Search Results (896)

Surfactin is a lipopeptide biosurfactant with significant industrial potential, but high production costs have hindered its commercialization. In this study, we developed a sustainable and cost-effective bioprocess for surfactin biosynthesis using Bacillus subtilis 55033, utilizing kitchen waste as the primary fermentation substrate without any previous pretreatment—an advantage that simplifies the process and reduces costs compared to previous reports. To maximize productivity, the fermentation parameters were systematically optimized through single-factor and orthogonal experimental designs. The optimal conditions were as follows: a fermentation temperature of 31 °C, a duration of 48 h, a 5% v/v inoculum, a 7% w/v solid-to-liquid ratio, an initial pH of 7.5, and an agitation speed of 200 rpm. Under these conditions, the surfactin yield reached 371.67 mg/L, an increase of 100.5% from 185.4 mg/L prior to optimization. We performed a comparative analysis of the surfactin biosynthetic gene clusters between B. subtilis 55033 and the model strain B. subtilis 168. The produced surfactin exhibited potent antagonistic activity against aquatic pathogens, significantly inhibiting the growth of several species of Vibrio and the division and hatching of Cryptocaryon irritans Tomonts. These findings demonstrate that our platform not only provides a high-value valorization route for organic waste but also enables preliminary exploration of surfactin applications in aquaculture, in line with the principles of a circular bioeconomy. Full article

The rhizosphere microbiome and phytohormone signaling are critical determinants of plant growth and stress resilience. This study evaluated the combined effects of Streptomyces sp. HU2014 and coronatine (COR) on maize (Zea mays L.) seedlings. Four treatments were established: control (CK), COR seed soaking (Cor), HU2014 soil inoculation (S), and combined S + Cor (SCor). Growth parameters, chlorophyll content, and antioxidant/oxidative stress markers were measured, and root and leaf transcriptomes, together with root metabolomes, were compared between SCor and CK, followed by qRT-PCR validation. Compared with CK, SCor treatment significantly increased stem diameter (~60%), plant height (~20%), and relative chlorophyll content (SPAD, ~50%). Soluble sugar levels were elevated by over 40% in both leaves and roots, accompanied by tissue-specific modulation of antioxidant enzymes. Transcriptomic analysis of SCor vs. CK revealed 2459 differentially expressed genes (DEGs) in leaves and 3444 DEGs in roots; leaves exhibited upregulation of photosynthetic pigment metabolism (porphyrin and carotenoid pathways) and volatile defense compounds (alkaloids and monoterpenoids), whereas roots showed enrichment in phenylpropanoid/flavonoid biosynthesis, benzoxazinoid synthesis, and starch/sucrose metabolism. Metabolomics of SCor vs. CK identified 526 differentially accumulated metabolites (DAMs) in roots, with significant enrichment in aminoacyl-tRNA biosynthesis, phenylalanine metabolism, and linoleic acid metabolism. Integrative multi-omics analysis further revealed that the JA precursor 13-epi-12-oxo-phytodienoic acid co-clustered with stress-responsive transcription factors (e.g., DREB1C), while tricarboxylic acid (TCA) intermediates and phenylpropanoid metabolites were linked to energy and lignin biosynthesis genes. qRT-PCR confirmed the expression trends of 14 out of 15 tested genes. Collectively, combined HU2014 and COR application triggers tissue-specific transcriptional and metabolic reprogramming in maize, coupling JA-mediated stress signaling with enhanced carbon metabolism and secondary defense compound synthesis to promote rhizosphere adaptation and seedling vigor. Full article

Aspergillus nidulans, a model filamentous fungus endowed with well-established genetic tools and a repertoire of cryptic secondary metabolite biosynthetic gene clusters (BGCs), is extensively exploited as a microbial chassis for heterologous biosynthesis. Mining of its secondary metabolites facilitates the discovery of novel bioactive compounds and the development and application of chassis cells. In the course of heterologous expression of exogenous genes in A. nidulans, we unexpectedly observed the activation of cryptic host BGCs, which resulted in substantial alterations to its secondary metabolic profile. Four previously undescribed compounds (1–4), together with six known analogs (5–10), were isolated from three recombinant A. nidulans strains. Notably, compounds 1–3 are the first naturally occurring examples of diketopiperazine–isoindolinone hybrid alkaloids, while compound 4 is a previously unreported benzofuran carboxylic acid derivative. Their structures and absolute configurations were assigned by interpretation of a combination of spectroscopic data and electronic circular dichroism calculations. Compounds 4 and 5 exhibited potent DPPH radical scavenging activity (IC₅₀, 6.01 and 7.00 μg·mL⁻¹, respectively). This study uncovers a “metabolic perturbation” effect on the host metabolic network during heterologous expression and offers a new strategy for activating silent gene clusters and discovering novel natural products through genetic manipulation. Full article

