Biosynthesis Of Secondary Metabolites Research Articles

Microbial Biodiversity in Sediment from the Amuyo Ponds: Three Andean Hydrothermal Lagoons in Northern Chile

The Amuyo Ponds (APs) are a group of three brackish hydrothermal lagoons located at 3700 m above sea level in a pre-Andean setting in the Atacama Desert. Each pond shows a conspicuous green (GP), red (RP), or yellow (YP) coloration, and discharges water rich in arsenic and boron into the Caritaya River (Camarones Basin, northern Chile). Microorganisms are subjected to harsh environmental conditions in these ponds, and the microbial composition and diversity in the Amuyo Ponds’ sediments are unknown. The microbial life colonizing AP sediments was explored by metagenomics analyses, showing a diverse microbial life dominated by members of the bacterial domain, with nearly 800 bacterial genome sequences, and sequences associated with Archaea, Eukarya, and viruses. The genus Pseudomonas was more abundant in GP and YP sediments, while the genera Pseudomonas, Aeromonas, and Shewanella were enriched in RP sediments. Archaeal composition was similar in all sediments, and enriched with methanogens sequences from the Archaeoglobi and Halobacteria classes. Abundant fungi sequences were detected in all sediments from the phyla Blastocladiomycota and Ascomycota. We also report putative functional capabilities related to virulence and defense genes, the biosynthesis of secondary metabolites, and tolerance to arsenic. Thirteen bacterial and fourteen viral metagenome-assembled genomes were reconstructed and informed here. This work expands our knowledge on the richness of the microorganisms in the APs and open further studies on the ecology and genomics of this striking Andean geosite.

The Impact of Nutrient Solution Electrical Conductivity on Leaf Transcriptome Contributing to the Fruit Quality of Cucumber Grown in Coir Cultivation

Soilless cultivation is increasingly utilized in supplying essential nutrients for greenhouse crops. However, the impact of coir cultivation under varying electrical conductivity (EC) conditions on cucumber growth and fruit quality, particularly through the regulation of gene expression during the vegetative stage, remains uncertain. In this study, we performed metabolic measurements on cucumber in both vegetative and reproductive stages under three different EC conditions and found metabolic products such as some primary metabolites (cellulose, many uncharged amino acids) and some secondary metabolites (rutin, cucurbitacin B) accumulated the most under EC of 5 dS·m−1. Next, we conducted transcriptome profiling in cucumber leaves, revealing that the function of genes significantly regulated by EC was associated with photosynthesis, many anabolic processes, and membrane transport. Finally, a set of genes contributed to metabolites related to the fruit quality of cucumber were identified by the Orthogonal Partial Least Squares (O2PLS) analysis, including genes involved in the biosynthesis of amino acids, polysaccharides, and many secondary metabolites. Taken together, these findings suggest that coir cultivation in greenhouses with moderate EC can induce a transcriptome-wide change in gene expression, thereby contributing to enhancing the abundance of metabolites associated with cucumber fruit quality.

Proteome Profiling of Cucurbita pepo Phyllosphere After Infection by Podosphaera xanthii and Application of Reynoutria sachalinensis Extract

Podosphaera xanthii is the main causal agent of powdery mildew (PM) disease for Cucurbita pepo. Disease control is attained principally by applications of chemical fungicides, along with parallel use of tolerant crop varieties and alternate application of elicitors to control development of disease resistance. To get insight into C. pepo molecular responses to P. xanthii infection and elicitor treatment we studied the proteomic profile differences at the phyllosphere of a zucchini cultivar susceptible to PM, at the onset of P. xanthii (PX) infection and after application of Reynoutria sachalinensis (RS) plant extract, respectively, using a nano-LC-HRMS/MS, Q-Exactive-Orbitrap approach. Analysis of peptide sequences regarding four treatment groups (Control; PX; RS; and RSPX (PX-infected priorly treated with RS)) resulted in 2070 CuGenDB annotations. Three comparisons (treatments vs. Control) encompassed most of the Differentially Expressed Proteins (DEPs). In these three comparisons, KEGG and Gene Ontology functional analyses highlighted unique differentially enriched pathways—some of which included highly expressed proteins—in PX-related (proteasome, pentose phosphate pathway, and carbon fixation), RS-related (biosynthesis of secondary metabolites, flavonoids, and starch and sucrose metabolism), and RSPX-related (pyruvate metabolism and polycomb repressive complex) comparisons, respectively, suggesting distinct mechanisms of early plant responses modulated by PX and RS. Furthermore, in four out of six comparisons the thiamine metabolism pathway was found to be enriched, suggesting a pivotal role in PX-induced responses.

