Search Results (1,593)

Climate change is intensifying soil salinization, posing a major threat to crop establishment and productivity, particularly in arid and semi-arid regions. Barley (Hordeum vulgare L.), one of the most salt-tolerant cereals, offers valuable genetic resources for improving salinity resilience at early growth stages. This study exploited the genetic diversity of the Nested Association Mapping (NAM) population Halle Exotic Barley-25 (HEB-25) to dissect salinity tolerance during germination and seedling developmental stages. First, the HEB-25 parental lines (25 wild barley genotypes and cv. Barke) were evaluated under salinity treatment to identify contrasting responses. Based on this screening, four HEB families (01, 04, 09, and 22) were selected out of 25 HEB families for detailed phenotypic and genomic analysis. Seeds of the selected HEB families were subjected to 40% seawater salinity stress and control treatments to assess germination percentage and seedling traits, including shoot length, root length, fresh weight (FW), dry weight (DW), DW/FW ratio, root–shoot ratio, and salt tolerance index (STI). Substantial variation was observed among families for all measured traits under salinity stress. STI values enabled clear differentiation among families: Family 01 exhibited the most consistent overall tolerance profile, Family 22 showed the strongest sensitivity in biomass traits, and Family 04 displayed a trait-specific response with sensitivity at the family-mean level but exceptional within-family diversity, harboring some of the highest individual TI values across the population. A genome-wide association study was conducted using 32,995 SNP markers. A total of 27 significant SNPs were identified, corresponding to 20 quantitative trait loci (QTLs). Of these, 12 QTLs were detected under control conditions, 16 under seawater treatment, and 21 based on tolerance indices, indicating both constitutive and stress-responsive genetic effects. Gene annotation within these regions revealed approximately 23 candidate genes associated with abiotic stress tolerance, including genes involved in ion transport, osmotic adjustment, kinases and stress signaling pathways. HEB_22_003, HEB_04_087, and HEB_01_013 represent the most promising genotypes for salinity breeding. These findings highlight the effectiveness of combining precise phenotyping with high-resolution genomic analysis in the HEB-25 population to uncover the genetic architecture of salinity tolerance at early developmental stages. We identified 20 salinity-responsive QTLs, including five major-effect loci on chromosomes 2H, 4H, 5H, and 7H that consistently explained the largest share of phenotypic variation. These loci co-localized with candidate genes linked to ion homeostasis, Ca²⁺-mediated signaling, protein glycosylation, epigenetic regulation, and root system plasticity, revealing key mechanisms underlying early-stage salt adaptation in barley. The strong and contrasting responses of Family 01 and Family 04 provide an excellent genetic framework for functional validation of tolerance alleles. Collectively, these genomic resources establish a robust foundation for QTL pyramiding, marker-assisted breeding, and the development of climate-resilient barley cultivars for saline agroecosystems. Full article

Microbial α-L-rhamnosidases are increasingly recognised as selective biocatalysts in food biotechnology, nutraceutical production, and health-related applications. These glycoside hydrolases catalyse the hydrolysis of terminal alpha-L-rhamnose residues from flavonoids, terpenoids, saponins, and other glycosylated natural products, thereby modulating sensory properties, solubility, intestinal absorption, and biological activity. While their traditional uses include debittering citrus juice and enhancing wine aroma, recent evidence demonstrates their wider value in selective flavonoid biotransformation, production of rare mono-glycosylated derivatives, probiotic fermentations, and microbiome-associated metabolism. This review summarises microbial sources, catalytic mechanisms, CAZy classification, substrate specificity, structure–function relationships, analytical methods, industrial process engineering, and emerging applications in functional foods and targeted nutraceutical applications. Particular attention is given to the distinction between alpha-(1→2)- and alpha-(1→6)-linked substrates, the production of isoquercitrin and prunin, recombinant enzyme platforms, immobilised biocatalysts, and potential future opportunities arising from metagenomics, synthetic biology, and AI-assisted protein engineering. Full article

