Biosynthesis Of Secondary Metabolites Research Articles

Identification of crucial drought-tolerant genes of barley through comparative transcriptomic analysis and yeast-based stress assay

Drought is a persistent and serious threat to crop yield and quality. The identification and functional characterization of drought tolerance-related genes is thus vital for efforts to support the genetic improvement of drought-tolerant crops. Barley is highly adaptable and renowned for its robust stress resistance, making it an ideal subject for efforts to explore genes related to drought tolerance. In this study, two barley materials with different drought tolerance were subjected to soil drought treatment, including a variety with strong drought tolerance (Hindmarsh) and a genotype with weaker drought tolerance (XZ5). Transcriptomic sequencing data from the aboveground parts of these plants led to the identification of 1,206 differentially expressed genes associated with drought tolerance. These genes were upregulated in Hindmarsh following drought stress exposure but downregulated or unchanged in XZ5 under these same conditions, or were unchanged in Hindmarsh but downregulated in XZ5. Pathway enrichment analyses suggested that these genes are most closely associated with defense responses, signal recognition, photosynthesis, and the biosynthesis of various secondary metabolites. Using protein-protein interaction networks, the ankyrin repeat domain-containing protein 17-like isoform X2 was predicted to impact other drought tolerance-related protein targets in Hindmarsh. In MapMan metabolic pathway analyses, genes found to be associated with the maintenance of drought tolerance in Hindmarsh under adverse conditions were predicted to include genes involved in the abscisic acid, cytokinin, and gibberellin phytohormone signaling pathways, genes associated with redox homeostasis related to ascorbate and glutathione S-transferase, transporters including ABC and AAAP, transcription factors such as AP2/ERF and bHLH, the heat shock proteins HSP60 and HSP70, and the sucrose non-fermenting-1-related protein kinase. Heterologous HvSnRK2 (one of the identified genes, which encodes the sucrose non-fermenting-1-related protein kinase) gene expression in yeast conferred significant drought tolerance, highlighting the functional importance of this gene as one linked with drought tolerance. This study revealed the drought tolerance mechanism of Hindmarsh by comparing transcriptomes while also providing a set of candidate genes for genetic efforts to improve drought tolerance in this and other crop species.

Genome Sequencing and Metabolic Potential Analysis of Irpex lacteus

Irpex lacteus is an edible and medicinal macrofungus with significant biological activity and broad pharmaceutical prospects that has received increasing attention in recent years. Although it is an important resource for macrofungi, knowledge of it remains limited. In this study, we sequenced, de novo assembled, and annotated the whole genome of I. lacteus using a PacBio Sequel II sequencer. The assembled 41.83 Mb genome contains 13,135 predicted protein-coding genes, 83.44% of which have searchable sequence similarity to other genes available in public databases. Using genome-based bioinformatics analysis, we identified 556 enzymes involved in carbohydrate metabolism and 103 cytochrome P450 proteins. Genome annotation revealed genes for key enzymes responsible for the biosynthesis of secondary metabolites, such as terpenoids and polyketides. Among them, we identified 14 terpene synthases, 8 NRPS-like enzymes, and 4 polyketide synthases (PKS), as well as 2 clusters of biosynthetic genes presumably related to terpene synthesis in I. lacteus. Gene family analysis revealed that the MYB transcription factor gene family plays an important role in the growth and development of I. lacteus. This study further enriches the genomic content of I. lacteus, provides genomic information for further research on the molecular mechanism of I. lacteus, and promotes the development of I. lacteus in the fields of drug research and functional food production.

Plant-specific microbial diversity facilitates functional redundancy at the soil-root interface

