Search Results (216)

Drought stress significantly impairs plant growth and productivity, which triggers complex adaptive responses mediated by diverse gene families. Among these, the TOPLESS (TPL)/TPL-related (TPR) family of transcriptional corepressors plays a crucial role by recruiting epigenetic modifiers through interactions with EAR motif-containing proteins. However, genome-wide studies of this corepressor family and its associated regulatory networks with EAR motif-containing repressors remain limited. This study aimed to characterize the TPL/TPR transcriptional corepressor family in Populus ussuriensis Kom., elucidate their regulatory networks with EAR motif-containing repressors, and validate their functional roles in drought stress adaptation. To this end, we identified 21 TPL/TPR genes in P. ussuriensis (PuTPLs), classified them into five subfamilies, and found they are evolutionarily conserved with Arabidopsis thaliana and Populus trichocarpa, harboring characteristic CTLH and WD40 domains. Given that TPL/TPR proteins are recruited by transcription factors containing repression motifs, we constructed a putative TPL/TPR-EAR motif interaction network representing a core paradigm of negative regulation. Expression profiling under drought stress showed significant upregulation of most PuTPLs in a tissue-specific and temporal manner. Functional validation using transgenic P. ussuriensis lines overexpressing five PuTPLs demonstrated enhanced drought tolerance, evidenced by reduced electrolyte leakage and malondialdehyde content and increased proline accumulation. Our study provides the first comprehensive genome-wide analysis of the TPL/TPR family in P. ussuriensis, establishes a core EAR-mediated negative regulatory network, and validates the critical role of these genes in drought stress adaptation, providing valuable resources for future mechanistic research and breeding of stress-resistant trees. Full article

Background/Objectives: Wilson’s disease (WD) is an autosomal recessive disorder characterized by pathological copper accumulation, primarily in the liver and brain. Severe hepatic involvement can be effectively treated with liver transplantation (LT). Geographic variation in ATP7B mutations suggests the presence of regional patterns that may impact disease presentation and management. This study aims to investigate the genetic basis of WD in patients from a major LT center in Iran. Methods: A retrospective analysis was conducted on clinical, biochemical, and pathological data from patients suspected of WD who underwent evaluation for LT between May 2020 and June 2025 at Shiraz University of Medical Sciences. Genetic testing was carried out on 20 patients at the Shiraz Transplant Research Center (STRC). Direct mutation analysis of ATP7B was performed for all patients, and the results correlated with clinical and demographic information. Results: In total, 20 WD patients who underwent liver transplantation (15 males, 5 females) carried 25 pathogenic or likely pathogenic ATP7B variants, 21 of which were previously unreported. Fifteen patients were homozygous, and five were compound-heterozygous; all heterozygous combinations occurred in the offspring of second-degree consanguineous unions. Recurrent changes included p.L549V, p.V872E, and p.P992S/L, while two nonsense variants (p.E1293X, p.R1319X) predicted truncated proteins. Variants were distributed across copper-binding, transmembrane, phosphorylation, and ATP-binding domains, and in silico AlphaMissense scores indicate damaging effects for most novel substitutions. Post-LT follow-up showed biochemical normalization in the majority of recipients, with five deaths recorded during the study period. Conclusions: This single-center Iranian study reveals a highly heterogeneous ATP7B mutational landscape with a large proportion of novel population-specific variants and underscores the benefit of comprehensive gene sequencing for timely WD diagnosis and family counseling, particularly in regions with prevalent consanguinity. Full article