Glycosylation, glycogen metabolism, and ubiquitination represent three fundamental cellular processes that are traditionally studied as distinct aspects of biology. Glycosylation and glycogen metabolism are unique carbohydrate-based pathways. The process of glycosylation generates structurally diverse glycans that regulate protein folding, cell signaling, and host–pathogen interactions, while glycogen serves as a glucose reserve essential for energy homeostasis. Emerging evidence reveals a deep mechanistic connection between these pathways, particularly in the context of brain biology and inherited metabolic diseases. Here, we present recent research linking glycosylation defects with glycogen metabolism, highlighting how changes in the shared metabolites and enzymatic pathways contribute to human health and disease. We then discuss the overlapping disease symptoms of congenital disorders of glycosylation and glycogen storage diseases, with particular emphasis on polyglucosan body-forming diseases. We also highlight the role of non-canonical ubiquitin ligase complexes such as laforin–malin and LUBAC and present emerging evidence for their potential role in the glycogen quality-control mechanism. Finally, we review current therapeutic strategies for CDGs and GSDs, including monosaccharide supplementation, glycogen synthase modulation, and gene therapy. Together, this review underscores glycogen as more than an energy store—as a key contributor to glycosylation homeostasis and cellular regulation in health and disease. Full article

Glioblastoma (GB) remains one of the most therapy-resistant solid tumors, characterized by profound metabolic plasticity, intratumoral heterogeneity, and a highly immunosuppressive microenvironment. While immunotherapies such as chimeric antigen receptor T (CAR-T) cells have shown promise in hematological malignancies, their efficacy in GB has been limited. Emerging evidence suggests that tumor-specific metabolic dependencies and post-translational modifications (PTMs) may represent exploitable vulnerabilities. This review discusses disulfidptosis, a recently described form of regulated cell death driven by disulfide stress under conditions of limited reducing capacity, as a context-dependent metabolic–redox vulnerability in GB. We further discuss how altered protein glycosylation and glycocalyx architecture in glioblastoma regulate cell survival, death signaling, and immune recognition. Particular emphasis is placed on the glycosylation of surface antigens targeted by CAR-T cells, including EGFR/EGFRvIII, IL-13Rα2, mesothelin, B7-H3, HER2, and GD2, and on how glycan-dependent epitope accessibility may limit therapeutic efficacy. Finally, we distinguish disulfidptosis, whose direct relevance to CAR-T-cell responses remains to be established, from glycosylation and glycocalyx remodeling as more direct determinants of target–antigen accessibility and immune recognition. Therapeutic strategies addressing these vulnerabilities may provide rational opportunities to improve CAR-T-based and combinatorial therapies for GB. Full article

Colorectal cancer (CRC) is the third most common malignancy worldwide. Detailed characterization of cell surface proteins (CSPs) is essential for the identification of prognostic biomarkers and the development of novel therapeutic strategies. Cancer progression and epithelial cell polarity influence the expression levels and subcellular localization of these proteins. However, quantitative information on the distribution of CSPs between the apical and basolateral membranes remains limited, particularly in CRC cells. Here, we developed a rapid, high-throughput method based on the enrichment of biotinylated peptides and proteins from the apical and basolateral surfaces of polarized CRC epithelial cells (HT29 and HCT116), followed by LC-MS/MS analysis. This approach enables the simultaneous identification of the side-specific distribution of ~1200 CSPs. In addition, almost 500 potential N-glycosylation sites with the canonical consensus sequence of these proteins were identified, which may serve as targets for future site-specific glycosylation analyses. To evaluate the sensitivity of the method, we altered the surface proteome by generating TKS4-knockout cells and identified several surface markers whose expression levels differed significantly from those of wild-type cells. Overall, our findings provide new insights into the role of CSPs in CRC cells and gene-edited models, particularly in the context of TKS4-dependent epithelial-to-mesenchymal transition (EMT)-like phenotypes that model cancer metastasis. Full article