Abstract Aims Plant-specific microbial diversity reflecting host-microbe coevolution was frequently shown at the structural level but less on the functional scale. We studied the microbiome of three compartments at the soil root interface (root endosphere, rhizosphere, bulk soil) of medicinal plants cultivated under organic management in Egypt. The study aimed to examine the impact of the rhizosphere on microbial community composition and diversity in desert agricultural soil, as well as to identify specific functions associated with the rhizosphere. Methods The microbiome community structure, diversity, and microbial functioning were evaluated through the utilization of 16S rRNA gene amplicon and shotgun metagenome sequencing. Results We found the typical rhizosphere effect and plant-species-specific enrichment of bacterial diversity. The annual plants Calendula officinalis and Matricaria chamomilla (Asteraceae) were more similar than the perennial Solanum distichum (Solanaceae). Altogether, plant species explained 50.5% of the variation in bacterial community structures in the rhizosphere. Our results indicate a stronger effect of the plant species in terms of modulating bacterial community structures in the rhizosphere than in root endosphere samples. The plant-driven rhizosphere effect could be linked to redundant plant beneficial functions in the microbiome, while enrichment of specific genes related to amino acid ion transport and metabolism, carbohydrate transport and metabolism, defense mechanisms, and secondary metabolites biosynthesis were more specific. Conclusions The study explores the microbiome continuum at the soil-root interface of medicinal plant species, revealing significant bacterial community structure shifts and plant specificity. The study provides insights into the essential microbiome components contributing to rhizosphere functionality.

Tailored culture strategies to promote antimicrobial secondary metabolite production in Diaporthe caliensis: a metabolomic approach

BackgroundIn the search for new antimicrobial secondary metabolites of fungi, optimizing culture conditions remains a critical challenge, as standard laboratory approaches often result in low yields. While non-selective methods, such as modifying culture media, have been effective in expanding the chemical diversity of fungal metabolites, they have not yet established a direct link to key process parameters crucial for further optimization. This study investigates the capacity of Diaporthe caliensis as a biofactory for biologically active secondary metabolites, employing tailored culture media to explore the relationship between chemical diversity and critical process variables.ResultsThe metabolomic profiles, antibacterial activities, and production yields of the extracts were analyzed to progressively adjust the culture conditions. This study was conducted in five steps, evaluating carbon and nitrogen source concentration, nitrogen source type, salt supplementation, and pH adjustment. Altering the rice starch concentration affected biomass yield per unit of oxygen consumed, while modifications to the nitrogen source concentration influenced both the bioactivity and chemical space by Diaporthe caliensis. Despite changes at the metabolome level, the extracts consistently exhibited potent antibacterial activities, influenced by the nitrogen source, added salts and pH adjustments. For instance, when using corn steep liquor and rice starch, supplemented with micronutrients, different metabolites were produced depending on whether buffer or water was used, though both conditions showed similar antibacterial activities (IC50 ≈ 0.10 mg mL− 1 against Staphylococcus aureus and ≈ 0.14 mg mL− 1 against Escherichia coli). In the treatment where buffer was used to stabilize pH change, there was an increase in the production of phomol-like compounds which are associated with known antibiotic properties. In contrast, in the treatments using water, the drop in pH stimulated the production of previously unidentified metabolites with potential antimicrobial activity.ConclusionsThis study proposes a strategic methodology for the tailored formulation of culture media aiming to promote the biosynthesis of diverse secondary metabolites. This approach revealed the critical role of nutrient limitation and pH regulation in stimulating the production of polyketide-lactone derivatives, including the antibiotic phomol. Ultimately, the systematic, custom-designed culture conditions developed in this work offer a promising strategy for expanding the chemical diversity of Diaporthe caliensis, while providing valuable insights into the key parameters needed for optimizing this fungal biofactory.Graphical

Antibiotic resistance genes and virulence factors in the plastisphere in wastewater treatment plant effluent: Health risk quantification and driving mechanism interpretation

Microplastics (MPs) are ubiquitous in wastewater treatment plants (WWTPs) and provide a unique niche for the spread of pollutants. To date, risk assessments and driving mechanisms of pathogens, antibiotic resistance genes (ARGs), and virulence factors (VFs) in the plastisphere are still lacking. Here, the microbiota, ARGs, VFs, their potential health risks, and biologically driving mechanisms on polythene (PE), polyethylene terephthalate (PET), poly (butyleneadipate-co-terephthalate) and polylactic acid blends (PBAT/PLA), PLA MPs, and gravel in WWTP effluent were investigated. The results showed that plastisphere and gravel biofilm harbored more distinctive microorganisms, promoting the uniqueness of pathogens, ARGs, and VFs compared to WWTP effluent. The abundance of major pathogens, ARGs, and VFs in the plastisphere was 1.01–1.35 times higher than that in the effluent. The high health risk of ARGs (HRA) calculated by fully considering the abundance, clinical relevance, pathogenicity, accessibility and mobility, and the high proportion of resistance contigs with mobile genetic elements confirmed that the plastisphere posed the highest potential health risk. Candidatus Microthrix and Candidatus Promineifilum were the essential hosts of ARGs and VFs in the plastisphere and gravel biofilm, respectively. High metabolic activity such as amino acid metabolism and biosynthesis of secondary metabolites, and highly expressed key genes increased the synthesis of ARGs and VFs. The primary mechanisms driving ARG enrichment in the plastisphere were enhanced microbial metabolic activity, increased frequency of horizontal gene transfer, heightened antibiotic inactivation and efflux, and reduced cell permeability. This study provided new insights into the ARGs, VFs, and health risks of the plastisphere and emphasized the importance of strict control of wastewater discharge.