Background: MYB transcription factors are key regulators of plant growth, development, secondary metabolism, and stress responses. However, this family has not been systematically characterized in the traditional medicinal plant Platycodon grandiflorus, and its roles in flavonoid biosynthesis remain largely unknown. Methods: We performed genome-wide identification of the MYB family using a combined HMMER and BLASTP approach with manual domain validation. Phylogenetic analysis was conducted on conserved MYB domains, followed by synteny, gene structure, conserved motif, and promoter cis-element analyses. Expression patterns under methyl jasmonate (MeJA) treatment were examined via transcriptomics and RT-qPCR. Protein-protein interaction networks were predicted using STRING based on Arabidopsis homologs. Subcellular localization of candidate proteins was tested in Nicotiana benthamiana leaf epidermal cells. Results: A total of 170 PgMYB members were identified, comprising 52.9% 1R-MYB and 44.1% 2R-MYB. They clustered into 26 subgroups (P1–P26), with 1R-MYBs enriched in subgroup P1 (82 members). Synteny analysis revealed 192 collinear blocks between P. grandiflorus and Arabidopsis, and all 26 syntenic gene pairs examined had Ka/Ks < 1, indicating strong purifying selection. Promoter regions were enriched in hormone- (72.9% ABA-responsive) and stress-responsive elements. Nine selected genes showed consistent MeJA-induced expression changes between RNA-seq and RT-qPCR. Integrated analysis of phylogeny, expression correlation, and predicted protein-protein interactions nominated PgMYB47, PgMYB142, and PgMYB151 as candidate regulators of flavonoid biosynthesis. All three proteins localized to the nucleus in N. benthamiana cells. Conclusions: This study provides the first comprehensive characterization of the P. grandiflorus MYB family, highlighting its evolutionary conservation and expression dynamics. The nominated candidates offer a foundation for future functional validation of flavonoid biosynthesis regulation. Full article

Streptomyces species are major producers of bioactive molecules via biosynthetic gene clusters (BGCs). However, many BGCs are silent or poorly expressed in their native hosts, making heterologous expression hosts a key strategy for discovering novel natural products and efficiently producing known compounds. In this study, Streptomyces albus ZD11, an industrial salinomycin producer capable of efficiently utilizing soybean oil to supply abundant polyketide precursors, was selected as a candidate host for the expression of polyketide BGCs. A genome-reduced derivative, designated ZD12, was constructed by deleting four endogenous polyketide BGCs from ZD11, aiming to reduce precursor competition and alleviate metabolic burden. To evaluate the polyketide biosynthesis capacity of ZD12, an engineered spectinabilin BGC was heterologously expressed in both ZD12 and a commonly used heterologous host S. albus J1074. The resulting ZD12-derived strain DHM produced 412 mg/L spectinabilin, while the J1074-derived strain J-DHM produced 114 mg/L, both of which were significantly higher than the native production level in S. spectabilis. Notably, the titer in DHM exceeded the highest previously reported heterologous titer by more than threefold. Furthermore, under identical integration conditions, DHM achieved a 2.6-fold higher spectinabilin titer than J-DHM, demonstrating the superior polyketide biosynthesis capacity of ZD12. Full article

Alternaria alternata causes major postharvest losses in melons. This dual RNA-seq study analyzed transcriptomic dynamics in both A. alternata strain A2022 and melon during infection. Genomic analysis revealed two conditionally dispensable chromosomes (CDCs) containing host-specific toxin genes, including a T1PKS cluster for βenone biosynthesis. Fungal transcriptomics identified upregulated virulence pathways: MAPK signaling (18 genes), autophagy (17 genes), and lipid metabolism. Melon mounted a biphasic defense: early lignin deposition via phenylpropanoid biosynthesis (15 genes) and late jasmonic acid/MAPK-mediated responses. Competitive nutrient acquisition emerged, with fungal amino acid transporters opposing host nitrogen metabolism. These findings reveal A. alternata’s genomic plasticity and melon’s layered resistance, suggesting RNAi-based silencing of CDC virulence genes or breeding for enhanced lignin/jasmonate pathways as sustainable control strategies. Full article

