specific ubiquitination events. In this protocol, we provide the ubiquitin research community with a chemical ubiquitination method enabled by an α-bromoketone-mediated ligation strategy. This method can be readily adapted to generate mono- and poly-ubiquitinated proteins of interest through a cysteine introduced to replace the target lysine, with the native cysteines mutated to serine. Using proliferating cell nuclear antigen (PCNA) as an example, we present herein a detailed protocol for generating di- and tri-Ub PCNA that contains a photo-activatable cross-linker for capturing potential reader proteins. The thioether-mediated protein ligation and purification typically takes 2-3 weeks. An important feature of our ubiquitination strategy is the ability to introduce a Michael-acceptor warhead to the linkage, allowing the generation of activity-based probes for deubiquitinases and ubiquitin-carrying enzymes such as HECT and RBR E3 ubiquitin ligases and E2 enzymes. As such, our method is highly versatile and can be readily adapted to investigate the readers and erasers of many proteins that undergo reversible ubiquitination.

Meisoindigo Acts as a Molecular Glue to Target PKMYT1 for Degradation in Chronic Myeloid Leukemia Therapy

Meisoindigo (Mei) has been clinically utilized for the treatment of chronic myeloid leukemia (CML), yet the precise molecular targets by which it exerts effects remain unclear. Through activity-based protein profiling (ABPP), the protein kinase, membrane-associated tyrosine/threonine 1 (PKMYT1) is identified as a direct target of Mei. Specifically, Mei forms a selective and reversible covalent bond with the Cys301 residue of PKMYT1, triggering its K48-linked polyubiquitination and accelerating proteasomal degradation, which is mediated by the E3 ligase TRIM25. The study reveals that Mei acts as a molecular glue, enhancing the interaction between PKMYT1 and TRIM25 by approximately 30-fold, thereby facilitating efficient PKMYT1 degradation. Further investigations reveal the pivotal role of PKMYT1 in cell growth. Knockdown of PKMYT1 in K562 cells induces G2/M phase arrest, enhances early apoptosis, and inhibits cell proliferation. In an orthotopic xenograft model, PKMYT1 knockdown delays leukemia progression and reduces lymph node metastasis, reinforcing its role in CML progression and metastasis. These findings provide a molecular rationale for the clinical efficacy of Mei and highlight PKMYT1 as a promising therapeutic target for CML. Additionally, it offers a valuable scaffold and inspiration for the development of novel molecular glue-based protein degraders.

MdDSK2a-Like-MdMTA Module Functions in Apple Cold Response via Regulating ROS Detoxification and Cell Wall Deposition

N6-methyladenosine (m6A) is the most abundant internal RNA modification in eukaryotic cells. Although the importance of its roles in mRNA metabolism, plant development, and stress responses has been well documented, regulation of its machinery is largely unknown in plants. Here, it is reported that MdMTA positively regulates cold tolerance. Combining MeRIP-seq and RNA-seq, it is found that MdMTA regulates the m6A and expression levels of cold-responsive genes under cold stress, including those involved in reactive oxygen species (ROS) detoxification and cell wall deposition. Further analysis reveals that MdMTA promotes ROS scavenging and the deposition of cellulose and hemicellulose by regulating the mRNA stability of the relevant genes under cold conditions. MdDSK2a-like, a ubiquitin receptor protein, mediates MdMTA degradation by the 26S ubiquitin-dependent proteasome and autophagy pathways. MdDSK2a-like negatively regulates cold tolerance by reducing the m6A levels of MdMTA target genes. Consistently, MdDSK2a-like inhibits ROS scavenging and the deposition of cellulose and hemicellulose under cold conditions. Genetic dissection shows that MdDSK2a-like acts upstream of MdMTA in cold response. The results not only reveal the degradation of MdMTA, but also illustrate the molecular mechanism of the MdDSK2a-like-MdMTA module in m6A modification and cold response.