Accumulation of secondary metabolites in the family Lamiaceae as influenced by foliar micronutrients

The Lamiaceae family is rich in secondary metabolites, such as essential oils comprising flavonoids, phenolic compounds, and terpenoids. Micronutrients play a crucial role in plant metabolism and secondary metabolites production. This review summarizes and emphasizes the significance of foliar micronutrient nutrition in facilitating the accumulation of secondary metabolites in the Lamiaceae family, based on research literature from 2010 to 2023 using dependable databases like Scopus, Google Scholar, PubMed, and Science Direct. Spraying micronutrients notably enhanced the biosynthesis of various secondary metabolites in Lamiaceae species, especially for nutrients that do not move easily (Fe, Zn, Mn, Cu, B, and Si). Using nano-micronutrients as foliar application on Lamiaceae medicinal plants was more effective than traditional soil treatment. This review highlighted the importance of additional investigation on Cerium, Titanium, and Boron. Genera such as Lavandula, Satureja, Origanum, Lippia, and Hyssopus require more research in the future.

Transcriptomic and Metabolomic Analysis Reveals Improved Fruit Quality in Grafted Watermelon

Grafting technology can improve the yield and quality of crops. In this study, we investigated the effects of grafting on watermelon using transcriptomic and metabolomic analysis. A total of 216 differentially accumulated metabolites (DAMs) were identified between pumpkin-grafted watermelon and self-grafted watermelon. KO (Kyoto Encyclopedia of Genes and Genomes Orthology) analysis revealed that the DAMs were mainly enriched in the flavone and flavonol biosynthesis pathway. In addition, high levels of phloretin and citric acid were found in pumpkin-grafted watermelon, which contributes to fruit quality. Meanwhile, compounds such as olivetol and ferulaldehyde, which confer a bitter taste, were downregulated in pumpkin-grafted watermelon. The transcriptome data indicated that the differentially expressed genes (DEGs) identified in the pulp were enriched in fructose and mannose metabolism, biosynthesis of secondary metabolites, and flavone and flavonol biosynthesis pathways. Moreover, genes related to the microtubule, cell wall, and fiber were highly expressed in the stem of pumpkin-grafted watermelon, suggesting that grafting could change the structure of the stem and improve the quality of watermelon fruit. Our study provides a comprehensive picture of the transcriptional and metabolic profile of watermelon induced by grafting, which furthers our understanding of the molecular mechanisms involved in improving watermelon fruit quality by grafting.

Genomic Features of Taiwanofungus gaoligongensis and the Transcriptional Regulation of Secondary Metabolite Biosynthesis