Lilac (Syringa spp.) is a widely cultivated ornamental plant prized for its fragrant aroma and attractive flower colors. However, the molecular mechanisms governing its flower pigmentation remain poorly understood. In this study, we performed integrated transcriptomic and metabolomic analyses on purple (Syringa oblata) and white (Syringa oblata var. alba) lilacs at the P1 stage, the point of deepest pigmentation. Compared with W1, P1 has a total of 918 differentially expressed genes, including 614 up-regulated genes and 304 down-regulated genes. And S. oblata exhibited significant upregulation of key anthocyanin biosynthesis genes, including the rate-limiting enzyme gene ObDFR, ObF3’H and transcriptional regulators such as ObWPA, which encodes a WD40 repeat protein. This transcriptional activation was accompanied by a substantial accumulation of 27 anthocyanins, including Petunidin Chloride, Cyanidin Chloride, Delphinidin and so on, while the Petunidin-3-O-rutinoside, Petunidin-3-O-(6-O-p-coumaroyl)-glucoside and Malvidin-3-O-sambubioside-5-O-glucoside were only detected in S. oblata. Furthermore, ATAC-seq analysis revealed that, in comparison to white lilac, purple lilac exhibited 3522 and 805 genes with increased and decreased chromatin accessibility, respectively. Integrative analysis with the transcriptome identified 135 genes that were both more accessible and transcriptionally upregulated in purple lilac, including ObWPA, Ob0214386, and Ob0227194 which belong to WD40 members. Subsequent qRT-PCR validation confirmed ObWPA as the most significantly upregulated gene in purple lilac, a finding consistent with the specific chromatin accessibility detected in its promoter region. To validate its function, we knocked down ObWPA expression in purple lilac using Virus-Induced Gene Silencing (VIGS). This intervention resulted in a dramatic color shift from purple to white, concomitant with a significant decrease in key anthocyanin metabolites such as Cyanidin-3-(6-O-p-caffeoyl)-glucoside, Cyanidin Chloride, Pelargonidin, Cyanidin-3-O-rutinoside, Dihydrokaempferol, and Petunidin Chloride. Collectively, our findings demonstrate that ObWPA is an indispensable positive regulator of purple color formation in S. oblata. Full article

Background/Objectives: The lifelong treatment of Wilson’s disease (WD) currently relies on copper chelators with relatively poor metal specificity, which frequently exhibit serious adverse effects. There is a real medical need for a specific copper chelator to regulate the copper excess efficiently, at lower doses than those used for penicillamine (DPA) or trientine (TETA), and with lower toxicity in long-term treatments. Methods: The efficiency of the specific Cu(II) chelator named TDMQ20 was evaluated by oral treatment of TX mice, used as a WD model, and compared with those of DPA, TETA, and also tetrathiomolybdate (bcTTM). We documented TDMQ20′s ability to (i) decrease the hepatic copper load, (ii) increase the amount and ferroxidase activity of ceruloplasmin (CP), and (iii) regulate liver proteins that are impaired in WD mice. Results: Compared to the other copper chelators, TDMQ20 was the only one that efficiently mediated excretion of Cu and restoration of active ceruloplasmin levels at doses 8 times lower than DPA. Such efficacy is related to the design of this chelator, which specifically coordinates Cu(II) as a discrete and soluble complex. Conversely, DPA, TETA, and bcTTM give rise to various complexes with copper ions, often with oligomeric or cluster structures that can be retained in blood circulation or sequestered by proteins. Conclusions: Taking into consideration all the advantages of TDMQ20 compared to other ligands, including its lack of toxicity during long-term administration in mice, the drug candidate TDMQ20 appears to be a first-class challenger to the currently used treatments, i.e., DPA, TETA, and bcTTM. Full article

Autophagy is a conserved catabolic pathway that degrades intracellular cargo through the lysosomal system. Canonically, this process is orchestrated by the autophagy-related (Atg)5-Atg7 conjugation system, which facilitates the formation of microtubule-associated protein 1 light chain 3 (LC3)-decorated double-membrane vesicles known as autophagosomes. However, accumulating evidence has revealed the existence of an Atg5-Atg7-independent, alternative autophagy pathway that still relies on upstream regulators such as the unc-51 like autophagy activating kinase 1 (Ulk1) kinase and the Beclin1 complex. In this review, we provide a comprehensive overview of the role of the Beclin1 complex in canonical autophagy and highlight its emerging importance in alternative autophagy. Notably, the recent identification of transmembrane protein 9 (TMEM9) as a lysosomal protein that interacts with Beclin1 to promote member RAS oncogene family 9 (Rab9)-dependent autophagosome formation has significantly advanced our understanding of alternative autophagy regulation. Furthermore, this Ulk1-Rab9-Beclin1-dependent mitophagy has been shown to mediate to mitochondrial quality control in the heart, thereby contributing to cardioprotection under ischemic and metabolic stress conditions. We further examine how the Beclin1 complex functions as a central scaffold in both canonical and alternative autophagy, with a focus on its modulation by novel factors such as TMEM9 and the potential therapeutic implications of these regulatory mechanisms. Full article