CHIRP-Seq: FOXP2 transcriptional targets in zebra finch brain include numerous speech and language-related genes

BACKGROUND

Vocal learning is a rare, convergent trait that is fundamental to both human speech and birdsong. The Forkhead Box P2 (FOXP2) transcription factor appears necessary for both types of learned signals, as human mutations in FOXP2 result in speech deficits, and disrupting its expression in zebra finches impairs male-specific song learning. In juvenile and adult male finches, striatal FOXP2 mRNA and protein decline acutely within song-dedicated neurons during singing, indicating that its transcriptional targets are also behaviorally regulated. The identities of these targets in songbirds, and whether they differ across sex, development and/or behavioral conditions, are largely unknown.

RESULTS

Here we used chromatin immunoprecipitation followed by sequencing (ChIP-Seq) to identify genomic sites bound by FOXP2 in male and female, juvenile and adult, and singing and non-singing birds. Our results suggest robust FOXP2 binding concentrated in putative promoter regions of genes. The number of genes likely to be bound by FOXP2 varied across conditions, suggesting specialized roles of the candidate targets related to sex, age, and behavioral state. We interrogated these binding targets both bioinformatically, with comparisons to previous studies, and biochemically, with immunohistochemistry using an antibody for a putative target gene. Gene ontology analyses revealed enrichment for human speech- and language-related functions in males only, consistent with the sexual dimorphism of song learning in this species. Fewer such targets were found in juveniles relative to adults, suggesting an expansion of this regulatory network with maturation. The fewest speech-related targets were found in the singing condition, consistent with the well-documented singing-driven down-regulation of FOXP2 in the songbird striatum.

CONCLUSIONS

Overall, these data provide an initial catalog of the regulatory landscape of FOXP2 in an avian vocal learner, offering dozens of target genes for future study and providing insight into the molecular underpinnings of vocal learning.

Ubiquitin-Specific Protease 7 (USP7) as a Promising Therapeutic Target for Drug Discovery: From Mechanisms to Therapies

Protein ubiquitination is a reversible post-translational modification regulated by ubiquitin-conjugating and deubiquitinating enzymes (DUBs). Ubiquitin-specific protease 7 (USP7), a well-characterized DUB, plays multifaceted roles in various cellular processes, making it a promising therapeutic target. The plasticity of its catalytic domain and unique allosteric regulation by substrates or external or intramolecular factors facilitate the identification of highly selective USP7 inhibitors. These inhibitors can engage distinct ubiquitin-binding sites through covalent or non-covalent mechanisms. Despite its therapeutic promise, no USP7 inhibitors have entered clinical trials, underscoring the urgent need for novel therapeutics. Here we provide a crystallographic and functional landscape of USP7's multilayer regulation and analyze the structure-activity relationship of inhibitors by chemotypes. Additionally, we explore USP7's roles in diseases and discuss the challenges in USP7-targeted drug discovery and future directions for therapeutic development. This Perspective aims to provide a systematic overview of USP7, from its regulatory mechanisms to its therapeutic potential.

TOM20-driven E3 ligase recruitment regulates mitochondrial dynamics through PLD6

Mitochondrial homeostasis is maintained through complex regulatory mechanisms, including the balance of mitochondrial dynamics involving fusion and fission processes. A central player in this regulation is the ubiquitin-proteasome system (UPS), which controls the degradation of pivotal mitochondrial proteins. In this study, we identified cullin-RING E3 ligase 2 (CRL2) and its substrate receptor, FEM1B, as critical regulators of mitochondrial dynamics. Through proteomic analysis, we demonstrate here that FEM1B controls the turnover of PLD6, a key regulator of mitochondrial dynamics. Using structural and biochemical approaches, we show that FEM1B physically interacts with PLD6 and that this interaction is facilitated by the direct association of FEM1B with the mitochondrial import receptor TOM20. Ablation of FEM1B or disruption of the FEM1B-TOM20 interaction impairs PLD6 degradation and induces mitochondrial defects, phenocopying PLD6 overexpression. These findings underscore the importance of FEM1B in maintaining mitochondrial morphology and provide further mechanistic insights into how the UPS regulates mitochondrial homeostasis.

