Search Results (1,132)

Glyphosate is one of the most widely used herbicides in agricultural, horticultural, and urban environments. However, its residue accumulation and oxidative damage pose serious threats to crop health and food safety. In this study, we evaluated the potential of epigallocatechin gallate, a natural polyphenol derived from tea, to alleviate glyphosate-induced stress in melon (Cucumis melo L.). LC-MS/MS analysis revealed that EGCG significantly reduced glyphosate residues in plant tissues. Transcriptome analysis indicated that glyphosate induced extensive transcriptional reprogramming, activating genes involved in detoxification and antioxidant defense. Co-treatment with glyphosate and EGCG partially mitigated this stress response and redirected gene expression toward secondary metabolic pathways, particularly flavonoid and phenylalanine biosynthesis. Under herbicide stress, EGCG restored the transcription of key flavonoid biosynthetic genes, including PAL, C4H, CHI, and OMT. Meanwhile, EGCG also modulated the expression of APX, SOD, and GST, suggesting a selective effect on antioxidant systems. Co-expression network analysis identified key hub genes associated with oxidative stress and flavonoid metabolism. These findings demonstrate the dual regulatory role of EGCG in suppressing acute oxidative stress while enhancing metabolic adaptability, highlighting its potential as a natural additive for reducing herbicide residues in fruit crops. Full article

Thermophilic microorganisms represent an untapped reservoir of thermostable biocatalysts and stress-resilient biomolecules for industrial biotechnology. Aeribacillus pallidus, a Gram-positive moderate thermophile, has attracted attention for its enzymatic versatility and environmental adaptability, yet its genomic potential remains underexplored. Here, we present a comparative genomic analysis of 13 A. pallidus strains to uncover conserved and strain-specific traits relevant to biotechnology. Genomes ranged from 3.24 to 4.98 Mb, with GC content largely conserved (~39%) except for GS3372 (57.4%), indicating possible horizontal gene transfer. All strains encoded complete central metabolic pathways, while carbohydrate-active enzyme profiling revealed abundant glycoside hydrolases and glycosyltransferases, with GS3372 and MHI3390 enriched for lignocellulose-degrading enzymes. Secondary metabolite mining identified diverse biosynthetic gene clusters, including terpenes, sactipeptides, and bacteriocins, with PI8, W-12, and 8m3 exhibiting the greatest biosynthetic diversity. A core set of heat shock and universal stress proteins underscored robust thermotolerance. Phylogenomic and pan-genome analyses revealed high intraspecific diversity and an open pan-genome structure. Collectively, these findings position A. pallidus as a promising thermophilic chassis organism for sustainable applications, including biomass conversion, biofuel production, bioremediation, and the synthesis of heat-stable antimicrobial agents. Full article

Neuroblastoma is a devastating pediatric solid tumor that, despite significant recent advances, still accounts for nearly 15% of all childhood cancer deaths. Patients are risk stratified based on a number of features, including amplification of the MYCN oncogene, yet targeting MYCN itself has been unsuccessful to date. The complex interplay between this oncogene and its many metabolic targets has proven challenging and is only beginning to be understood in the context of pediatric tumors. It is increasingly recognized, however, that MYCN-driven metabolic rewiring and concomitant increases in biosynthetic precursors has the potential to drive many aspects of tumor development. Furthermore, emerging research suggests that improving overall therapeutic outcomes for neuroblastoma patients may well require individual metabolic profiling, allowing personalized simultaneous targeting of multiple metabolic nodes. In this review, we outline clinically relevant research involving MYCN-driven metabolic derangements, including increased glucose uptake, polyamine synthesis, glycosylation, and others, and attempt to summarize the influence of MYCN on important metabolic genes and druggable protein targets. We spotlight emerging research in glycosylation and its modulation as an often overlooked but increasingly promising therapeutic area. It is our hope that this document will provide utility for both clinicians and scientists seeking to understand how the MYCN oncogene and metabolism are critically intertwined. Full article

