Search Results (2,333)

Banana bunchy top virus (BBTV) is a devastating pathogen threatening global banana production. The plant ubiquitin–proteasome system (UPS) governs immune signaling and is frequently subverted by invading viruses, yet the molecular mechanism through which BBTV interferes with host UPS remains unclear. Here, we show that BBTV nuclear shuttle protein (NSP) serves as the core viral effector to disrupt banana ubiquitination homeostasis. RT-qPCR time-series assays confirmed that BBTV infection dynamically remodels the transcription of eight phylogenetically divergent RING-type E3 ubiquitin ligases: four subfamily I E3-SIS3 paralogs and E3-HIP1 are significantly upregulated at 14 dpi and 21 dpi, while E3-BOI and E3-RHA1B are suppressed at 21 dpi. Transient expression screening of all six BBTV-encoded proteins verified that only NSP reproduces the UPS perturbation signature triggered by viral infection. Cross-species sequence alignment identified an evolutionarily conserved FNGSF motif within NSP orthologs of all Nanoviridae members. Alanine substitution mutagenesis (NSP^AAAAA) completely abolished NSP’s capacity to alter E3 ligase transcription. Western blot assays further validated that wild-type NSP induces massive accumulation of ubiquitinated host proteins, whereas the FNGSF-deficient mutant does not disrupt cellular ubiquitination. Phylogenetic analysis revealed that NSP-targeted E3 ligases share low overall sequence similarity but retain conserved catalytic RING domains, indicating that NSP exerts broad-spectrum regulatory effects on host UPS via the FNGSF motif. Collectively, this study reveals a novel pathogenic strategy whereby BBTV NSP recruits diverse host RING E3 ligases via its conserved FNGSF motif to dysregulate plant ubiquitination and elicit plant pathogenicity. Our findings provide two promising targets—the NSP FNGSF motif and defense-associated E3-SIS3 ligases—for developing antiviral agents and breeding BBTV-resistant banana germplasm. Full article

Regular exercise mediates inter-tissue communication between skeletal muscle and the immune system through skeletal muscle-derived secretory factors, providing an important molecular basis for the beneficial effects of exercise on chronic inflammation, metabolic dysregulation, and impaired tissue repair. As key effector cells of the innate immune system, macrophages do not simply conform to a dichotomous classification of classically activated M1 macrophages and alternatively activated M2 macrophages; rather, their functional states constitute a dynamic spectrum shaped by exercise load, recovery time window, tissue microenvironment, and disease context. This review focuses on recent advances in exercise-induced skeletal muscle secretory factors involved in macrophage functional remodeling. Representative signals, including interleukin-6 (IL-6), irisin, meteorin-like protein (METRNL), fibroblast growth factor 21 (FGF21), oncostatin M (OSM), decorin, myostatin, chemokines, and extracellular vesicles, are systematically summarized in terms of their exercise responsiveness, evidence for skeletal muscle origin, and evidence supporting macrophage regulation. Based on these dimensions, an evidence-strength grading framework is further proposed. Moreover, this review integrates key signaling axes, including glycoprotein 130 (gp130)/Janus kinase (JAK)/signal transducer and activator of transcription (STAT), signal transducer and activator of transcription 6 (STAT6)/peroxisome proliferator-activated receptor gamma (PPARγ), AMP-activated protein kinase (AMPK)/nuclear factor erythroid 2-related factor 2 (Nrf2)/nuclear factor kappa B (NF-κB), transforming growth factor beta (TGF-β)/Smad, and chemokine receptor pathways, to explain how exercise-induced secretory networks participate in the dynamic regulation of the macrophage functional spectrum through immune cell recruitment, inflammatory clearance, immunometabolic reprogramming, matrix remodeling, and repair-niche formation. Current evidence indicates the translational potential of exercise-induced skeletal muscle secretory factors in skeletal muscle repair, metabolic inflammation, aging-related functional decline, and cancer rehabilitation. However, this field still faces several major challenges, including insufficient tracing of skeletal muscle-derived signals, limited direct causal validation, a lack of human tissue-level evidence, and unclear exercise dose–response relationships. Future studies should combine tissue-specific genetic interventions, receptor blockade, single-cell and spatial omics, metabolic flux analysis, and standardized human exercise interventions to further clarify the mechanistic basis and application boundaries of exercise-induced skeletal muscle–macrophage communication, thereby providing a theoretical foundation for precision exercise prescription and chronic inflammation intervention. Full article