Background: Steatotic liver disease (SLD) and sarcopenia are lifestyle-related conditions for which prevention is critical. The phase angle, which is derived from impedance, reactance, and resistance values obtained via bioelectrical impedance analysis, has emerged as a potential marker of sarcopenia. Additionally, amino acids have been implicated in the pathogenesis of both SLD and sarcopenia. This epidemiological study investigated the association between SLD and sarcopenia in a general population cohort. Methods: This cross-sectional study included 281 participants with metabolic dysfunction-associated steatotic liver disease (MASLD), 72 with metabolic alcohol-associated liver disease (MetALD), and 54 with alcohol-associated liver disease (ALD). Associations between phase angle, Mac-2-binding protein glycosylation isomer (M2BPGi) as a marker of liver fibrosis, and serum amino acid levels were analyzed. Results: The phase angle was significantly higher in the MetALD group than in the MASLD and ALD groups. Multivariate analysis identified MASLD as an independent risk factor for a low phase angle compared with MetALD. M2BPGi levels were lower in MetALD than in MASLD, and M2BPGi showed a negative correlation with the phase angle. Furthermore, MetALD was characterized by lower serine and glutamine levels than MASLD, with serine demonstrating a negative correlation with the phase angle. Conclusions: Although the possibility of residual confounding factors cannot be excluded, the present study suggests that phase angle may serve as a sensitive marker for the early decline in muscle mass in patients with SLD, comparable to grip strength and skeletal muscle mass index. Full article

Glycosylation is a critical structural modification that shapes the pharmacological properties of bioactive ingredients from Traditional Chinese Medicine (TCM), and UDP-glycosyltransferases (UGTs) are the core rate-limiting biocatalysts mediating this process. Traditional plant extraction methods are constrained by resource scarcity, long growth cycles, low target content and high environmental costs, which cannot meet the large-scale industrial demand for high-value medicinal glycosides. This review systematically outlines the latest global advances in medicinal plant UGT research, covering family classification and physiological functions, multi-omics and AI-assisted gene mining, molecular basis of substrate recognition and catalytic specificity, protein engineering for performance optimization, and the construction of full-spectrum biomanufacturing systems including in vitro multi-enzyme cascades, microbial cell factories and plant suspension cell cultures. We further discuss the core challenges of industrial scale-up, regulatory compliance and clinical translation, as well as the significant economic and technical advantages of synthetic biology-based UGT biomanufacturing platforms. This work provides a complete technical framework for the engineering application of medicinal plant UGTs, to support the green and scalable production of rare natural therapeutic glycosides. Full article

Tyrosinase-related protein 1 (Tyrp1) is a melanosomal glycoprotein required for eumelanin biosynthesis through the oxidation of 5,6-dihydroxyindole-2-carboxylic acid (DHICA). Pathogenic variants in Tyrp1 cause oculocutaneous albinism type 3 (OCA3), but the molecular basis by which individual substitutions impair Tyrp1 stability and activity remains incompletely understood. Here, we examined wild-type Tyrp1 and three missense variants associated with OCA3: R356Q and R326H as OCA3-related variants, and D308N as a benign control; these were under conditions relevant to melanosome maturation. To assess stability, we developed a urea-induced unfolding assay in which His-tagged Tyrp1 variants were immobilized to Ni-NTA magnetic beads before chemical denaturation. R356Q was the most destabilized variant, with a ΔΔG of 0.695 kcal/mol at pH 5.0 (acidic conditions) and 1.998 kcal/mol at pH 7.4 (near-neutral conditions) relative to wild-type. R326H showed intermediate destabilization, whereas D308N behaved similarly to wild-type. DHICA oxidation assays in the presence of MBTH showed about 20% reduced catalytic activity for R356Q, particularly under acidic conditions. Molecular dynamics simulations and ligand docking were consistent with these findings and indicated that R356Q increases conformational flexibility and perturbs structural integrity. In contrast, glycosylation reduced conformational fluctuations and enhanced stability across Tyrp1 and mutant variants examined. Together, these results show that pH, glycosylation, and disease-associated substitutions collectively modulate Tyrp1 folding energetics and catalytic competence and identify R356Q as a strongly destabilizing OCA3 variant. By defining how disease-associated Tyrp1 substitutions affect protein stability and function, this study may provide a framework for interpreting genotype–phenotype relationships and improving molecular diagnosis of OCA3. Full article