Comprehensive analysis of secondary metabolite biosynthetic gene clusters in Helianthus annuus L.: A bioinformatics approach

Plant secondary metabolite gene clusters are regions within the plant genome that encode enzymes and proteins involved in the biosynthesis of secondary metabolites. Helianthus annuus L. is a significant oilseed plant with economic importance. This study aims to comprehensively identify secondary metabolite biosynthetic gene clusters within H. annuus using bioinformatics tools, shedding light on the functions of the enzymes involved. In this study, the plantiSMASH software was utilized to predict secondary metabolite biosynthetic gene clusters in H. annuus. The results from plantiSMASH were analyzed to identify the biosynthetic gene clusters for secondary metabolites on each chromosome. The biological and molecular functions of the enzymes within these clusters were predicted using data from the relevant articles. According to the obtained data, H. annuus lacks a biosynthetic gene cluster on chromosomes four, seven, and fifteen. The identified gene clusters in this plant are polyketide, saccharide, saccharide-terpene, alkaloid, putative, and terpene. The enzyme categories found in secondary metabolite biosynthetic gene clusters include Methyltransferase, Ketosynthase, Glycosyltransferase, BAHD acyltransferase, Dioxygenase, CoA-ligase, Epimerase, PRISE enzymes, Prenyltransferase, Oxidoreductase, Aminotransferase, Copper amine oxidase, Cytochrome P450, Terpene synthase, and Pictet-Spengler enzyme (Bet v1). This comprehensive analysis provides a foundation for further investigations into the biosynthesis of secondary metabolites in H. annuus, offering valuable insights for researchers exploring the medicinal and pharmaceutical potential of this plant species.

Magnesium-Doped Carbon Quantum Dot Nanomaterials Alleviate Salt Stress in Rice by Scavenging Reactive Oxygen Species to Increase Photosynthesis.

Salt stress has strongly impacted the long-term growth of eco-friendly farming worldwide. By targeting the oxidative stress induced by salt, the utilization of biomass-derived carbon dots (CDs) that possess high-efficiency antioxidant properties, are nontoxic, and have excellent biocompatibility represents a viable and effective approach for enhancing the salt tolerance of plants. In this study, we blended magnesium oxide nanoparticles with carbon sources derived from durian shells to construct Mg-doped carbon dots (Mg-CDs) through a hydrothermal reaction. We demonstrated that the foliar application of 150 μg/mL Mg-CDs to rice plants after treatment with 100 mM salt effectively increased the plant height (9.52%), fresh weight (22.41%), dry weight (33.33%), K+ content (21.46%), chlorophyll content (36.21%), and carotenoid content (16.21%); decreased the malondialdehyde (MDA) (9.43%), Na+ (25.75%), H2O2 (17.50%), and O2•- contents (37.99%); and promoted the photosynthetic system and antioxidant activity. Transcriptome analysis revealed that Mg-CD pretreatment triggered transcriptional reprogramming in rice seedlings. The enrichment analysis of the Kyoto Encyclopedia of Genes and Genomes pathways based on trend groups of gene expression patterns of Profile 8 and Profile 15 indicated that priming with Mg-CDs activated stress signaling- and defense-related pathways, such as metabolic pathways, biosynthesis of secondary metabolites, and photosynthesis pathways. These activations subsequently prompted the expression of genes related to the mitogen-activated protein kinase signaling pathway, hormone signal transduction, the oxidative stress response, and the photosynthetic system. This study demonstrated that the use of Mg-CDs represents a potential strategy to increase plant salt tolerance, creating the possibility for the regulation of crop salinity stress and offering valuable advancements in sustainable agriculture.

