Search Results (205)

Fungal effectors play an important role in plant immunity. The Magnaporthe oryzae effector PWL2 plays a significant role in rice blast disease caused by this fungus. However, the function of PWL2 in rice immunity is not fully understood. In this study, transgenic rice lines overexpressing PWL2 showed resistance to rice blast. Subcellular localization showed that PWL2-GFP fusion protein is localized on the plasma membrane and cytoplasm. Salicylic acid (SA) induces rice resistance to M. oryzae. Notably, the expression of the NPR1 gene exhibited a rhythmic pattern during the early stages of M. oryzae infection in the transgenic rice lines. However, during later stages of infection, transgenic plants showed reduced levels of the NPR1, WRKY45, PR1a and PR10a genes, along with decreased H₂O₂ accumulation, while SA levels remained unchanged. Transcriptome analysis revealed that SA treatment induced the expression of the ARGONAUTE11 (AGO11) gene in rice. Furthermore, during the later infection stage in the transgenic rice lines, the expression levels of both AGO11 and PWL2 genes increased. Intriguingly, PWL2-derived small interfering RNAs (siRNA) were detected in these transgenic rice lines. It suggests that both the SA signaling pathway and PWL2-derived siRNAs function in rice resistance to blast disease caused by M. oryzae. Full article

Transfer RNA-derived fragments (tRFs) have become a significant category of small non-coding RNAs that likely play vital roles in various cellular functions. Initially, research on small RNAs overlooked tRFs as simple byproducts of tRNA degradation, but recent findings show they are precisely produced molecules that regulate gene expression. Studies have demonstrated that tRFs regulate genes and proteins through various mechanisms, from miRNA-like targeting that relies on Argonaute (AGO) protein to lesser-known modes of action. Recent reports also suggest that tRFs are involved in multiple diseases, including cancer, where they may be utilized as biomarkers. Notably, tRFs can be transported between different cells and tissues of an organism or even across different organisms, further emphasizing their biological significance. Although evidence increasingly indicates that tRFs may function as new regulatory agents in health and disease, their biogenesis and underlying mechanisms are not yet fully understood. Conducting a thorough exploratory analysis of the tRF modes of action could be a valuable resource for advancing this growing field. Our goal in this review is to gather and examine the latest research on tRF biology, focusing on its diverse and dynamic molecular mechanisms discovered in different disease contexts, with a view toward potential applications in medicine. We aim to gain a deeper understanding of tRFs and explore their potential for new therapeutic breakthroughs by combining insights from molecular studies, disease models, and clinical research. Full article

The localization and remodeling of mRNPs is inextricably linked to translational control. In recent years there has been great progress in the field of mRNA translational control due to the characterization of the proteins and small RNAs that compose mRNPs. But our initial assumptions about the physical nature and participation of germ cell granules/condensates in mRNA regulation may have been misguided. These “granules” were found to be non-membrane-bound liquid–liquid phase-separated (LLPS) condensates that form around proteins with intrinsically disordered regions (IDRs) and RNA. Their macrostructures are dynamic as germ cells differentiate into gametes and subsequently join to form embryos. In addition, they segregate translation-repressing RNA-binding proteins (RBPs), selected eIF4 initiation factors, Vasa/GLH-1 and other helicases, several Argonautes and their associated small RNAs, and frequently components of P bodies and stress granules (SGs). Condensate movement, separation, fusion, and dissolution were long conjectured to mediate the translational control of mRNAs residing in contained mRNPs. New high-resolution microscopy and tagging techniques identified order in their organization, showing the segregation of similar mRNAs and the stratification of proteins into distinct mRNPs. Functional transitions from repression to activation seem to corelate with the overt granule dynamics. Yet increasing evidence suggests that the resident mRNPs, and not the macroscopic condensates, exert the bulk of the regulation. Full article