Fungal secondary metabolites (SMs) have broad applications in biomedicine, biocontrol, and the food industry. In this study, whole-genome sequencing and annotation of Taiwanofungus gaoligongensis were conducted, followed by comparative genomic analysis with 11 other species of Polyporales to examine genomic variations and secondary metabolite biosynthesis pathways. Additionally, transcriptome data were used to analyze the differential expression of polyketide synthase (PKS), terpene synthase (TPS) genes, and transcription factors (TFs) under different culture conditions. The results show that T. gaoligongensis differs from other fungal species in genome size (34.58 Mb) and GC content (50.72%). The antibiotics and Secondary Metabolites Analysis Shell (AntiSMASH) analysis reveals significant variation in the number of SM biosynthetic gene clusters (SMBGCs) across the 12 species (12–29), with T. gaoligongensis containing 25 SMBGCs: 4 PKS, 6 non-ribosomal peptide synthetase (NRPS), and 15 TPS clusters. The TgPKS1 gene is hypothesized to be involved in the biosynthesis of orsellinic acid or its derivatives, while TgPKS2 might catalyze the synthesis of 6-methylsalicylic acid (6MSA) and its derivatives. The TgTRI5 genes are suggested to synthesize tetracyclic sesquiterpene type B trichothecene compounds, while TgPentS may be involved in the synthesis of δ-cadinol, β-copaene, and α-murolene analogs or derivatives. Comparative genomic analysis shows that the genome size of T. gaoligongensis is similar to that of T. camphoratus, with comparable SMs. Both species share four types of PKS domains and five distinct types of TPS. Additionally, T. gaoligongensis exhibits a high degree of similarity to Laetiporus sulphureus, despite belonging to a different genus within the same family. Transcriptome analysis reveals significant variation in the expression levels of PKS and TPS genes across different cultivation conditions. The TgPKS1 and TgPKS4 genes, along with nine TgTFs, are significantly upregulated under three solid culture conditions. In contrast, under three different liquid culture conditions, the TgPKS3, TgTRI5-1, and TgTRI5-2 genes, along with twelve TgTFs, exhibit higher activity. Co-expression network analysis and TgTFs binding site prediction in the promoter regions of TgPKS and TgTPS genes suggest that TgMYB9 and TgFTD4 regulate TgPKS4 expression. TgHOX1, TgHSF2, TgHSF3, and TgZnF4 likely modulate TgPKS3 transcriptional activity. TgTRI5-1 and TgTRI5-5 expression is likely regulated by TgbZIP2 and TgZnF15, respectively. This study provides new insights into the regulatory mechanisms of SMs in T. gaoligongensis and offers potential strategies for enhancing the biosynthesis of target compounds through artificial intervention.

Volatile metabolomics and metagenomics reveal the effects of lactic acid bacteria on alfalfa silage quality, microbial communities, and volatile organic compounds

Lactic acid bacteria metabolism affects the composition of volatile organic compounds (VOCs) in alfalfa silage, which results in differences of odor and quality. The aim of this study was to reveal the effects of commercial Lactobacillus plantarum (CL), screened Lactobacillus plantarum (LP), and screened Pediococcus pentosaceus (PP) on quality, microbial community, and VOCs of alfalfa silage based on volatile metabolomics and metagenomics. The results showed that the LP and PP groups had higher sensory and quality grades, and the dominant bacteria were Lactiplantibacillus plantarum and Pediococcus pentosaceus. The main VOCs in alfalfa silage were terpenoids (25.29%), esters (17.08%), and heterocyclic compounds (14.43%), and esters such as methyl benzoate, ethyl benzoate, and ethyl salicylate were significantly increased in the LP and PP groups (P < 0.05). Correlation analysis showed that terpenoids, esters, and alcohols with aromatic odors were positively correlated with Lactiplantibacillus plantarum and Pediococcus pentosaceus. Microbial functions in carbohydrate and amino acid metabolism, biosynthesis of secondary metabolites, and degradation of aromatic compounds were significantly enriched. In conclusion, the addition of lactic acid bacteria can increase the aromatic substances in silage and further improve silage odor and quality.

Transcriptomic analysis reveals differential transcriptional regulation underlying Citrus Bacterial Canker (CBC) tolerance in Citrus sinensis

The sustainable development of the citrus industry is greatly affected by citrus canker, an important bacterial disease. To explore the transcriptional regulatory mechanism of citrus resistance to canker disease, this study used the susceptible Citrus sinensis cv. ‘Newhall’ and its citrus canker-resistant bud mutation variety ‘Longhuitian’ (LHT) as materials. Through analysing the variances in leaf phenotypes between Newhall and LHT, as well as the variations in their transcriptional expression under Xanthomonas citri subsp. citri (Xcc) inoculation, our study concluded that LHT displays markedly greater resistance to Xcc compared to Newhall. Additionally, the spongy parenchyma of LHT leaves is significantly thicker than that of Newhall, and the stomatal number is significantly higher in LHT leaves, while the length and width of individual stomata in LHT leaves are significantly smaller than those in Newhall. RNA-seq analysis indicates that the differentially expressed genes between LHT and Newhall are involved in biotic stress-related biological processes, secondary metabolite biosynthesis, as well as phytohormone signalling pathways. Furthermore, significant differences were observed in reactive oxygen metabolism and phenylalanine metabolism pathways. The findings of our study provide data support for a deeper understanding of the citrus-Xcc interactions and offer valuable clues for unravelling citrus resistance to citrus canker.