Antiviral Potential and Chemical Composition of Wild Baccharis crispa Spreng. Populations (Asteraceae) from Córdoba, Argentina: Perspective on Population Variability

Medicinal plants have been explored worldwide as potential alternatives for the prevention and treatment of different diseases, including viral infections. Baccharis crispa Spreng. (Asteraceae) is a native medicinal species widely used in South America. Given the influence of genetic and environmental factors on secondary metabolites biosynthesis and accumulation, this study aimed to evaluate the in vitro antiviral activity of four wild populations of B. crispa from Córdoba, Argentina, and assess the variability in their bioactivity and chemical composition. The cytotoxicity of chloroform, ethanol, and aqueous extracts from aerial parts was evaluated by the neutral red uptake method. Antiviral and virucidal activity against herpes simplex virus type 1 (HSV-1) and chikungunya virus (CHIKV) were assessed via plaque-forming unit (PFU) reduction assay. Phytochemical analyses of the extracts were conducted using HPLC-ESI- MS/MS. The Puesto Pedernera population showed the strongest antiviral activity, with inhibition rates of 82% for CHIKV and 79% against HSV-1, as well as potent virucidal effects, reducing PFU formation by up to 5 logarithms for both viruses. Remarkably, ethanol extract exhibited the least toxicity and strongest inhibitory activity. Villa del Parque population was inactive. We identified 38 secondary metabolites, predominantly phenolic acids (12) and flavonoids (18), in varying proportions. Delphinidin and delphinidin-3-glucoside are described for the first time in the species. Differences in phytochemical profiles were observed among extract types and populations. Key phenolic compounds showed moderate positive correlations with the evaluated bioactivities, emphasizing the complexity of phytochemical properties and interactions. These results highlight the therapeutic potential of B. crispa extracts against viral infections and underscore the importance of considering the geographical source of plant material in bioactivity evaluations.

Genomic characterization and probiotic potency of Bacillus velezensis CPA1-1 reveals its potential for aquaculture applications

Biological prevention and control are increasingly applied in sustainable aquaculture, and Bacillus spp. has been revealed to good alternatives to antibiotics. This research examined the probiotic capabilities of Bacillus velezensis CPA1-1 by genomic and phenotypic analysis. The genome sequence showed that B. velezensis CPA1-1 has a 3,925,520 bp chromosome with 46.49 % GC content and 3762 CDSs. And eight clusters of secondary metabolite biosynthesis genes related to antibacterial compounds were predicted in CPA1-1 genome, including surfactin, difficidin, bacillibactin, fengycin, bacilysin, bacillaene, macrolactin H, butirosin A. Besides, the antimicrobial assay indicated that strain CPA1-1 exhibited strong antagonistic capacity against non-O1/O139 Vibrio cholerae GXFL1-4 isolated from diseased Macrobrachium rosenbergii, and MIC of CPA1-1 fermentation broth against GXFL1-4 was 1.0 × 105 CFU/mL. Furthermore, administering CPA1-1 markedly elevated the activities of ACP, AKP, and SOD in M. rosenbergii, and the immune-related genes, including ALF, Crustin, Hemocyanin, Prophenoloxidase, C-type lectin and HSP70, also exhibited higher expression in the CPA1-1 treated groups. Additionally, M. rosenbergii in the test group treated with CPA1-1 could resist non-O1/O139 V. cholerae GXFL1-4 infection by the challenge test. Our study contributed to reveal biocontrol mechanisms of B. velezensis CPA1-1, and demonstrated that CPA1-1 has promise as a probiotic agent for aquaculture.

Impact of nitrogen rates on biosynthesis pathways: A comparative study of diterpene synthases in clerodane diterpenoids and enzymes in benzylisoquinoline alkaloids

