Search Results (190)

Lactic acid bacteria (LAB)-mediated fermentation has been widely explored as a strategy to enhance the nutritional functionality of cereal processing by-products. In this study, 50 LAB strains previously isolated from Korean traditional fermented foods and obtained from the National Agrobiodiversity Center (KACC, Jeonju-si, Republic of Korea) were systematically screened for bifunctional carbohydrate and protein degradation capacities, and their potential to improve the nutritional functionality of wheat bran was evaluated. Paper disc assays revealed substantial inter-strain variability, with clear zone diameters ranging from 12.35 to 29.52 mm for carbohydrate degradation and 11.61 to 25.45 mm for protein degradation. Ten strains exceeding both upper-quartile enzymatic degradation cutoff thresholds (≥25.25 mm for carbohydrate degradation and ≥17.98 mm for protein degradation, respectively) were putatively identified as Lactiplantibacillus plantarum and Lacticaseibacillus paracasei based on 16S rRNA gene sequencing (99.73–100% similarity). Substrate-specific fermentation using L. paracasei KS 595 across four substrates (brewed soy sauce soybean meal, pea, floury rice, and wheat bran) demonstrated substrate-dependent differences in growth and branched-chain amino acid (BCAA) accumulation, with the highest increase observed in pea fermentation. Strain-specific evaluation during wheat bran fermentation revealed distinct differences in growth kinetics, pH reduction, and BCAA production driven by cell-envelope proteinases and intracellular peptidases, with viable cell counts reaching 9–10 log CFU/mL after 48 h. Biogenic amine analysis indicated that histamine levels remained below commonly accepted safety limits in all strains, while L. paracasei KS 543 showed no detectable tyramine or histamine. Although the potential improvement in plant protein bioavailability was indirectly inferred through the free BCAA enrichment rather than directly measured in vivo, these results support a systematic screening approach for selecting LAB strains capable of producing BCAA-enriched fermented wheat bran, with potential implications for improving plant protein bioavailability and addressing nutritional needs in aging and active populations. Full article

Cabbage (Brassica oleracea var. capitata), a member of the Brassicaceae family, is an important vegetable crop grown worldwide. Self-incompatibility (SI) in cabbage is a key trait that prevents self-fertilization and inbreeding, thereby maintaining genetic diversity within populations. Although several genes related to SI have been reported, its genetic control remains unclear. In this study, we developed an F₂ population from the highly self-compatible (SC) cabbage line 87-534 and the highly self-incompatible (SI) line 01-20, both of which exhibit the S5 haplotype. The segregation analysis of the F₂ population revealed the possible control of SI by a major gene with additional modifying genetic factors. Bulk segregant analysis sequencing (BSA-Seq) and RNA sequencing (RNA-Seq) were performed on SI and SC samples selected from the F₂ population. BSA-Seq revealed a candidate region on chromosome 7 (C07: 7.45 Mb to 8.93 Mb), including 32 differentially expressed genes (DEGs). RNA-Seq identified a total of 2400 DEGs between the two pools, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses suggested that plant hormone biosynthesis and signaling, plant immune response were significantly enriched and may be involved in SI. The combined analysis of BSA-Seq and RNA-Seq identified six candidate genes associated with SI, and their expression was confirmed using quantitative real-time PCR (qRT-PCR). Among them, Bol023956 encodes fructokinase, Bol023986 is involved in plant defense response, Bol024018 is related to pollen development, Bol024012 encodes a transport protein for phytohormones, Bol023943 encodes chorismate mutase 3, and Bol012515 is an important regulatory gene for chloroplast synthesis. These six genes, potentially linked to SI, should be targets for further validation. These findings provide insights into the molecular mechanisms of SI in cabbage and the selection of superior cabbage varieties. Full article

