Ubiquitination Process Research Articles

The other side of the coin: protein deubiquitination by Ubiquitin-Specific Protease 1 in cancer progression and therapy.

Reversible protein ubiquitination is a crucial factor in cellular homeostasis, with Ubiquitin-Specific Protease 1 (USP1) serving as a key deubiquitinase involved in DNA damage response (DDR) and repair mechanisms in cancer. While ubiquitin ligases have been extensively studied, research on the reverse process of ubiquitination, particularly the mechanisms involving USP1, remains relatively limited. USP1 is overexpressed in various cancers, influencing tumor initiation and progression by regulating multiple associated proteins. Inhibiting USP1 effectively suppresses tumor proliferation and migration and may help overcome resistance to cisplatin and PARP inhibitors. As a potential synthetic lethal target, USP1 demonstrates significant research potential. This review highlights the biological mechanisms of USP1 in cancer progression, the signaling pathways it regulates, and the latest advancements in USP1 inhibitors, while also analyzing the opportunities and challenges of targeting USP1. By adopting the perspective of "the other side of the coin," this review aims to underscore the crucial yet often overlooked role of the deubiquitinase USP1, contrasting it with the extensively studied ubiquitin ligases, and emphasizing its therapeutic potential in cancer treatment.

Male sex determination maintains proteostasis and extends lifespan of daf-18/PTEN deficient C. elegans.

Although females typically have a survival advantage, those with PTEN functional abnormalities face a higher risk of developing tumors than males. However, the differences in how each sex responds to PTEN dysfunction have rarely been studied. We use Caenorhabditis elegans to investigate how male and hermaphrodite worms respond to dysfunction of the PTEN homolog daf-18. Our study reveals that male worms can counterbalance the negative effects of daf-18 deficiency, resulting in longer adult lifespan. The survival advantage depends on the loss of DAF-18 protein phosphatase activity, while its lipid phosphatase activity is dispensable. The deficiency in DAF-18 protein phosphatase activity leads to the failure of dephosphorylation of the endoplasmic reticulum membrane protein C18E9.2/SEC62, causing increased levels of unfolded and aggregated proteins in hermaphrodites. In contrast, males maintain proteostasis through a UNC-23/NEF-mediated protein ubiquitination and degradation process, providing them with a survival advantage. We find that sex determination is a key factor in regulating the differential expression of unc-23 between sexes in response to daf-18 loss. These findings highlight the unique role of the male sex determination pathway in regulating protein degradation.

Dementia with lewy bodies patients with high tau levels display unique proteome profiles

BackgroundClinical studies have long observed that neurodegenerative disorders display a range of symptoms and pathological features and, in some cases, overlap, suggesting that these diseases exist on a spectrum. Dementia with Lewy Bodies (DLB), a synucleinopathy, is a prominent example, where symptomatic similarities with tauopathy, Alzheimer’s disease, are observed. Although tau pathology has been observed in DLB, the interplay between tau and α-synuclein is poorly understood at a molecular level.MethodsQuantitative mass spectrometry analysis was used to measure protein abundance in the insoluble fraction from cortical brain tissue from pathologically diagnosed DLB subjects (n = 30) and age-matched controls (n = 29). Using tau abundance, we stratified the DLB subjects into two subgroups termed DLBTau+ (higher abundance) and DLBTau− (lower abundance). We conducted proteomic analysis to characterize and compare the cortical proteome of DLB subjects exhibiting elevated tau, as well as the molecular modifications of tau and α-synuclein to explore the dynamic between tau and α-synuclein pathology in these patients.ResultsProteomic analyses revealed distinct global protein dysregulations in DLBTau+ and DLBTau− subjects when compared to controls. Notably, DLBTau+ patients exhibited increased levels of tau, along with ubiquitin, and APOE, indicative of cortical proteome alterations associated with elevated tau. Comparing DLBTau+ and DLBTau− groups, we observed significant upregulation of cytokine signaling and metabolic pathways in DLBTau− patients, while DLBTau+ subjects showed increases in protein ubiquitination processes and regulation of vesicle-mediated transport. Additionally, we examined the post-translational modification patterns of tau and α-synuclein. Our analysis revealed distinct phosphorylation and ubiquitination sites on α-synuclein between groups. Moreover, we observed increased modifications on tau specifically within the DLBTau+ subgroup.ConclusionThis molecular-level data supports the idea of neurodegenerative disease as a continuum of diseases with distinct PTM profiles DLBTau+ and DLBTau− patients in comparison to AD. These findings further emphasize the importance of identifying specific and tailored therapeutic approaches targeting the involved proteopathies in the neurodegenerative disease spectrum.