Transcriptome sequencing and SSR prediction of Clematis calyx based on SMRT sequencing platform

Clematis is an excellent vertical greening plant for garden viewing vines, with great ornamental and high medicinal value. To obtain transcriptome information and functional gene data for the Clematis calyx, this study utilized three biological replicates of the calyx from each of the three Clematis varieties: ‘Henryi’, ‘Polish spirit’, and ‘Mme Julia Correvon’ Single-molecule real-time sequencing technology was employed for full-length transcriptome sequencing. The study revealed that 21,673,173 non-chimeric sequences were identified through full-length transcriptome sequencing. After clustering, correction, and redundancy removal, 40,465 high-quality, full-length transcripts were obtained. Among these transcripts, there were 15,488 long non-coding RNA (lncRNA), 9,212 simple sequence repeats (SSR) sites, 1,247 transcription factors (TFs), 1,228 alternative splicing events, and 7,189 selectively polyadenylation sites predicted. In addition, 7,442 primer pairs were designed based on the SSR sites, covering 80.76% of the total SSR. 15 primer pairs were randomly selected for amplification, and 73.3% of them were successfully amplified. Transcript annotation results showed that 38,439, 38,094, 26,815, and 33,407 transcripts were annotated to the Nr, KEGG, KOG, and SwissProt databases, respectively. Among these, the KEGG database identified 137 metabolic pathways, including biosynthesis of secondary metabolites, carbon metabolism, and amino acid biosynthesis. 104 and 7 transcripts are involved in the flavonoid and anthocyanin metabolism pathways, respectively. The above results provide initial insights into the transcriptome information and functional characteristics of Clematis calyx. This critical data supports future research on marker primers for the color mechanism of Clematis calyx, the pathways and regulatory mechanisms of flavonoids and other products, as well as specific trait genes.

Identification and characterization of a novel bacteriocin PCM7-4 and its antimicrobial activity against Listeria monocytogenes

Listeria monocytogenes, a pathogenic bacterium causing zoonotic diseases, necessitates the urgent search for novel anti-Listeria monocytogenes drugs due to the continuous emergence of drug-resistant bacteria. In this study, we isolated and identified a bacteriocin-producing strain CM7–4 from seawater as Bacillus velezensis through 16S rRNA sequence analysis. Moreover, we successfully purified a novel bacteriocin named PCM7–4 from Bacillus velezensis CM7–4. The molecular weight of PCM7–4 was determined to be 40,228.99 Da. Notably, PCM7–4 exhibited broad-spectrum antibacterial activity against both Gram-positive and Gram-negative bacteria with a minimum inhibitory concentration (MIC) of 5.625 μg/mL against Listeria monocytogenes specifically. It demonstrated heat resistance and high stability within the pH range of 2–12 while being sensitive to proteinase K degradation without any observed hemolytic activity. Furthermore, SEM analysis revealed that PCM7–4 effectively inhibited biofilm formation and disrupted cell membranes in Listeria monocytogenes cells. Transcriptome analysis revealed that PCM7–4 exerts an impact on genes associated with crucial metabolic pathways, encompassing the biosynthesis of secondary metabolites, phosphotransferase systems (PTS), and starch/sucrose metabolism. These findings highlight the significant potential of bacteriocin PCM7–4 for the development of effective antimicrobial interventions targeting food-borne pathogenic bacteria.

Transcriptome analysis under pecan scab infection reveals the molecular mechanisms of the defense response in pecans.