Tinospora sagittata is rich in secondary metabolites used in traditional medicine. However, environmental factors impact key enzymes in metabolite synthesis, highlighting the need for improved growth conditions. This study employs transcriptomics and metabolomics to assess nitrogen's impact on enzymes in secondary metabolites biosynthesis pathways. The gene expressions of berberine bridge enzymes (BBEs) like TsBBE2 had peak expression in low nitrogen treatments (A0 and A1) but were absent in higher nitrogen treatments (A2 and A3). Similar trends were observed for other enzymes such as (S)-scoulerine 9-O-methyltransferase (TsCMT3), Tetrahydroberberine oxidase (TsSTOX), and Columbamine O-methyltransferase (TsCoCOMT2-4) in response to nitrogen levels. In examining gene families related to diterpene synthases (diTPS), 1-deoxyxylulose 5-phosphate synthase (TsDXR1) expression increased with higher nitrogen fertilizer, while TsDXR2 peaked at maximal nitrogen levels. Geranylgeranyl diphosphate synthase (TsGGPP3 and TsGGPP5) decreased with nitrogen levels. (−)-kolavenyl diphosphate synthase (KPS) genes had higher expression in treatments, while ent-kaurene synthase (KSL) genes, especially TsKSL1 and TsKSL2, showed higher expression in control conditions with lower nitrogen fertilizer. Metabolite analysis confirmed more upregulated compounds in A3 compared to A0. These findings have practical implications for agriculture and pharmaceuticals, highlighting the link between nitrogen fertilization and specialized metabolism in medicinal plants.

Methyl jasmonate mitigates Fusarium graminearum infection in wheat by inhibiting deoxynivalenol synthesis.

Methyl jasmonate (MeJA), a plant growth regulator, coordinates a diverse array of physiological responses, including the inhibition of seed germination, modulation of secondary metabolite biosynthesis, and activation of defence responses. The external application of MeJA has been demonstrated to effectively diminish the severity of fungal diseases. Here, we unveil a novel mechanism through which exogenous MeJA alleviates Fusarium head blight (FHB) by inhibiting the synthesis of deoxynivalenol (DON) in Fusarium graminearum, rather than by enhancing the wheat resistance response. MeJA treatment reduced the infection by wild-type F. graminearum in wheat coleoptiles, but exhibited no significant influence on that of the DON-deficient mutant strain (∆Tri5). The production of DON in F. graminearum was significantly inhibited both in vitro and in planta. MeJA affected the expression of genes related to DON biosynthesis, without influencing the formation of toxisomes as observed under microscopic analysis. Exogenous MeJA demonstrated a limited impact on the early genes of plant jasmonic acid signalling pathway, in contrast to the wild-type pathogen strain, which induced the upregulation of these genes. The expression levels of defence marker genes induced by MeJA were notably lower compared to those induced by the pathogen. This study elucidates the molecular mechanisms of MeJA in modulating the wheat-F. graminearum interaction, providing new insights into the development of environmentally friendly strategies against fungi.

Effects of exogenous calcium on flavonoid biosynthesis and accumulation in peanut roots under salt stress through multi-omics

Flavonoids possess antioxidant properties and are crucial in enhancing plant resistance to abiotic stress. Exogenous calcium has been found to regulate the biosynthesis and accumulation of secondary metabolites, including flavonoids. However, the mechanism by which exogenous calcium influences flavonoid regulation in peanut roots under salt stress remains unclear. In this study, four treatment conditions were established: no salt stress, salt stress, exogenous calcium, and a combination of salt stress and exogenous calcium. The peanut root flavonoid profile was comprehensively analyzed using both a broadly targeted metabolomic approach and an absolute quantitative flavonoid metabolome. A total of 168 flavonoids were identified in the broad-target metabolome, while 68 were quantified in the absolute quantification analysis. The findings revealed that salt stress generally increased flavonoid content in peanut roots, while co-treatment with exogenous calcium significantly reduced this accumulation. Additionally, the activities of key enzymes and the expression of genes involved in the flavonoid biosynthesis pathway were upregulated under salt stress, but downregulated following the combined treatment. This study offers valuable insights into the physiological and ecological roles of flavonoids in response to environmental stressors in economically important crops.

Whole-genome sequence of Bacillus subtilis TR6 strain isolated from tomato (Solanum lycopersicum L.) roots.

Here, we announce the sequence of endophyte Bacillus subtilis TR6 strain isolated from tomato roots growing in a greenhouse in St. Petersburg, Russia. With a length of 4,071,622 bp, this strain contained 4,073 potential coding sequences and 10 predicted secondary metabolite biosynthesis gene clusters.