GPX4 knockdown suppresses M2 macrophage polarization in gastric cancer by modulating kynurenine metabolism

Background: Glutathione peroxidase 4 (GPX4), an important factor regulating redox homeostasis, plays an important role in tumor microenvironment and progression. However, the role of GPX4 in gastric cancer (GC) is unclear. Methods: Spectral flow cytometry and multiplex immunohistochemistry were employed to assess the correlation between GPX4 expression and immune cell infiltration. Metabolomics analysis of conditioned media from GPX4 knockdown NUGC3 cells identified metabolic alterations. Additionally, both in vitro and in vivo functional studies were conducted to elucidate the mechanistic role of GPX4 in regulating the tumor microenvironment and progression. Results: Knockdown of GPX4 in GC cells inhibited tumor growth, enhanced CD8+ T cell infiltration, and suppressed the polarization of tumor-associated macrophages (TAMs) toward the pro-tumor M2 phenotype. Multiplex immunohistochemistry revealed a positive correlation between GPX4 expression and M2 macrophage infiltration in clinical samples from patients with GC. Metabolomics revealed that GPX4 knockdown regulate kynurenine metabolism pathway. Furthermore, mechanistic studies reveal that GPX4 silencing elevates lipid peroxidation, triggering the conversion of KYNU ubiquitin chain modifications from K48 to K63. Such ubiquitination remodeling stabilizes KYNU expression (a key kynurenine-metabolizing enzyme), reduces kynurenine accumulation, and ultimately reprograms TAM polarization to enhance antitumor immunity. We also identified that the K96 and K163 sites are important for KYNU's modification by K48 and K63 ubiquitin chains. Conclusion: Our study not only affirm the role of GPx4 in GC progression but also highlight it as a promising target for reshaping the immune microenvironment.

Regulation of PEST-containing nuclear proteins in cancer cells: implications for cancer biology and therapy

The PEST-containing nuclear protein (PCNP) is a nuclear protein involved in the regulation of cell cycle progression, protein degradation, and tumorigenesis. PCNP contains a PEST sequence, a polypeptide structural motif rich in proline (P), glutamic acid (E), serine (S), and threonine (T), which serves as a proteolytic recognition signal. The degradation of specific proteins via the PEST sequence plays a crucial role in modulating signaling pathways that control cell growth, differentiation, apoptosis, and stress responses. PCNP is primarily degraded through the ubiquitin-proteasome system (UPS) and the calpain pathway, with phosphorylation of threonine and serine residues further accelerating its degradation. The ubiquitination of PCNP by the ring finger protein NIRF in an E3 ligase-dependent manner is well documented, along with its involvement in the MAPK and PI3K/AKT/mTOR signaling pathways. Additionally, PCNP is implicated in p53-mediated cell cycle arrest and apoptosis, which are essential for inhibiting tumor growth. To explore the role of PCNP in cancer, this review examines its effects on cell growth, differentiation, proliferation, and apoptosis in lung adenocarcinoma, thyroid cancer, ovarian cancer, and other malignancies derived from glandular epithelial cells. By focusing on PCNP and its regulatory mechanisms, this study provides a scientific basis for further research on the biological functions of the PEST sequence in tumor development and cancer progression.

Proteolysis targeting chimera, molecular glue degrader and hydrophobic tag tethering degrader for targeted protein degradation: Mechanisms, strategies and application

Targeted protein degradation (TPD) represents a revolutionary approach to drug discovery, offering a novel mechanism that outperforms traditional inhibitors. This approach employs small molecule drugs to induce the ubiquitination and subsequent degradation of target protein via the proteasome or lysosomal pathways. Key strategies within TPD include proteolysis targeting chimeras (PROTACs), hydrophobic tag tethering degraders (HyTTDs), and molecular glue degraders (MGDs). PROTACs have been undergone clinical evaluations, MGDs have been used in the clinic, and HyTTDs have shown significant progress in cancer treatment. Each of these strategies presents unique advantages and approaches to target protein degradation. This review summarizes five years of research on PROTACs, HyTTDs, and MGDs, highlighting their design principles, advantages, limitations, and future challenges to provide clear guidance and in-depth insights for advancing drug development.