Long-term warming and acidification interaction drives plastic acclimation in the diatom Pseudo-nitzschia multiseries.

Ocean warming (OW) and acidification (OA) are expected to interactively impact key phytoplankton groups such as diatoms, but the underlying mechanisms, particularly under long-term acclimation, remain poorly understood. In this study, we investigated the responses of the toxic diatom Pseudo-nitzschia multiseries to combined changes in temperature (20°C and 30°C) and CO2 concentration (pCO2 400μatm and 1000μatm) using a multi-omics approach over an acclimation period of at least 251 generations. Physiological data suggest that elevated temperature, either alone or in combination with CO2, reduced the net photosynthesis and nitrate uptake rate, thus inhibiting P. multiseries growth. Conversely, elevated CO2 alone stimulated P. multiseries growth. Comparative genome analysis revealed the phenotypic plasticity in response to temperature and pCO2 variations, even after more than 251 generations acclimation period. Temperature was identified as the dominant environmental factor, showing stronger effects than CO2. Transcriptomic profiles indicated that genes involved in stress- and intracellular homeostasis such as Hsps, ubiquitination process and antioxidant defense were mostly down-regulated under long-term warming acclimation. This study demonstrates that P.multiseries responds similarly to both short-term and long-term experimental selection, suggesting that short-term experiments can be used to predict long-term responses.

Regulation of ubiquitination in sepsis: from PAMP versus DAMP to peripheral inflammation and cell death.

Sepsis (sepsis) is a systemic inflammatory response triggered by infection, and its pathologic features include overproduction of peripheral inflammatory factors (e.g., IL-1β, IL-6, TNF-α), which ultimately leads to cytokine storm and multiple organ dysfunction syndrome (MODS). Pathogen-associated molecular patterns (PAMP) and damage-associated molecular patterns (DAMP) induce strong immune responses and exacerbate inflammation by activating pattern recognition receptors (PRRs) in the host. Ubiquitination, as a key protein post-translational modification, dynamically regulates the activity of several inflammation-associated proteins (e.g., RIPK1, NLRP3) through the coordinated action of the E1, E2, and E3 enzymes, affects cell death pathways such as necroptosis and pyroptosis, and ultimately regulates the release of peripheral inflammatory factors. Deubiquitinating enzymes (DUBs), on the other hand, influence the intensity of the inflammatory response in sepsis by counter-regulating the ubiquitination process and balancing pro- and anti-inflammatory signals. This review focuses on how PAMP and DAMP activate inflammatory pathways via PRRs, and the central role of ubiquitination and deubiquitination in the development of sepsis, especially the mechanisms in regulating the secretion of peripheral inflammatory factors and cell death. By deeply dissecting the impact of the balance of ubiquitination and deubiquitination on inflammatory regulation, we further envision its potential as a therapeutic target in sepsis.

Neural Precursor Cell-Expressed Developmentally Downregulated Protein 4 (NEDD4)-Mediated Ubiquitination of Glutathione Peroxidase 4 (GPX4): A Key Pathway in High-Glucose-Induced Ferroptosis in Corpus Cavernosum Smooth Muscle Cells.