Multiple Omics Analyses Reveal Activation of Nitrogen Metabolism and Flavonoid Glycosylation in Toxicodendron vernicifluum Under High Temperature

Lacquer trees (Toxicodendron vernicifluum), economically vital, face high-temperature stress in summer. Transcriptomic, proteomic, and metabolomic analyses were employed to investigate the mechanisms by which lacquer trees respond to high temperatures. High-temperature treatment led to notable metabolite changes with 224 upregulated and 69 downregulated. Indole-3-acetic acid remained stable while abscisic acid decreased, with increases in jasmonic acid and jasmonoyl-L-isoleucine indicating complex hormonal responses. JAR1 and ABA 8′-hydroxylase encoding genes were upregulated. The rise in JAs boosted the alkaloid content and activated nitrogen transport. High temperatures also increased specific amino acids and upregulated aminotransferase and protease-encoding genes. Metabolomic analysis showed elevated flavonoid glycosides and the upregulation of glycosyltransferase genes. WPCNA found 35 protein modules involved in secondary metabolite biosynthesis, protein phosphorylation, and signal transduction. Protein–protein interaction analysis revealed MYC6’s link with flavonoid biosynthesis, indicating its role in promoting flavonoids.

Transcriptomic and metabolomic reveal OsCOI2 as the jasmonate-receptor master switch in rice root.

Jasmonate is an essential phytohormone involved in plant development and stress responses. Its perception occurs through the CORONATINE INSENSITIVE (COI) nuclear receptor allowing to target the Jasmonate-ZIM domain (JAZ) repressors for degradation by the 26S proteasome. Consequently, repressed transcription factors are released and expression of jasmonate responsive genes is induced. In rice, three OsCOI genes have been identified, OsCOI1a and the closely related OsCOI1b homolog, and OsCOI2. While the roles of OsCOI1a and OsCOI1b in plant defense and leaf senescence are well-established, the significance of OsCOI2 in plant development and jasmonate signaling has only emerged recently. To unravel the role of OsCOI2 in regulating jasmonate signaling, we examined the transcriptomic and metabolomic responses of jasmonate-treated rice lines mutated in both the OsCOI1a and OsCOI1b genes or OsCOI2. RNA-seq data highlight OsCOI2 as the primary driver of the extensive transcriptional reprogramming observed after a jasmonate challenge in rice roots. A series of transcription factors exhibiting an OsCOI2-dependent expression were identified, including those involved in root development or stress responses. OsCOI2-dependent expression was also observed for genes involved in specific processes or pathways such as cell-growth and secondary metabolite biosynthesis (phenylpropanoids and diterpene phytoalexins). Although functional redundancy exists between OsCOI1a/b and OsCOI2 in regulating some genes, oscoi2 plants generally exhibit a weaker response compared to oscoi1ab plants. Metabolic data revealed a shift from the primary metabolism to the secondary metabolism primarily governed by OsCOI2. Additionally, differential accumulation of oryzalexins was also observed in oscoi1ab and oscoi2 lines. These findings underscore the pivotal role of OsCOI2 in jasmonate signaling and suggest its involvement in the control of the growth-defense trade-off in rice.

Aquificae overcomes competition by archaeal thermophiles, and crowding by bacterial mesophiles, to dominate the boiling vent-water of a Trans-Himalayan sulfur-borax spring.