The alkaline pectate lyase A from Paenibacillus barcinonensis, encoded by pelA (GenBank accession no. CAB40884), is an enzyme with high activity on pectin and potential application in sustainable industrial biotechnology. In this study, pelA was expressed in Saccharomyces cerevisiae by using different domains of the cell wall protein Pir4 as translational fusion partners. Given the presence of five potential N-glycosylation sites in the amino acid sequence coded by pelA, and two of them in conserved regions of class III pectate lyases, the effect of glycosylation on the enzymatic activity of the recombinant enzyme was investigated by expressing the recombinant fusion proteins in both standard and glycosylation deficient strains of S. cerevisiae. The correct targeting of the recombinant fusion proteins was confirmed by Western blot analysis using Pir-specific antibodies, whilst enzymatic activity on polygalacturonic acid was demonstrated on both plate assays and colorimetric assays. Maximum activities were over two and a half times higher when the enzyme was expressed in the glycosylation deficient strain, suggesting a better adaptation of this strain to the secretion of the functional enzyme. Full article

Myocardial fibrosis is a common pathological feature of multiple cardiovascular diseases, including heart failure, hypertension, and myocardial infarction, and is associated with poor prognosis. Despite extensive research, clinically validated molecular biomarkers for early diagnosis and reliable therapeutic targets for myocardial fibrosis remain limited. Post-translational modifications (PTMs), including phosphorylation, acetylation, ubiquitination, SUMOylation, and glycosylation, are critical regulators of fibrosis-related signaling pathways, yet a systematic bioinformatics-driven identification of PTM-related hub genes has not been performed. Three publicly available GEO datasets (GSE57345, GSE133054, GSE76314) comprising cardiac tissue from heart failure and control patients were integrated. Differentially expressed genes (DEGs) were identified using the limma package, then intersected with a curated PTM gene set derived from PhosphoSitePlus and UniProt databases. Weighted gene co-expression network analysis (WGCNA) identified fibrosis-associated modules, and protein–protein interaction (PPI) network analysis via STRING and CytoHubba pinpointed hub genes. Diagnostic performance was assessed by receiver operating characteristic (ROC) analysis across independent validation cohorts. Immune cell infiltration was estimated using CIBERSORT.Molecular docking with AutoDock Vina (version 1.2.3) was performed to evaluate binding affinity of FDA-approved cardiovascular drugs against identified hub protein targets. A total of 863 DEGs were identified in the training cohort (|log₂FC| > 1.0, adjusted p < 0.05), of which 138 overlapped with the PTM gene set. WGCNA revealed a turquoise module (r = 0.79, p < 0.001) most significantly correlated with fibrosis severity. PPI analysis identified five hub genes: SIRT3, SMAD3, NEDD4L, UBC9, and CAMK2D. ROC analysis demonstrated strong diagnostic performance (AUC range: 0.82–0.92) validated in independent cohorts. Hub genes showed significant correlations with M2 macrophage infiltration. Molecular docking identified spironolactone and finerenone as top-ranked ligands with binding energies of −8.7 and −8.4 kcal/mol against SMAD3 and SIRT3, respectively. This study, which is entirely in silico and based on publicly available transcriptomic datasets, systematically identifies five PTM-related hub genes as candidate diagnostic biomarkers and prioritised drug-repurposing targets in myocardial fibrosis. These findings are hypothesis-generating and require experimental validation (protein-level confirmation, cell- and animal-based functional assays, and biophysical binding studies) before any diagnostic or therapeutic claim can be made. Full article

