Search Results (2,036)

High-Mobility Group Box (HMGB) proteins belong to the family of high-mobility proteins characterized by two DNA-binding domains and an unstructured, negatively charged C-terminal domain that modulates DNA–protein and protein–protein interactions. These proteins participate in multiple cellular processes, including DNA replication, transcription, recombination, and repair. The functional activity of HMGB proteins is associated with various physiological and pathological conditions, including malignant tumors and cardiovascular diseases, highlighting the need for strict regulation of their levels and activity to maintain cellular homeostasis. Such regulation can occur at multiple levels, including proteolytic degradation. In recent years, a number of E3 ubiquitin ligases that promote the degradation of HMGB proteins, as well as deubiquitinases (DUBs) that stabilize them by removing ubiquitin tags, have been identified. This review summarizes these enzymes and their proposed roles in controlling the functions of the HMGB family proteins, both through direct interaction with these proteins and via mediator proteins. Full article

Ubiquitin-specific protease 22 (USP22) regulates epigenetic gene expression by deubiquitinating histone H2B (H2Bub1) and upregulating oncogenic proteins and pathways, while antagonizing p53-mediated tumor suppression. USP22 is frequently overexpressed in cancers and associated with therapy resistance and poor prognosis yet remains largely untargeted pharmacologically. Here, using a fluorescence-based USP22 deubiquitinase assay to screen the LOPAC^®1280 library, we identified β-Lapachone, a natural ortho-naphthoquinone with strong anticancer activities, as a potent USP22 inhibitor. β-Lapachone potently inhibited USP22 enzymatic activity, with a half-maximal inhibitory concentration (IC₅₀) of ~0.75 μM, and molecular docking revealed its occupation of the catalytic pocket adjacent to the USP22 active-site triad, supporting a potential binding mode. Functionally, β-Lapachone suppressed proliferation and induced apoptosis in A549 and H1299 RAS-mutant lung adenocarcinoma (LUAD) cells, while USP22 knockout conferred marked resistance, indicating partial USP22 dependence. In patient-derived LUAD models, β-Lapachone inhibited sphere formation and reduced CD133⁺ cancer stem cell populations. Notably, it synergized with cisplatin to enhance DNA damage and apoptosis. In vivo, β-Lapachone significantly suppressed tumor growth in a syngeneic KRAS-mutant/p53-Null mouse lung cancer model and further potentiated cisplatin-induced antitumor effects. Collectively, these findings identify β-Lapachone as a potent inhibitor of USP22 and validate USP22 inhibition as a key mechanism underlying its anticancer activity in LUAD cells, both in vitro and in vivo. Full article

Identifying cold-resistance genes is essential for improving the ability of apples (Malus × domestica) to tolerate low temperatures, as cold stress significantly limits their growth and productivity. The MdWRKY31 gene was cloned from apple, and its sequence characteristics, expression pattern, and biological function were systematically investigated. Bioinformatic analysis indicated that MdWRKY31 belongs to the group II WRKY transcription factors and is localized in the nucleus. Expression analysis revealed that MdWRKY31 transcript levels were markedly upregulated under low-temperature stress. To further explore its function, MdWRKY31 was heterologously overexpressed in tomato (Solanum lycopersicum). Following low-temperature treatment, transgenic tomato plants exhibited significantly reduced accumulation of reactive oxygen species, markedly enhanced activities of antioxidant enzymes (SOD, POD, and CAT), increased contents of proline and soluble protein, and a notable decrease in malondialdehyde levels. Additionally, transcript levels of SlCBF1, SlCBF2, SlCBF3, SlICE1, along with the ABA signaling-related genes SlNCED1 and SlABI5, were markedly elevated. Further molecular docking showed that the MdWRKY31 protein has strong binding affinity to the W-box elements in the promoters of SlCBF1 suggesting that it may regulate the expression of these genes through direct protein–DNA interactions. These findings indicate that MdWRKY31 improves plant cold tolerance by CBF-dependent pathways to modulate antioxidant defenses and osmotic balance. These findings identify candidate genetic resources for breeding cold-resistant apple cultivation. Full article