Ginger possesses both significant edible and medicinal value. Sprouting of ginger is a critical phase that influences the yield and quality of the crop. While silica nanoparticles (SiNPs) are known to promote the growth of ginger, their impact on sprouting remains unclear. The results show that sprouting 100 mg L⁻¹ SiNPs (SiNP100) significantly improved ginger sprouting rate and respiratory intensity while reducing weight loss. It also elevated fructose, sucrose, and glucose contents, as well as sucrose phosphate synthase (SPS), sucrose synthase (SS), neutral invertase (NI), acid invertase (AI) activities, indicating that SiNP100 is associated with enhanced sprouting by modulating sugar metabolism. Concurrently, starch content decreased and α- and β-amylase activities increased. Hormonal profiling showed that SiNP100 increased auxin (IAA), trans-zeatin (TZR), isoamylalkenyladenin (IP), and gibberellic acid (GA₃) levels, while decreasing abscisic acid (ABA), further supporting its role in promoting sprouting. RNA-seq and RT-qPCR validated that SiNP100 significantly enriched the plant hormone signal transduction and starch and sucrose metabolism pathways, upregulating genes related to sugar transport and metabolism (ZoSweet7, ZoSSIVa, ZoSPS1, and ZoSUS5). Field trials over two consecutive years confirmed that SiNP100 application improved ginger growth, photosynthesis, antioxidant capacity, and ultimately yield and quality. This study demonstrated the potential of SiNPs to improve seed sprouting and promote ginger growth under field conditions. Full article

Non-alcoholic fatty liver disease (NAFLD) is characterized by excessive hepatic lipid accumulation and can progress to severe liver injury. Kaempferol (KPF), a plant-derived flavonoid, exhibits lipid-regulatory properties. Tripartite motif-containing protein 56 (TRIM56), an E3 ubiquitin ligase, has been reported to interact with fatty acid synthase (FASN) and limit hepatic lipogenesis. This study investigated whether KPF alleviates NAFLD through modulation of TRIM56-associated lipid metabolic pathways. Molecular docking, molecular dynamics simulations, and cellular thermal shift assays (CETSA) were employed to evaluate the interaction between KPF and TRIM56. High-fat diet-induced NAFLD mice and fatty acid-treated HepG2 cells were used to assess the effects of KPF on hepatic lipid accumulation. Histological analysis, lipid profiling, Oil Red O staining, Western blotting, immunofluorescence, and quantitative PCR were performed. Endogenous co-immunoprecipitation examined the association between TRIM56 and FASN, and siRNA-mediated knockdown of TRIM56 evaluated its functional contribution. KPF significantly reduced serum triglyceride, total cholesterol, and low-density lipoprotein cholesterol levels, ameliorated hepatic steatosis in vivo, and decreased intracellular lipid accumulation in vitro. In silico and CETSA analyses supported the engagement of TRIM56 by KPF. KPF restored TRIM56 expression under steatotic conditions, whereas TRIM56 silencing attenuated its lipid-lowering effects. TRIM56 was confirmed to associate with FASN, and KPF treatment suppressed multiple lipogenic enzymes. These findings indicate that KPF alleviates hepatic steatosis, at least in part, through modulation of TRIM56-associated lipogenic pathways, highlighting TRIM56 as a potential therapeutic target in NAFLD. Full article