Pecan scab, caused by the fungal pathogen Venturia effusa, is the most devastating disease of pecan (Carya illinoinensis) in the southeastern United States. Resistance to this pathogen is determined by a complex interaction between host genetics and disease pathotype with even field-susceptible cultivars being resistant to most scab isolates. To understand the underlying molecular mechanisms of scab resistance in pecan, we performed a transcriptome analysis of the pecan cultivar, 'Desirable', in response to inoculation with a pathogenic and a non-pathogenic scab isolate at three different time points (24, 48, and 96 hrs. post-inoculation). Differential gene expression and gene ontology enrichment analyses showed contrasting gene expression patterns and pathway enrichment in response to the contrasting isolates with varying pathogenicity. The weighted gene co-expression network analysis of differentially expressed genes detected 11 gene modules. Among them, two modules had significant enrichment of genes involved with defense responses. These genes were particularly upregulated in the resistant reaction at the early stage of fungal infection (24 h) compared to the susceptible reaction. Hub genes in these modules were predominantly related to receptor-like protein kinase activity, signal reception, signal transduction, biosynthesis and transport of plant secondary metabolites, and oxidoreductase activity. Results of this study suggest that the early response of pathogen-related signal transduction and development of cellular barriers against the invading fungus are likely defense mechanisms employed by pecan cultivars against non-virulent scab isolates. The transcriptomic data generated here provide the foundation for identifying candidate resistance genes in pecan against V. effusa and for exploring the molecular mechanisms of disease resistance.

TMT-based quantitative proteomics analysis of defense responses induced by the Bph3 gene following brown planthopper infection in rice.

The brown planthopper (BPH) is an economically significant pest of rice. Bph3 is a key BPH resistance gene. However, the proteomic response of rice to BPH infestation, both in the presence and absence of Bph3, remains largely unexplored. In this study, we employed tandem mass tag labeling in conjunction with liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis to identify differentially expressed proteins (DEPs) in rice samples. We detected 265 and 125 DEPs via comparison of samples infected with BPH for 2 and 4 days with untreated samples of the BPH-sensitive line R582. For the Bph3 introgression line R373, we identified 29 and 94 DEPs in the same comparisons. Bioinformatic analysis revealed that Bph3 significantly influences the abundance of proteins associated with metabolic pathways, secondary metabolite biosynthesis, microbial metabolism in diverse environments, and phenylpropanoid biosynthesis. Moreover, Bph3 regulates the activity of proteins involved in the calcium signaling pathway, mitogen-activated protein kinase (MAPK) signaling pathway, and plant hormone signal transduction. Our results indicate that Bph3 enhances the resistance of rice to BPH mainly by inhibiting the down-regulation of proteins associated with metabolic pathways; calcium signaling, the MAPK signaling pathway, and plant hormone signal transduction might also be involved in BPH resistance induced by Bph3.

Description of the first marine-isolated member of the under-represented phylum Gemmatimonadota, and the environmental distribution and ecogenomics of Gaopeijiales ord. nov.

The phylum Gemmatimonadota is widespread but rarely cultured and, in fact, there are only six described species isolated from soil, freshwater, and wastewater treatment. However, no isolates of Gemmatimonadota from marine environment have been described; thus, little is known about the physiology and metabolism of members of the marine lineages. In this study, four novel facultatively anaerobic bacterial strains belonging to Gemmatimonadota were isolated from marine sediments collected from Xiaoshi Island in Weihai, China, using an aerobic enrichment method. The integrated results of phylogenetic and phenotypic characteristics supported that these four strains represent one novel species in a novel genus, for which the name Gaopeijia maritima gen. nov., sp. nov. is proposed, as the first representative of novel taxa, Gaopeijiales ord. nov., Gaopeijiaceae fam. nov. in the class Longimicrobiia. Gaopeijiales was detected in 22,884 out of 95,549 amplicon data sets, mainly from soil. However, the highest mean relative abundances were in sponge (0.7%) and marine sediment (0.35%), showing salt-related character. Most of the Gaopeijiales subgroups potentially belong to the rare bacterial biosphere. The aerobic enrichment in this study could significantly increase the relative abundance of Gaopeijiales (from 0.37% to 2.6%). Furthermore, the metabolic capabilities inferred from high-quality representative Gaopeijiales genomes/MAGs suggest that this group primarily performs chemoorganoheterotrophic metabolism with facultatively anaerobic characteristics and possesses various secondary metabolite biosynthesis gene clusters (BGCs), mirroring those observed in the four novel strains.IMPORTANCEDespite rapid advances in molecular and sequencing technologies, obtaining pure cultures remains a crucial research goal in microbiology, as it is essential for a deeper understanding of microbial metabolism. Gemmatimonadota is a widespread but rarely cultured bacterial phylum. Currently, there are only six cultured strains of this interesting group, all isolated from non-marine environments. Little is known about the physiology and metabolism of members of the marine lineages. Here we isolated and characterized four novel marine strains, and proposed a new order Gaopeijiales within Gemmatimonadota. Furthermore, the global distribution, environmental preference, and metabolic potential of Gaopeijiales are analyzed using public data. Our work enriches the resources available for the under-represented phylum Gemmatimonadota and provides insights into the physiological and metabolic characteristics of the marine lineage (Gaopeijiales) through culturology and omics.