Pharmacological treatment of diabetes mellitus-induced erectile dysfunction (DMED) has become increasingly challenging due to the limited efficacy of phosphodiesterase type 5 inhibitors (PDE5i). As the global prevalence of DM continues, there is a critical need for novel therapeutic strategies to address DMED. In our previous studies, we found that Glutathione peroxidase 4 (GPX4), a ferroptosis inhibitor, can ameliorate DMED in diabetic rats. However, the specific role of GPX4 in corpus cavernosum smooth muscle cells (CCSMCs) and its regulatory mechanisms remain unclear. In this study, we established primary cultures of CCSMCs and systematically analyzed the role of GPX4 under high-glucose conditions. To further elucidate the upstream regulatory pathways of GPX4, we employed immunoprecipitation coupled with mass spectrometry (IP-MS) to identify potential interacting proteins. Additionally, co-immunoprecipitation (Co-IP) and cycloheximide (CHX) chase assays were conducted to explore the regulatory dynamics and post-translational stability of GPX4. Under high-glucose conditions, the expression of GPX4 in CCSMCs is significantly downregulated, leading to an increase in intracellular oxidative stress and heightened levels of ferroptosis, accompanied by dysfunction in smooth muscle cell relaxation. Furthermore, the CHX chase assay revealed that high glucose accelerates GPX4 protein degradation via the ubiquitin-proteasome pathway. Subsequent IP-MS identified NEDD4, an E3 ubiquitin ligase, as a potential interacting partner of GPX4. Further validation demonstrated that NEDD4 modulates the ubiquitination process of GPX4, thereby influencing its stability and expression. In conclusion, we identified NEDD4 as a key regulator of GPX4 stability through ubiquitin-mediated proteasomal degradation. These findings suggest potential therapeutic strategies targeting the NEDD4-GPX4 axis to alleviate DMED pathology.

Genome-Wide Identification of the GbUBC Gene Family in Sea-Island Cotton (Gossypium barbadense) and the Active Regulation of Drought Resistance in Cotton by GbUBC23.

Cotton is an economically critical crop worldwide, and drought stress strongly affects its growth and development. Ubiquitination modifies protein activity and is crucial in numerous biological processes. Ubiquitin-conjugating enzymes serve as intermediaries in the protein ubiquitination process and play important roles in plant responses to abiotic stress. However, the impact of ubiquitination on the response of cotton to abiotic stress is not fully understood. Bioinformatic methods were employed in this study to analyze the physiochemical characteristics, gene structure, collinearity, expression patterns, and evolutionary relationships of GbUBC gene family members in sea-island cotton. In sea-island cotton, a minimum of 125 GbUBC genes are irregularly distributed across the 26 chromosomes, with multiple instances of gene duplication observed among the members. Phylogenetic analysis categorized the GbUBC gene family into 15 ubiquitin-conjugating enzyme (E2) subgroups, one ubiquitin E2 enzyme variant (UEV) subgroup, and one COP10 subgroup. GbUBC gene expression pattern analyses revealed that most GbUBC genes responded differently to cold, heat, NaCl, and polyethylene glycol (PEG) treatments, with certain GbUBC genes exhibiting high expression levels in specific fiber development period and organs. Furthermore, molecular biology methods were employed to elucidate the biological functions of GbUBC23. The GbUBC23 gene was highly expressed in the cotyledons of sea-island cotton and was activated by PEG treatment. GbUBC23 is localized to the nucleus and cytomembrane. The silencing of the GbUBC23 gene under drought conditions led to decreased drought tolerance and survival rates in sea-island cotton. Compared with those in the control plants, the activity of proline and superoxide dismutase and the expression levels of the drought-induced genes GbNCED3, GbRD22, GbRD26 were significantly lower, but the levels of malondialdehyde and hydrogen peroxide were significantly higher. Our findings revealed 125 members of the GbUBC gene family in sea-island cotton, with the GbUBC23 gene critically contributing to the abiotic stress response. These findings indicate that the GbUBC gene family may play a crucial role in the drought stress response in sea-island cotton.

Deubiquitinases as novel therapeutic targets for diseases

AbstractDeubiquitinating enzymes (DUBs) regulate substrate ubiquitination by removing ubiquitin or cleaving within ubiquitin chains, thereby maintaining cellular homeostasis. Approximately 100 DUBs in humans counteract E3 ubiquitin ligases, finely balancing ubiquitination and deubiquitination processes to maintain cellular proteostasis and respond to various stimuli and stresses. Given their role in modulating ubiquitination levels of various substrates, DUBs are increasingly linked to human health and disease. Here, we review the DUB family, highlighting their distinctive structural characteristics and chain‐type specificities. We show that DUB family members regulate key signaling pathways, such as NF‐κB, PI3K/Akt/mTOR, and MAPK, and play crucial roles in tumorigenesis and other diseases (neurodegenerative disorders, cardiovascular diseases, inflammatory disorders, and developmental diseases), making them promising therapeutic targets Our review also discusses the challenges in developing DUB inhibitors and underscores the critical role of the DUBs in cellular signaling and cancer. This comprehensive analysis enhances our understanding of the complex biological functions of the DUBs and underscores their therapeutic potential.