Ecology and adaptive differentiation of Epimedium are central to understanding both its taxonomic complexity and medicinal value. In this study, we integrate transcriptomic and plastid data from four natural populations of E. brevicornu (HZ, QLH, TS, WD) to reconstruct their phylogenetic relationships, estimate divergence times, and identify candidate genes associated with local adaptation. Nuclear gene-based phylogenies provide higher resolution and greater topological consistency than plastid data, underscoring the utility of nuclear data in lineages affected by hybridization and incomplete lineage sorting. Molecular dating indicated that major intraspecific divergence occurred during the mid-Quaternary (0.61–0.45 Ma), coinciding with climatic oscillations and montane isolation. Population structure showed strong correlations with temperature and precipitation gradients, suggesting environmentally driven selection. Signatures of positive selection and accelerated evolutionary rates revealed population-specific enrichment of genes involved in stress response, protein modification, signaling, and carbohydrate metabolism—key pathways linked to high-elevation adaptation. Protein–protein interaction networks further indicated a two-tier adaptation mechanism: ancestral network rewiring combined with population co-evolution of interacting genes. Together, these findings advance our understanding of alpine plant adaptation and provide candidate genes for further functional and breeding studies in Epimedium. Full article

Alcohol Use Disorder (AUD) poses global health challenges, and causes hematological alterations such as macrocytosis and oxidative stress. Disruption of protein structures by alcohol and/or its metabolites may exacerbate AUDs; proteomics can elucidate the underlying biological mechanisms. This study examined the proteins differentially expressed in the cytosol and membrane fractions of erythrocytes obtained from 30 male patients with AUD, comparing them to samples from 15 age- and BMI-matched social drinkers (SDs) and 15 non-drinkers (control). The analysis aimed to identify the molecular differences related to alcohol consumption. The AUD patient subgrouping was based on mean corpuscular volume (MCV), with 16 individuals classified as having a normal MCV and 14 having a high MCV. Proteins were separated via two-dimensional(2D)-gel electrophoresis, digested with trypsin, and identified via Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (TOF) mass spectrometry (MALDI-TOF/TOF). Additionally, levels of malondialdehyde and 4-hydroxyalkenals (MDA + HAE), reduced glutathione (GSH), oxidized glutathione (GSSG), serum carbohydrate-deficient transferrin (%CDT), disialotransferrin (%DST), and sialic acid (SA) were analyzed. The results showed increased MDA + HAE and decreased total thiols in AUD patients, with GSSG elevated and the GSH/GSSG ratio reduced in the AUD MCV-high subgroup. Serum %CDT, %DST, and SA were significantly higher in AUD. Compared to the control profiles, the AUD group exhibited differential protein expression. Few proteins, such as bisphosphoglycerate mutase, were downregulated in AUD versus control and SD, as well as in the MCV-high AUD subgroup. Conversely, endoplasmin and gelsolin were upregulated in AUD relative to control. Cytoskeletal proteins, including spectrin-alpha chain, actin cytoplasmic 2, were overexpressed in the AUD group and MCV-high AUD subgroup. Several proteins, such as 14-3-3 isoforms, alpha-synuclein, translation initiation factors, heat shock proteins, and others, were upregulated in the MCV-high AUD subgroup. Under-expressed proteins in this subgroup include band 3 anion transport protein, bisphosphoglycerate mutase, tropomyosin alpha-3 chain, uroporphyrinogen decarboxylase, and WD repeat-containing protein 1. Our findings highlight the specific changes in protein expression associated with oxidative stress, cytoskeletal alterations, and metabolic dysregulation, specifically in AUD patients with an elevated MCV. Understanding these mechanisms is crucial for developing targeted interventions and identifying biomarkers of alcohol-induced cellular damage. The complex interplay between oxidative stress, membrane composition, and cellular function illustrates how chronic alcohol exposure affects cellular physiology. Full article

