Search Results (26)

Post-translational modification (PTM) encompasses diverse modifications, including phosphorylation, methylation, ubiquitin-like modifications (UBLs), and so on, which profoundly influence cellular functions. UFMylation is a recently identified ubiquitin-like modification, which is mediated by the Ubiquitin-like Ubiquitin Fold Modifier 1 (UFM1) conjugation system. The UFM1 conjugation system comprises UFM1, Ubiquitin-like protein activating enzyme 5 (UBA5), UFM1-conjugating enzyme 1 (UFC1), UFM1-specific ligase 1 (UFL1), UFM1-specific protease 1 (UFSP1), UFM1-specific protease 2 (UFSP2), UFM1-binding protein 1 (UFBP1), and CDK5 regulatory subunit-associated protein 3 (CDK5RAP3). Accumulating research has demonstrated that the UFM1 conjugation system regulates various cellular stress responses, including endoplasmic reticulum (ER) stress, protein trafficking, DNA damage repair, and autophagy. Additionally, abnormal stress adaptations of the UFM1 conjugation system contribute to the pathophysiological complications of inflammatory diseases and cancer, underscoring its significance as a key regulatory node in human health and disease. Therefore, this review provides a comprehensive exploration of the structural characteristics of UFM1 conjugation system members and the mechanistic roles of UFMylation by UFM1 conjugation system-mediated diseases related to cellular stress responses, which will not only facilitate the identification of novel diagnostic and prognostic indicators but also enable the identification of specific therapeutic targets for UFM1 conjugation system-related diseases. Full article

Anthocyanins are widespread specialized metabolites that provide pigmentation and antioxidant capacity, contributing to pollinator and seed-disperser attraction and to plant resistance to diverse environmental stresses. In human diets, anthocyanins are valued for their antioxidant and health-promoting properties. The biosynthetic pathway of anthocyanins is relatively conserved across plant species and is controlled by structural genes that encode the enzymes of the pathway along with regulatory genes, particularly transcription factors. This network integrates developmental and environmental signals, with light serving as a dominant cue: anthocyanins typically accumulate in light-exposed tissues and are repressed in darkness. A key node in this light-dependent switch is CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), an E3 ubiquitin ligase that, in the dark, promotes polyubiquitination and proteasome-mediated turnover of positive regulators of anthocyanin production. Although ELONGATED HYPOCOTYL 5 (HY5) is a canonical COP1 target and major activator of anthocyanin biosynthesis, COP1 control of this pathway extends well beyond HY5. Evidence from Arabidopsis and multiple horticultural crops, including apple, pear, eggplant, and tomato, indicates that COP1 also regulates anthocyanin accumulation through interactions with additional transcription factors and regulatory modules. Here, we synthesize recent advances in COP1-centered regulation of anthocyanin biosynthesis, with an emphasis on post-translational mechanisms and COP1 targets beyond HY5. We also discuss emerging opportunities to leverage this regulatory axis for nutritional improvement in horticultural species. Full article

Root rot disease severely threatens tropical fruit production, leading to plant mortality and reduced yields; however, the mechanisms of host defense responses and pathogen infection remain poorly understood. In this study, Fusarium acutatum was isolated from diseased Annona squamosa roots and identified through morphological features and ITS phylogeny (99.8% identity). Infection triggered a marked activation of antioxidant defenses, with elevated POD, SOD, PAL, PPO, and CAT activities. Transcriptomic and TMT-based quantitative proteomic analyses identified 23,791 and 74,403 differentially expressed genes (DEGs) and 367 and 609 differentially expressed proteins (DEPs) in root at 5 and 10 days post inoculation, respectively, relative to the control. These DEGs and DEPs were consistently enriched in pathways involving redox regulation, protein synthesis and processing, ubiquitin-mediated proteolysis, phenylpropanoid and flavonoid metabolism, cell wall remodeling, plant–pathogen interaction and MAPK signaling. Integrated transcriptomic–proteomic correlation analysis showed clear positive associations between key defense-related genes and proteins, suggesting that phenylpropanoid metabolism and reactive oxygen species (ROS) scavenging play central roles in resistance. Key genes such as CHI2, CHS, and CYP were strongly induced and validated by qPCR, supporting coordinated activation of the defense systems. Furthermore, F. acutatum exhibited upregulation of 50 pathogenic-related proteins, including 4 cell wall-degrading enzymes (e.g., CBH1, pectate lyase), 5 metabolic regulation or signal transduction enzymes (e.g., gabD, TPI, and ENO) and 3 potential effectors, suggesting coordinated pathogen strategies for host colonization. Collectively, this study provides comprehensive multi-omics insight into the molecular mechanisms underlying A. squamosa defense against F. acutatum and offers candidate targets supported by omics evidence, serving as a theoretical reference for the management of root rot. Full article