The flower color of Rhododendron is primarily determined by anthocyanin biosynthesis, with cytochrome P450 CYP75 family members, particularly flavonoid 3′,5′-hydroxylase (F3′5′H), playing a central role. However, the composition and functional characterization of CYP75 genes in Rhododendron remain insufficiently explored. This study performed genome-wide identification of the CYP75 gene family using the Rhododendron simsii reference genome and functionally characterized the corresponding F3′5′H homolog cloned from Rhododendron × hybridum petals (red cultivar and pink cultivar). Seven RsCYP75 genes were identified, categorized into two subfamilies: RsCYP75A (A1–A5) and RsCYP75B (B1–B2), with a prominent cluster on chromosome 13. All encoded proteins contained a conserved cytochrome P450 domain and typical heme-binding motifs. Among these, RhCYP75A2 showed the highest expression level in red petals at full blooming period and was designated as RhF3′5′H. RhF3′5′H encodes a basic membrane protein with the characteristic F3′5′H motif, with its transcript most abundant in flowers. Transient overexpression of RhF3′5′H in red R. × hybridum petals resulted in a 9.74-fold increase in its transcript levels and a 1.25-fold increase in anthocyanin content compared to that in the control accompanied by the up-regulation of CHS, F3H, DFR and ANS. Conversely, RhF3′5′H silencing reduced anthocyanin accumulation but increased CHS and F3H transcript levels, suggesting a compensatory transcriptional response in the upstream anthocyanin pathway. Moreover, RhF3′5′H was heterologously expressed in E. coli Rosetta as an MBP fusion protein, purified, and identified by LC-MS/MS and ELISA. The protein showed the ability to promote anthocyanin accumulation. Molecular docking analysis demonstrated that RhF3′5′H can bind to naringenin and dihydrokaempferol. These results confirm that RhF3′5′H is a functional F3′5′H-type CYP75A enzyme and a positive regulator of anthocyanin accumulation in Rhododendron petals. This work enriches the CYP75 gene catalog in Rhododendron and provides candidate genes for future studies on flower color regulation and molecular breeding. Full article

This study presents a high-quality chromosome-level genome assembly of Morchella sextelata (54.64 Mb, 26 pseudochromosomes) and systematically characterizes its genomic and evolutionary features. Phylogenetic analysis indicates that M. sextelata diverged early within the Morchella genus (~14.2 million years ago) and underwent substantial genomic remodeling, with 1124 expanded and 1961 contracted gene families. Enrichment analysis of rapidly expanded gene families highlights two prominent functional themes: genes associated with small molecule/ion binding and secondary metabolite biosynthesis, and genes linked to the Fanconi anemia pathway and DNA repair/recombination. Notably, 56.96% of the COG-annotated M. sextelata-specific genes encode retrotransposon-related proteins, and this enrichment coincides with the expansion of DNA repair systems—a pattern reminiscent of the “transposon domestication” model. Functional genomic analyses further reveal that the glycoside hydrolase system is dominated by GH5, GH43, and GH3 families, suggesting a predicted capacity for plant cell wall polysaccharide degradation, while 12 biosynthetic gene clusters indicate genetic potential for terpenoid and non-ribosomal peptide biosynthesis. These findings provide a valuable genomic resource for M. sextelata and offer new insights into the role of transposable element mediated remodeling in fungal genome evolution. Full article

The transition of blueberry fruits from the ripening stage to the post-harvest senescence stage is rapid. However, the internal physiological, biochemical, and molecular mechanisms underlying this process have not been elucidated. This study analyzed changes during blueberry fruit development and post-harvest storage senescence to examine processes associated with quality loss. Post-harvest senescence was associated with a marked metabolic transition, which coincided with a transient ethylene peak at maturity and the accumulation of sugars and anthocyanins. This ripening phase was followed by increased oxidative stress, reflected in higher membrane damage, elevated malondialdehyde (MDA) levels, and shifts in conductivity and antioxidant activities, including reduced superoxide dismutase (SOD) levels and increased catalase (CAT), peroxidase (POD), and polyphenol oxidase (PPO) activities. The oxidative conditions were associated with higher rotting rates and coincided with fruit softening and increased polygalacturonase (PG) and β-galactosidase (β-Gal) activities. Correlation analysis identified a “ripening stress-activation cluster” (ethylene, sugars, anthocyanin, CAT/POD/PPO, MDA, PG/β-Gal, and RR) and a “textural integrity cluster” (hardness, chewiness, titratable acidity (TA), and ascorbic acid); these clusters represent correlation-based groupings of variables rather than experimentally validated functional modules. Transcriptomic profiling further showed extensive gene expression changes during storage. Functional enrichment analysis supported a shift from developmental metabolism toward senescence-associated pathways, including starch and sucrose metabolism, phenylpropanoid biosynthesis, flavonoid biosynthesis, mitogen activated protein kinase (MAPK) signaling, and cell wall modification. Overall, the results support a model in which ethylene signaling, oxidative stress, and cell wall disassembly are associated with the transition from ripening to senescence, offering insights for improving blueberry post-harvest quality and extending shelf life. Full article