Base excision repair (BER) and nucleotide excision repair (NER) are traditionally regarded as independent pathways; however, accumulating evidence indicates that ultraviolet (UV)-damaged DNA-binding protein (UV-DDB), a core NER factor, stimulates BER DNA glycosylases, including alkyladenine DNA glycosylase (AAG). Despite this functional link, the molecular basis of the UV-DDB/AAG interaction and its regulation by DNA remain unclear. This study investigated the direct interaction between AAG and UV-DDB using electrophoretic mobility shift assays (EMSA), surface plasmon resonance (SPR), biolayer interferometry (BLI) and AlphaFold3-based structural modeling under DNA-free and DNA-bound conditions. SPR analysis revealed that AAG and UV-DDB form a high-affinity complex in the absence of DNA ($K_D$ ≈ 17.5 nM), which is maintained but reduced approximately 2.6-fold upon binding to apurinic/apyrimidinic site (AP site)-containing dsDNA ($K_D$ ≈ 46.2 nM). BLI analysis independently confirmed this interaction under both DNA-free and DNA-bound conditions, with inter-platform differences consistent with previously reported BLI/SPR variability. EMSA showed UV-DDB-mediated ternary complex formation accompanied by redistribution of binary AAG/DNA species. AlphaFold3 modeling predicted that AAG associates with DDB1 in the DNA-free state, whereas under DNA-bound conditions, DDB2 recognizes the AP site while AAG repositions toward the lesion with multiple active site residues placed in close proximity. These findings support a model in which DNA binding acts as a molecular switch that reconfigures the UV-DDB/AAG interaction, potentially enabling UV-DDB to function as a recruitment platform that facilitates directional progression of AAG through the BER cycle, and providing a structural basis for coordinated integration of BER and NER. Full article

Biosensing performance in graphene-derived field-effect transistors (BioFETs) is widely attributed to surface chemistry, yet the role of the underlying charge transport mechanism remains poorly understood. This work establishes a direct correlation between disorder-driven transport and biosensing transduction in vertical graphene (VG) and nanocrystalline graphite (NCG) FET devices. Temperature-dependent electrical characterization (15–500 K) reveals a hybrid transport regime: three-dimensional Mott variable-range hopping below 240 K, transitioning to thermally activated Arrhenius-type conduction above 240 K. The extracted VRH parameters characteristic temperature T₀, localization length ξ, and density of states N(E_F) quantify fundamentally distinct disorder landscapes: VG operates in a strongly localized, edge-dominated regime, while NCG forms a continuous percolative network with greater transport stability. Surface functionalization via PASE and amine-terminated ssDNA probes, followed by DNA hybridization across four nucleobase systems, demonstrates that the sequence-dependent electrical response is mechanistically interpretable within the VRH–transconductance framework. NCG transduces biomolecular binding through direct charge transfer and hopping pathway perturbation, whereas VG responds through interfacial electrostatic reorganization. These results introduce a unified VRH–transconductance–sensing framework, providing a rational physical basis for next-generation graphene BioFET design. Full article