Plant responses to heat stress include complex transcriptional networks and protein regulations in which BTB/POZ-MATH (BPM) proteins participate as a part of ubiquitin-mediated protein degradation. Arabidopsis thaliana contains six BPM genes involved in responses to environmental changes, including heat. Seedlings overexpressing BPM1 (oeBPM1), seedlings with downregulation of BPM1, 4, 5, and 6 (amiR-bpm) and wild type were exposed to 37 °C for 6 h. Treatment caused stronger decline of photosynthesis in oeBPM1 than in amiR-bpm and wild type, although all seedlings recovered after 24 h at 24 °C. The activity of the antioxidant enzymes catalase, guaiacol peroxidase, and ascorbate peroxidase remained unchanged in oeBPM1, but increased in amiR-bpm and wild type. Heat stress induced HSP70 and HSP90 in all seedlings but expression remained notably higher in amiR-bpm after recovery. DREB2A and HSFA3 expression increased in all seedlings immediately after stress, with the strongest induction in amiR-bpm. In amiR-bpm and wild type, BPM2 expression was induced immediately after exposure, while BPM1, BPM3, BPM4, and BPM6 were upregulated in wild type after recovery. In oeBPM1 seedlings, BPM4 expression decreased and BPM6 expression increased immediately after treatment at 37 °C for 6 h. The results suggest that BPM proteins modulate heat stress response by influencing photosynthesis, activation of antioxidant enzymes, accumulation of HSPs, and expression of heat-responsive genes, thus contributing to the different physiological strategies observed in A. thaliana lines with altered expression of BPM genes. Full article

Drought stress caused a significant threat to apple growth and production. Although there is an increasing studies concerning the molecular mechanism in apple response to drought, most of these studies focus on the leaves. However, the roots is the first organism to sense the drought signal and play important role in drought response. The molecular mechanisms underlying the apple roots in response to drought needs to be further explored. In this study, we conducted a comparative transcriptomic analysis of roots from drought-resistant (Malus prunifolia) and drought-susceptible (Malus hupehensis) apple genotypes under different soil water contents with 60% (control), 30% (mild drought), 10% (moderate drought), and 5% (severe drought). The further Mapman pathways analysis showed that Malus prunifolia exhibited more rapid activation of abscisic acid (ABA) biosynthesis (NCED, PYL) and signaling pathway, as well as the induction of transcription factors (NAC, WRKY, MYB) compare to Malus prunifolia under mild and moderate drought treatments. This might be one of the reasons why Malus prunifolia exhibits greater drought resistance. Furthermore, weighted gene co-expression network analysis (WGCNA) was adopted for the identification of core drought-responsive genes. Notably, three hub genes, ubiquitin-conjugating enzyme 32 (UBC32), basic leucine-zipper 4 (bZIP4), and highly ABA-induced PP2C gene 2 (HAI2), were selected from the different modules, suggesting their vital roles in drought response. Taken together, our results gain insights into the global expression alterations in drought-resistance and susceptible germplasms under different drought conditions and identify some key genes involved in drought response, which is helpful for drought-resistant apple breeding in future. Full article

Background: Anti-MDA5 antibody-bearing (anti-MDA5⁺)-dermatomyositis (DM) or polymyositis (PM) is notorious for causing rapidly progressive interstitial lung disease (RPILD) and/or cancers with high mortality rate. However, anti-MDA5 antibodies (Abs) are also found in other connective tissue diseases and their link with RPILD, especially with regard to the mortality rate, are unknown. Methods: We retrospectively recruited 71 patients bearing anti-MDA5-Abs in serum, stratified them in terms of a presence or absence of RPILD, and evaluated their clinical features, laboratory findings, associated myositis antibodies, concurrent connective tissue disease (CTD) as well as newly developed malignancies. Results: In total, 39 (55%) patients presented with DM/PM, but 32 (45%) did not. In total, 22 of the former and 11 of the latter developed RPILD eventually, accounting for a total of 46% of all MDA-5 bearing patients. On the other hand, 15 of all 71 (21.1%) patients had cancers. Among the 32 patients who did not have DM/PM, 27 (38.0% of all 71) had other CTDs, indicating that only 5 (7.0% of 71) patients did not have CTDs. Senility (odds ratio (OR) = 1.816, p = 0.032), presence of anti-Ro-52 antibody (OR = 1.676, p = 0.018), elevated C-reactive protein (CRP, OR = 4.354, p < 0.001) and carcinoembryonic antigen (CEA, OR = 2.625, p = 0.005) posed risks for RPILD. High lactose dehydrogenase (LDH, p = 0.009), CRP (p = 0.001) and CEA (p = 0.001), ferritin (p ≤ 0.001) and low albumin (p ≤ 0.001) were significantly associated with mortality. Anti-SAE antibodies were negatively correlated with RPILD as analyzed by univariate (OR = 0.245, p = 0.017) and multivariate (OR = 0.058, p = 0.036) regressions, indicating that they may be a protective factor in relation to RPILD (OR = 0.543, p = 0.008) or fatality (OR = 0.707, p = 0.012), which was also demonstrated in subgroup analyses. Conclusions: In contrast to various risk factors for RPILD or mortality, anti-SAE antibodies might conversely be a protective factor in anti-MDA5⁺ patients. Full article

