Search Results (1,608)

In contrast to foreign nucleic acids, some of our own endogenously synthesized nucleic acids may become immunologically active without being considered “foreign”. For example, abnormalities in chromatin organization, transcription termination, ribonucleic acid (RNA) splicing, and RNA editing, together with damage to mitochondrial integrity, may render normally functional deoxyribonucleic acid (DNA) and RNA persistently available and aberrantly structured ligands for innate immunity. Z-DNA-binding protein 1 (ZBP1), recently identified as an important component of this innate immune system, recognizes both left-handed DNA (Z-DNA) and left-handed RNA (Z-RNA) using its tandem Z-alpha (Zα) domains and couples recognition of these conformational states to receptor-interacting serine/threonine-protein kinase 1 (RIPK1)-, receptor-interacting serine/threonine-protein kinase 3 (RIPK3)-, and mixed-lineage kinase domain-like pseudokinase (MLKL)-dependent inflammatory and cell-death pathways. More recent studies have also shown that ZBP1 plays a role in recognizing damaged self-nucleic acids associated with tauopathies, Alzheimer’s disease (AD), traumatic brain injury (TBI), and amyloid-associated neuroinflammation. The nucleic-acid forms associated with these conditions include transposable-element activation, extended repeat-containing transcripts, RNA–RNA duplexes or RNA:DNA hybrids, oxidized mitochondrial DNA (mtDNA), and intercellularly transferred nucleic acids, all of which may exhibit substrate structures compatible with Z-form formation. Signaling by ZBP1 does not occur simply based upon nucleic-acid abundance; rather, signaling occurs after prolonged exposure to a nucleic acid when it persists in a structurally competent state, sufficient receptors are present to bind its exposed regions, the receptor proteoforms are competent to participate in signaling, receptor-interacting protein homotypic interaction motif (RHIM)-dependent assembly occurs, and the appropriate adaptor molecules are present. Furthermore, the identity of the cell type expressing ZBP1 determines whether the response produces RIPK3–MLKL-dependent neuronal injury, microglia-mediated inflammation, apoptosis, or mixed cell death. Finally, competition with adenosine deaminase acting on RNA 1 (ADAR1), melanoma differentiation-associated protein 5 (MDA5), double-stranded RNA-dependent protein kinase (PKR), the cyclic guanosine monophosphate–adenosine monophosphate synthase–stimulator of interferon genes (cGAS–STING) pathway, and other nucleic-acid-sensing proteins divides the available pool of endogenous nucleic acids among the outcomes of immune tolerance, type I interferon (IFN-I) signaling, translational inhibition, neuroinflammation, and necroptosis. Full article

Extracellular vesicle RNAs (EV-RNAs) possess important biological functions and strong therapeutic potential. Their composition, however, is not yet fully understood. To obtain a comprehensive insight of the composition for healthy individuals, we adopted RNA-based T oligo-primed PCR (RNA TOP-PCR) to amplify all EV-RNA species for three healthy males. The constituent sequences were then sequenced and analyzed. The results showed that rRNAs constitute the major species (31.1–43.6%) of EV-RNAs, followed by ncRNAs (including lncRNAs, 4.3–7.9%, and sncRNAs, 0.4–1.2%), Y RNAs (3.9–9.3%), mRNAs (0.7–1.7%), and tRNAs (~0.1%), together with small amounts of mitochondrial tRNA, pseudogenes, and miRNAs (<0.004% over mappable reads). Noticeably, ~40% of the EV-RNAs remain unannotated, while the annotated EV-mRNAs seem to bear a major mission focusing on signal transduction and oxidative phosphorylation. Motif sequences for lncRNA vesicle localization highly agree with previous reports. Among Y RNAs, RNY3 and RNY4 are the major isoforms. Interestingly, many sequences overlap with precursor miRNAs but do not overlap with mature miRNAs. Taken together, RNA TOP-PCR is a robust method suitable for the study of EV-RNAs complexity, and EV-RNAs-mediated intercellular regulation seems to be much more complicated than previously thought. Full article