Skeletal muscle differentiation relies on transient DNA strand breaks (DSBs), yet excessive DNA damage remains harmful to myogenic progression. The RNA-binding protein Zfp36l1 is expressed in skeletal muscle and contributes to muscle regeneration; nevertheless, its role in preserving genome stability during myogenic differentiation has not been defined. Here, we investigated the role and mechanism of Zfp36l1 in regulating DNA damage using C2C12 myoblast cells, combining loss- and gain-of-function assays, RNA-seq, and rescue experiments. The results revealed that Zfp36l1 expression is strongly induced during early myogenic differentiation, coinciding with the onset of physiological DSBs. Functional assays revealed that silencing Zfp36l1 aggravates DSB accumulation, reinforces G0/G1 cell cycle arrest, and promotes apoptosis, whereas Zfp36l1 overexpression attenuates these abnormalities. Transcriptomic profiling shows that Zfp36l1 knockdown impairs homologous recombination (HR)-mediated DNA repair by downregulating core repair factors, including Rad51 and Brca1. Gene set enrichment analysis further confirms significant suppression of the HR-dependent DSB repair pathway. Mechanistically, Zfp36l1 regulates HR repair by suppressing p21 expression, thereby relieving inhibition of E2F1-mediated Rad51 transcription. Co-silencing p21 restores Rad51 expression and reduces DNA damage in Zfp36l1-knockdown cells. Collectively, these findings identify Zfp36l1 as an essential safeguard of genome stability during myogenic differentiation by balancing DNA damage levels through the p21-E2F1-Rad51 signaling axis, and provide new insights into the regulatory basis of muscle development and genomic instability-associated muscle diseases. Full article

Legume–rhizobium symbiosis represents a crucial biological nitrogen fixation system. The AP2/ERF transcription factor ERN1 plays a vital role in nodulation of model legumes; however, its function in peanut (Arachis hypogaea), a typical crack-entry infection legume, remains unclear. To explore this, we performed transcriptome sequencing of peanut roots at 3 days post-inoculation (dpi) with rhizobium. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that differentially expressed genes (DEGs) were mainly enriched in DNA-binding transcription factor activity, plant–pathogen interaction, and plant hormone signal transduction pathways. The most strongly up-regulated gene was AhERN1, which was highly expressed in peanut roots and nodules. Subcellular localization indicated that AhERN1 was a nuclear-localized protein, and yeast transcriptional activation assays confirmed that AhERN1 functions as a transcriptional activator relying on its C-terminal domain. Furthermore, hairy root overexpression of AhERN1 significantly increased the number of peanut nodules. Collectively, these results reveal that AhERN1 acts as a positive regulator to promote rhizobium-induced nodule development in peanut, providing new insights into the regulatory mechanism of nodulation in dalbergoid legumes. Full article

Epithelial ovarian cancer (EOC) remains one of the most aggressive gynecological malignancies, largely due to late-stage diagnosis, therapeutic resistance, and molecular heterogeneity. This study aimed to identify biologically relevant hub genes and evaluate potential dual-target compounds against Cyclin-Dependent Kinase 1 (CDK1) and DNA Topoisomerase II Alpha (TOP2A) through an integrated computational framework. Transcriptomic datasets from GSE28799, GSE54388, and GSE14407 were analyzed to identify overlapping differentially expressed genes, followed by protein–protein interaction analysis, functional enrichment, survival assessment, molecular docking, ADMET profiling, and molecular dynamics simulations. Mechanistically, CDK1 and TOP2A participate in coordinated cell-cycle regulation associated with G2/M progression and chromosomal dynamics in ovarian cancer. Among the identified hub genes, CDK1 and TOP2A demonstrated marked overexpression and central topological importance within the interaction network. Functional enrichment analyses highlighted significant associations with mitotic cell-cycle regulation, DNA replication, and proliferative signaling pathways. Molecular docking analyses identified Naringin as a potential dual-target candidate with favorable binding affinity toward both CDK1 and TOP2A. ADMET profiling suggested acceptable pharmacokinetic and toxicity characteristics, while molecular dynamics simulations supported stable protein–ligand interactions under dynamic conditions. Although survival analyses did not demonstrate statistically significant independent prognostic associations, the findings support the biological relevance of CDK1 and TOP2A in EOC progression. Collectively, this study provides an integrated computational perspective on CDK1/TOP2A-associated oncogenic signaling and prioritizes Naringin as a preliminary candidate for future experimental investigation in epithelial ovarian cancer. Full article