Global analysis of protein and small-molecule substrates of ubiquitin-like proteins (UBLs)

Ubiquitin-like proteins (UBLs) constitute a family of evolutionarily conserved proteins that share similarities with ubiquitin in 3D structures and modification mechanisms. For most UBLs including Small-Ubiquitin-like Modifiers (SUMO), their modification sites on substrate proteins cannot be identified using the mass spectrometry-based method that has been successful for identifying ubiquitination sites, unless a UBL protein is mutated accordingly. To identify UBL modification sites without having to mutate UBL, we have developed a dedicated search engine pLink-UBL on the basis of pLink, a software tool for identification of cross-linked peptide pairs. pLink-UBL exhibited superior precision, sensitivity, and speed than "make-do" search engines such as MaxQuant, pFind, and pLink. For example, compared to MaxQuant, pLink-UBL increased the number of identified SUMOylation sites by 50 ∼ 300% from the same datasets. Additionally, we present a method for identifying small-molecule modifications of UBLs. This method involves antibody enrichment of a UBL C-terminal peptide following enrichment of a UBL protein, followed by LC-MS/MS analysis and a pFind 3 blind search to identify unexpected modifications. Using this method, we have discovered non-protein substrates of SUMO, of which spermidine is the major one for fission yeast SUMO Pmt3. Spermidine can be conjugated to the C-terminal carboxylate group of Pmt3 through its N1 or also likely, N8 amino group in the presence of SUMO E1, E2, and ATP. Pmt3-spermidine conjugation does not require E3 and can be reversed by SUMO isopeptidase Ulp1. SUMO-spermidine conjugation is present in mice and humans. Also, spermidine can be conjugated to ubiquitin in vitro by E1 and E2 in the presence of ATP. The above observations suggest that spermidine may be a common small molecule substrate of SUMO and possibly ubiquitin across eukaryotic species.

F-box protein 22: A prognostic biomarker for colon cancer associated with immune infiltration and chemotherapy resistance

BACKGROUND

Colon cancer represents a significant malignant neoplasm within the digestive system, characterized by a high incidence rate and substantial disease burden. The F-box protein 22 (FBXO22) plays a role in forming a specific type of ubiquitin ligase subunit, which is expressed abnormally in various malignant neoplasms and shows a notable relationship with prognosis in patients with cancer. Nevertheless, the function of FBXO22 in the context of colon cancer remains inadequately elucidated.

AIM

To explore the role of FBXO22 in colon cancer by examining FBXO22 expression patterns and analyzing how the protein affects the prognosis in patients who have undergone surgery.

METHODS

Samples of cancerous and nearby normal tissues from patients with colon cancer were gathered, along with pertinent clinical data. Expression levels of the FBXO22 gene in both cancerous and paracancerous tissues were assessed through immunohistochemistry. The median H score served as a criterion for categorizing FBXO22 gene expression into high and low levels in cancerous tissues, and the relationship between these expression levels and various pathologic characteristics of patients, such as age, sex, and clinical stage, was analyzed. Colon cancer cell lines HCT116 and DLD-1 were used and divided into three groups: A blank control group, a negative control group, and a si-FBXO22 group. FBXO22 gene mRNA and protein expression were measured 24 hours post-transfection using real-time fluorescence quantitative polymerase chain reaction and western blotting. The proliferation capabilities of the cells in each group were assessed using the Cell Counting Kit-8 assay and 5-ethynyl-2'-deoxyuridine assay, while cellular migration and invasion abilities were evaluated using scratch healing and Transwell assays. Various online platforms, including the Timer Immune Estimation Resource, were used to analyze pan-cancer expression, promoter methylation levels, and mutation frequencies of the FBXO22 gene in colon cancer patients. Additionally, the correlation between FBXO22 gene expression, patient prognosis, immune cell infiltration, and the expression of immune molecules in the colon cancer microenvironment was investigated. The relationship between FBXO22 gene expression and chemotherapy resistance, along with the potential mechanisms of action of the FBXO22 gene, were analyzed using The Cancer Genome Atlas dataset and the Genomics of Drug Sensitivity in Cancer drug training set via R software.