C-type lectins (CTLs) are important pattern recognition receptors (PRRs) involved in innate immune defense in crustaceans. In this study, a novel C-type lectin, designated LvCTL, was identified and functionally characterized from Litopenaeus vannamei. Sequence analysis revealed that the open reading frame (ORF) of LvCTL is 495 bp in length and encodes a 164-amino acid polypeptide containing a typical C-type lectin-like domain but lacking the classical carbohydrate-binding motifs. Notably, two novel EPF motifs were identified in the CTLD region, suggesting a potential non-canonical ligand recognition pattern. Phylogenetic analysis revealed that LvCTL clustered with other crustacean CTLs. Tissue expression analysis revealed that LvCTL exhibited the highest transcript level in the hepatopancreas. After immune stimulation, LvCTL expression in the hepatopancreas was significantly regulated by LPS, Vibrio parahaemolyticus, Staphylococcus aureus, WSSV and Poly(I: C), indicating its involvement in antimicrobial immune responses. RNA interference assays showed that knockdown of LvCTL significantly increased the bacterial burden and reduced the survival rate of shrimp after V. parahaemolyticus infection. Furthermore, recombinant LvCTL displayed broad bacterial binding activity to Gram-negative and Gram-positive bacteria and induced calcium-dependent agglutination of V. parahaemolyticus and S. aureus. Taken together, these results demonstrate that LvCTL functions as an important immune recognition molecule and contributes to antibacterial defense against V. parahaemolyticus in L. vannamei. These findings broaden our understanding of the functional diversity of shrimp CTLs and their contributions to crustacean innate immunity. Full article

Respiratory syncytial virus (RSV) RNA synthesis relies on RNA-dependent RNA polymerase, a complex composed of the L and P proteins. We recently resolved four major structural states of the RSV nucleotide addition cycle (NAC), establishing a framework for viral RNA elongation. However, reaction-derived complexes are influenced by catalytic efficiency and intermediate occupancy and may incompletely sample the NAC conformational landscape. Here, we report two cryo-electron microscopy (cryo-EM) structures of unreacted RSV polymerase bound to a post-translocation RNA product mimic. One structure closely recapitulates the previously determined reaction-derived post-translocation state, demonstrating that the canonical architecture can be recovered independently of nucleotide incorporation. The second structure reveals an additional post-translocation intermediate that retains the same RNA register and vacant +1 product-binding site while adopting a two-domain L organization. Structural comparisons further identify localized rearrangements near the catalytic center, including changes in the motif A loop and supporting helix. Together, these findings expand the structural landscape of the RSV post-translocation stage and refine the current NAC model. More broadly, our results highlight unreacted state-matched complexes as a complementary approach to reaction-derived structures for capturing more complete structural snapshots of dynamic reaction cycles. Full article