Mechanistic exploration of ubiquitination-mediated pathways in cerebral ischemic injury.

The ubiquitin-proteasome system (UPS) plays a pivotal role in regulating protein homeostasis and cellular processes, including protein degradation, trafficking, DNA repair, and cell signaling. During cerebral ischemia, ischemic conditions profoundly disrupt UPS activity, leading to proteasomal dysfunction and the accumulation of abnormal proteins. This imbalance contributes to neuronal injury and cell death observed in ischemic stroke. The UPS is intricately linked to various signaling pathways crucial for neuronal survival, inflammation, and cellular stress response, such as NF-κB, TRIM, TRIP, JAK-STAT, PI3K/Akt, and ERK1/2. Alterations in the ubiquitination process can significantly impact the activation and regulation of these pathways, exacerbating ischemic brain injury. Therapeutic approaches targeting the UPS in cerebral ischemia aim to rebalance protein levels, reduce proteotoxic stress, and mitigate neuronal injury. Strategies include proteasome inhibition, targeting specific ubiquitin ligases and deubiquitinating enzymes, and modulating ubiquitination-mediated regulation of key signaling pathways implicated in ischemia-induced pathophysiology. Therefore, the present review discusses the molecular mechanisms underlying UPS dysfunction in ischemic stroke is crucial for developing effective therapeutic interventions. Modulating ubiquitination-mediated pathways through therapeutic interventions targeting specific UPS components holds significant promise for mitigating ischemic brain injury and promoting neuroprotection and functional recovery in patients with cerebral ischemia.

Chelerythrine triggers the prolongation of QT interval and induces cardiotoxicity by promoting the degradation of hERG channels

Cardiotoxicity is a serious adverse reaction during drug treatment. The cardiac hERG channels play a crucial role in driving cardiac action potential repolarization and are a key target for drug-induced cardiac toxicity. Chelerythrine has anti-cancer effects on various human cancer cells. But little is known about its drug safety currently. The purpose of this study is to explore the key mechanism of cardiac toxicity induced by Chelerythrine under pathological conditions. Chelerythrine and hypoxia prolonged QT interval and action potential duration compared with control group in guinea pigs, as measured by BL-420S biological acquisition and processing system in conjunction with optical mapping technology. HERG current was measured by patch-clamp technique and the interaction between ubiquitin molecules and hERG channels was assessed using immunoprecipitation method at the molecular level. The co-localization of proteins and the function of lysosomes were determined via confocal laser scanning microscopy. Further research indicates that Chelerythrine enhances the ubiquitination process of hERG proteins by catalyzing the formation of K63 ubiquitin chains, the ubiquitination modification disrupts hERG channel homeostasis and promotes the degradation of the channel. Mechanistically, Chelerythrine accelerates the degradation of hERG channels through lysosomes via HDAC6, which may easily induce cardiotoxicity caused by prolonged QT interval under hypoxic conditions.

Dynamic Expression of Genes Encoding Ubiquitin Conjugating Enzymes (E2s) During Neuronal Differentiation and Maturation: Implications for Neurodevelopmental Disorders and Neurodegenerative Diseases.

Background: The ubiquitination process plays a crucial role in neuronal differentiation and function. Numerous studies have focused on the expression and functions of E3 ligases during these different stages, far fewer on E2 conjugating enzymes. In mice, as in humans, these E2s belong to 17 conjugating enzyme families. Objectives: We analyzed by real-time PCR the expression dynamics of all known E2 genes during an in vitro differentiation of mouse hippocampal neuronal cultures, and after, we analyzed their stimulation with N-methyl-D-aspartate (NMDA). Results: We found that 36 of the 38 E2 genes were expressed in hippocampal neurons. Many were up-regulated during neuritogenesis and/or synaptogenesis stages, such as Ube2h, Ube2b, and Aktip. Rapid and delayed responses to NMDA stimulation were associated with the increased expression of several E2 genes, such as Ube2i, the SUMO-conjugating E2 enzyme. We also observed similar expression profiles within the same E2 gene family, consistent with the presence of similar transcription factor binding sites in their respective promoter sequences. Conclusions: Our study indicates that specific expression profiles of E2 genes are correlated with changes in neuronal differentiation and activity. A better understanding of the regulation and function of E2s is needed to better understand the role played by the ubiquitination process in physiological mechanisms and pathophysiological alterations involved in neurodevelopmental or neurodegenerative diseases.