Trans-Himalayan hot spring waters rich in boron, chlorine, sodium and sulfur (but poor in calcium and silicon) are known based on PCR-amplified 16S rRNA gene sequence data to harbor high diversities of infiltrating bacterial mesophiles. Yet, little is known about the community structure and functions, primary productivity, mutual interactions, and thermal adaptations of the microorganisms present in the steaming waters discharged by these geochemically peculiar spring systems. We revealed these aspects of a bacteria-dominated microbiome (microbial cell density ~8.5 × 104 mL-1; live:dead cell ratio 1.7) thriving in the boiling (85°C) fluid vented by a sulfur-borax spring called Lotus Pond, situated at 4436 m above the mean sea-level, in the Puga valley of eastern Ladakh, on the Changthang plateau. Assembly, annotation, and population-binning of >15-GB metagenomic sequence illuminated the numeral predominance of Aquificae. While members of this phylum accounted for 80% of all 16S rRNA-encoding reads within the metagenomic dataset, 14% of such reads were attributed to Proteobacteria. Post assembly, only 25% of all protein-coding genes identified were attributable to Aquificae, whereas 41% was ascribed to Proteobacteria. Annotation of metagenomic reads encoding 16S rRNAs, and/or PCR-amplified 16S rRNA genes, identified 163 bacterial genera, out of which 66 had been detected in past investigations of Lotus Pond's vent-water via 16S amplicon sequencing. Among these 66, Fervidobacterium, Halomonas, Hydrogenobacter, Paracoccus, Sulfurihydrogenibium, Tepidimonas, Thermus and Thiofaba (or their close phylogenomic relatives) were presently detected as metagenome-assembled genomes (MAGs). Remarkably, the Hydrogenobacter related MAG alone accounted for ~56% of the entire metagenome, even though only 15 out of the 66 genera consistently present in Lotus Pond's vent-water have strains growing in the laboratory at >45°C, reflecting the continued existence of the mesophiles in the ecosystem. Furthermore, the metagenome was replete with genes crucial for thermal adaptation in the context of Lotus Pond's geochemistry and topography. In terms of sequence similarity, a majority of those genes were attributable to phylogenetic relatives of mesophilic bacteria, while functionally they rendered functions such as encoding heat shock proteins, molecular chaperones, and chaperonin complexes; proteins controlling/modulating/inhibiting DNA gyrase; universal stress proteins; methionine sulfoxide reductases; fatty acid desaturases; different toxin-antitoxin systems; enzymes protecting against oxidative damage; proteins conferring flagellar structure/function, chemotaxis, cell adhesion/aggregation, biofilm formation, and quorum sensing. The Lotus Pond Aquificae not only dominated the microbiome numerically but also acted potentially as the main primary producers of the ecosystem, with chemolithotrophic sulfur oxidation (Sox) being the fundamental bioenergetic mechanism, and reductive tricarboxylic acid (rTCA) cycle the predominant carbon fixation pathway. The Lotus Pond metagenome contained several genes directly or indirectly related to virulence functions, biosynthesis of secondary metabolites including antibiotics, antibiotic resistance, and multi-drug efflux pumping. A large proportion of these genes being attributable to Aquificae, and Proteobacteria (very few were ascribed to Archaea), it could be worth exploring in the future whether antibiosis helped the Aquificae overcome niche overlap with other thermophiles (especially those belonging to Archaea), besides exacerbating the bioenergetic costs of thermal endurance for the mesophilic intruders of the ecosystem.

Novel Strain Bacillus velezensis LAFUEL 03: Activity Against Xanthomonas vasicola pv. vasculorum, Control of Bacterial Leaf Streak of Corn and Genome Insights into Its Antagonistic Activity

The main objective of this study was to investigate the antimicrobial activity of three putative antagonist bacterial strains of Bacillus spp. against Xanthomonas vasicola pv. vasculorum (Xvv) and their potential to control bacterial leaf streak (BLS) of corn. Additionally, the study included investigations on the genome of one of these antagonist bacteria, such as genome sequencing and mining of genes involved in biofilm formation, swarming motility, and synthesis of secondary metabolites. The growth of Xvv was inhibited by both cell suspensions and cell-free supernatants of the bacterial strains LAFUEL 01, LAFUEL 02, and LAFUEL 03 in agar diffusion tests. All three antagonist strains significantly reduced the severity of BLS in the 3rd and 4th leaves of corn plants that were artificially inoculated at the V3 growth stage under greenhouse conditions. The 16S rRNA sequencing confirmed that the antagonistic bacterial strains belong to the genus Bacillus, with LAFUEL 03 having approximately 97% similarity to B. velezensis. B. velezensis LAFUEL 03 harbors genes related to the biosynthesis of secondary metabolites, biofilm formation/regulation, and swarming motility that enhances its potential for controlling BLS in corn and suggests a promising candidate for the development of a commercial biocontrol agent.