The FMD is an endangered species under first-class national protection in China. Comparative genomic investigation of microsatellite (SSR) in CDS may provide insights into adaptive evolutionary mechanisms and may inform conservation management strategies for captive populations. Here, we analyzed the FMD genome alongside five closely related ruminants: cattle (Bos taurus), red deer (Cervus elaphus), white-tailed deer (Odocoileus virginianus), sheep (Ovis aries), and goat (Capra hircus). Through genome-wide bioinformatic identification, we systematically compared the abundance, density, structural categories, repeat motifs, chromosomal distribution, and pathway enrichment analysis of SSR-containing genes in CDS. Furthermore, we performed synteny analysis and evaluated population genetic diversity. A total of 2509 SSRs in CDS were identified in the FMD, with a relative density of 62.61 loci/Mb. Trinucleotide SSRs were overwhelmingly dominant (88.46%) in the FMD. Notably, the FMD exhibited the highest relative abundances of both tetranucleotide and pentanucleotide repeats among the six species (2.37 and 2.18 loci/Mb, respectively), with pentanucleotide abundance approximately 5.6- to 9.1-fold higher than that of the other species. Chromosomal mapping revealed the highest SSR density in CDS regions on chromosome 27, while SSR-containing genes exhibited a heterogeneous pattern characterized by localized clustering. Synteny analysis demonstrated relatively conserved syntenic relationships between the FMD and goat, sheep, and cattle, with moderate conservation also observed with red deer and white-tailed deer, suggesting that SSR-containing genes in ruminants may remain highly conserved during chromosomal rearrangements. GO and KEGG analyses indicated that SSR-containing genes across all species were predominantly enriched in transcriptional regulation, RNA processing, and signal transduction pathways. Specifically, the FMD showed enrichment patterns associated with hypoxia response, mRNA processing, and epigenetic regulation, which may reflect lineage-specific transcriptional patterns, though the functional involvement of these SSRs remains to be experimentally validated. In addition, the five primer pairs screened in this study exhibited high polymorphism, with a mean polymorphism information content (PIC) of 0.93. The observed heterozygosity (Ho) was significantly lower than the expected heterozygosity (He), and the mean inbreeding coefficient (FIS) was 0.57, indicating heterozygote deficiency and an elevated risk of inbreeding in this captive FMD population. Collectively, our findings provide preliminary insights into the conserved patterns of microsatellite evolution and lineage-specific divergence in ruminants, offering a reference framework for comparative genomics and adaptive evolution research, as well as practical molecular markers for genetic management of captive populations. Full article

Background: The efficacy of chemotherapy in triple-negative breast cancer (TNBC) is limited by intrinsic resistance and the tumor microenvironment (TME). Accumulating evidence reveals a mechanistic connection between programmed death-ligand 1 (PD-L1) and c-x-c motif chemokine receptor 4 (CXCR4), which dominate stroma barriers, immune escape, and cancer metastasis. Earlier studies have shown that dual suppression of c-x-c motif ligand 12 (CXCL12)/CXCR4 and programmed cell death-1 (PD-1)/PD-L1 pathways regulates extracellular matrix (ECM) deposition, activation of cancer-associated fibroblasts (CAFs), and epithelial–mesenchymal transition (EMT) of pancreatic cancer cells. Methods: We combined BsNb PX4, a bispecific nanobody targeting PD-L1 and CXCR4, with paclitaxel or gemcitabine in multiple tumor cell lines and human peripheral blood mononuclear cell (hPBMC)-reconstituted xenograft mouse models. Antitumor activity was assessed by CCK-8, flow cytometry, and ELISA, and immune cell infiltration and TME remodeling were examined by immunofluorescence, immunohistochemistry, cytokine assays, and RNA-seq. Results: In MDA-MB-231 cells, BsNb PX4 synergistically enhanced paclitaxel-induced growth inhibition and apoptosis via G₂/M cycle arrest. This combinatorial strategy profoundly remodeled tumor immunity by expanding CD8⁺ T cells and depleting Foxp3⁺ CD4⁺ regulatory T cells (Tregs), while concurrently restoring T-cell cytotoxicity and skewing the cytokine balance toward an antitumor state, with elevated IFN-γ and reduced TGF-β1. Notably, compared with paclitaxel monotherapy, the combination significantly elevated intratumoral CD8⁺ T-cell infiltration, decreased Treg abundance, and exerted robust inhibitory effects on tumor growth and metastasis in humanized TNBC xenografts. Conclusions: These findings reveal that dual blockade of PD-L1 and CXCR4 acts synergistically with chemotherapy by triggering tumor cell apoptotic effects and reversing the immunosuppressive microenvironment, thereby emerging as a promising therapeutic strategy for TNBC. Full article