Soybean yield is governed by key agronomic traits such as main stem node number, lowest pod height, and branch number. These polygenic traits exhibit substantial environmental variation, and the instability of associated genetic loci identified in single-environment studies constrains their application in molecular breeding. To uncover their stable genetic basis, we conducted multi-environment phenotyping over three years and six locations using a panel of 320 soybean accessions. The Best Linear Unbiased Prediction (BLUP) model was employed to integrate phenotypic data and control for genotype-by-environment interactions. Subsequently, genome-wide association studies (GWAS) were performed using BLUP-integrated phenotypic values to capture stable genetic effects, with optimal model using the Mixed Linear Model (MLM). As a result, a total of 22 significant single-nucleotide polymorphism (SNP) loci were identified. Among these, 10, 7, and 5 significant loci were associated with main stem node number, lowest pod height, and branch number, respectively, representing stable genetic signals across multiple environments. These loci primarily clustered on chromosomes 19, 8, and 18. Within these associated regions, we predicted eight high-confidence candidate genes. Functional annotation revealed that these genes are significantly enriched in pathways related to cell wall biosynthesis, energy metabolism, and stress response. This study provides effective genomic resources derived from a multi-environment GWAS framework. These stable loci and candidate genes directly facilitate the molecular breeding of soybean varieties with improved yield-related traits and environmental adaptability. Full article

Background: Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal infections (PANDAS) are characterized by neuropsychiatric symptoms linked to immune dysregulation. Emerging evidence highlights the role of host–microbiome interactions in modulating neuro-immune functions via gut–brain axis signaling; however, its contribution to PANDAS pathophysiology remains poorly understood. Methods: We conducted microbiome analysis from samples collected across multiple sites of PANDAS patients including nasal, throat and stool. We performed an integrated multi-omics analysis of stool samples from pediatric PANDAS cases and healthy controls, including discordant twin pairs. Microbial composition and function were assessed using 16S rRNA gene sequencing, shotgun metagenomics, while untargeted metabolomic profiling was performed using ultra-performance liquid chromatography-mass spectrometry (UPLC-MS/MS). Results: PANDAS cases exhibited reduced alpha diversity and significantly altered beta diversity compared to controls, indicating shifts in gut microbial composition. Shotgun metagenomic analysis revealed differential enrichment of functional pathways, including diminished quorum sensing, altered gamma-aminobutyric acid (GABA) biosynthesis, and microbial degradation processes. Multiple gut–brain modules (GBMs) and gut metabolic modules (GMMs) associated with neurotransmission, transport activities and metabolism were significantly perturbed in PANDAS. Metabolomic profiling showed reduced functional diversity and distinct clustering of metabolic profiles, with differential abundance of amino acids, bile acids, and neuroactive compounds. Integrative analysis further identified disrupted microbe–metabolite networks allied to gut–brain signaling. Conclusions: Our findings reveal significant functional shifts in gut microbiota composition, functional capacity and metabolite profile in PANDAS, suggesting dysregulation of the gut–brain axis signaling. This study provides a foundation for development of microbiome-based biomarkers and therapeutic strategies for pediatric neuropsychiatric disorders. Full article

Tropodithietic acid (TDA) is a sulfur-containing secondary metabolite with pronounced antimicrobial activity that has been primarily described in marine Alphaproteobacteria of the Roseobacter clade. Despite extensive studies of these bacteria, the occurrence and genetic organization of the TDA biosynthetic pathway in other bacterial groups remain poorly understood. In this study, we report the production of TDA by the freshwater bacterium Janthinobacterium sp. PLB04 isolated from diseased cell cultures of the primmorphs from the Baikal sponge Lubomirskia baikalensis. The presence of a TDA biosynthetic gene cluster homologous to the canonical tda operon previously described in the marine Roseobacter clade was found in Janthinobacterium sp. PLB04 by genome mining with bioinformatic analysis. However, comparative analysis of the cluster architecture demonstrated the absence of the gene tdaC in the Janthinobacterium sp. PLB04 genome. Despite this difference, the strain retained the ability to synthesize TDA. TDA was extracted from the culture medium and identified using chromatographic and MALDI-TOF mass spectrometric analysis. These results suggest that tdaC may not be strictly required for TDA biosynthesis in this strain and may be functionally replaced with alternative enzymatic steps or functional redundancy within the pathway. The discovery of TDA production in a freshwater Janthinobacterium strain expands the known phylogenetic and ecological diversity of TDA-producing bacteria and provides new insights into the plasticity of the TDA biosynthetic gene cluster. Full article