The discovery of bidirectional microRNA transfer between two organisms during plant–microbe interactions and the ability of some fungal pathogens to absorb double-stranded RNA (dsRNA) or short interfering RNA (siRNA) from the environment provided an impetus for exploiting this mechanism in plant defense against pathogens. In this study, we investigated the role of conserved wheat microRNAs (miRNAs), miRNA408 and miRNA159, in inducing plant defense responses and suppressing the virulence of the phytopathogenic ascomycete fungus Parastagonospora nodorum, mediated by necrotrophic effectors (NEs) encoded by SnTox genes regulated by fungal transcription factors (TFs). The foliar spraying with in vitro synthesized siRNA408 and siRNA159 duplexes before inoculation with SnTox3-producing P. nodorum isolate increased wheat plant resistance to the SnB isolate and suppressed the pathogen growth and development. Most likely, silencing of the miRNA408 target genes TaCAT-2A, TaCAT-2B, and TaCLP1, and the miRNA159 target gene TaMYB65, led to the induction of a defense response of wheat plants against P. nodorum. This defense response was characterized by a decrease in the catalase activity, accumulation of hydrogen peroxide, activation of the expression of salicylic acid signaling pathway genes (TaWRKY13, TaPR1), and suppression of the expression of ethylene signaling pathway genes (TaEIN3, TaPR3). We demonstrated for the first time the ability of siRNA159 and siRNA408 to penetrate the mycelium of the pathogen P. nodorum and be involved in the cross-kingdom regulation of fungal genes to suppress the expression of some genes of NE (SnToxA, SnTox3) and fungal TFs (SnStuA). We predicted potential targets for wheat miRNA408 and miRNA159 in the P. nodorum transcriptome, making spray-induced gene silencing (SIGS) promising for use against this pathogen. These results provide valuable insights for studying the cross-kingdom transfer of plant miRNAs. Full article

Coding transcripts-derived small interfering RNAs (ct-siRNAs) have emerged as a special class of endogenous siRNAs and have been implicated in the regulation of gene expression in plants, particularly under conditions where RNA metabolic pathways are perturbed. When the RNA quality control (RQC) system is impaired, the aberrant mRNA fragments were converted to double stranded forms by RNA-directed RNA polymerase 6 (RDR6) with the assistance of Suppressor of Gene Silencing 3 (SGS3) and subsequently processed by DICER-LIKE proteins into 21-nt and 22-nt ct-siRNAs. The accumulation of ct-siRNAs and the resulting suppression of their cognate genes are usually associated with altered plant growth and stress response. In this review, we summarize our current understanding of the ct-siRNAs, particularly their biogenesis under different RNA metabolic defective conditions. Comparative analysis of these genetic contexts indicates that ct-siRNAs act through translation inhibition and/or mRNA cleavage, with regulatory outcomes influenced by siRNA length and genetic background. We further summarize the biological consequence of ct-siRNA accumulation, which are frequently associated with impaired plant growth and stress adaptation. Finally, we discuss current controversies on ct-siRNAs research and highlight key unsolved questions for future investigation. Collectively, this review highlights ct-siRNAs as a link between impaired RNA metabolisms and post-transcriptional gene silencing, with context-dependent effects on plant growth and stress responses. Full article

Potyvirus genomes are expressed as a single large open reading frame, which is translated into a polyprotein that is post-translationally cleaved by three virus-encoded proteases into 10 functional proteins. Several of these potyviral proteins, including nuclear inclusion protein b (NIb), are multifunctional. Here, using the classic GFP silencing in Nicotiana benthamiana gfp-transgenic plants, we show that potato virus Y (PVY) NIb, in addition to its canonical role as the viral RNA-dependent RNA polymerase (RdRP), functions as a suppressor of RNA silencing. Mutational analyses reveal a previously unreported NIb nuclear localization signal (NLS) consisting of a triple-lysine motif. NIb suppression of RNA silencing activity was lost when the NLS was mutated, suggesting that nuclear localization is required for NIb suppression of RNA silencing activity. Analysis of sequenced GFP siRNAs revealed three reproducible hotspot regions at ≈175 nt, ≈320–330 nt, and a broader 3′-proximal region spanning ≈560–700 nt that contains multiple local maxima. These data show differences in the positional distribution of siRNAs between samples expressing NIb and those expressing NIb^Del3×2, the NIb null mutant that does not suppress RNA silencing. However, the positional distribution of GFP-derived small RNAs across the transgene differed modestly between NIb and NIb^Del3×2, while both treatments showed the same three reproducible hotspot regions. Furthermore, NIb was found to interact with four key RNA silencing pathway proteins—AGO4, HSP70, HSP90, and SGS3. Except for HSP90, each of these proteins showed degradation products that were absent in NIb mutants that did not suppress RNA silencing. These findings support a role for NIb in countering host defense during virus infection. Full article