C-C motif chemokine ligand 2 (CCL2) interacts with cytokines, adipokines, miRNAs, and multiple synovial cell populations. Experimental studies indicate that these interactions can form a CCL2-associated inflammatory amplification network across cell types. In cellular and animal models, increased CCL2 is associated with monocyte recruitment, synovial fibroblast activation, osteoclast-related bone remodelling, and vascular responses. Therapeutic strategies targeting the CCL2-centered inflammatory network include antagonists of the CCL2/CCR2 axis, natural products, synthetic compounds, conventional antirheumatic drugs, and emerging delivery-based approaches. Notably, direct CCL2/CCR2 inhibition has shown biological activity in experimental models but has not produced consistent clinical benefit in established rheumatoid arthritis (RA). Although these findings do not establish CCL2 as a dominant causal driver of RA, human observational studies suggest that circulating CCL2 may complement established markers in preclinical RA risk assessment, disease activity and remission classification, estimation of treatment response, and evaluation of RA-related complications such as interstitial lung disease. Of note, no validated concentration cut-off or standardized assay currently supports its routine clinical use. This review examines the CCL2-related inflammatory network in RA and evaluates its cellular mechanisms, therapeutic implications, and potential clinical applications. Full article

RNA-dependent RNA polymerases (RdRPs) are essential enzymes involved in RNA virus replication and eukaryotic RNA silencing. They are generally absent in vertebrates but present in some invertebrate lineages, such as nematodes and certain arthropods. Brevipalpus yothersi is a phytophagous mite of agricultural relevance due to its role as a vector of plant-infecting viruses. We have identified two RdRPs on the genome of this mite species that, unexpectedly, are not of eukaryotic origin. Phylogenetic reconstruction and comparisons of 3D protein structures revealed similarity with viral RdRPs of the Partitiviridae family. Both RdRPs retain conserved catalytic motifs at the protein sequence level, and expression was confirmed by RNAseq and qPCR across mite developmental stages, with a peak during the nymphal stage. K-mer profiles showed similarity with mite endogenous genes, suggesting gene amelioration after the integration, or being derived from a viral donor already adapted to the mite. Our study also identified orthologs in other Brevipalpus species, but not in other Acari relatives, supporting that the horizontal gene transfer event is circumscribed to the Brevipalpus genus. These findings highlight an intriguing case of viral gene domestication in arthropods that might influence their developmental biology and the host–virus interaction. Full article

Bovine viral diarrhea virus (BVDV) is a pathogen of globally significance in cattle that has two biotypes: non-cytopathogenic (non-cp) and cytopathogenic (cp). The cp biotype arises from the non-cp through genome rearrangements, which frequently involve the insertion of host cellular RNA sequences, often accompanied by viral genome duplications. Here, we performed a systematic analysis of insertions across all complete BVDV genomes available in GenBank. Despite a 10-fold increase in available sequences over the past 10 years (from 59 to 670), the repertoire of known rearrangements associated with the cp phenotype has expanded only modestly, with insertions occurring predominantly at five conserved genomic hotspots. Notably, independent acquisitions of similar insertions—such as DNAJC14 (Jiv), ubiquitin-like sequences, the NS4B-NS5A cleavage site, and the PYPDPQTLG motif—in phylogenetically unrelated virus lineages reflect a limited number of permissive sites. Our analysis further demonstrates that many insertions are mosaic and suggests multiple recombination events that are poorly compatible with template switching by viral polymerase. Mechanistically, we propose that non-replicative recombination provides the most consistent explanation for the observed insertion patterns, particularly common coupling of cellular RNA acquisitions with viral sequence duplications. Both the steric proximity of virus replication to the endoplasmic reticulum and the RNA end requirements (2′-3′ cyclic phosphate and 5′-OH) suggest that non-replicative recombination is likely mediated by the endoplasmic reticulum-associated IRE1 RNase and RtcB ligase, which are responsible for the alternative cytoplasmic splicing of cellular mRNA. Full article

This comprehensive literature review delves into the multifaceted roles of RNA-binding motif protein 3 (RBM3) in cellular processes, disease pathogenesis, and therapeutic potential. RBM3 has been implicated in shaping cell morphology, synaptic protection in neurodegenerative conditions, and regulating gene expression through binding to specific RNA sequences. In cancer, RBM3 exhibits contrasting effects, influencing cell proliferation, tumorigenic potential, and RNA splicing. Clinical studies suggest RBM3 as a predictive biomarker in chemotherapy response for muscle-invasive bladder cancer. Despite promising therapeutic implications in neuroprotection and cancer, challenges persist in understanding the regulatory mechanisms and clinical behavior of RBM3. Further research is warranted to elucidate the molecular mechanisms underlying RBM3’s diverse functions and its significance as a potential target for personalized medicine in cancer therapy. This review underscores the pivotal role of RBPs, particularly RBM3, in disease progression and highlights the need for continued investigation to harness their therapeutic potential effectively. This review evaluates evidence available through December 2025, with particular emphasis on studies published between 2010 and 2025. Full article