Ubiquitin carboxyl-terminal hydrolase L1 (UCHL1), also known as Parkinson’s disease protein 5, is a highly expressed protein in the brain. It plays an important role in the ubiquitin–proteasome system (UPS), where it acts as a deubiquitinase (DUB) enzyme. Being the smallest member of the UCH family of DUBs, it catalyzes the reaction of ubiquitin precursor processing and the cleavage of ubiquitinated protein remnants, thus maintaining the level of ubiquitin monomers in the brain cells. UCHL1 mutants, containing amino acid substitutions, influence catalytic activity and its aggregability. Some of them protect cells and transgenic mice in toxin-induced Parkinson’s disease (PD) models. Studies of putative protein partners of UCHL1 revealed about sixty individual proteins located in all major compartments of the cell: nucleus, cytoplasm, endoplasmic reticulum, plasma membrane, mitochondria, and peroxisomes. These include proteins related to the development of PD, such as alpha-synuclein, amyloid-beta precursor protein, ubiquitin-protein ligase parkin, and heat shock proteins. In the context of the catalytic paradigm, the importance of these interactions is not clear. However, there is increasing understanding that UCHL1 exhibits various effects in a catalytically independent manner through protein–protein interactions. Since this protein represents up to 5% of the soluble protein in the brain, PD-related changes in its structure will have profound effects on the proteomes/interactomes in which it is involved. Growing evidence is accumulating that the role of UCHL1 in PD is obviously determined by a balance of canonic catalytic activity and numerous activity-independent protein–protein interactions, which still need better characterization. Full article

Mass spectrometry-based chemical proteomic approaches using limited proteolysis have become a powerful tool for the identification and analysis of the interactions between a small molecule (SM) and its protein target(s). Gracilioether A (GeA) is a polyketide isolated from a marine sponge, for which we aimed to trace the interactome using this strategy. DARTS (Drug Affinity Responsive Target Stability) and t-LiP-MS (targeted-Limited Proteolysis-Mass Spectrometry) represented the main techniques used in this study. DARTS was applied on HeLa cell lysate for the identification of the GeA target proteins, and t-LiP-MS was employed to investigate the protein’s regions involved in the binding with GeA. The results were complemented through the use of binding studies using Surface Plasmon Resonance (SPR) and in silico molecular docking experiments. Ubiquitin carboxyl-terminal hydrolase 5 (USP5) was identified as a promising target of GeA, and the interaction profile of the USP5-GeA complex was explained. USP5 is an enzyme involved in the pathway of protein metabolism through the disassembly of the polyubiquitin chains on degraded proteins into ubiquitin monomers. This activity is connected to different cellular functions concerning the maintenance of chromatin structure and receptors and the degradation of abnormal proteins and cancerogenic progression. On this basis, this structural information opens the way to following studies focused on the definition of the biological potential of Gracilioether A and the rational development of novel USP5 inhibitors based on a new structural skeleton. Full article

Protein arginine methyltransferase 5 (PRMT5) is the primary enzyme generating symmetric dimethylarginine (sDMA) on numerous substrates, through which it regulates many cellular processes, such as transcription and DNA repair. Aberrant expression and activation of PRMT5 is frequently observed in various human cancers and associated with poor prognosis and survival. However, the regulatory mechanisms of PRMT5 remain poorly understood. Here, we report that TRAF6 serves as an upstream E3 ubiquitin ligase to promote PRMT5 ubiquitination and activation. We find that TRAF6 catalyzes K63-linked ubiquitination of PRMT5 and interacts with PRMT5 in a TRAF6-binding-motif-dependent manner. Moreover, we identify six lysine residues located at the N-terminus as the primarily ubiquitinated sites. Disruption of TRAF6-mediated ubiquitination decreases PRMT5 methyltransferase activity towards H4R3 in part by impairing PRMT5 interaction with its co-factor MEP50. As a result, mutating the TRAF6-binding motifs or the six lysine residues significantly suppresses cell proliferation and tumor growth. Lastly, we show that TRAF6 inhibitor enhances cellular sensitivity to PRMT5 inhibitor. Therefore, our study reveals a critical regulatory mechanism of PRMT5 in cancers. Full article