RESULTS

Compared with normal colonic tissues, the FBXO22 gene was highly expressed in colon cancer tissues. Post-operative patients with colon cancer elevated FBXO22 reduced survival and exhibited resistance to various chemotherapeutic agents. FBXO22 expression suppresses the infiltration of anti-tumor immune cells. In vitro, FBXO22 knockdown inhibited the proliferation and migration of colon cancer cells.

CONCLUSION

The FBXO22 gene is a biomarker of poor prognosis in patients with colon cancer and has potential as a target for immunotherapy and overcoming chemotherapy resistance.

Protein modifications in hepatic ischemia-reperfusion injury: molecular mechanisms and targeted therapy

Ischemia-reperfusion injury refers to the damage that occurs when blood supply is restored to organs or tissues after a period of ischemia. This phenomenon is commonly observed in clinical contexts such as organ transplantation and cardiac arrest resuscitation. Among these, hepatic ischemia-reperfusion injury is a prevalent complication in liver transplantation, significantly impacting the functional recovery of the transplanted liver and potentially leading to primary graft dysfunction. With the growing demand for organ transplants and the limited availability of donor organs, effectively addressing hepatic ischemia-reperfusion injury is essential for enhancing transplantation success rates, minimizing complications, and improving graft survival. The pathogenesis of hepatic ischemia-reperfusion injury is multifaceted, involving factors such as oxidative stress and inflammatory responses. This article focuses on the role of protein post-translational modifications in hepatic ischemia-reperfusion injury, including phosphorylation, ubiquitination, acetylation, ADP-ribosylation, SUMOylation, crotonylation, palmitoylation, and S-nitrosylation. Initially, we examined the historical discovery of these protein post-translational modifications and subsequently investigated their impact on cellular signal transduction, enzymatic activity, protein stability, and protein-protein interactions. The emphasis of this study is on the pivotal role of protein post-translational modifications in the progression of hepatic ischemia-reperfusion injury and their potential as therapeutic targets. This study aims to conduct a comprehensive analysis of recent advancements in research on protein modifications in hepatic ischemia-reperfusion injury, investigate the underlying molecular mechanisms, and explore future research trajectories. Additionally, future research directions are proposed, including the exploration of interactions between various protein modifications, the identification of specific modification sites, and the development of drugs targeting these modifications. These efforts aim to deepen our understanding of protein post-translational modifications in hepatic ischemia-reperfusion injury and pave the way for innovative therapeutic interventions.

Spatial mechanisms of quality control during chaperone-mediated assembly of the proteasome

Cellular protein degradation requires a complex molecular machine, the proteasome. To mitigate the fundamental challenge of assembling the 66-subunit proteasome, cells utilize dedicated chaperones to order subunit addition. However, recent evidence suggests that proteasome assembly is not simply a series of subunit additions, but each step may be scrutinized so that only correct assembly events advance to proteasomes. Here, we find an unexpected mechanism of quality control (QC) during proteasome assembly-via the proteasomal nuclear localization signal (NLS). This mechanism specifically sequesters defective assembly intermediates to the nucleus, away from ongoing assembly in the cytoplasm, thereby antagonizing defective proteasome formation. This NLS, a bona fide proteasomal component, provides continuous surveillance throughout proteasome assembly. Even a single incorrect event activates spatial QC. Our findings illuminate a two-decade-old mystery in proteasome regulation; proteasomal NLSs, dispensable for proteasome localization, instead provide QC by compartmentalizing assembly defects to ensure that only correct proteasomes form.