Background: Acacetin, a naturally occurring flavone present in various plants, is known as a promising drug candidate for cardiovascular disorders. Our previous study demonstrated that acacetin ameliorates atherosclerosis through endothelial cell protection; however, its pharmacological effects on vascular smooth muscle cells (VSMCs) remain unexplored. This study investigates the therapeutic potential of acacetin against lysophosphatidylcholine (LysoPC)-induced VSMC injury and elucidates the underlying molecular mechanisms. Methods and Results: Multiple biochemical techniques were employed in the present study. The results showed that acacetin significantly attenuated LysoPC-induced apoptosis and reactive oxygen species (ROS) generation in cultured VSMCs. Western blot analysis revealed that the cytoprotection of acacetin was associated with upregulated expression of antioxidant defense proteins, including nuclear factor erythroid 2-related factor 2 (Nrf2), catalase (CAT), NADPH quinone oxidoreductase 1 (NQO-1), and superoxide dismutase 1 (SOD1). Nrf2 silencing completely abolished these protective effects. Mechanistically, siRNA-silencing of Sirtuin 1 (Sirt1) abrogated acacetin-induced modulation of the Nrf2/Keap1/p62 signaling. In vivo validation using aortic tissues from high-fat-diet-fed ApoE^−/− mice confirmed that acacetin effectively suppressed VSMC apoptosis and ROS overproduction associated with restoring the downregulated Sirt1 expression levels. Conclusions: These findings establish a novel mechanistic paradigm wherein acacetin confers protection against LysoPC-induced VSMC apoptosis and oxidative stress through Sirt1-dependent activation of the Nrf2/p62 signaling pathway, suggesting that acacetin is a promising therapeutic drug candidate for atherosclerotic plaque stabilization. Full article

The phenomenon of transgene silencing was first observed shortly after the generation of the initial transgenic plants. The vast body of experimental data accumulated since then constitutes an invaluable resource for dissecting the mechanisms of epigenetic gene regulation. Silencing operates at either the transcriptional (TGS) or post-transcriptional (PTGS) level and is predominantly mediated by small interfering RNAs (siRNAs). Although these two epigenetic pathways involve distinct sets of proteins and enzymes, they share fundamental mechanistic features: the generation of double-stranded RNA (dsRNA), its processing into siRNAs by DICER-LIKE (DCL) enzymes, and the assembly of an Argonaute-centered effector ribonucleoprotein complex (RISC). Guided by sequence-specific siRNAs, this complex identifies complementary target sequences with high precision. A comprehensive understanding of these regulatory pathways enables the targeted induction or suppression of specific plant genes. This review traces the history of experimental findings regarding the loss of recombinant gene activity in transformants and their progeny, which collectively established the foundation for elucidating the molecular mechanisms of transgene silencing. Full article

Wheat dwarf virus (WDV) is a major constraint to global wheat production, causing severe yield losses and economic disruption. Understanding the molecular basis of wheat–WDV interactions is essential for developing resistant cultivars. Non-coding RNAs (ncRNAs), including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), are key regulators of gene expression and defence. This study identified ncRNAs involved in wheat responses to WDV, including host lncRNAs, miRNAs, and viral small interfering RNAs (siRNAs) targeting WDV genomic regions. High-throughput sequencing revealed extensive ncRNA reprogramming under WDV infection. A total of 437 differentially expressed lncRNAs (DElncRNAs) and 58 miRNAs (DEmiRNAs) were detected. Resistant genotypes displayed more DElncRNAs (204 in Svitava; 163 in Fengyou 3) than the susceptible Akteur (141). In Akteur, 66.7% of DElncRNAs were downregulated, whereas in Svitava, 56.9% were upregulated. Akteur also exhibited more DEmiRNAs (28) than resistant genotypes (15), with predominant downregulation. A co-expression network analysis revealed 391 significant DElncRNA–mRNA interactions mediated by 16 miRNAs. The lncRNA XLOC_058282 was linked to 298 transcripts in resistant genotypes, suggesting a central role in the host defence. Functional annotation showed enrichment in signalling, metabolic, and defence-related pathways. Small RNA profiling identified 1166 differentially expressed sRNAs targeting WDV, including conserved hotspots and 408 genotype-specific sites in Akteur versus Fengyou 3. Infected plants displayed longer sRNAs, a sense-strand bias, and a 5′ uridine preference, but lacked typical 21–24 nt phasing. These findings highlight the central roles of ncRNAs in orchestrating wheat antiviral defence and provide a molecular framework for breeding virus-resistant wheat. Full article