Fusarium wilt, caused by Fusarium oxysporum f. sp. phaseoli (Fop), is a major constraint to global common bean (Phaseolus vulgaris L.) production. Thiamine (vitamin B1), an essential coenzyme in plant metabolism, has recently emerged as a potential regulatory factor in plant defense. Here, we performed a comprehensive genome-wide analysis of thiamine biosynthesis-related genes in common bean and elucidated their roles in resistance to Fusarium wilt. Five key thiamine biosynthetic genes were identified and characterized, showing conserved functional domains and evolutionary conservation across species. Expression profiling revealed tissue-specific patterns, with PvTHI1-1 and PvTHIC being highly expressed in reproductive and photosynthetic organs, with their relative expression levels 0.28–0.57 higher than other members in the same tissue, while PvTPK maintained a basal expression level in the roots. Upon Fop infection, resistant genotypes exhibited significantly higher expression of thiamine biosynthetic genes and greater accumulation of endogenous thiamine and its derivatives than susceptible ones. Functional analysis using Agrobacterium rhizogenes-mediated transformation demonstrated that overexpression of PvTPK enhanced thiamine metabolism and conferred resistance in susceptible genotypes. Similarly, exogenous application of thiamine upregulated biosynthetic genes and improved disease resistance. Together, these results reveal that thiamine biosynthesis is intricately linked to Fusarium wilt resistance and that both genetic and biochemical manipulation of thiamine pathways can enhance disease tolerance. This study provides new insights into thiamine-mediated plant immunity and establishes a foundation for its application in the control of Fusarium wilt in common bean. Full article

Marine Bacteroidota are recognized bacterial producers of bioactive metabolites, yet their biosynthetic potential remains cryptic under standard laboratory conditions. Here, we developed chemically defined media for Fulvivirga kasyanovii 48LL (Cytophagia) and Tenacibaculum mesophilum fLL (Flavobacteriia) to evaluate the effect of environmentally relevant carbon sources on growth and secondary metabolism. F. kasyanovii utilized 31 of 34 tested carbon sources whereas T. mesophilum grew on only five substrates, underscoring a distinct nutritional preferences. Substrate significantly influenced the antibacterial activity of F. kasyanovii extracts. Growth on β-1,3-glucan, glycerol, poly(β-hydroxybutyrate) (PHB), fish gelatin, or pectin resulted in extracts generating the largest inhibition zones (10–13 mm) against Bacillus subtilis or Rossellomorea marisflavi. Genome analysis revealed F. kasyanovii to be enriched in biosynthetic gene clusters (BGCs), notably harboring a ~570 kb genomic island comprising five large NRPS/PKS-type clusters. Quantitative PCR confirmed carbon-source-dependent regulation of these operons: glucose induced BGC1, BGC3, and BGC4, while κ-carrageenan and PHB upregulated BGC2. Conversely, yeast–peptone medium (analogous to standard marine broth) repressed transcription across all active clusters. These findings demonstrate that naturally occurring carbon sources can selectively activate cryptic BGCs and modulate antibacterial activity in F. kasyanovii, suggesting that similar strategy can be used for natural-product discovery in marine Bacteroidota. Full article

The global transition to a circular bioeconomy is accelerating the demand for sustainable, high-performance materials. Filamentous fungi represent a promising solution, as they function as living foundries that transform low-value biomass into advanced, self-assembling materials. While mycelium-based composites have proven potential, progress has been predominantly driven by empirical screening of fungal species and substrates. To unlock their full potential, a paradigm shift from empirical screening to rational design is required. This review introduces a conceptual framework centered on the biochemical programming of the fungal cell wall. Viewed through a materials science lens, the cell wall is a dynamic, hierarchical nanocomposite whose properties can be deliberately tuned. We analyze the contributions of its principal components—the chitin–glucan structural scaffold, the glycoprotein functional matrix, and surface-active hydrophobins—to the bulk characteristics of mycelium-derived materials. We then identify biochemical levers for controlling these properties. External factors such as substrate composition and environmental cues (e.g., pH) modulate cell wall architecture through conserved signaling pathways. Complementing these, an internal synthetic biology toolkit enables direct genetic and chemical intervention. Strategies include targeted engineering of biosynthetic and regulatory genes (e.g., CHS, AGS, GCN5), chemical genetics to dynamically adjust synthesis during growth, and modification of surface chemistry for specialized applications like tissue engineering. By integrating fungal cell wall biochemistry, materials science, and synthetic biology, this framework moves the field from incidental discovery toward the intentional creation of smart, functional, and sustainable mycelium-based materials—aligning material innovation with the imperatives of the circular bioeconomy. Full article