Human immunodeficiency virus (HIV) is an enveloped virus with a remarkable capacity for genetic diversification, enabling rapid escape from host immune responses and therapeutic interventions. Despite extensive global efforts, the development of an effective vaccine has remained elusive owing to the virus’s high genetic variability and antigenic diversity. Consequently, considerable effort has been directed toward the development of therapeutic agents targeting viral entry, reverse transcriptase, integrase, protease, and more recently, capsid. Although antiretroviral therapy (ART) remains the cornerstone of HIV treatment, it is associated with challenges including drug resistance, adverse side effects, and limitations in access and affordability. Targeting viral entry offers distinct advantages by blocking infection at the earliest stage of the viral life cycle and enabling the neutralization of free virions, as well as Fc-mediated elimination of HIV-infected cells in some cases. This review highlights promising protein-based HIV entry inhibitors that have demonstrated efficacy in preclinical studies, and discusses ongoing efforts to optimize their valency, avidity, specificity, serum half-life, effector functions, and production platforms to improve their therapeutic potential and economic feasibility. Full article

Self-labeling enzymes, like SNAP-, CLIP- and Halo-tag have found wide application in biology, biochemistry, materials science and bioengineering. For example, they have been applied with high versatility to rewrite genetic information inside the living cell by providing rationally programmable RNA-targeting strategies of protein-based effectors. Such approaches benefit from the engineering capability of the small molecule-based self-labeling moieties. Here, we further engineered that approach to control RNA-targeting by light. Specifically, we combined two orthogonal self-labeling enzymes for the recruitment of two distinct fusion proteins to a target RNA inside the living cell and achieved concurrent assembly and disassembly of distinct guide RNA–protein conjugates. We applied this to control RNA base editing and achieved a photo-induced swap of two distinct editing events. Overall, this work describes new ways for tool development, RNA imaging, and transcript engineering. Full article

(1) Background: methicillin‑resistant Staphylococcus aureus (MRSA) is a zoonotic pathogen, and its hemolysins serve as key virulence factors. Functional membrane microdomains (FMMs) are protein-enriching platforms and regulate diverse physiological functions by recruiting and assembling various proteins. However, whether and how FMMs regulate the hemolytic ability of MRSA remains unclear. This study aimed to investigate FMM-mediated regulation of MRSA hemolysins and the underlying mechanisms. (2) Methods: Homologous recombination was employed to generate FMM-disrupted (N315ΔfloA) and complemented (N315ΔfloA::floA) strains from the MRSA N315 wild-type strain (N315 WT). The three strains were compared with respect to hemolytic activity, transcript levels of key virulence and regulatory genes, and in vivo virulence. (3) Results: Disruption of FMMs significantly enhanced hemolytic activity compared with N315 WT and complemented strains. Meanwhile, FMM disruption repressed the two-component system genes (vraS and vraR), while activating the agr operon (agrB, agrD, agrC and agrA) and its effector molecule RNAIII, leading to upregulation of hemolysin genes (hla, hlb, hld). In vivo, N315ΔfloA infection markedly increased mortality in G. mellonella larvae and BALB/c mice, with significantly elevated pro-inflammatory factors (TNF-α, IL-6, and IL-1β) in mouse plasma. All these phenotypes were effectively reversed in N315ΔfloA::floA. (4) Conclusions: Disruption of FMMs potentiates both hemolytic activity and overall virulence in MRSA, with the potential underlying mechanism involving the VraS/R-Agr regulatory axis that drives transcriptional upregulation of hemolysin-encoding genes. Full article