Brassinosteroid signaling kinases (BSKs) act as core signal transducers downstream of Brassinosteroid (BR) perception and integrate plant growth regulation with broad-spectrum biotic and abiotic stress tolerance. Despite well-established functional characterizations of BSK gene families in Arabidopsis thaliana and rice, comprehensive genome-wide profiling and salt response analysis of BSK homologs remain lacking in wheat. In this study, we systematically identified 18 TaBSK family members. Phylogenetic analysis separated wheat TaBSKs into three distinct evolutionary subgroups. The 18 TaBSK loci were unevenly distributed across 14 chromosomes derived from the A, B, and D subgenomes. Motif scanning uncovered 10 universal conserved amino acid motifs, including two signature functional domains: the tetratricopeptide repeat (TPR) and protein kinase catalytic domain (PKc). Intra-genomic collinearity analysis confirmed that segmental duplication constituted the primary evolutionary driver underlying TaBSK family expansion. Extensive cis-regulatory element profiling identified abundant hormone- and stress-responsive cis-motifs. Transcriptome profiling RNA-seq datasets revealed five TaBSK genes exhibiting significant differential transcription under salt stress. Specifically, TaBSK16, TaBSK17, and TaBSK18 were markedly upregulated following salt exposure. Collectively, this study delivers an evolutionary and transcriptional atlas of the wheat TaBSK family and provides candidate genes for functional validation and molecular breeding toward salt-tolerant wheat varieties. Collectively, this study explores the evolution and transcriptional patterns of the wheat TaBSK gene family and provides candidate genes for subsequent functional validation and molecular breeding of salt-tolerant wheat varieties. Full article

The nuclear ITS1–5.8S rDNA–ITS2 region is among the most widely used markers for phylogenetic studies in plants. We sequenced the ITS1–5.8S rDNA–ITS2 region in several species of Selenicereus, two species of Deamia and Epiphyllum chrysocardium. The newly generated sequences were found to be more closely related to ITS and 5.8S rDNA sequences from representatives of other cactus tribes than to the Selenicereus ITS sequences previously deposited in GenBank by research group O. Plume. Importantly, all these sequences retained three conserved motifs of the 5.8S rRNA gene that are commonly used to distinguish functional copies from pseudogenes. Then we analyzed available genome assemblies representing 12 species of Cactaceae. In contrast to the ribotypes identified in this study, the previously reported 5.8S rDNA variants in the assembled genomes of Selenicereus and Carnegiea were represented by a single copy flanked by highly degraded 18S and 28S rDNA sequences. Phylogenetic analyses based on the newly generated ITS sequences and Genbank data supported the monophyly of the subtribes Hylocereinae, Rhipsalideae, and Trichocereinae, as well as the tribes Rhipsalideae, Notocacteae, and Cylindropuntieae. These results demonstrate that the functional ITS1-5.8S rDNA–ITS2 region represents an informative marker for phylogenetic studies within the Cactaceae. Full article