Tumor necrosis factor (TNF) receptor-associated factor 7 (TRAF7) is a signal transducer in the TNF receptor superfamily. TRAF7 is unique among its superfamily in that it does not contain a TRAF-C domain but does contain WD-40 domains. TRAF7 interacts with mitogen-activated protein kinases (MAPK), which are known regulators of inflammation and shear stress response. Notably, these molecular interactions have profound implications for the function of brain endothelial cells (ECs), which are pivotal for sustaining the integrity of the blood–brain barrier (BBB), orchestrating neurovascular coupling (NVC), and modulating the vascular architecture. By directly influencing MAPK signaling pathways, particularly the shear stress-responsive MAPK kinase kinase 3 (MEKK3)–MAPK kinase 5 (MEK5)–extracellular-regulated protein kinase 5 (ERK5) cascade, TRAF7 contributes to vascular homeostasis, as exemplified by its role in phosphorylating ERK5. Such molecular events underpin the capacity of brain ECs to regulate substance exchange, adjust blood flow in response to neural activity, and maintain efficient cerebral perfusion, all of which are essential for preserving brain health and cognitive performance. By synthesizing the current evidence regarding TRAF7’s molecular functions and its impact on brain endothelial integrity, cerebrovascular aging, and exploring implications for therapeutic strategies targeting vascular dysfunction in the aging brain, this review fills a crucial gap in the literature. Given the limited number of original studies directly addressing these contexts, the review will integrate broader insights from related literature to provide a foundational overview for future research in this developing field. The culmination of this literature will provide a rationale for the development of novel TRAF7-targeted therapies to restore vascular integrity in the context of aging, which could maintain cognitive health. Although TRAF7 has been implicated in regulating endothelial permeability during inflammation, its precise functions in brain ECs and the subsequent effects on cerebrovascular structure and cognitive function remain to be fully elucidated. Full article

Colored wheat lines, which feature elevated anthocyanin content and associated traits, represent valuable genetic resources for enhancing the plant’s nutritional and aesthetic properties. This genome-wide association study (GWAS) utilized a set of radiation-induced mutant lines to identify genetic loci linked to agricultural and biochemical traits. The GWAS models Fixed and Random Model Circulating Probability Unification, and the Bayesian-information and Linkage-Disequilibrium Iteratively Nested Keyway were employed to increase the reliability of marker–trait associations (MTAs). In total, 35 significant MTAs were identified, and seven single-nucleotide polymorphisms (SNPs) were commonly detected by both models. To explore candidate genes, a ± 1.5-Mb window around each significant SNP was analyzed according to the estimated linkage disequilibrium decay, revealing 635 genes. Among these, several genes were annotated as transcription factors and enzymes associated with flavonoid biosynthesis and modification, including MYB, WD-repeat proteins, and UDP-glycosyltransferases. Expression profiling and RT-qPCR further supported the functional relevance of selected SNP–gene pairs, particularly for anthocyanin accumulation and seed color variation. In summary, the integration of GWAS, gene annotation, and expression data could provide valuable insights into the genetic basis of complex traits in wheat, providing data for future molecular studies and marker-assisted breeding of colored wheat mutant cultivars. Full article

Seed oil represents a key trait in soybeans, which holds substantial economic significance, contributing to roughly 60% of global oilseed production. This research employed genome-wide association mapping to identify genetic loci associated with oil content in soybean seeds. A panel comprising 341 soybean accessions, primarily sourced from Northeast China, was assessed for seed oil content at Heilongjiang Province in three replications over two growing seasons (2021 and 2023) and underwent genotyping via whole-genome resequencing, resulting in 1,048,576 high-quality SNP markers. Phenotypic analysis indicated notable variation in oil content, ranging from 11.00% to 21.77%, with an average increase of 1.73% to 2.28% across all growing regions between 2021 and 2023. A genome-wide association study (GWAS) analysis revealed 119 significant single-nucleotide polymorphism (SNP) loci associated with oil content, with a prominent cluster of 77 SNPs located on chromosome 8. Candidate gene analysis identified four key genes potentially implicated in oil content regulation, selected based on proximity to significant SNPs (≤10 kb) and functional annotation related to lipid metabolism and signal transduction. Notably, Glyma.08G123500, encoding a receptor-like kinase involved in signal transduction, contained multiple significant SNPs with PROVEAN scores ranging from deleterious (−1.633) to neutral (0.933), indicating complex functional impacts on protein function. Additional candidate genes include Glyma.08G110000 (hydroxycinnamoyl-CoA transferase), Glyma.08G117400 (PPR repeat protein), and Glyma.08G117600 (WD40 repeat protein), each showing distinct expression patterns and functional roles. Some SNP clusters were associated with increased oil content, while others correlated with decreased oil content, indicating complex genetic regulation of this trait. The findings provide molecular markers with potential for marker-assisted selection (MAS) in breeding programs aimed at increasing soybean oil content and enhancing our understanding of the genetic architecture governing this critical agricultural trait. Full article