G protein-coupled receptors (GPCRs) are dynamic allosteric proteins whose signaling properties are governed by reciprocal communication between extracellular ligand-binding sites and intracellular transducer interfaces. Although classical pharmacological models established the concept that ligand binding and G protein coupling are thermodynamically linked, recent structural, biophysical, and computational studies have revealed a far more complex picture in which GPCRs exist as ensembles of interconverting conformational states. Accumulating evidence indicates that G proteins function not only as downstream signaling effectors but also as endogenous allosteric modulators. By reshaping receptor conformational landscapes, G protein coupling can influence the structure and dynamics of orthosteric ligand-binding pockets, thereby regulating ligand affinity, binding kinetics, and receptor selectivity. These findings support a bidirectional model of GPCR signaling in which information is transmitted not only from ligand-binding sites to intracellular signaling partners but also in the reverse direction through receptor-wide allosteric networks. Disease-associated mutations of endothelin A receptor (ETAR) provide in vivo evidence that structural perturbations located far from orthosteric ligand-binding sites can alter ligand recognition through long-range allosteric communication. In addition, emerging studies of positive allosteric modulators demonstrate the therapeutic potential of selectively stabilizing ligand–receptor–G protein complexes. These observations suggest that ligand recognition, receptor activation, and transducer coupling should be viewed as integrated properties of a dynamic receptor–ligand–transducer ensemble. This perspective provides a conceptual framework that links classical GPCR pharmacology, structural biology, disease mechanisms, and next-generation drug discovery. Full article

Chimeric antigen receptor (CAR) T-cell therapy has revolutionized the treatment landscape of hematologic malignancies but has demonstrated limited efficacy in solid tumors, mainly due to the complex and immunosuppressive tumor microenvironment (TME). Among the strategies to overcome this challenge, targeting the tumor stroma rather than the tumor cells themselves has gained increasing interest. In this context, fibroblast activation protein alpha (FAP), a cell surface protease overexpressed by cancer-associated fibroblasts, represents a promising target. With the aim of remodeling the TME, enhancing immune infiltration, and suppressing tumor growth, numerous FAP-directed CAR T-cell therapies have been developed in the last decade, leading to the clinical translation of two candidates. To improve the flexibility and safety profile of CAR T-cell therapies, several groups have designed more controllable and modular approaches, including adapter CAR T-cell systems, which enable on-demand activation of effector cells through the administration of an adapter molecule. In parallel, the development of FAP-targeted radiotracers, particularly FAP inhibitors (FAPIs), has enabled high-contrast imaging of solid tumors and introduced attractive opportunities for radioligand therapy. The convergence of these advances has given rise to immunotheranostic strategies that integrate CAR T-cell immunotherapy and radioligand delivery within a unified framework. This review traces the evolution of FAP-directed CAR T-cell strategies, from conventional designs to adapter-based and theranostic platforms, and examines how modular adapters bring immunotherapy and radioligand delivery together within a single immunotheranostic framework, across preclinical and clinical settings. Full article