Background/Objectives: Protein–carbohydrate interactions are implicated in amyloid aggregation pathways associated with Alzheimer’s disease (AD). Designing glycomimetics that modulate amyloid assembly represents a promising strategy. In addition, the interaction of Aβ_1–42 oligomers (Aβo) with prion protein (PrP^C) activates Fyn kinase and leads to Tau hyperphosphorylation, another process characterizing AD. Thus, we generated a library of phenyl 2-acetamidoselenogalactoside mimetics to evaluate their interactions with Aβo and disruption of Aβo–PrP^C binding, and consequently their potential to inhibit Fyn kinase activation. Methods: The synthetic approach comprised azidophenylselenylation, a modified one-pot Staudinger reduction–acylation, a selective α-glycosylation, and deacetylation. Structural diversity was achieved mainly via acylation or ureation. The compounds were screened for binding to Aβo using STD-NMR, ¹⁹F-NMR, and rapid equilibrium dialysis (RED). ADME properties were assessed through microsomal metabolism and solubility assays, while cytotoxicity was evaluated by MTT assays in human embryonic kidney (HEK) cells. Results: Several compounds bound Aβo in STD-NMR experiments, mainly through aromatic and anomeric protons, and phenyl 2-deoxy-2-phenylureido-1-seleno-α-d-galactopyranoside (34) showed the most consistent response, with >50% increase in relative binding signal in competition assays, demonstrating also some inhibition of Aβo–PrP^C interactions (12%). Selenium at the anomeric position enhanced binding compared to sulphur and oxygen analogs. RED experiments confirmed weak binding interactions, consistent with STD-NMR results. ADME revealed that acetylated compounds undergo microsomal metabolism, whereas deacetylated derivatives displayed high aqueous solubility (>100 μM) and showed no cytotoxicity. Conclusions: Phenyl 2-acetamidoselenogalactosides are a novel class of amyloid-binding glycomimetics. Among them, 34 emerges as the most promising compound, combining favorable solubility, metabolic stability, low toxicity, and measurable interference with Aβo and Aβo–PrP^C interactions, thus supporting further developments toward therapeutic applications in AD. Full article

ATP-binding cassette (ABC) transporters are one of the largest superfamilies of membrane proteins, but little is known about the structural and evolutionary features of their non-domain regions. To clarify the diversity of these non-canonical regions across evolutionary lineages, we performed an analysis of intrinsically disordered regions, site-specific selection and predicted post-translational modification (PTM) sites among five architectural classes involving 1581 prokaryotic and eukaryotic sequences. Linker and flanking regions were more disordered than transmembrane and nucleotide-binding domains in all architectures. Disorder fraction was significantly different between region types after phylogenetic correction (Pagel’s λ ≈ 0.97). Predicted PTM sites are enriched in disordered non-domain segments, with N-linked glycosylation and phosphoserine showing the strongest positive enrichment. A total of 140 sites satisfied a tiered conservation criterion (MusiteDeep score ≥ 0.5; cross-species conservancy ≥ 30%), including 40 high-confidence or moderate-confidence sites (conservancy ≥ 50%) as well as novel phosphotyrosine candidates in half transporters and NBD-only proteins. Site-specific selection analyses showed pervasive purifying selection across domain cores and architecture-dependent enrichment of episodic positive selection in non-domain regions, with significant non-domain enrichment in full reverse and half forward transporters (Fisher’s exact, BH-adjusted p < 0.05). In summary, these findings establish that non-canonical regions of ABC transporters are evolutionarily dynamic and contain conserved predicted modification sites, supporting the idea that these regions are evolutionary dynamic segments that deserve experimental characterization as candidate regulatory interfaces. Full article