Background/Objectives: Natural products have long been regarded as a cornerstone in the discovery and development of novel therapeutic agents. Accumulating evidence indicates that natural products represent promising pharmacological candidates for cancer treatment. This review provides a holistic overview of novel identified natural products as a continuing source of bioactive compounds, with particular emphasis on recent advances and their applications in anticancer therapy over the past five years. Methods: A literature search was conducted using PubMed, Scopus, and Web of Science to identify relevant studies published within the past five years. Predefined keywords and Boolean operators (e.g., “natural products”, “anticancer”, “drug discovery”, “secondary metabolites”, “signaling pathways”, “epigenetics”) were applied, with search strategies adapted to each database. Eligible studies included original research articles and reviews reporting on newly identified natural products with anticancer activity, with emphasis on chemical diversity, biological effects, and molecular mechanisms of action. Additional references were identified through manual screening of bibliographies. The selected literature was evaluated using a qualitative, interpretative approach consistent with narrative review methodology, and findings were critically synthesized and thematically organized. Results: Growing evidence indicates that multiple newly identified natural products target mitochondrial metabolism and interact with alternative tubulin binding sites, thereby highlighting their potential as anticancer agents. In addition, emerging compounds have been shown to affect DNA integrity and transcriptional regulation, while also acting as systems-level modulators of key oncogenic signaling pathways, including PI3K/Akt, NF-κB, and MAPK. Recent studies further demonstrate that natural products can modulate multiple layers of epigenetic regulation, including DNA methylation, histone acetylation, histone methylation, and non-coding RNA networks. Conclusions: Current evidence supports the concept that natural products primarily function as multi-target biological modulators rather than classical single-target inhibitors in cancer biology. A persistent challenge remains the translational gap between preclinical efficacy and clinical application, as the majority of naturally derived candidate compounds remain confined to in vitro or early in vivo validation. Future progress will therefore depend on systematically aligning the multi-target pharmacology of natural products with defined cancer vulnerabilities and clinically actionable therapeutic strategies. Full article

RNA-binding proteins (RBPs) are essential regulators of all aspects of RNA metabolism, including splicing, stability, localisation, translation, and degradation. Through their ability to recognise specific cis-elements in target transcripts, often via RNA-recognition motifs or other conserved domains, RBPs enable rapid cellular adaptation to stress and maintain proteostasis, particularly in post-mitotic tissues with limited transcriptional flexibility. Accumulating evidence positions RBPs as both modulators and drivers of the molecular hallmarks of ageing, including genomic instability, loss of proteostasis, mitochondrial dysfunction, cellular senescence, and chronic inflammation. This review synthesises peer-reviewed studies on the multifaceted roles of RNA-binding proteins in organismal ageing and age-related diseases. Key themes include the tissue- and age-dependent changes in expression of turnover and translation regulatory RBPs such as HuR (ELAVL1), AUF1 (HNRNPD), TIA-1, and tristetraprolin (ZFP36), which alter the stability of mRNAs encoding cell-cycle regulators, pro-inflammatory cytokines, and stress-response proteins. Systematic downregulation of core splicing factors, including PTBP1 and several heterogeneous nuclear ribonucleoproteins, drives widespread senescence-associated splicing alterations in pathways governing cell division, autophagy, DNA repair, and mitochondrial function, suggesting a causal contribution to the senescent phenotype. Prion-like RBPs such as TDP-43 and FUS exhibit age-dependent mislocalisation, nuclear depletion, and cytoplasmic aggregation, contributing to splicing defects, impaired RNA transport, and neurodegeneration in amyotrophic lateral sclerosis, frontotemporal dementia, and limbic-predominant age-related TDP-43 encephalopathy. Interactions between RBPs and non-coding RNAs, together with disrupted liquid–liquid phase separation dynamics, further exacerbate age-related decline. By integrating mechanistic studies from cellular and animal models with observations in human cohorts, this review underscores RBPs as central nodes linking multiple ageing hallmarks and highlights their potential as biomarkers and therapeutic targets to promote healthy ageing. Limitations of current models and priorities for future translational research are discussed. Full article