Endometrial carcinoma (EC) is the most common malignancy of the female reproductive tract, with increasing incidence driven by aging populations and obesity. While molecular classification has improved diagnostic precision, the identification of clinically relevant metabolic biomarkers remains incomplete, and targeted therapies are not yet standardized. In this study, we investigated metabolic alterations in four EC cell lines (AN3-CA, EFE-184, HEC-1B and MFE-296) compared to non-malignant controls under normoxic and stress conditions (hypoxia and lactic acidosis) to identify metabolomic differences with potential clinical relevance. Untargeted gas chromatography–mass spectrometry (GC/MS) and targeted liquid chromatography–mass spectrometry (LC/MS) profiling revealed two distinct metabolic subtypes of EC. Cells of metabolic subtype 1 (AN3-CA and EFE-184) exhibited high biosynthetic and energy demands, enhanced cholesterol and hexosyl-ceramides synthesis and increased RNA stability, consistent with classical cancer-associated metabolic reprogramming. Cells of metabolic subtype 2 (HEC-1B and MFE-296) displayed a phospholipid-dominant metabolic profile and greater hypoxia tolerance, suggesting enhanced tumor aggressiveness and metastatic potential. Key metabolic findings were validated via real-time quantitative PCR. This study identifies and characterizes distinct metabolic subtypes of EC within the investigated cancer cell lines, thereby contributing to a better understanding of tumor heterogeneity. The results provide a basis for potential diagnostic differentiation based on specific metabolic profiles and may support the identification of novel therapeutic targets. Further validation in three-dimensional culture models and ultimately patient-derived samples is required to assess clinical relevance and integration with current molecular classifications. Full article

A pathogenic fungus was isolated from the leaves of strawberry black spot in Zhengzhou China. Based on morphological and phylogenetic analysis, the isolate was identified as Alternaria alstroemeriae. Hybrid sequencing and assembly yielded a high-quality 38.7 Mb genome with 12,781 predicted genes and 99.6% Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness. Functional annotation revealed enrichment in carbohydrate metabolism, secondary metabolite biosynthesis, and virulence-associated genes. Strain L6 harbored 45 biosynthetic gene clusters(BGCs), including 12 clusters for terpenes, 7 for non-ribosomal peptide synthetases, and 7 for polyketide synthases. Six BGCs showed high similarity to known pathways producing alternariol (phytotoxic/mycotoxic compound), alternapyrone (phytotoxin), choline (osmoprotectant), terpestacin (anti-angiogenic agent), clavaric acid (anticancer terpenoid), and betaenone derivatives (phytotoxins). CAZyme analysis identified 596 carbohydrate-active enzymes, aligning with L6’s biotrophic lifestyle. Additionally, 996 secreted proteins were predicted, of which five candidate effectors contained the conserved RxLx [EDQ] host-targeting motif, suggesting potential roles in virulence. This genome resource highlights L6’s exceptional secondary metabolites (SMs) diversity, featuring both plant-pathogenic toxins and pharmacologically valuable compounds, indicating that this endophytic fungus is a potential producer of metabolites meriting further exploration and development. Full article

Polyamines, particularly spermidine, have emerged as key dietary factors with roles in cellular health, autophagy, and longevity. However, strategies for scalable production of polyamine-rich food ingredients remain limited. Here, we report the development of a high-spermidine-producing Saccharomyces cerevisiae strain, 3L63, obtained via ultraviolet mutagenesis of the K7 strain. This strain exhibited a 5.9-fold increase in the total polyamine content, with spermidine being the most abundant. A scalable fermentation system of up to 10⁴ L was established, yielding a dried yeast product that met food safety criteria. Whole-genome sequencing identified mutations in central metabolic pathways, including ARG3, and functional enrichment analysis suggested broad metabolic rewiring, supporting an enhanced biosynthetic capacity, including polyamines. Free amino acid profiling revealed higher arginine levels in 3L63 than in K7, which is consistent with its role as a polyamine precursor. The 3L63 yeast-derived product was enriched in essential amino acids and polyamines. Functionally, this strain promoted the proliferation of normal and senescent human dermal fibroblasts, and its autophagy-inducing activity exceeded that of equivalent concentrations of pure spermidine, suggesting synergistic effects of yeast-derived bioactive compounds. This study demonstrates a non-genetically modified, high-spermidine yeast strain as a promising functional food ingredient with potential applications in healthy aging. Full article