DNA methylation profiles of transgenerational rat hyperactivity primed by silver nanoparticles: Comparison with valproate model rats of autism

There is an increasing body of evidence suggesting that a single exposure to certain chemicals can have transgenerational effects, with the underlying mechanism believed to be epigenetic. However, it remains largely unknown whether psychiatric conditions like ADHD or autism, induced by environmental chemicals, can be inherited across generations. Pregnant rats were purchased from a commercial breeder. On the 7th day of gestation (E7), they were divided into two groups: one group was orally exposed to silver nanoparticles (AgNP; 4 mg/kg), while the control group received vehicle alone. The subsequent generation (F1) underwent spontaneous motor activity (SMA) measurements at 8–11 weeks of age. For breeding at 26 weeks of age, rats with higher SMA were selected from hyperactive litters, while untreated rats were randomly selected. This process was continued for four generations in both groups. The AgNP-primed rats at 4th generation displayed significantly higher SMA, 1.8 times greater than that of untreated rats. Intraperitoneal injection of valproic acid (150 mg/kg), an epigenetic modifier to 5-day-old rats causes adult hyperactivity (1.4-fold), suggesting that epigenetic modification contributes to rat hyperactivity. Global DNA methylation profiles in the mesencephalon were positively correlated in both groups of hyperactive rats. Furthermore, there were 7–8 common genes showing both hypermethylation and hypomethylation, which are involved in neuronal development, neuronal function, transcriptional activity, DNA binding activity, cell differentiation, ubiquitination processes, or histone modification, including Pax 6 and Mecp 2. Thus, it is most likely that rats retain hyperactivity through mesencephalic DNA methylation status across transgeneration.

UBC18 E2 conjugating enzyme depends on SINAT1 E3 ligase to destabilize the ESCRT component FREE1 in plant iron deficiency responses.

E2 ubiquitin-conjugating enzymes play a crucial role in the ubiquitination process by catalyzing ubiquitin transfer. Although the function of ubiquitin-protein ligases (E3s) in plants response to diverse abiotic stress by targeting specific substrates has been well studied, the involvement of E2s in environmental responses and their downstream targets are not well understood. In this study, we demonstrated that the E2 ubiquitin-conjugating enzyme 18 (UBC18) influences the stability of FREE1 to modulate iron deficiency stress. UBC18 affects the ubiquitination of FREE1 and promotes its degradation, and overexpression of UBC18 decreases plants' sensitivity to iron deficiency by reducing FREE1 level, whereas the ubc18 mutant exhibits sensitivity due to elevated FREE1 accumulation. This study also identified that lysine residues K227, K295, K315, and K540 are required for FREE1 ubiquitination and stability regulation. Mutating these lysine residues in FREE1 resulted in plants' sensitivity to iron starvation. Taken together, our findings shed light on the mechanism of UBC18 in responding to iron deficiency stress by modulating the abundance of FREE1, and further elucidate the role of ubiquitination sites in FREE1 stability regulation and the plant iron deficiency response.

FBXO family genes promotes hepatocellular carcinoma via ubiquitination of p53

FBXO protein family plays an essential role in the ubiquitination process acting as E3 ligases, which may contribute to the progression of cancers. However, the molecular functions of FBXOs in hepatocellular carcinoma (HCC) remain incompletely understood. Here, we investigated the overlapping genes between the FBXOs and differentially expressed genes (DEGs) of HCC identified by utilizing The Cancer Genome Atlas (TCGA) dataset, then, a prognostic model with effective predictive capacity was constructed based on the uni-cox and LASSO regression analyses. To elucidate the underlying mechanism of the FBXO model genes, KEGG analysis was carried out. Drug metabolism-cytochrome P450 and retinol metabolism were revealed as the potential pathway, which Increased the credibility of subsequent drug prediction research. Meanwhile, patients divided by the prognostic model showed a different immune infiltrating status and we also found FBXO model genes may ubiquitinate P53, inducing TP53 more prone to mutations, thereby promoting the occurrence and development of tumors. Consistent with these findings, the result of immunohistochemistry (IHC) validated an elevated expression of these model genes in HCC tissues than in the adjacent tissues. The primary aim of this investigation is to formulate a prognostic model while exploring the underlying mechanisms associated with FBXO genes in HCC. These findings offer initial research perspectives on the involvement of FBXO genes in HCC and contribute to the discovery of dependable biomarkers for the management, prognostication, and early detection of HCC in patients.