Cultivated strawberry (Fragaria × ananassa) is an allo-octoploid for which the genetic basis of fruit appearance traits has not been comprehensively elucidated. This study investigated the genetic architecture of fruit color and morphological traits using integrated digital phenotyping and genome-wide association analysis of a core collection of diverse strawberry germplasm maintained for Korean breeding programs. A 108-accession core collection was assembled, genotyped, and phenotyped for 12 fruit quality traits. Population structure analysis identified K = 10 genetic clusters, and a Mantel test confirmed significant genotype–phenotype correspondence (r = 0.38, p < 0.001). Genome-wide association studies (GWAS) using BLINK and MLMM identified 15 significant marker–trait associations across six traits. Pleiotropic loci on chromosomes 15 (4C) and 22 (6B) were consistently associated with fruit lightness (L*) and red channel intensity (R) in both models, and the 6B locus explained approximately 18% of the phenotypic variance for each trait. Gene Ontology enrichment implicated transcriptional regulation, SUMOylation, and plastid-to-chromoplast transition, suggesting that the identified loci influenced fruit coloration through cellular regulatory mechanisms rather than direct pigment biosynthesis. These findings provide a genomic foundation for dual-trait marker-assisted selection targeting light and vividly red fruits for strawberry breeding. Full article

Quorum Quenching (QQ) is a mechanism that disrupts Quorum Sensing (QS) signaling systems, which regulate gene expression based on bacterial population density. Many fish pathogens, such as Aeromonas, utilize QS systems to regulate the expression of their virulence factors. Disrupting these systems using QQ is a promising approach for infection control in aquaculture and may provide a safe alternative to antibiotics. Therefore, identifying microorganisms with QQ activity is a relevant task in agricultural microbiology and veterinary medicine. This study examines the identification of isolates with QQ activity in the microbial community of perch and assesses their probiotic potential for the prevention of aeromonosis. In this study, we isolated 32 strains of microorganisms capable of degrading N-acylhomoserine lactone (AHL), six of which exhibited stable QQ activity. Five strains were found to belong to the genus Rhodococcus, and one strain to the genus Exiguobacterium. The selected strains were tested for the enzymatic/non-enzymatic and intra-/extracellular QQ activity, pathogen growth inhibition, biofilm formation, and hemolytic activity, as well as growth ability under various environmental conditions (salinity, pH, bile acids, and temperature). Based on the results of these tests, the R. erythropolis PFS1.20 strain was selected as the most promising probiotic. The genomic analysis revealed that the studied strain contains genes encoding QQ enzymes, siderophore biosynthesis clusters, osmoprotectors, and compounds with antimicrobial properties. These results indicate the high probiotic potential of the R. erythropolis PFS1.20. Full article

Plant pathogens pose a severe threat to global agricultural production, and their pathogenicity is closely linked to the biosynthesis of secondary metabolites. Basidiomycete within the family Ustilaginaceae represent significant plant pathogens, among which Ustilago maydis, as a model species, has been extensively studied for its secondary metabolites. However, the biosynthetic potential of other species within this family remains poorly understood. In this study, we conducted whole-genome bioinformatic analyses of 16 Ustilaginaceae species, including U. maydis, to systematically identify the distribution of biosynthetic gene clusters (BGCs), core gene domain compositions, and interspecies similarities. A total of 181 predicted BGCs were identified, averaging approximately 11 per species. BGCs for mannosylerythritol lipids (MELs), siderophores, and itaconic acid, as well as the melanin-associated genes pks1 and pks2, were widely distributed across most species. Conversely, an additional melanin biosynthetic gene cluster was found exclusively in U. maydis strain 521, indicating species-specific occurrence. Furthermore, this study identified a novel class of polyketide synthase (PKS) gene clusters with uncharacterized functions across 15 species, exhibiting high sequence and structural conservation between species. These findings reveal the rich metabolic diversity and species-specific biosynthetic potential of Ustilaginaceae, and by using U. maydis as a reference model, we highlight several BGCs (e.g., for MELs, siderophores, itaconic acid, and melanin) that are known to contribute to virulence or pathogenicity in plant hosts. This provides new insights into their pathogenic mechanisms. Full article