Preterm infants are at high risk of developing long-term brain injury such as encephalopathy of prematurity (EoP). Hyperoxia is a major contributor to EoP, affecting white and grey matter, with immature oligodendrocytes and hippocampal neurons being particularly vulnerable. While no causal therapy is available, mesenchymal stromal cells (MSCs) show therapeutic potential and are considered a promising candidate, although their effector mechanisms remain incompletely understood. Primary oligodendrocytes were isolated from mixed glial cultures of P0–P2 rats and hippocampal neurons from E16 rat embryos. On day 3 (oligodendrocytes) and day 5 (neurons) after isolation, cells were exposed to hyperoxia for 8 h and subsequently co-cultured indirectly with naive or hypoxic-preconditioned human MSCs (hMSCs) for 48 h under standard culture conditions. Degeneration, proliferation, differentiation and mitochondrial respiration were assessed in both cell types. Both naive and hypoxic-preconditioned hMSCs attenuated hyperoxia-induced degeneration, reduced proliferation and mitochondrial respiration failure. Although oligodendrocyte differentiation, assessed by myelin basic protein (MBP) expression, was modulated neither by hyperoxia nor by hMSC treatment, the dendritic structure in hippocampal neurons was impaired by hyperoxia and improved by hMSC treatment. Notably, hypoxic-preconditioned hMSCs showed a stronger therapeutic effect than naive hMSCs on hyperoxia-damaged hippocampal neurons. These findings indicate that indirect hMSC co-culture mitigates hyperoxia-induced impairment of immature oligodendrocytes and hippocampal neurons and that hypoxic preconditioning may modulate this effect in a cell type-specific manner. Full article

Muscle stem cells (MuSCs) are the cellular source for the generation and regeneration of skeletal muscle. Proper muscle growth requires precise control over the differentiation and self-renewal of MuSCs. Signaling systems, such as bone morphogenetic proteins (BMPs) and Notch, suppress the myogenic differentiation of MuSCs. This allows the expansion of the progenitor pool necessary for muscle growth. To better understand the molecular mechanisms and target genes of BMPs during myogenesis, we examined the response of adult mouse MuSCs to BMP6. BMP6 stimulation of freshly isolated MuSCs suppressed myogenic differentiation. Short-term stimulation (one hour) rapidly increased the expression of classical BMP target genes, such as Id1, as well as Notch pathway genes, including Hes1, Hey1, Lfng, and Snai1. We used Cleavage Under Targets and Tagmentation (CUT&Tag) to generate whole-genome binding profiles for pSMAD1/5/9 and SMAD4, which are transcriptional effectors of the BMP pathway. This method detected dynamic binding in promoters and regulatory elements of direct BMP targets, including Notch pathway genes. Our data demonstrate that BMP6 is a potent suppressor of MuSC differentiation and reveal that a subset of well-characterized anti-myogenic genes (i.e., Hes1 and Hey1) are shared targets of the BMP and Notch pathways. Full article

Claviceps purpurea is a highly specialized biotrophic ascomycete that colonizes floral tissues of grasses, including economically important cereal crops, causing ergot disease and producing ergot alkaloids with significant agricultural, pharmaceutical, and biotechnological relevance. Despite extensive research on its biology and secondary metabolism, the molecular mechanisms underlying host recognition, floral specificity, establishment of biotrophy, and developmental differentiation remain incompletely understood. This review integrates current knowledge derived from genomic, transcriptomic, proteomic, metabolomic, and functional genetic studies to provide an overview of the molecular basis of the C. purpurea–host interaction. Particular emphasis is placed on recent advances in fungal development, host immune modulation, hormonal signalling, sclerotial differentiation, and ergot alkaloid biosynthesis. Current evidence indicates that successful colonization depends on coordinated regulation of host recognition, secretion of effector proteins, carbohydrate-active enzymes, and manipulation of host signalling pathways to establish and maintain a biotrophic lifestyle. The transition from the sphacelial stage to sclerotial development represents a major developmental and metabolic reprogramming event associated with fungal differentiation and activation of the ergot alkaloid biosynthetic pathway. Recent multi-omics approaches have further revealed complex regulatory networks connecting fungal development and secondary metabolism. Claviceps purpurea has emerged as a valuable model for studying floral biotrophy and fungal secondary metabolism; however, key questions remain regarding the molecular basis of host specificity, effector function, hormonal crosstalk, and developmental regulation. Future integration of multi-omics approaches with functional genomics will be essential to resolve these processes and to support sustainable disease management strategies and the biotechnological exploitation of ergot alkaloids. Full article