Screening of the Candidate Metabolite to Evaluate the Mycelium Physiological Maturation of Lyophyllum decastes Based on Metabolome and Transcriptome Analysis

Lyophyllum decastes is a commercially cultivated rare edible mushroom with high dietary and medicinal value. The mycelium physiological maturation was an important factor to the yield and quality of mushrooms obtained. However, it was impossible to obtain discriminative characteristics represented the maturity level of the mycelia from morphological features. In this article, we screened a candidate metabolite for evaluating the mycelium physiological maturation by metabolomic and transcriptomic analysis during mycelial vegetative growth stages of L. decastes. The results showed that mycelial vegetative growth 55 d had reached to physiological maturation according to the yield and quality of L. decastes, which the single bottle yield (307 g/bottle), the contents of flavonoids (2.94 mg/g dry weight), and 5 flavor amino acids (glutamate 177.90 μg/g, aspartate 95.74 μg/g, phenylalanine 31.68 μg/g, tyrosine 13.79 μg/g, and alanine 10.99 μg/g) were the highest. In addition, the metabolomic and transcriptomic analysis results showed that biosynthesis of secondary metabolites and amino acid had significant different during mycelial vegetative growth stages, and glutamine may be a candidate indicator to evaluate the mycelial physiological maturation. These findings contribute to improve our knowledge of mycelium physiological maturation and it will be used to increase mushroom yield and quality.

Global regulator AdpA directly binds to tunicamycin gene cluster and negatively regulates tunicamycin biosynthesis in Streptomyces clavuligerus.

Since a transcriptional regulator has yet to be identified within the tunicamycin biosynthetic gene cluster in Streptomyces clavuligerus, we conducted a comprehensive investigation by focusing on the possible function of the pleiotropic regulator AdpA on tunicamycin. The genes encoding early steps of tunicamycin biosynthesis were significantly upregulated in S. clavuligerus ΔadpA. At the same time, they were downregulated in adpA overexpressed strain as shown by RNA-sequencing (RNA-seq) and reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) analysis. The tunicamycin gene cluster's co-transcription pattern was understood by reverse transcriptase polymerase chain reaction (RT-PCR). Our Electrophoretic Mobility Shift Assay (EMSA) data clearly showed AdpA's binding to the upstream sequence of the tunA gene, asserting its regulatory control. In addition to its direct negative regulation of tunicamycin biosynthesis, AdpA operates at a global level by orchestrating various regulatory genes in S. clavuligerus, such as wblA, whiB, bldM, arpA, brp, and adsA involved in morphological differentiation and secondary metabolite biosynthesis as depicted in RNA-seq data. This study represents a significant milestone by unveiling the AdpA regulator's pathway-specific and global regulatory effect in S. clavuligerus.

Exogenously Applied Gibberellic Acid Alters Cannabinoid Profile in Cannabis sativa L.

Cannabis sativa (C. sativa L.) has garnered significant attention worldwide due to its widespread use as a pharmaceutical agent. With the increasing clinical application of C. sativa and cannabinoid therapeutics, there is strong interest in the development of superior plant varieties and optimisation of growth conditions to enhance secondary metabolite yield. Our RNA sequencing analysis revealed differential expression of hormone-related transcripts in developing C. sativa trichomes, suggesting the involvement of hormone signalling pathways in cannabinoid production. Leveraging the potency of exogenous hormones on plants, this study sought to determine if the application of cytokinin (CK), gibberellic acid (GA) and jasmonic acid (JA) modified trichome morphology and the cannabinoid profile over an 8-week period following the induction of flowering. Exogenous hormone application led to alterations in trichome morphology, with each treatment significantly reducing trichome head width by the final week of assessment. Interestingly, GA application also resulted in a significant reduction in the concentration of Δ-9-tetrahydrocannabinol (THC), Δ-9-tetrahydrocannabinolic acid (THCA), cannabidiol (CBD) and cannabidiolic acid (CBDA) by week 8 post floral induction, however, JA and CK treatment did not consistently modulate the accumulation of these cannabinoids. The minor cannabinoids, cannabidivaranic acid (CBDVA), cannabicyclolic acid (CBLA), cannabicyclol (CBL), cannabichromene (CBC), cannabigerolic acid (CBGA) and cannabigerol (CBG), were also affected by hormone treatments, with varying degrees of accumulation observed. These findings underscore the intricate interplay between phytohormones and secondary metabolite biosynthesis in C. sativa. Our study highlights the potential of hormone modulation as a strategy to enhance cannabinoid yield and offers some insights into the regulatory mechanisms governing cannabinoid biosynthesis in C. sativa trichomes.