Protein arginine methyltransferases (PRMTs) are key regulators of diverse cellular processes in eukaryotes, including transcriptional regulation, RNA processing, signal transduction and DNA repair. However, the biological functions of PRMTs in Verticillium dahliae remain largely unexplored. In this study, we identified a PRMT1 homolog in V. dahliae. Targeted deletion of VdPRMT1 resulted in severely impaired hyphal growth, sporulation, stress responses and pathogenicity. Subcellular localization analysis showed that VdPRMT1 is distributed in both the nucleus and cytoplasm of hyphae. Host-induced gene silencing (HIGS) of VdPRMT1 in cotton significantly reduced disease severity, supporting its important role in pathogenicity. Furthermore, VdLuc7, a U1 snRNP-associated protein containing multiple RG/RGG motifs, was identified as a putative interacting partner of VdPRMT1 through yeast two-hybrid (Y2H) screening, bimolecular fluorescence complementation (BiFC) and luciferase complementation imaging (LCI) assays. Together, our results demonstrate that VdPRMT1 is required for normal fungal development and full virulence in V. dahliae, and suggest that arginine methylation may contribute to pathogenicity through regulation of RNA processing-related pathways. These findings provide new insights into the molecular mechanisms underlying fungal virulence and identify VdPRMT1 as a potential target for disease control. Full article

The fennel shoot borer, Evergestis extimalis (Scopoli) (Lepidoptera: Crambidae: Glaphyriinae), is a widespread and economically significant pest across the Qinghai–Tibet Plateau. However, its geographic distribution, comprehensive genomic resources and the phylogenetic position have not been systematically examined. Our findings reveal a broad distribution for E. extimalis, spanning extensive regions across Asia, Europe, and North America. Furthermore, we present the first complete mitochondrial genome (mitogenome) of this species and conduct extensive phylogenetic analyses to clarify its evolutionary relationships within Crambidae. The circular mitogenome is 15,301 bp in length and exhibits typical lepidopteran organization, comprising 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and an AT-rich control region. Comparative analysis of E. junctalis revealed conserved gene arrangement and high structural similarity. Among the 13 PCGs, nad6 exhibited the highest nucleotide diversity, whereas cox1 was the most conserved. Most PCGs were under purifying selection (Ka/Ks < 1) except atp8, nad2, and nad6. The AT-rich region (367 bp) contained tandem repeat motifs characteristic of Pyraloidea. Phylogenetic reconstruction based on concatenated sequences of 13 PCGs and 2 rRNAs from 58 species strongly supported the monophyly of Crambidae and revealed Glaphyriinae as a sister group to Odontiinae. Our results confirm the basal divergence between the “PS clade” (Pyraustinae + Spilomelinae) and the “non-PS clade” (Glaphyriinae, Odontiinae, Crambinae, Scopariinae, Schoenobiinae, and Acentropinae) but reveal discordant relationships within the “CAMMSS clade” (Crambinae, Acentropinae, Midilinae, Musotiminae, Schoenobiinae, and Scopariinae) compared to earlier nuclear gene-based studies. This study fills a significant gap in Glaphyriinae mitogenomics and provides valuable genomic resources for future population genetics on this economically important pest. Full article

This study investigated the RNA virome associated with the phlebotomine sand fly Pintomyia fischeri using a metatranscriptomic approach applied to the Meta29 library, composed of 21 specimens collected at the São Paulo Zoo, Brazil. Read-based taxonomic analysis revealed a diverse viral community composed of viruses associated with the families Iflaviridae, Narnaviridae, Partitiviridae, Reoviridae, Solemoviridae, Tombusviridae, Totiviridae, and Tymoviridae, in addition to highly abundant unclassified RNA viruses related to the ShiM 2016 group. Assembly and annotation analyses enabled the characterization of four viral RNA genomes associated with the families Partitiviridae (PfPartitiV-1a-SP, PfPartitiV-1b-SP, and PfPartitiV-2-SP) and Narnaviridae (PfNarnaV-1-SP). Sequence comparisons revealed low amino acid identity relative to currently available reference viral sequences, supporting the classification of these sequences as highly divergent and potentially novel viral lineages. Structural modeling of the RNA-dependent RNA polymerase (RdRp) proteins identified the viral polymerase-specific catalytic motifs A, B, and C. Phylogenetic analyses further supported the evolutionary divergence of the identified viruses relative to currently described taxa. Overall, these findings expand current knowledge of viral RNA diversity associated with Neotropical sand flies and highlight the value of metatranscriptomic approaches for the detection and characterization of previously undescribed viruses associated with medically important insect vectors. Full article