The Molecular Toolbox for Linkage Type-Specific Analysis of Ubiquitin Signaling

Modification of proteins and other biomolecules with ubiquitin regulates virtually all aspects of eukaryotic cell biology. Ubiquitin can be attached to substrates as a monomer or as an array of polyubiquitin chains with defined linkages between the ubiquitin moieties. Each ubiquitin linkage type adopts a distinct structure, enabling the individual linkage types to mediate specific functions or outcomes in the cell. The dynamics, heterogeneity, and in some cases low abundance, make analysis of linkage type-specific ubiquitin signaling a challenging and complex task. Herein, the strategies and molecular tools available for enrichment, detection, and characterization of linkage type-specific ubiquitin signaling, are reviewed. The molecular "toolbox" consists of a range of molecularly different affinity reagents, including antibodies and antibody-like molecules, affimers, engineered ubiquitin-binding domains, catalytically inactive deubiquitinases, and macrocyclic peptides, each with their unique characteristics and binding modes. The molecular engineering of these ubiquitin-binding molecules makes them useful tools and reagents that can be coupled to a range of analytical methods, such as immunoblotting, fluorescence microscopy, mass spectrometry-based proteomics, or enzymatic analyses to aid in deciphering the ever-expanding complexity of ubiquitin modifications.

Olfactomedin 4 promotes gastric cancer cell G2/M progression and serves as a therapeutic target in gastric adenocarcinoma

Olfactomedin 4 (OLFM4) is a member of the olfactomedin domain-containing olfactomedin glycoprotein family and plays important roles in innate immunity, inflammation, and cancer. It exhibits increased expression in gastric cancer patient tissues and has been shown to regulate proliferation and apoptosis in gastric cancer cells. However, the molecular mechanism(s) underlying OLFM4's role in gastric cancer remain unknown. In this study, we found that OLFM4 knockdown significantly inhibited YCC3 gastric cancer cell proliferation and induced G2/M cell cycle arrest. Yeast two-hybridization screening revealed that OLFM4 directly interacts with cyclin B1 interacting protein 1 (CCNB1IP1), an E3 ubiquitin protein ligase. In YCC3 cells, OLFM4 co-immunoprecipitated and colocalized with CCNB1IP1 and underwent cell cycle phase-specific nucleo-cytoplasmic shuttling. OLFM4 knockdown decreased both cyclin B1 protein levels and CDK1 activity in YCC3 cells. Screening of a cohort of OLFM4-targeted microRNAs (miRNAs) for their impact on cell proliferation identified several that significantly downregulated OLFM4 protein levels and inhibited YCC3 cell proliferation in vitro. Rescue experiments demonstrated that these miRNAs' inhibitory effect on cell proliferation was partially related to their downregulation of OLFM4. When three of these miRNAs were individually administered intratumorally to nude mice bearing YCC3 cell xenografts, tumor growth was significantly inhibited when compared with tumors treated with a negative control miRNA. These results suggest that OLFM4 promotes cell cycle progression and cell proliferation in gastric cancer cells and may have utility as a therapeutic target in gastric adenocarcinoma.

Chemical approaches to explore ubiquitin-like proteins

Chemical protein synthesis has emerged as a powerful approach for producing ubiquitin (Ub) and ubiquitin-like modifiers (Ubls) in both their free and conjugated forms, particularly when recombinant or enzymatic strategies are challenging. By providing precise control over the assembly of Ub and Ubls, chemical synthesis enables the generation of complex constructs with site-specific modifications that facilitate detailed functional and structural studies. Ub and Ubls are central regulators of protein homeostasis, regulating a wide range of cellular processes such as cell cycle progression, transcription, DNA repair, and apoptosis. Ubls share an evolutionary link with Ub, resembling its structure and following a parallel conjugation pathway that results in a covalent isopeptide bond with their cellular substrates. Despite their structural similarities and sequence homology, Ub and Ubls exhibit distinct functional differences. Understanding Ubl biology is essential for unraveling how cells maintain their regulatory networks and how disruptions in these pathways contribute to various diseases. In this review, we highlight the chemical methodologies and strategies available for studying Ubls and advancing our comprehensive understanding of the Ubl system in health and disease.