Background: Triple-negative breast cancer (TNBC) remains a clinical challenge due to its aggressive nature and the frequent emergence of therapeutic resistance. While the role of protein-coding genes in DNA repair is well-documented, the regulatory contributions of the non-coding genome, specifically long intergenic non-coding RNAs (lincRNAs), remain largely undefined. Objectives: In this study, we characterize the biological significance of LincRNA-BC7, a novel transcript identified within the breast cancer field effect. Methods: Through a combined in silico and in vitro approach, we investigated the transcriptional dynamics of the LincRNA-BC7/miR-663a/BRCA1 axis in response to the PARP inhibitor, Olaparib. Results: Our results demonstrate that Olaparib induces selective cytotoxicity in BRCA1-deficient MDA-MB-231 cells while sparing non-cancerous HEK293 cells, a response accompanied by a significant downregulation of LincRNA-BC7 and a reciprocal upregulation of BRCA1. Bioinformatics analysis through BLASTN, miRBase, and KEGG revealed that LincRNA-BC7 contains highly complementary binding sites for miR-663a, suggesting it functions as a competing endogenous RNA (ceRNA) or “molecular sponge.” Conclusions: By sequestering miR-663a, LincRNA-BC7 appears to modulate the expression of critical signaling nodes within the PI3K-AKT and TP53 pathways, thereby influencing cellular sensitivity to DNA-damaging agents. These findings suggest that LincRNA-BC7 is a key determinant of the aggressive TNBC phenotype and the response to PARP inhibition. Our study establishes the LincRNA-BC7/miR-663a axis as a novel biomarker for precision risk stratification and a promising therapeutic target to enhance treatment outcomes in BRCA1-associated breast cancers. Full article

Leaf architecture critically impacts crop yield. The Auxin Response Factor (ARF) family is a key regulator of leaf development, yet remains uncharacterized in the important legume crop chickpea (Cicer arietinum L.), which bears pinnate compound leaves. Here, we performed a genome-wide identification and analysis of ARF genes in chickpea. We identified 33 CaARF genes and resolved their phylogenetic structure through comparison with six other key dicot species. The analysis revealed a deeply conserved core set of ARF proteins across species, all sharing the N-terminal DNA-binding domain (DBD), with most the C-terminal PB1 domain, connected by a middle region (MR). We also uncovered instances of lineage-specific expansion, e.g., a chickpea-specific ARF clade, which is characterized by the absence of the C-terminal PB1 domain. Expression profiling using public transcriptome data and qRT-PCR revealed distinct spatiotemporal expression patterns for CaARF genes across tissues and during compound leaf development. Detailed in situ hybridization analysis for selected candidates, chosen based on phylogenetic proximity to known leaf-development-related ARFs in other species, localized their transcripts to specific regions within compound leaf primordia. Focusing on CaARF5, the closest ortholog of Arabidopsis MONOPTEROS/ARF5, we confirmed its nuclear localization and dynamic expression during chickpea leaf development. Functional complementation assays demonstrated that CaARF5 could restore developmental defects in the Arabidopsis mp mutant. Our study establishes an evolutionary and molecular framework for the chickpea ARF family, highlighting conserved features and species-specific innovations, and provides essential resources for future research on auxin-mediated leaf development and ARF-targeted legume breeding. Full article