Obesity is a major global health challenge characterized by chronic low-grade inflammation, oxidative stress, and an increased risk of cardiometabolic disorders. Although sex-related differences in inflammatory and redox biomarkers have been reported in obese populations, the molecular mechanisms underlying this heterogeneity remain incompletely understood. In this study, we applied a proteomics-based approach to investigate urinary extracellular vesicles from 45 obese individuals (BMI 30–40 kg/m²; age 50–70 years) in order to identify molecular signatures associated with metabolic dysregulation. Shotgun proteomics analysis performed by nanoLC–MS/MS enabled the identification of 3822 proteins. Hierarchical clustering of proteomic profiles revealed two distinct molecular groups, predominantly enriched in males (Group I) and females (Group II). Label-free quantitative analysis identified 466 differentially abundant proteins between the two clusters. Functional enrichment analysis highlighted pathways associated with immune response, metabolic regulation, and redox homeostasis, including glycolysis/gluconeogenesis, lysosome activity, leukocyte transendothelial migration, and glutathione, cysteine and methionine metabolism. Notably, proteins related to ferroptosis were enriched, suggesting the involvement of iron-dependent oxidative cell death mechanisms in the metabolic imbalance observed in a subset of subjects. Furthermore, the non-enzymatic glycosylation of urinary proteins was significantly higher in Group I compared with Group II (p = 0.0002), indicating increased formation of advanced glycation products in individuals with a more pronounced pro-oxidant state. Preliminary follow-up data suggested a higher incidence of pathological events, including cardiovascular complications, among individuals belonging to Group I. Overall, these findings demonstrate that urinary proteomic profiling can identify distinct molecular phenotypes among obese individuals and highlight oxidative stress, ferroptosis, and protein glycation as potential determinants of metabolic vulnerability, supporting the use of non-invasive proteomic approaches for improved risk stratification in obesity. Full article

Human metapneumovirus (HPMV) is a significant pathogen that causes lower respiratory tract infections. Given the weak immunogenicity thereof, and the few relevant studies, the utility of the viral membrane protein G as a vaccine remains controversial. In this study, the G extracellular domain (RMG) of HMPV was expressed either alone or fused with the cholera toxin B subunit (CTB) and “cross-reacting material 197” (CRM197) carrier proteins (giving G-CTB/G and CRM197), to enhance immunogenicity. The non-glycosylated G protein (REG) expressed in Escherichia coli served as a control. SDS-PAGE and anti-His tag Western blotting verified that each protein was successfully expressed and correctly identified. BALB/c mice were immunized with each protein and subjected to challenge with HMPV. The results showed that, although immunization with RMG alone failed to induce potent neutralizing antibodies, it modestly reduced viral loads in the lungs of mice. However, the pathological damage caused by lung inflammation was more aggravated than that of the control challenge group. The level of specific IgG antibody induced by the recombinant G-CTB was significantly higher than that elicited by RMG. Compared to the RMG group, the viral load in the lungs of the G-CTB group tended to be reduced. Also, the damage caused by lung inflammation was significantly alleviated. Our study proves that HMPV G may be a valuable antigen in terms of HMPV vaccine development and offers a promising strategy for modulating the immunogenicity and safety thereof. Full article

Cancer progression is closely linked to the enhanced uptake of extracellular amino acids, mediated by specific transporters that support biosynthesis, metabolic activity, and energy production through the tricarboxylic acid cycle. By increasing the expression of these transporters, tumor cells secure a continuous amino acid supply that sustains the proliferation, metabolic balance, and activation of major signaling pathways. While most studies have emphasized post-translational control of amino acid transporters, such as phosphorylation, ubiquitination, glycosylation, and palmitoylation, emerging evidence highlights regulatory crosstalk between these transporters and other membrane proteins, including G protein-coupled receptors and receptor tyrosine kinases. This review summarizes the current literature on the receptor-mediated mechanisms governing amino acid uptake and explores how interactions among families of membrane proteins contribute to the regulation of transporter activity. Full article