Ubiquitination and deubiquitination are reversible processes that modify the characteristics of target proteins, including stability, intracellular localization, and enzymatic activity. Ubiquitin-specific proteases (USPs) constitute the largest deubiquitinating enzyme family. To date, accumulating evidence indicates that several USPs positively and negatively affect metabolic diseases. USP22 in pancreatic β-cells, USP2 in adipose tissue macrophages, USP9X, 20, and 33 in myocytes, USP4, 7, 10, and 18 in hepatocytes, and USP2 in hypothalamus improve hyperglycemia, whereas USP19 in adipocytes, USP21 in myocytes, and USP2, 14, and 20 in hepatocytes promote hyperglycemia. In contrast, USP1, 5, 9X, 14, 15, 22, 36, and 48 modulate the progression of diabetic nephropathy, neuropathy, and/or retinopathy. USP4, 10, and 18 in hepatocytes ameliorates non-alcoholic fatty liver disease (NAFLD), while hepatic USP2, 11, 14, 19, and 20 exacerbate it. The roles of USP7 and 22 in hepatic disorders are controversial. USP9X, 14, 17, and 20 in vascular cells are postulated to be determinants of atherosclerosis. Moreover, mutations in the Usp8 and Usp48 loci in pituitary tumors cause Cushing syndrome. This review summarizes the current knowledge about the modulatory roles of USPs in energy metabolic disorders. Full article

Gold nanoparticles (AuNPs) are widely used in biomedicine due to their remarkable therapeutic applications. However, little is known about their cytotoxic effects on the ubiquitin proteasome system (UPS). Herein, the cytotoxicity of different sizes of AuNPs (5, 10, and 80 nm) on the UPS was investigated with a particular focus on deubiquitinating enzymes (DUBs) such as ubiquitin-specific proteases (USP) and ubiquitin carboxyl-terminal hydrolases (UCHL-1) in human alveolar epithelial adenocarcinoma (A549). It was found that all sizes of AuNPs reduced the percentage of viable A549 cells and increased lactate dehydrogenase (LDH) release, measured using the MTT and LDH assays, respectively. Furthermore, the 5 nm AuNPs were found to exhibit greater cytotoxicity than the 10 and 80 nm AuNPs. In addition, apoptosis and necrosis were activated through reactive oxygen species (ROS) generation due to AuNPs exposure. The internalisation of AuNPs in A549 cells increased with increasing particle size (80 > 10 > 5 nm). Interestingly, the expression of USP7, USP8, USP10, and UCHL-1 was significantly (p < 0.001) downregulated upon treatment with 5–30 µg/mL of all the AuNPs sizes compared to control cells. Moreover, the inhibition of these proteins triggered mitochondrial-related apoptosis through the upregulation of poly (ADP-ribose) polymerase (PARP), caspase-3, and caspase-9. Collectively, these results indicate that AuNPs suppress the proliferation of A549 cells and can potentially be used as novel inhibitors of the proteasome. Full article

Background: In 2019, the world witnessed the onset of an unprecedented pandemic. By February 2022, the infection by SARS-CoV-2 has already been responsible for the death of more than 5 million people worldwide. Recently, we and other groups discovered that SARS-CoV-2 infection induces ER stress and activation of the unfolded protein response (UPR) pathway. Degradation of misfolded/unfolded proteins is an essential element of proteostasis and occurs mainly in lysosomes or proteasomes. The N-terminal arginylation of proteins is characterized as an inducer of ubiquitination and proteasomal degradation by the N-degron pathway. Results: The role of protein arginylation during SARS-CoV-2 infection was elucidated. Protein arginylation was studied in Vero CCL-81, macrophage-like THP1, and Calu-3 cells infected at different times. A reanalysis of in vivo and in vitro public omics data combined with immunoblotting was performed to measure levels of arginyl-tRNA-protein transferase (ATE1) and its substrates. Dysregulation of the N-degron pathway was specifically identified during coronavirus infections compared to other respiratory viruses. We demonstrated that during SARS-CoV-2 infection, there is an increase in ATE1 expression in Calu-3 and Vero CCL-81 cells. On the other hand, infected macrophages showed no enzyme regulation. ATE1 and protein arginylation was variant-dependent, as shown using P1 and P2 viral variants and HEK 293T cells transfection with the spike protein and receptor-binding domains (RBD). In addition, we report that ATE1 inhibitors, tannic acid and merbromine (MER) reduce viral load. This finding was confirmed in ATE1-silenced cells. Conclusions: We demonstrate that ATE1 is increased during SARS-CoV-2 infection and its inhibition has potential therapeutic value. Full article