Background/Objectives: The bean beetle (Callosobruchus maculatus) exhibits population density-dependent plasticity in the terminal oocyte maturation rate. DNA methyltransferase 1 (DNMT1) plays a conserved function in reproduction that is independent of DNA methylation. However, whether DNMT1 is involved in the population density-dependent reproductive plasticity of bean beetles remains unclear. Methods: Two and twenty pairs of beetles were reared with approximately 100 seeds per bottle to establish a low-density population and a high-density population, respectively. Quantitative real-time PCR was used to unveil the mRNA levels of DNMT1, MBD2/3, and insulin-like peptides (ILPs). RNA interference was used to determine the function of DNMT1 and MBD2/3 in terminal oocyte development. The length of terminal oocytes was measured under a microscope. Results: Individuals reared under high-population-density conditions showed a faster terminal oocyte maturation rate compared to those under low-density conditions. The bean beetle genome encodes DNMT1 but lacks DNMT3, and only a single methyl-DNA-binding domain protein (MBD2/3) was identified. Population density could modulate the expression levels of both DNMT1 and MBD2/3. RNA interference (RNAi)-mediated knockdown demonstrated that suppressing either DNMT1 or MBD2/3 significantly reduced the terminal oocyte maturation rate. Moreover, silencing DNMT1 and MBD2/3 resulted in decreased expression of ILP3 and all ILPs in the fat body, respectively. ILPs are known to be involved in regulating terminal oocyte development. Conclusions: Taken together, these findings suggest that DNMT1 and MBD2/3 modulate the population density-dependent terminal oocyte maturation rate in the bean beetle by influencing the expression of ILPs. Full article

Regulation of the endothelial stress response is important for blood vessel homeostasis and angiogenesis, processes disrupted in common vascular diseases and ageing. Here, we discovered that the Y-box factor ZONAB (ZO-1-associated nucleic acid binding protein; YBX3), a gene associated with risk loci for severe vascular disorders, regulates endothelial homeostasis and angiogenesis. By combining cell-based assays with primary endothelial cells and genome-wide expression and methylation measurements, we found that ZONAB depletion results in mitochondrial deregulation, increased reactive oxygen species, and a defective oxidative stress response, which correlates with increased promoter methylation of cell cycle genes. ZONAB depletion triggered cellular senescence via a phosphatidylinositol 3-kinase (PI3K)/Akt-dependent pathway, which was attenuated by PIK3 inhibitors, an antioxidant, or by drugs targeting mitochondrial function or fragmentation. Thus, our results reveal that ZONAB repression in endothelial cells leads to genome-wide changes in gene expression and DNA methylation, regulating endothelial proliferation and inflammation, as well as mitochondrial deregulation to promote cellular senescence. Hence, ZONAB supports endothelial homeostasis and may play a role in vascular health. Full article

Sulfane sulfur species are increasingly recognized as integral cellular components involved in signaling pathways and cytoprotection against oxidative stress in mammals. While their production in bacteria has been extensively studied, their functional role in bacterial oxidative stress defense remains poorly understood. Here, we demonstrate that sulfane sulfur generated by sulfide: quinone oxidoreductase decreases H₂O₂ sensitivity in Pseudomonas aeruginosa PAO1. Notably, this protective mechanism does not depend on sulfane sulfur acting as a direct H₂O₂ scavenger via nucleophilic reactions. Through persulfidation proteomic profiling, we reveal that persulfidation is a prominent post-translational modification in P. aeruginosa, reflecting the prevalence of deprotonated sulfane sulfur species. These species modify cysteine residues in proteins, including the well-known oxidative stress regulator OxyR. Specifically, sulfane sulfur modifies OxyR at Cys199 to form persulfidated OxyR C199-SSH, contributing to a single-Cys activated state that modulates promoter activity and DNA-binding affinity. Furthermore, sulfane sulfur-mediated persulfidation protects the critical cysteine residue of LpdG, a ROS-vulnerable dihydrolipoamide dehydrogenase, from irreversible overoxidation. Although LpdG is not part of the canonical H₂O₂-scavenging system, its preservation is essential for cell viability under oxidative stress. These findings establish endogenous sulfane sulfur species as key mediators of antioxidant defense in P. aeruginosa. Full article