Argonaute (Ago) proteins are ubiquitous across all domains of life. Some prokaryotic Agos (pAgos) function as endonucleases that utilize short nucleic acid guides to recognize and cleave complementary targets. Yet, considerable diversity within pAgos leaves many of their biochemical and functional features insufficiently understood. This study characterizes CalAgo, an pAgo from the mesophilic bacterium Cohnella algarum, which demonstrates DNA-guided DNA endonuclease and RNA endonuclease activities at physiological temperatures. CalAgo’s cleavage activity depends on Mn²⁺ and Mg²⁺ ions and remains effective across a wide range of temperatures and pH levels. CalAgo utilizes only short guides ranging from 15 to 21 nucleotides (nt) in length, in contrast to other reported pAgos that target both DNA and RNA, which often exhibit broad guide selectivity. CalAgo preferentially loads 5′-phosphorylated guides and shows no significant preference among guides with different 5′-end nucleotides. CalAgo is sensitive to guide–target mismatches, and introducing a single mismatch at positions 12 or 15 of the guide strand abolished detectable activity. Structural modeling suggests that this unique guide specificity may originate from structural features in its PAZ domain involved in 3′-guide binding. In summary, this study deepens insight into mesophilic pAgos and supports their potential utility in nucleic acid-based applications. Full article

MicroRNAs (miRNAs) are small non-coding RNAs that play pivotal roles in post-transcriptional gene regulation, influencing development, differentiation, and disease pathogenesis. Since their discovery in 1993, miRNAs have been recognized for their evolutionary conservation and pleiotropic effects, with the 2024 Nobel Prize underscoring their significance in post-transcriptional regulation via the RNA interference (RNAi) pathway. This review synthesizes the complete life cycle of miRNAs—from transcription and processing to function and decay—emphasizing regulatory mechanisms and their implications in human diseases, particularly cancer. We discuss how epitranscriptomic modifications influence miRNA biogenesis and activity, explore their nuclear and mitochondrial functions, and address emerging challenges in miRNA-based therapeutics, including the expanding small RNA landscape such as tRNA-derived small RNAs (tsRNAs), and Argonaute (AGO)-independent activities. Despite hurdles such as modest multi-target effects, off-target interactions, and delivery challenges, miRNAs remain promising as both biomarkers and therapeutic agents, underscoring the need for sustained research to bridge preclinical insights with clinical applications. Full article

The RNA-directed DNA methylation (RdDM) pathway is a crucial epigenetic mechanism governing plant responses to environmental stress. While the RdDM pathway has been extensively studied in Arabidopsis thaliana, the comprehensive understanding of its components in cucumber (Cucumis sativus L.) remains lacking. In this study, we performed a genome-wide identification and characterization of RdDM pathway genes in cucumber, followed by an analysis of their expression patterns across various tissues and under multiple abiotic stress conditions. A total of 67 putative CsRdDM genes were identified, which are unevenly distributed across the cucumber’s chromosomes. Phylogenetic and gene structure analyses revealed considerable evolutionary divergence, particularly within the key Argonaute gene family (CsAGO). Crucially, the promoter regions of CsRdDM genes were found to contain cis-regulatory elements associated with abiotic stress, light signaling, and development, suggesting their potential involvement in complex regulatory networks. RT-qPCR assays confirmed that CsRdDM genes exhibit distinct and stress-specific transcriptional patterns. Notably, several genes such as CsAGO4 and CsIDN2 showed antagonistic expression between roots and leaves under drought (PEG-6000) stress, implying a sophisticated, tissue-specific defense mechanism. Among them, CsAGO4 emerged as a candidate gene responsive to abiotic stress. Those findings provide new insights into the regulatory roles of CsRdDM genes under abiotic stress and highlight candidate genes for the genetic improvement of stress tolerance in cucumber. Full article

MicroRNAs (miRNAs), as an integral component of gene regulatory networks, play a critical role in post-transcriptional regulation, maintaining a dynamic balance between miRNA biogenesis and turnover essential for maintaining cellular homeostasis. The regulation of miRNA turnover, particularly through target-directed microRNA degradation (TDMD), is emerging as a key mechanism in gene expression control in response to physiological, developmental, and environmental changes. This process is mediated by the ubiquitin–proteasome system (UPS), where the E3 ligase ZSWIM8 functions as an adaptor to facilitate the recognition and degradation of Argonaute (AGO) proteins, essential components of the miRNA-induced silencing complex (miRISC), thus negatively regulating gene expression. The ZSWIM8–UPS axis contributes to the precise modulation of miRNA levels by targeting AGO proteins for degradation, thereby influencing miRNA stability and function. This review summarizes the mechanisms underlying ZSWIM8-mediated TDMD, its molecular interactions, and the potential therapeutic applications of targeting miRNA turnover pathways. By understanding the regulation of miRNA degradation, we aim to inform future strategies for the clinical manipulation of miRNA-based therapeutics. Full article