Background/Objectives: Advanced-stage hepatocellular carcinoma is characterized by a very poor prognosis; thus, highly effective medication is still needed. Often overexpressed heat shock protein 90 is a promising target due to its pivotal role in carcinogenesis. Methods: Antiproliferative effects of 246TMP-3SF5 on HepG2 and HuH-7 cells were assessed by crystal violet staining. Apoptosis was evaluated via subG1 peak, caspase-3 activity and PARP cleavage, and ferroptosis via ROS, glutathione and malondialdehyde levels. Migration was assessed by scratch assay, and in ovo models were used to study angiogenesis and drug effects on microtumors. CAM vascular networks were quantified by semi-automatic segmentation, morphometric and box-counting fractal analysis. Molecular docking and molecular dynamics simulation of heat shock protein 90 were carried out using Autodock Vina and Gromacs respectively. Results: Profound dose- and time-dependent antiproliferative effects of 246TMP-3SF5 against HCC cell lines were observed, revealing low micromolecular IC₅₀ values and selectivity for carcinoma cells with selectivity indices > 1. A significant increase in the sub-G1 peak, key effector caspase-3 activity, as well as cleavage of PARP strongly suggested apoptosis playing a crucial role in the antiproliferative effects. Additionally, HuH-7 cells revealed an elevation of reactive oxygen species and both cell lines showed significant glutathione depletion concomitant with an increase in malondialdehyde concentration upon treatment. The observed effect could be partially reversed by applying ferrostatin-1, suggesting ferroptosis as an additional relevant mode of action. Changes in the cell cycle as well as impaired tumor cell migration were observed. Upon treatment, angiogenesis was impaired and mass of microtumors was significantly reduced. Quantitative CAM analysis showed that vascularized area fraction increased in controls but decreased under both 17-AAG and 246TMP-3SF5. Likewise global mean vessel width decreased relative to controls, while box-counting dimension was reduced under 246TMP-3SF5. Molecular docking and molecular dynamics simulation analysis predicts 246TMP-3SF5 to be binding in catalytic site of heat shock protein 90. Conclusions: 246TMP-3SF5 is a promising novel inhibitor meriting further research as a potential treatment against hepatocellular carcinoma. Full article

Glioblastoma multiforme is the most aggressive primary brain tumor in adults, which displays extremely poor prognosis. Protease-activated receptor 2 (PAR2) and its downstream effector SerpinB3 are overexpressed in aggressive glioblastomas. In this study we evaluated the antitumor activity of 1-piperidine propionic acid (1-PPA), an allosteric PAR2 inhibitor, in in vitro preclinical models of glioblastoma. PAR2 and SerpinB3 were analyzed at the transcriptional and protein level in glioblastoma cell lines and primary cultures. These were treated with 1-PPA alone or in association with temozolomide (TMZ) and the effects evaluated by Incucyte^® technology. Pharmacokinetics and tissue distribution of 1-PPA were assessed in mice by LC-MS/MS. 1-PPA significantly reduced glioma cell proliferation, migration, and invasion, thus promoting apoptotic cell death, in a concentration-dependent manner. The combined treatment with TMZ led to a concentration-dependent decrease in cell proliferation (12–20%) compared to TMZ alone. Molecularly, 1-PPA downregulated PAR2 and SerpinB3 expression. Pharmacokinetic studies in healthy mice showed that 1-PPA is systemically bioavailable and distributes to several organs, including the brain. These data indicate that 1-PPA shows brain exposure and capability to affect different hallmarks of aggressiveness in glioblastoma cells, including hyperproliferation and invasion, supporting its further development as a novel therapeutic strategy in these tumors. Full article