USP33 PROMOTES CERULEIN-INDUCED APOPTOTIC, OXIDATIVE, AND INFLAMMATORY INJURIES IN ACUTE PANCREATITIS BY DEUBIQUITINATING TRAF3

ABSTRACT

Background: Tumor necrosis factor receptor associated factor 3 (TRAF3) and deubiquitinating enzyme ubiquitin-specific protease 33 (USP33) have been identified to play important roles in inflammatory diseases, including acute pancreatitis (AP). Here, we aimed to explore whether USP33 affected AP progression by affecting TRAF3 expression through deubiquitination. Methods: Cerulein-treated HPDE6-C7 cells were used to mimic AP conditions in vitro . Levels of mRNAs and proteins were examined by qRT-PCR and western blot. Cell proliferation and apoptosis were evaluated using CCK-8 assay, EdU assay, and flow cytometry. Cell oxidative stress was assessed by detecting the production of superoxide dismutase and malonaldehyde. ELISA analysis detected IL-6 and TNF-α levels. Macrophage M1 polarization was evaluated by flow cytometry. Cellular ubiquitination analyzed the ubiquitination effect on TRAF3. Protein interaction between USP33 and TRAF3 was identified by immunofluorescence staining. Results: Cerulein dose-dependently induced apoptosis, oxidative stress, and inflammatory response in HPDE6-C7 cells and promoted macrophage M1 polarization to enhance inflammation ( P < 0.05). TRAF3 was highly expressed in AP patients (3.5±1.10 vs. 1.0 ±0.74, P < 0.05) and cerulein-induced HPDE6-C7 cells (3.3 ±0.34 vs. 1.0 ±0.10, P < 0.05). Knockdown of TRAF3 protected HPDE6-C7 cells from cerulein-induced apoptotic, oxidative and inflammatory injuries. Mechanistically, USP33 interacted with TRAF3 and induced TRAF3 deubiquitination to upregulate its expression ( P < 0.05). Further analyses showed that USP33 knockdown reversed cerulein-induced apoptosis, oxidative stress and inflammation in HPDE6-C7 cells by TRAF3 ( P < 0.05). Moreover, USP33-TRAF3 activated the NF-κB pathway ( P < 0.05). Conclusion: USP33 promoted cerulein-induced apoptosis, oxidative stress and inflammation in pancreatic ductal cells by deubiquitinating TRAF3, indicating a novel insight into the pathogenesis of AP.

Boronic Acid-Linked Apo-Zinc Finger Protein for Ubiquitin Delivery in Live Cells

Delivering cargo into live cells has extensive applications in chemistry, biology, and medicine. Cell-penetrating peptides (CPPs) provide an ideal solution for cellular delivery. Enhancing CPPs with additional functional units can improve delivery efficiency. We investigate the conjugation of boronic acid modules to enhance internalization through interactions with cell surface glycans. The aim of this study is to determine whether adding boronic acid can transform a peptide that typically lacks CPP properties into one that functions as a CPP, enabling the delivery of crucial biological cargo like ubiquitin (Ub). The zinc finger protein in its apo state was selected as a "boronate-enabled" CPP. Results indicate that skeletal point mutations and post-synthetic modifications, combined with conjugated benzoboroxole derivatives, enable the apo-ZFP the ability to transport Ub within A549 cells, confirmed through microscopy and flow cytometry. This effective internalization of cargo offers valuable insights for advancing the development of boronic acid-mediated cell-penetrating peptides.