In Drosophila gonads, transposable elements (TEs) are repressed by the Piwi-interacting RNA (piRNA) pathway operating both co-transcriptionally and post-transcriptionally. In the non-gonadal tissues, TEs are mainly repressed by the short interfering RNA (siRNA) pathway with Argonaute 2 (Ago2) functioning as an effector protein. It is generally assumed that this pathway acts at the post-transcriptional level. However, recent data point to its possible involvement in co-transcriptional silencing as well. Here, using DamID, we found a drastic decrease in HP1a on TEs (especially on the LTR-containing retrotransposons) and other heterochromatin regions in Ago2-mutant Drosophila brain. HP1a reduction is accompanied by the increased chromatin accessibility of TEs, indicating their derepression. Accordingly, several LTR-containing retrotransposons were up-regulated in the larval brain of Ago2 mutants. Moreover, upon the knock-down of lamin Dm0 in neurons, HP1a was increased predominantly on the same set of TEs that had reduced HP1a binding in Ago2 mutants. We hypothesize that, since Ago2 was localized to the common complex with lamin Dm0, the depletion of the latter may release Ago2 in the nucleoplasm, thus enhancing the recruitment of HP1a on TEs. Our findings support the hypothesis that TEs in the Drosophila brain are silenced, in part, through Ago2-mediated recruitment of HP1a. Full article

Background/Objectives: Transfer RNA-derived fragments (tRFs) are small non-coding RNAs increasingly implicated in gene regulation and disease, yet their target specificity and disease relevance remain poorly understood. This is an exploratory study that investigates the phenomenon of identical tRF sequences reported in distinct disease contexts and evaluates the consistency between experimental findings and predictions from both target-based and abundance-based tRF databases. Methods: Five tRFs with identical sequences across at least two peer-reviewed disease studies were selected from a recent systematic review. Their validated targets and disease associations were extracted from the literature. Motifs and predicted targets were cross-referenced using three target-oriented databases: tatDB, tRFTar, and tsRFun. In parallel, the abundance enrichment of cancer-associated tRFs was assessed in OncotRF and MINTbase using TCGA-based abundance data. Results: Among the five tRFs, only LeuAAG-001-N-3p-68-85 showed complete alignment between experimental data and both tatDB and tRFTar predictions. Most of the other four displayed at least partial overlaps in motif/binding regions with some of validated targets. tRF abundance data from MINTbase and OncotRF showed inconsistent enrichment, with only AlaAGC-002-N-3p-58-75 exhibiting concordance with its experimentally validated cancer type. Most functionally relevant tRFs were not strongly represented in abundance-only databases. Conclusions: Given the limited number of tRFs analyzed, this study serves primarily as a pilot analysis designed to generate hypotheses and guide future in-depth research, rather than offering comprehensive conclusions. We did, however, illustrate how the analysis of tRFs can benefit from utilizing currently available databases. Target-based databases more closely reflected experimental evidence for mechanistic details when a tRF or a motif match is found. Yet all database types are incomplete, including the abundance-focused tools, which often fail to capture disease-specific regulatory roles of tRFs. These findings underscore the importance of using integrated data sources for tRF annotation. As a pilot analysis, the study provides insights into how identical tRF sequences might function differently across disease contexts, highlighting areas for further investigation while pointing out the limitations of relying on expression data alone to infer functional relevance. Full article