Dietary advanced glycation end-products (dAGEs) contained in high-sugar/fat and ultra-processed foods of the “Western diet” (WD) pattern predispose to several diseases by altering protein function or increasing oxidative stress and inflammation via RAGE (receptor for advanced glycation end-products). Although elevated endogenous AGEs are associated with loss of muscle mass and functionality (i.e., muscle wasting; MW), the impact of dAGEs on MW has not been elucidated. Here, we show that the most common dAGEs or their precursor, methylglyoxal (MGO), induce C2C12 myotube atrophy as endogenous AGE-derived BSA. ROS production, mitochondrial dysfunction, mitophagy, ubiquitin–proteasome activation, and inhibition of myogenic potential are common atrophying mechanisms used by MGO and AGE-BSA. Although of different origins, ROS are mainly responsible for AGE-induced myotube atrophy. However, while AGE-BSA activates the RAGE-myogenin axis, reduces anabolic mTOR, and causes mitochondrial damage, MGO induces glycolytic stress and STAT3 activation without affecting RAGE expression. Among thirty selected natural compounds, Vaccinium macrocarpon (VM), Camellia sinensis, and chlorophyll showed a surprising ability in counteracting in vitro AGE formation. However, only the standardized VM, containing anti-glycative metabolites as revealed by UHPLC-HRMS analysis, abrogates AGE-induced myotube atrophy. Collectively, our data suggest that WD-linked dAGE consumption predisposes to MW, which might be restricted by VM food supplements. Full article

Hippeastrum, a perennial herbaceous plant belonging to the Amaryllidaceae family, is widely cultivated for its large, vibrant flowers with diverse petal colors, which have significant ornamental and economic value. However, the mechanisms underlying anthocyanin accumulation in Hippeastrum petals remain poorly understood. To fully explore the involved regulation mechanism was significant for the breeding of Hippeastrum and other Amaryllidaceae family plants. In this study, we selected six Hippeastrum cultivars with distinctly different petal colors. We used metabolomic profiling and high-throughput transcriptomic sequencing to assess varied anthocyanin profiles and associated expression of genes in their biosynthetic pathways. Four key anthocyanins were identified: cyanidin, cyanidin-3-O-rutinoside, delphinidin-3-glucoside, and delphinidin-3-rutinoside. Weighted gene co-expression network analysis (WGCNA) correlated the abundance of these four anthocyanins with transcriptomic data, to suggest three regulatory modules. Nine transcription factors families in these modules were identified and some of them were validated using qRT-PCR. Y2H assay isolated some transcription factors interacted with TTG1 (WD40 protein), including MYB3/39/44/306 and bHLH13/34/110, illustrating the possibility of forming MBW complexes. Our study provides a comprehensive characterization of anthocyanin composition. These findings laid a theoretical foundation for future research on the regulatory mechanisms of pigment accumulation and the breeding of Hippeastrum cultivars with novel petal colors. Full article