Outlook of SNCA (α-synuclein) transgenic fly models in delineating the sequel of mitochondrial dysfunction in Parkinson's disease

Parkinson's disease (PD) is a progressive neurodegenerative disorder associated with mechanisms that results in loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc) region of the brain. Being a complex heterogeneous disorder, there is a requisite in discovering the underlying molecular signatures that could potentially help in resolving challenges associated with diagnosis as well as therapeutic management. SNCA gene that encodes for the protein α-synuclein is widely known for its indispensable role in aggravating the progression of sporadic and familial PD, upon mutations. Likewise, mitochondrial dysfunction is inferred to be playing a central role in both forms of PD. Observations from experimental models and human PD cases displayed strong evidence for disruption of mitochondrial dynamics, inhibition of mitochondrial complex I protein's function and elevation in reactive oxygen species (ROS) by the toxic aggregation of α-synuclein. Further, recent studies have raised the possibility of an underlying relationship, where the α-synuclein toxicity is exacerbated by the mutant mitochondrial complex proteins and vice-versa. In this review, we provide an overview of mechanisms influencing α-synuclein-related neurodegeneration, particularly, emphasizing the role of SNCA (α-synuclein) gene in leading to altered mitochondrial biogenesis during PD. We have described how transgenic Drosophila models were reliable at recapitulating some of the essential characteristics of PD. In addition, we highlight the capability of utilizing transgenic fly models in deciphering the altered α-synuclein toxicity and mitochondrial dysfunction, as induced by defects in the mitochondrial DNA.

Unraveling the role of deubiquitinating enzymes on cisplatin resistance in several cancers

The use of platinum-based drugs in cancer treatment is one of the most common methods in chemotherapy. Especially, cisplatin induces cell death by interrupting DNA synthesis by binding to the DNA bases, thereby leading to the apoptosis via multiple pathways. However, the major hurdle in chemotherapy is drug resistance. To overcome drug resistance, the ubiquitin-proteasome system (UPS) has emerged as a potential therapeutic target. The UPS is a pivotal signaling pathway that regulates the majority of cellular proteins by attaching ubiquitin to substrates, leading to proteasomal degradation. Conversely, deubiquitinating enzymes (DUBs) remove tagged ubiquitin from the substrate and inhibit degradation, thereby maintaining proteostasis. Recently, studies have been conducted to identify the substrates of DUBs and investigated the cellular mechanisms, and now the development of therapeutics using DUB inhibitors is in clinical trials. However, the mechanism of the DUB response to cisplatin remains still unclear. In this review, we summarize the research reported on the function of DUBs responding to cisplatin.

Mdm2-Mediated Ubiquitination Plays a Pivotal Role in Differentiating the Endocytic Roles of GRK2 and Arrestin3

Upon activation of certain G protein-coupled receptors, Mdm2 promotes the ubiquitination of both GRK2 and arrestin3. Similar to arrestin3, GRK2 ubiquitination was associated with its endocytic activity and proteasomal degradation. Ubiquitination of GRK2 was essential for arrestin3 ubiquitination, and vice versa. Cellular components involved in arrestin3 ubiquitination, including Gβγ, clathrin, and 14-3-3η, were also necessary for GRK2 ubiquitination. Additionally, the arrestin-biased signaling pathway contributed to the ubiquitination of both GRK2 and arrestin3. By employing Mdm2-knockdown cells alongside GRK2 and arrestin3 mutants deficient in ubiquitination sites, as well as receptors lacking phosphorylation sites, we established that the ubiquitinated forms of GRK2 and arrestin3 facilitate clathrin-dependent endocytosis, whereas non-ubiquitinated GRK2 and arrestin3 are responsible for caveolar and a distinct third endocytic pathway, respectively. In the context of clathrin-mediated endocytosis, arrestin3's interaction with clathrin and GRK2's interaction with the β2-adaptin subunit of adaptor protein complex 2 were critical. These findings suggest that GRK2 and arrestin3 ubiquitination are mutually dependent, with their ubiquitination states determining their roles in distinct endocytic pathways.