Secondary metabolites, including alkaloids, flavonoids, and tannins, are crucial for human health, agriculture, and ecosystem functioning. Their synthesis is often species-specific, influenced by both genetic and environmental factors. The increasing demand for these compounds across various industries highlights the need for advancements in plant breeding and biotechnological approaches. Transcription activator-like effector nucleases (TALENs) have emerged as a powerful tool for precise genome editing, offering significant potential for enhancing the synthesis of secondary metabolites in plants. However, while plant genome editing technologies have advanced significantly, the application of TALENs in improving secondary metabolite production and expanding genetic diversity remains underexplored. Therefore, this review aims to provide a comprehensive analysis of TALEN-mediated genome editing in plants, focusing on their role in enhancing secondary metabolite biosynthetic pathways and improving genetic diversity. The mechanisms underlying TALENs are examined, including their ability to target specific genes involved in the synthesis of bioactive compounds, highlighting comparisons with other genome editing tools such as CRISPR/Cas9. This review further highlights key applications in medicinal plants, particularly the modification of pathways responsible for alkaloids, flavonoids, terpenoids, and phenolic compounds. Furthermore, the role of TALENs in inducing genetic variation, improving stress tolerance, and facilitating hybridization in plant breeding programs is highlighted. Recent advances, challenges, and limitations associated with using TALENs for enhancing secondary metabolite production are critically evaluated. In this review, gaps in current research are identified, particularly regarding the integration of TALENs with multi-omics technologies and synthetic biology approaches. The findings suggest that while underutilized, TALENs offer sustainable strategies for producing high-value secondary metabolites in medicinal plants. Future research should focus on optimizing TALEN systems for commercial applications and integrating them with advanced biotechnological platforms to enhance the yield and resilience of medicinal plants. Full article

The early stages of plant–microbe interaction are critical for establishing beneficial symbioses. We investigated how the endophytic fungus Fusarium solani strain FsK modulates tomato (Solanum lycopersicum) development and hormone pathways during in vitro co-cultivation. Seedlings were sampled at three early interaction stages (pre-contact, T1; initial contact, T2, 3 days post-contact, T3). Root traits and root and leaf transcripts for abscisic acid (ABA) and ethylene (ET) pathways were quantified, alongside fungal ET-biosynthesis genes. FsK altered root system architecture, increasing root area, lateral root number, root-hair length, and fresh biomass. These morphological changes coincided with tissue- and time-specific shifts. In leaves, FsK broadly affected ABA biosynthetic and homeostasis genes (ZEP1, NCED1, ABA2, AAO1, ABA-GT, BG1), indicating reduced de novo synthesis with enhanced deconjugation of stored ABA. ET biosynthesis was curtailed in leaves via down-regulation of ACC oxidase (ACO1–3), with isoform-specific changes in ACC synthase (ACS). The ET receptor ETR1 was transiently expressed early (T1–T2). FsK itself showed staged activation of fungal ET-biosynthesis genes. These results reveal coordinated fungal–plant hormone control at the transcriptional level that promotes root development during early interaction and support FsK’s potential as a biostimulant. Full article

The color of flowers constitutes one of the most significant ornamental characteristics in roses. Red pigmentation in rose flowers is generally controlled by the biosynthetic pathway of anthocyanins. In this study, the red petals from the rose cultivar ‘Silk Road’ (SR) and the white petals from its color mutant ‘Arctic Road’ (AR) were investigated. Transcriptomic and metabolomic analyses were utilized to identify the crucial genes and metabolites associated with the biosynthesis of flavonoids. A total of 479 flavonoid- related metabolites and 39,201 genes were detected in the rose petals. Comparative analyses revealed significant differences in 277 metabolites and 2556 genes between the blooming flowers of AR and SR. The contents of 11 anthocyanins, 11 proanthocyanidins, as well as the expression levels of CHS, ANS, 3GT, COMT, and CCoAOMT differ significantly between the two cultivars, which may contribute to the formation of white petals in AR. Additionally, 5 GSTs, 4 ABCCs, and 8 MATEs were found to be downregulated in AR, potentially resulting in reduced sequestration of anthocyanins in petal vacuoles. Through comprehensive data analyses, the correlations between genes and metabolites associated with anthocyanin variation in rose petals were identified. The MYB gene (Chr1g0360311) may serve as a key regulator in anthocyanin biosynthesis. This study offers new perspectives on the specific genes and metabolites regulating petal pigmentation, as well as the molecular mechanisms underlying flavonoid synthesis in roses. The candidate key genes associated with anthocyanin biosynthesis and sequestration could serve as important genetic resources for developing ornamental plant varieties with specific pigmentation traits. Full article