Redox control of the deubiquitinating enzyme Ubp2 regulates translation during stress

Protein ubiquitination is essential to govern cells’ ability to cope with harmful environments by regulating many aspects of protein dynamics from synthesis to degradation. As important as the ubiquitination process, the reversal of ubiquitin chains mediated by deubiquitinating enzymes (DUBs) is critical for proper recovery from stress and re-establishment of proteostasis. Although it is known that ribosomes are decorated with K63-linked polyubiquitin (K63-ub) chains that control protein synthesis under stress, the mechanisms by which these ubiquitin chains are reversed and regulate proteostasis during stress recovery remain elusive. Here, we showed in budding yeast that the DUB Ubp2 is redox-regulated during oxidative stress in a reversible manner, which determines the levels of K63-ub chains present on ribosomes. We also demonstrate that Ubp2 can cleave single ubiquitin moieties out of chain and its activity is modulated by a series of repeated domains and the formation of disulfide bonds. By combining cellular, biochemical, and proteomics analyses, we showed that Ubp2 is crucial for restoring translation after stress cessation, indicating an important role in determining the cellular response to oxidative stress. Our work demonstrates a novel role for Ubp2, revealing that a range of signaling pathways can be controlled by redox regulation of DUB activity in eukaryotes, which in turn will define cellular states of health and diseases.

Identification of key ubiquitination-related genes in gestational diabetes mellitus: A bioinformatics-driven study.

Gestational diabetes mellitus (GDM) is characterized by glucose intolerance that occurs during pregnancy. This study aimed to identify key ubiquitination-related genes associated with GDM pathogenesis. Microarray data from GSE154377 was analyzed to identify differentially expressed genes (DEGs) in GDM vs normal pregnancy samples. Weighted gene co-expression network analysis was performed on ubiquitination-related genes. Functional enrichment, protein-protein interaction network, and TF-mRNA-miRNA interaction network analyses were conducted on differentially expressed ubiquitination-related genes (DE-URGs). We identified 2337 DEGs and 65 DE-URGs in GDM. Functional enrichment analysis of the 65 DE-URGs revealed involvement in protein ubiquitination and ubiquitin-dependent catabolic processes. Protein-protein interaction network analysis identified 8 hub genes, including MAP1LC3C, USP26, USP6, UBE2U, USP2, USP43, UCHL1, and USP44. ROC curve analysis showed these hub genes have high diagnostic accuracy for GDM (AUC > 0.6). The TF-mRNA-miRNA interaction network suggested USP2 and UCHL1 may be key ubiquitination genes in GDM. In conclusion, this study contributes to our understanding of the molecular landscape of GDM by uncovering key ubiquitination-related genes. These findings may serve as a foundation for further investigations, offering potential biomarkers and therapeutic targets for clinical applications in GDM management.

LUCAT1 Activates the Malignant Phenotypes of Lung Cancer Cells via Regulating P53 Ubiquitination.

Long non-coding RN (lncRNAs) have been implicated in lung cancer, but the mechanisms stay unclear. We investigated the theatrical role and mechanism of lncRNA Lung cancer associated transcript 1 LUCAT1 in the malignant progress of lung cancer. From May 2022 to March 2023, a total of thirty normal and cancerous tissues were collected from patients diagnosed with non-small cell lung cancer at Zhongke Gengjiu Hospital in Anhui Province, China. The human SPC-A1 and A549 cell lines were chosen as the subjects for the relevant cellular experiments in this study. LncRNAs were expressed in a different manner identified by bioinformatics methods, and the expression levels in lung cancer tissues as well as cells were verified by the qRT-PCR assay. The biological role of LUCAT1 in NSCLC was determined by CCK-8, EdU, and transwell assay. The regulation of ubiquitin of P53 by LUCAT1 was studied, which showed that LUCAT1 was significantly elevated in NSCLC cell lines and patients' tissues (P<0.05). High levels of LUCAT1 promoted the proliferation, invasion, and migration of NSCLC cells. Mechanism studies showed that LUCAT1 was mainly located in the nucleus, which bound to P53 and mediated the ubiquitinated degradation of P53. Meanwhile, LUCAT1 knockdown attenuated the ubiquitination process of P53. In addition, rescue experiments illustrated that LUCAT1 induced the proliferation and invasion of NSCLC cells, and played a key role in the survival and tumorigenicity of NSCLC cells by mediating the ubiquitination of P53. Collectively, LUCAT1 activated the malignant phenotypes of NSCLC cells via regulating P53 ubiquitination, which provided a new idea for the diagnosis and treatment of NSCLC.