ARGONAUTE 1 (AGO1) selectively recruits microRNAs (miRNAs) and some small interfering RNAs (siRNAs) to form an RNA-induced silencing complex (RISC) to regulate gene expressions and also promotes the transcription of certain genes through direct chromatin binding. Complete dysfunction of AGO1 causes extremely serious growth arrest and sterility in Arabidopsis. Here, we characterize an ago1-38 allele with distinctive morphological abnormalities obviously distinguishing it from the other ago1 alleles, such as ago1-25 and ago1-45. The aberrant phenotypes of ago1-38 were completely restored in its transgenic complementation lines harboring an AGO1 promoter and coding sequence. To investigate the mechanism underlying the unique phenotype of ago1-38, integrated transcriptomic and metabolomic analysis was employed. The glutathione metabolism pathway was significantly co-enriched in the integrated analysis of ago1-38, suggesting an altered balance of the glutathione-related redox system. Transcriptomic analysis showed that many genes in the siRNA processing pathway were significantly changed in ago1-38, suggesting the dysregulation of the siRNA pathway. Meanwhile, numerous genes, particularly the large set of transcriptional factors associated with plant–pathogen interaction networks and phytohormone signaling cascades, exhibited altered expression patterns, implying perturbed immune defense and hormonal signaling. Collectively, these findings provide new insights into the multifaceted roles of AGO1 in siRNA processing, pathogen response, and phytohormone signaling. Full article

Plant viral diseases cause significant agricultural losses worldwide and are shaped by complex virus-host and virus-virus interactions. Unlike fungal or bacterial pathogens, viruses cannot be directly controlled with chemicals, and their management relies on insect vector control and the development of virus-resistant plant varieties. Plants deploy endogenous epigenetic (DNA/chromatin-based) and epitranscriptomic (RNA-based) mechanisms to limit viral infections. RNA silencing pathways, particularly post-transcriptional gene silencing (PTGS) mediated by small RNAs, restrict viral replication and shape viral populations. Additional layers, including RNA-directed DNA methylation (RdDM), N6-methyladenosine (m⁶A) RNA modifications, histone modifications and chromatin remodeling, further modulate host–virus interactions. DNA methylation can be inherited and may confer resistance to future generations, although its stability is partial and context-dependent. Virus-derived 24-nt small interfering RNAs (siRNAs) act as mobile signals, inducing systemic gene silencing and potentially influencing viral population dynamics. Understanding these epigenetic and epitranscriptomic mechanisms can improve virus diagnosis, pathogenesis studies and disease management, while also providing insights into viral diversity and co-infection dynamics. This review synthesizes current knowledge of these mechanisms and discusses their implications for developing sustainable antiviral strategies. Full article