The maintenance of muscle homeostasis is vital for life and health. Skeletal muscle atrophy not only seriously reduces people’s quality of life and increases morbidity and mortality, but also causes a huge socioeconomic burden. To date, no effective treatment has been developed for skeletal muscle atrophy owing to an incomplete understanding of its molecular mechanisms. Exercise therapy is the most effective treatment for skeletal muscle atrophy. Unfortunately, it is not suitable for all patients, such as fractured patients and bedridden patients with nerve damage. Therefore, understanding the molecular mechanism of skeletal muscle atrophy is crucial for developing new therapies for skeletal muscle atrophy. In this review, PubMed was systematically screened for articles that appeared in the past 5 years about potential therapeutic strategies for skeletal muscle atrophy. Herein, we summarize the roles of inflammation, oxidative stress, ubiquitin-proteasome system, autophagic-lysosomal pathway, caspases, and calpains in skeletal muscle atrophy and systematically expound the potential drug targets and therapeutic progress against skeletal muscle atrophy. This review focuses on current treatments and strategies for skeletal muscle atrophy, including drug treatment (active substances of traditional Chinese medicine, chemical drugs, antioxidants, enzyme and enzyme inhibitors, hormone drugs, etc.), gene therapy, stem cell and exosome therapy (muscle-derived stem cells, non-myogenic stem cells, and exosomes), cytokine therapy, physical therapy (electroacupuncture, electrical stimulation, optogenetic technology, heat therapy, and low-level laser therapy), nutrition support (protein, essential amino acids, creatine, β-hydroxy-β-methylbutyrate, and vitamin D), and other therapies (biomaterial adjuvant therapy, intestinal microbial regulation, and oxygen supplementation). Considering many treatments have been developed for skeletal muscle atrophy, we propose a combination of proper treatments for individual needs, which may yield better treatment outcomes. Full article

Aqueous humor (AH) can be easily and safely used to evaluate disease-specific biomarkers in ocular disease. The aim of this study was to identify specific proteins biomarkers in the AH of retinoblastoma (RB) patients at various stages of the disease. We analyzed the proteome of 53 AH samples using high-resolution mass spectrometry. We grouped the samples according to active vitreous seeding (Group 1), active aqueous seeding (Group 2), naive RB (group 3), inactive RB (group 4), and congenital cataracts as the control (Group 5). We found a total of 889 proteins in all samples. Comparative parametric analyses among the different groups revealed three additional proteins expressed in the RB groups that were not expressed in the control group. These were histone H2B type 2-E (HISTH2B2E), InaD-like protein (PATJ), and ubiquitin conjugating enzyme E2 V1 (UBE2V1). Upon processing the data of our study with the OpenTarget Tool software, we found that glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and CD44 were more highly expressed in the RB groups. Our results provide a proteome database regarding AH related to RB disease that may be used as a source of biomarkers. Further prospective studies should validate our finding in a large cohort of RB patients. Full article

Ubiquitin-fold modifier 1 (UFM1), a newly identified ubiquitin-like molecule (UBLs), is evolutionarily expressed in multiple species except yeast. Similarly to ubiquitin, UFM1 is covalently attached to its substrates through a well-orchestrated three-step enzymatic reaction involving E1, the UFM1-activating enzyme (ubiquitin-like modifier-activating enzyme 5, UBA5); E2, the UFM1-conjugating enzyme 1 (UFC1); and E3, the UFM1-specific ligase 1 (UFL1). To date, numerous studies have shown that UFM1 modification is implicated in various cellular processes, including endoplasmic reticulum (ER) stress, DNA damage response and erythroid development. An abnormal UFM1 cascade is closely related to a variety of diseases, especially tumors. Herein, we summarize the process and functions of UFM1 modification, illustrating the relationship and mechanisms between aberrant UFMylation and diversified tumors, aiming to provide novel diagnostic biomarkers or therapeutic targets for cancer treatments. Full article