Plant viruses have been traditionally considered pathogens restricted to plant hosts. However, recent studies have shown that some plant viruses can infect and replicate in filamentous fungi and oomycetes, suggesting that their host range is broader than previously thought, and that their ecological interactions are more complex. In this study, we investigated the ability of the well-characterized positive-sense RNA plant virus Tobacco mosaic virus (TMV) to replicate in four major phytopathogenic fungi from different taxonomic groups: Botrytis cinerea, Fusarium oxysporum f. sp. lycopersici, Verticillium dahliae, and Monilinia fructicola. Using a recombinant TMV-based vector expressing a green fluorescent protein (TMV-GFP-1056) as reporter, we demonstrated that TMV can enter, replicate, and persist within the mycelia of B. cinerea and V. dahliae—at least through the first subculture. However, it cannot replicate in F. oxysporum f. sp. lycopersici and M. fructicola. RNA interference (RNAi) is a conserved eukaryotic epigenetic mechanism that provides an efficient defence against viruses. We explored the role of RNAi in the interaction between TMV and the mycelia of V. dahliae and B. cinerea. Our results revealed a strong induction of the Dicer-like 1 and Argonaute 1 genes, which are key compounds of the RNA silencing pathway. This RNAi-based response impaired TMV-GFP replication in both fungi. Notably, despite viral replication and RNAi activation, the virulence of V. dahliae and B. cinerea on their respective host plants remained unaffected. These findings reinforce the emerging recognition of cross-kingdom virus transmission and interactions, which likely play a crucial role in pathogen ecology and viral evolution. Understanding these virus–fungus interactions not only sheds light on RNAi interference silencing mechanisms but also suggests that plant viruses like TMV could serve as simple and effective tools for functional genomic studies in fungi, such as in V. dahliae and B. cinerea. Full article

MicroRNAs (miRNAs) are key post-transcriptional regulators controlling gene expression across several cellular processes, including development, proliferation, and apoptosis. Their biogenesis involves a multi-step pathway, including the processing of primary transcripts and the assembly of the RNA-Induced Silencing Complex (RISC) with Argonaute (AGO) proteins at its core. This review provides a comprehensive overview of the molecular dynamics of miRNA-loaded RISC (miRISC), focusing on the post-translational modifications, the interactors of AGOs and the mechanisms that fine-tune and coordinate miRISC activity. The composition of miRISC influences AGO stability, localization, and silencing efficiency, thereby maintaining cellular homeostasis and development and mediating the response to various types of cellular stress. Uncommon regulatory mechanisms, including AGO modifications during, e.g., hypoxia or Type 2 T cell responses and miRISC functionality, with myriad RNA-binding proteins (RBPs), will be discussed. This review aims at highlighting the recent advances in the understanding of the intricate regulation of miRISC-driven gene silencing. Full article

Contact unmodified antisense DNA biotechnology (CUADb), developed in 2008, employs short antisense DNA oligonucleotides (oligos) as a novel approach to insect pest control. These oligonucleotide-based insecticides target pest mature rRNAs and/or pre-rRNAs and have demonstrated high insecticidal efficacy, particularly against sap-feeding insect pests, which are key vectors of plant DNA viruses and among the most economically damaging herbivorous insects. To further explore the potential of CUADb, this study evaluated the insecticidal efficacy of short 11-mer antisense DNA oligos against Coccus hesperidum, in comparison with long 56-mer single-stranded and double-stranded DNA sequences. The short oligos exhibited higher insecticidal activity. By day 9, the highest mortality rate (97.66 ± 4.04%) was recorded in the Coccus-11 group, while the most effective long sequence was the double-stranded DNA in the dsCoccus-56 group (77.09 ± 6.24%). This study also describes the architecture of the DNA containment (DNAc) mechanism, highlighting the intricate interactions between rRNAs and various types of DNA oligos. During DNAc, the Coccus-11 treatment induced enhanced ribosome biogenesis and ATP production through a metabolic shift from carbohydrates to lipid-based energy synthesis. However, this ultimately led to a ‘kinase disaster’ due to widespread kinase downregulation resulting from insufficient ATP levels. All DNA oligos with high or moderate complementarity to target rRNA initiated hypercompensation, but subsequent substantial rRNA degradation and insect mortality occurred only when the oligo sequence perfectly matched the rRNA. Both short and long oligonucleotide insecticide treatments led to a 3.75–4.25-fold decrease in rRNA levels following hypercompensation, which was likely mediated by a DNA-guided rRNase, such as RNase H1, while crucial enzymes of RNAi (DICER1, Argonaute 2, and DROSHA) were downregulated, indicating fundamental difference in molecular mechanisms of DNAc and RNAi. Consistently, significant upregulation of RNase H1 was detected in the Coccus-11 treatment group. In contrast, treatment with random DNA oligos resulted in only a 2–3-fold rRNA decrease, consistent with the normal rRNA half-life maintained by general ribonucleases. These findings reveal a fundamental new mechanism of rRNA regulation via complementary binding between exogenous unmodified antisense DNA and cellular rRNA. From a practical perspective, this minimalist approach, applying short antisense DNA dissolved in water, offers an effective, eco-friendly and innovative solution for managing sternorrhynchans and other insect pests. The results introduce a promising new concept in crop protection: DNA-programmable insect pest control. Full article