Whole-Genome Sequencing of the Entomopathogenic Fungus Fusarium solani KMZW-1 and Its Efficacy Against Bactrocera dorsalis.

Fusarium solani KMZW-1 is recognized for its potential as a biocontrol agent against agricultural and forestry pests, particularly due to its compatibility with integrated pest management (IPM) strategies. This study aimed to investigate the complete genome of F. solani KMZW-1 and assess its pathogenicity against Bactrocera dorsalis. Whole-genome sequencing revealed a genome size of 47,239,278 bp, comprising 27 contigs, with a GC content of 51.16% and fungus identified as F. solani KMZW-1. The genome completeness was assessed as 97.93% using BUSCO analysis, the DFVF sequence identifier was Fusarium 0G092560.1, and AntiSMASH analysis identified 35 gene clusters associated with secondary metabolite biosynthesis, providing insights into the genetic basis of its pathogenic mechanisms and biocontrol potential. Comparative genomic analysis found 269 unique genes for F. solani KMZW-1, and collinearity analysis exhibited a high degree of synteny with Fusarium solani-melongenae. The pathogenicity of F. solani KMZW-1 was assessed using concentrations ranging from 1 × 104 to 1 × 1011 conidia/mL. Higher concentrations (1 × 1010 to 1 × 1011 conidia/mL) resulted in significantly increased cumulative mortality rates of B. dorsalis adults compared to the control group. Notably, the pathogenicity was higher in male adults than in females. Probit analysis yielded LC50 (50% lethal concentration) values of 5.662 for female and 4.486 for male B. dorsalis adults. In summary, F. solani, KMZW-1 exhibits strong insecticidal activity against B. dorsalis and shows potential as a biocontrol agent with IPM strategies. These findings provide robust genomic evidence supporting the use of F. solani KMZW-1 in managing against B. dorsalis populations.

Metabolome and Metagenome Integration Unveiled Synthesis Pathways of Novel Antioxidant Peptides in Fermented Lignocellulosic Biomass of Palm Kernel Meal.

Approximately one-third of the entire world's food resources are deemed to be wasted. Palm kernel meal (PKM), a product that is extensively generated by the palm oil industry, exhibits a unique nutrient-rich composition. However, its recycling is seldom prioritized due to numerous factors. To evaluate the impact of enzymatic pretreatment and Lactobacillus plantarum and Lactobacillus reuteri fermentation upon the antioxidant activity of PKM, we implemented integrated metagenomics and metabolomics approaches. The substantially enhanced (p < 0.05) property of free radicals scavenging, as well as total flavonoids and polyphenols, demonstrated that the biotreated PKM exhibited superior antioxidant capacity. Non-targeted metabolomics disclosed that the Lactobacillus fermentation resulted in substantial (p < 0.05) biosynthesis of 25 unique antioxidant biopeptides, along with the increased (p < 0.05) enrichment ratio of the isoflavonoids and secondary metabolites biosynthesis pathways. The 16sRNA sequencing and correlation analysis revealed that Limosilactobacillus reuteri, Pediococcus acidilactici, Lacticaseibacillus paracasei, Pediococcus pentosaceus, Lactiplantibacillus plantarum, Limosilactobacillus fermentum, and polysaccharide lyases had significantly dominated (p < 0.05) proportions in PMEL, and these bacterial species were strongly (p < 0.05) positively interrelated with antioxidants peptides. Fermented PKM improves nutritional value by enhancing beneficial probiotics, enzymes, and antioxidants and minimizing anti-nutritional factors, rendering it an invaluable feed ingredient and gut health promoter for animals, multifunctional food elements, or as an ingredient in sustainable plant-based diets for human utilization, and functioning as a culture substrate in the food sector.