The Altai Republic remains a geographic region with an uncovered microbial diversity hiding yet undescribed potential species. Here, we describe the strain al37.1^T from the Altai soil. It showed genomic similarity with the Bacillus mycoides strain DSM 2048^T. However, the in silico DNA–DNA hybridization (DDH) was 61.6%, which satisfies the accepted threshold for delineating species. The isolate formed circular, smooth colonies, in contrast to the rhizoidal morphology typical of B. mycoides. The strain showed optimal growth under the following conditions: pH 6.5, NaCl concentration 0.5% w/v, and +30 °C. The major fraction of fatty acids was composed of C_16:0 (34.77%), C_18:1 (15.20%), C_14:0 (9.06%), and C_18:0 (7.88%), which were sufficiently lower in DSM 2048^T (C_16:0–15.6%, C_14:0–3.7%). In contrast to DSM 2048^T, al37.1^T utilized glycerol, D-mannose, and D-galactose, while being unable to assimilate D-sorbitol, D-melibiose, and D-raffinose. The strain contains biosynthetic gene clusters (BGCs) associated with the production of fengycin, bacillibactin, petrobactin, and paeninodin, as well as loci coding for insecticidal factors, such as Spp1Aa, chitinases, Bmp1, and InhA1/InhA2. The comparative analysis with the 300 closest genomes demonstrated that these BGCs and Spp1Aa could be considered core for the whole group. Most of the strains, coupled with al37.1^T, contained full nheABC and hblABC operons orchestrating the synthesis of enteric toxins. We observed a cytotoxic effect (≈19 and 22% reduction in viability) of the strain on the PANC-1 cell line. Given the unique morphological features and genome-derived data, we propose a new species, B. altaicus, represented by the type strain al37.1^T. Full article

Chronic metabolic disorders have increased recently due to changes in dietary habits and lifestyle. Red-coloured fruits, such as sweet cherries, are rich in anthocyanins and other (poly)phenolic compounds with health-promoting properties, which has garnered growing scientific interest. Melatonin elicitation has emerged as a promising strategy to improve the functional quality of these fruits. This research investigates, for the first time, the combined effect of pre- and postharvest melatonin treatments, followed by a cold storage (2 °C) of 21 days, on the endogenous melatonin and phenolic compound levels of 90 sweet cherries (n = 3) from the ‘Sunburst’ cultivar and harvested from 9 trees per treatment. Single preharvest or postharvest melatonin treatments increased the endogenous melatonin content via direct absorption and activation of key biosynthetic genes, while they reduced anthocyanin, hydroxycinnamic acid, and flavonol levels, likely due to a ripening-delaying effect at harvest. Nevertheless, the combined treatment increased endogenous melatonin levels 5-fold compared to harvest and increased all measured polyphenolic compound levels, including a 29% rise in total anthocyanins reverting the delay in the ripening process. These effects suggest upregulation of genes in the phenylpropanoid pathway and could improve fruit’s functional quality. The response to melatonin is cultivar- and dose-dependent. Future research should investigate genetic and transcriptomic validation to confirm these potential effects and assess whether increased bioactive compound content would translate into measurable human health benefits. Full article

Maize stalk rot (MSR) is one of the most devastating fungal diseases affecting maize worldwide. In recent years, biological control agents have emerged as an environmentally friendly and highly attractive strategy for managing MSR. In this study, two Bacillus strains—B. subtilis KP3P9 and B. siamensis K13C—were shown to effectively inhibit the growth of the MSR pathogen Fusarium graminearum in vitro. Pot experiments showed that inoculation with KP3P9 significantly increased plant height, stem width, above-ground part fresh weight, and total plant fresh weight, whereas K13C significantly improved the stem width and under-ground part fresh weight of maize seedlings (p < 0.05), demonstrating their plant-growth-promoting potential. Moreover, both strains markedly reduced the disease severity indices (DSIs) of maize seedlings, indicating that they can enhance maize resistance to the pathogen. Whole-genome sequencing using Oxford Nanopore (ONT) and Illumina technologies showed that the complete genomes of KP3P9 and K13C contained biosynthetic gene clusters involved in the biosynthesis of antimicrobial secondary metabolites, including fengycin, bacillibactin, subtilin, pulcherriminic acid, subtilosin A, bacilysin, and others. Moreover, both strains exhibited strong antagonistic activity against F. solani (the causal pathogen of apple replant disease), as well as F. oxysporum f. sp. cubense race 1 (Foc1) and tropical race 4 (FocTR4) (pathogens responsible for banana wilt disease), with inhibition rates exceeding 70% in vitro. These results indicate that KP3P9 and K13C are promising biocontrol agents for MSR and other devastating Fusarium diseases. Full article