Highly conserved LOR structural domains are found in proteins encoded by LURP-ONE-RELATED (LOR) family genes, which is named after LATE UP-REGULATED IN RESPONSE TO HYALOPERONOSPORA PARASITICA 1 (LURP1), the first characterized member in Arabidopsis thaliana. Members of the AtLOR gene family play a role in the biotic stress responses in Arabidopsis. In contrast, functional studies on the role of the LOR gene in plant responses to abiotic stresses (such as drought) remain relatively scarce. Using foxtail millet (Setaria italica), a drought-tolerant C4 model plant, this study systematically investigates the LOR gene family. It provides a foundation for improving crop stress tolerance. In this study, forty-two LOR family members were identified via genome-wide analysis of foxtail millet, and phylogenetic tree analysis revealed that the SiLOR gene family could be divided into seven subgroups, which are distributed across six chromosomes of the genome. Furthermore, RNA-Seq data analysis showed that SiLOR genes exhibited differential expression across roots, stems, leaves, and panicles, with the majority predominantly expressed in roots. Cis-acting element analysis indicated that SiLOR genes may be implicated in multiple biological processes, including hormone response, low-temperature response, and dehydration response. The involvement of foxtail millet LOR gene family members in abiotic stress was strongly supported by RNA-Seq and quantitative real-time PCR (qRT-PCR) results, which confirmed their drought stress-induced expression and demonstrated that SiLOR3, SiLOR11, SiLOR12, SiLOR16, and SiLOR18 were significantly upregulated. Collectively, this study provides vital starting points for further investigation into the functional roles of SiLOR genes in foxtail millet. Full article

With emerging viruses and drug resistance on the rise, the discovery and development of innovative antiviral substances and agents are necessary for the effective treatment and control of viral outbreaks. Surrogate viruses are safer alternatives used in research to mimic dangerous or hard-to-culture viruses. They enable efficient, ethical, and cost-effective screening of antiviral compounds. In this study, we used a recombinant viral hemorrhagic septicemia virus (rVHSV) expressing enhanced green fluorescent protein as a surrogate for RNA viruses for the high-throughput screening of antiviral agents. An optimized mixture of viruses and EPC host cells was distributed in 96-well plates containing chemical compounds or plant extracts for screening. Using this system, 44,642 chemical compounds and 8104 plant and marine organism extracts were tested; 140 candidates were selected from primary screening, and 8 compounds and 5 plant extracts were further selected based on the selectivity index (SI), representing the ratio of the cytotoxic concentration (CC₅₀) to the inhibition concentration (IC₅₀). Among these, compound 3, which had the highest SI value of 1046, was further tested, considering in vitro activity against VHSV and another fish rhabdovirus, snakehead rhabdovirus (SHRV). Full article

Salt stress is a major form of abiotic stress that disrupts soybean germination and early seedling establishment. In this study, physiological, biochemical, and transcriptomic analyses—including germination index, antioxidant enzyme activity, and RNA-seq profiling—were conducted during soybean germination to elucidate early responses to salt stress and biostimulant treatment. A preliminary screening of six biostimulants (nanoparticle zinc oxide (NP-ZnO), nanoparticle silicon dioxide (NP-SiO₂), silicon dioxide (SiO₂), glucose, humic acid, and fulvic acid) revealed NP-SiO₂ as the most effective in promoting germination under salt stress. Under 150 mM NaCl, NP-SiO₂ increased the germination rate and length of the radicle compared with the control, also enhancing peroxidase and ascorbate peroxidase activities while reducing malondialdehyde accumulation, suggesting alleviation of oxidative stress. RNA sequencing revealed extensive transcriptional reprogramming under salt stress, identifying 4579 differentially expressed genes (DEGs) compared with non-stress conditions, while NP-SiO₂ treatment reduced this number to 2734, indicating that NP-SiO₂ mitigated the transcriptional disturbance caused by salt stress and stabilized gene expression networks. Cluster analysis showed that growth- and hormone-related genes suppressed by salt stress were restored under NP-SiO₂ treatment, whereas stress-responsive genes that were induced by salt were attenuated. Hormone-related DEG analysis revealed that NP-SiO₂ down-regulated the overactivation in the abscisic acid, jasmonic acid, and salicylic acid pathways while partially restoring gibberellin, auxin, cytokinin, and brassinosteroid signaling. Overall, NP-SiO₂ at 100 mg/L mitigated salt-induced oxidative stress and promoted early soybean growth by fine-tuning physiological and transcriptional responses, representing a promising nano-based biostimulant for enhancing salt tolerance in plants. Full article