Ultraconserved elements (UCEs) are among the most evolutionarily conserved DNA sequences in vertebrate genomes, yet the biological mechanisms underlying their extraordinary conservation remain poorly understood. Using the recently developed dedUCE database comprising 12,813 human UCEs, we performed a comprehensive genome-wide analysis of their distribution relative to protein-coding genes, transcription factor (TF) genes, and long noncoding RNA (lncRNA) genes. UCEs showed a highly non-random genomic organization, with approximately 40% occurring in clusters within 20 kb genomic intervals. Non-KRAB transcription factor genes exhibited a striking sevenfold enrichment of UCEs compared with random expectation, whereas KRAB zinc-finger genes displayed an approximately tenfold depletion. Beyond TFs, UCE-rich genes were predominantly involved in developmental regulation, chromatin remodeling, RNA processing, and embryonic neurogenesis, whereas similarly large UCE-poor genes primarily encoded membrane proteins, ion channels, and synaptic components required for mature neuronal function. UCEs also demonstrated strong positional bias, with approximately fourfold enrichment near the 3′ ends of protein-coding genes but no comparable distribution pattern in lncRNAs. Although lncRNA genes showed only modest overall UCE enrichment, a small subset contained numerous UCEs. These findings demonstrate that UCEs preferentially associate with master developmental regulators rather than downstream neuronal effector genes, providing new insights into the functional organization and evolutionary conservation of the human genome. Full article

Glioblastoma (GBM) is one of the most aggressive and treatment-resistant cancers, shaped by a tumor microenvironment (TME) that is both metabolically demanding and strongly immunosuppressive. GBM relies heavily on fatty acid (FA) metabolism to sustain growth of rapidly dividing tumor cells and survive metabolic stress. GBM cells enhance lipid uptake, activate sterol regulatory element-binding protein 1 (SREBP-1)-driven lipogenesis, store excess lipids in droplets to prevent toxicity, and depend on fatty acid oxidation (FAO) to generate adenosine triphosphate (ATP) and maintain redox balance, particularly under nutrient-limited conditions. GBM TME is also consistently enriched with regulatory T cells (Tregs), which maintain suppressive activity despite the nutrient restrictions that impair effector T cells (Teffs). In hypoxia and nutrient limitation within the TME, Tregs can adapt by using FAO, lactate oxidation, and OXPHOS, supported by forkhead box P3 (Foxp3)-dependent metabolic programming, cluster of differentiation 36 (CD36)-mediated FA uptake, and hypoxia-related signals. At the same time, programmed cell death protein 1 (PD-1)/programmed death-ligand 1 (PD-L1) signaling reduces glycolytic activity in Teffs and contributes to metabolic dysfunction, while also supporting the stability of oxidative metabolism in Tregs. Evidence from pre-clinical and clinical studies suggests a possible association between Treg enrichment in GBM and reduced responsiveness to immune checkpoint inhibitors (ICIs), although this relationship is not yet fully defined. Overall, current findings point to FA metabolism as a shared metabolic axis that supports both tumor progression and Treg-mediated immune resistance. Targeting lipid-driven pathways may offer an opportunity to disrupt these advantages and improve the effectiveness of existing immunotherapies for GBM. Full article

There is a growing interest in methods that illuminate the contributions of individual positions to a protein’s function by site-saturating mutagenesis. However, a commonly used approach for assessing variant libraries with deep mutational scanning relies on readouts of biological fitness, which is influenced by many protein properties (ligand binding, catalysis, allosteric effector binding, allosteric coupling between effector and substrate, etc.). Biochemical assays are required to distinguish among these factors. To facilitate the generation and biochemical evaluation of the functions of large numbers of substituted positions, we co-express updated plasmids coding a series of amber suppressor tRNA in a high-throughput workflow; these plasmids are available at Addgene. As an example, our goal is to evaluate whether allosteric mechanisms are conserved among homologs. Because homologs often have <50% identity, and up to 30% of a protein’s positions can contribute to allosteric function, we reason that the set of “allosteric” positions likely differs among homologs. Our high-throughput workflow includes the following steps: Step (1) an amber suppressor tRNA-based mutagenesis protocol; Step (2) a robotic system for protein expression/purification and functional assays; and Step (3) a method for aggregating results from multiple substitutions at each position into a composite score. Full article