Wilson’s disease (WD) is an autosomal recessive disorder of copper metabolism caused by mutations in the ATP7B gene. While hepatic manifestations are frequent, psychiatric symptoms occur in up to 30% of patients and may precede neurological signs. This study was the first to assess the relationship between oxidative stress, selected genetic polymorphisms, and psychiatric symptoms in WD. A total of 464 patients under the care of the Institute of Psychiatry and Neurology in Warsaw were studied. Genotyping for GPX1 (rs1050450), SOD2 (rs4880), and CAT (rs1001179) was performed, along with biochemical analyses of copper metabolism, oxidative DNA, lipid and protein damage, and systemic antioxidant capacity. Among the most important observations are the following: the homozygous GPX1 rs1050450 TT and SOD2 rs4880 CC genotypes were associated with the lowest prevalence of psychiatric symptoms. The CAT rs1001179 TT genotype was linked to a delayed onset of psychiatric symptoms by 6.0–8.5 years. Patients with or without psychiatric symptoms did not differ significantly in saliva 8-OHdG, total antioxidant capacity, serum glutathione (GSH), catalase, and MnSOD; however, patients reporting psychiatric symptoms had significantly higher prostaglandin F2α 8-epimer (8-iso-PGF2α) concentrations and tended to have lower serum glutathione peroxidase (Gpx) concentrations compared to those without such symptoms. Our data firstly provide consistent evidence that oxidative stress balance associated with copper overload in the CNS may be associated with CNS damage and the development of psychiatric symptoms of WD. In particular, our findings of increased oxidative lipid damage together with decreased Gpx activity indirectly suggest that damage to neuronal membrane lipids, which may be potentially related to abnormalities in GSH metabolism, may have an etiological role in CNS damage and related symptoms. Full article

The production of food with a naturally enriched protein content is a strategic response to the growing global demand for sustainable protein sources. Wood distillate (WD), a by-product of the pyrolysis of woody biomass, has previously been shown to increase the protein concentration and bioavailability in chickpea seeds. Here, we evaluated the effect of 0.5% (v/v) WD soil drenching on chickpea productivity, nutritional profile, and proteomic pattern. WD treatment significantly improved the yield by increasing plant biomass (+144%), number of pods and seeds (+148% and +147%), and seed size (diameter: +6%; weight: +25%). Nutritional analyses revealed elevated levels of soluble proteins (+15%), starch (+11%), fructose (+135%), and polyphenols (+14%) and a greater antioxidant capacity (25%), alongside a reduction in glucose content, albeit not statistically significant, suggesting an unchanged or even lowered glycemic index. Although their concentration decreased, Ca (−31%), K (−12%), P (−5%), and Zn (−14%) in WD-treated plants remained within normal ranges. To preliminary assess the quality and safety of the protein enrichment, a differential proteomic analysis was performed on coarse flours from individual seeds. Despite the higher protein content, the overall protein profiles of the WD-treated seeds showed limited variation, with only a few storage proteins, identified as legumin and vicilin-like isoforms, being differentially abundant. These findings indicate a general protein concentration increase without a major alteration in the proteoform composition or differential protein synthesis. Overall, WD emerged as a promising and sustainable biostimulant for chickpea cultivation, capable of enhancing both yield and nutritional value, while maintaining the proteomic integrity and, bona fide, food safety. Full article

Drought severely limits crop yield every year, making it critical to clarify the genetic basis of drought tolerance for breeding of improved varieties. As drought tolerance is a complex quantitative trait, we analyzed three phenotypic groups: (1) agronomic traits under well-watered (WW) and water-deficit (WD) conditions, (2) stress tolerance indices of these traits, and (3) phenotypic plasticity, using a multi-parent doubled haploid (DH) population assessed in multi-environment trials. Genome-wide association studies (GWAS) identified 130, 171, and 71 quantitative trait loci (QTL) for the three groups of phenotypes, respectively. Only one QTL was shared among all trait groups, 25 between stress indices and agronomic traits, while the majority of QTL were specific to their group. Functional annotation of candidate genes revealed distinct pathways of the three phenotypic groups. Candidate genes under WD conditions were enriched for stress response and epigenetic regulation, while under WW conditions for protein synthesis and transport, RNA metabolism, and developmental regulation. Stress tolerance indices were enriched for transport of amino/organic acids, epigenetic regulation, and stress response, whereas plasticity showed enrichment for environmental adaptability. Transcriptome analysis of 26 potential candidate genes showed tissue-specific drought responses in leaves, ears, and tassels. Collectively, these results indicated both shared and independent genetic mechanisms underlying drought tolerance, providing novel insights into the complex phenotypes related to drought tolerance and guiding further strategies for molecular breeding in maize. Full article