Chemical modifications are the standard for small interfering RNAs (siRNAs) in therapeutic applications, but predicting their off-target effects remains a significant challenge. Current approaches often rely on sequence-based encodings, which fail to fully capture the structural and protein–RNA interaction details critical for off-target prediction. In this study, we developed a framework to generate reproducible structure-based chemical features, incorporating both molecular fingerprints and computationally derived siRNA–hAgo2 complex structures. Using an RNA-Seq off-target study, we generated over 30,000 siRNA–gene data points and systematically compared nine distinct types of feature representation strategies. Among the datasets, the highest predictive performance was achieved by Dataset 3, which used extended connectivity fingerprints (ECFPs) to encode siRNA and mRNA features. An energy-minimized dataset (7R), representing siRNA–hAgo2 structural alignments, was the second-best performer, underscoring the value of incorporating reproducible structural information into feature engineering. Our findings demonstrate that combining detailed structural representations with sequence-based features enables the generation of robust, reproducible chemical features for machine learning models, offering a promising path forward for off-target prediction and siRNA therapeutic design that can be seamlessly extended to include any modification, such as clinically relevant 2′-F or 2′-OMe. Full article

Myocardial injury is a critical determinant of prognosis in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection; however, its underlying mechanisms remain incompletely understood. In this study, we examined the effects of SARS-CoV-2-derived RNA fragments on human cardiomyocytes. We identified a 19-nucleotide sequence within the viral genome that shares complete sequence homology with the human F1F0 ATP synthase subunit alpha gene (ATP5A). This sequence was found to associate with Argonaute 2 (AGO2) and downregulate ATP5A expression via a mechanism analogous to RNA interference. Consequently, oxidative phosphorylation was suppressed in cardiomyocytes, leading to impaired myocardial maturation and the emergence of heart failure-like phenotypes. Notably, exosome-mimetic liposomal delivery of this RNA fragment to cardiomyocytes reproduced the ATP5A-suppressive effect. These findings suggest that SARS-CoV-2-derived RNA fragments may contribute to myocardial injury through the siRNA-like modulation of mitochondrial gene expression. Further validation in animal models and patient-derived materials is warranted. Full article

In recent years, global public health security has encountered significant challenges, with infectious diseases accounting for approximately 25% of global mortality annually. The worldwide pandemic instigated by the novel coronavirus, alongside the persistent threats posed by Ebola, influenza, and multidrug-resistant bacteria, has severely compromised human health, economic development, and social stability. Within this context, the development of rapid and precise pathogen detection technologies has emerged as a critical frontline defense for epidemic prevention and control, serving as a pivotal component in the implementation of the “early detection, early isolation, and early treatment” strategy. The Argonaute (Ago) protein, recognized as a programmable and target-specific activated nuclease, has demonstrated substantial potential in the realm of nucleic acid detection due to its distinctive biological properties, garnering considerable attention. In this study, we delineate the structural characteristics of Ago proteins and elucidate the mechanism underlying their nuclease activity. Furthermore, we review the principles of nucleic acid detection based on Argonaute and provide a comprehensive analysis of recent advancements in related detection systems. Additionally, we compare the advantages of detection based on Argonaute with other detection methodologies. Through a comprehensive analysis, we aim to provide a robust theoretical foundation and an advanced technical reference for the development of new-generation nucleic acid detection platforms with high sensitivity and high specificity. Full article