NUSAP1 promotes gastric cancer radioresistance by inhibiting ubiquitination of ANXA2 and is suppressed by miR-129-5p

BackgroundRadiotherapy is an important strategy for the treatment of advanced gastric cancer (GC), while the radioresistance limits its effectiveness. Nucleolar and spindle associated protein 1 (NUSAP1) was implicated in cancer progression and chemoresistance. However, the underlying mechanisms of NUSAP1 influencing GC radioresistance remain largely unknown.MethodsMeta-analysis was conducted to systematically evaluate the prognostic value of NUSAP1 in human cancers. Gene set enrichment analysis (GSEA) was conducted using The Cancer Genome Atlas (TCGA) and gene expression omnibus (GEO) datasets. MRNA and protein expressions were detected by qRT-PCR and western blot, respectively. The radiosensitivity of GC cells was observed by colony formation, flow cytometry, comet, immunofluorescence, and animal assays. Immunoprecipitation assay and mass spectrometry were utilized to identify protein associations. MiRNAs binding with NUSAP1 were determined by starbase prediction, luciferase reporter, and RNA immunoprecipitation (RIP) assays.ResultsNUSAP1 high expression predicted worse overall survival (OS) and disease-free survival (DFS) with no statistical heterogeneity through the meta-analysis. Downregulation of NUSAP1 significantly increased GC radiosensitivity by inhibiting colony formation, DNA damage repair, and promoting apoptosis following irradiation. Additionally, NUSAP1 silencing combined with radiation resulted in a synergistic anti-tumor effect in xenograft mouse model. Mechanistically, NUSAP1 interacted with ANXA2, protecting it against protein degradation via impeding its ubiquitination process. NUSAP1 was confirmed as a target of miR-129-5p and negatively regulated by it.ConclusionOur results suggested that NUSAP1 enhanced the radioresistance of GC cells. NUSAP1 could be a promising target to increase GC radiosensitivity.

Ubiquitination and De-Ubiquitination in the Synthesis of Cow Milk Fat: Reality and Prospects.

Ubiquitination modifications permit the degradation of labelled target proteins with the assistance of proteasomes and lysosomes, which is the main protein degradation pathway in eukaryotic cells. Polyubiquitination modifications of proteins can also affect their functions. De-ubiquitinating enzymes reverse the process of ubiquitination via cleavage of the ubiquitin molecule, which is known as a de-ubiquitination. It was demonstrated that ubiquitination and de-ubiquitination play key regulatory roles in fatty acid transport, de novo synthesis, and desaturation in dairy mammary epithelial cells. In addition, natural plant extracts, such as stigmasterol, promote milk fat synthesis in epithelial cells via the ubiquitination pathway. This paper reviews the current research on ubiquitination and de-ubiquitination in dairy milk fat production, with a view to providing a reference for subsequent research on milk fat and exploring new directions for the improvement of milk quality.

ResUbiNet: A Novel Deep Learning Architecture for Ubiquitination Site Prediction

Introduction: Ubiquitination, a unique post-translational modification, plays a cardinal role in diverse cellular functions such as protein degradation, signal transduction, DNA repair, and regulation of cell cycle. Method: Thus, accurate prediction of potential ubiquitination sites is an urgent requirement for exploring the ubiquitination mechanism as well as the disease pathogenesis associated with ubiquitination processes. Results: This study introduces a novel deep learning architecture, ResUbiNet, which utilized a protein language model (ProtTrans), amino acid properties, and BLOSUM62 matrix for sequence embedding and multiple state-of-the-art architectural components, i.e., transformer, multi-kernel convolution, residual connection, and squeeze-and-excitation for feature extractions. Conclusion: The results of cross-validation and external tests showed that the ResUbiNet model achieved better prediction performances in comparison with the available hCKSAAP_UbSite, RUBI, MDCapsUbi, and MusiteDeep models.