Activation of Cryptic Secondary Metabolite Biosynthesis in Tobacco BY-2 Suspension Cells by Epigenetic Modifiers.

Cultured plant cells often biosynthesize secondary metabolites to a lesser extent relative to the mother plants. This phenomenon is associated with epigenetic alterations of the biosynthetic gene(s). Here we investigated the effectiveness of epigenetic modifiers, such as inhibitors of histone deacetylase (HDAC) and DNA methyltransferase (DNMT), to activate cryptic secondary metabolite biosynthesis in tobacco (Nicotiana tabacum) BY-2 cells. The BY-2 suspension cells cultured with an HDAC inhibitor, suberoyl bis-hydroxamic acid, exhibited strong biosynthesis of four compounds that were originally present at trace concentrations. The induced compounds were identified as caffeoylputrescine (1), 4-O-β-D-glucopyranosylferulic acid (2), 5-O-caffeoylquinic acid (3), and feruloylputrescine (4). Biosynthetic activation of compounds 1-4 was reproduced by two other HDAC inhibitors. Treatment of the cells with a DNMT inhibitor (zebularine) also activated the biosynthesis of compounds 1-4, but had a limited effectiveness relative to the HDAC inhibitors, indicating that histone acetylation levels are involved more than DNA methylation levels in the epigenetic regulation of the biosynthesis of compounds 1-4 in the BY-2 cells. Following our previous demonstration using cultured cells of a monocotyledonous plant, this study demonstrates the utility of epigenetic modifiers to activate cryptic secondary metabolite biosynthesis in cultured cells of a dicotyledonous plant.

A respiro-fermentative strategy to survive nanoxia in Acidobacterium capsulatum.

Microbial soil habitats are characterized by rapid shifts in substrate and nutrient availabilities, as well as chemical and physical parameters. One such parameter that can vary in soil is oxygen; thus, the microbial survival is dependent on adaptation to this substrate. To better understand the metabolic abilities and adaptive strategies to oxygen-deprived environments, we combined genomics with transcriptomics of a model organism, Acidobacterium capsulatum, to explore the effect of decreasing, environmentally relevant oxygen concentrations. The decrease from 10 to 0.1µM oxygen (3.6 to 0.036 pO2% present atmospheric level, respectively) caused the upregulation of the transcription of genes involved in signal transduction mechanisms, energy production and conversion and secondary metabolites biosynthesis, transport and catabolism based on COG categories. Contrary to established observations for aerobic metabolism, key genes in oxidative stress response were significantly upregulated at lower oxygen concentrations, presumably due to a NADH/NAD+ redox ratio imbalance as the cells transitioned into nanoxia. Furthermore, A. capsulatum adapted to nanoxia by inducing a respiro-fermentative metabolism and rerouting fluxes of its central carbon and energy pathways to adapt to high NADH/NAD+ redox ratios. Our results reveal physiological features and metabolic capabilities that allowed A. capsulatum to adapt to oxygen-limited conditions, which could expand into other environmentally-relevant soil strains.

Genome-Wide Identification and Characterization of bHLH Gene Family in Hevea brasiliensis

The basic helix-loop-helix (bHLH) transcription factors play crucial roles in plant growth, development, and stress responses. However, their identification and insights into the understanding of their role in rubber trees remain largely uncovered. In this study, the bHLH gene family was explored and characterized in rubber trees using systematic bioinformatics approaches. In total, 180 bHLH genes were identified in the rubber tree genome, distributed unevenly across 18 chromosomes, and phylogenetic analysis classified these genes into 23 distinct subfamilies. Promoter regions revealed a high density of cis-elements responsive to light and hormones. Enrichment analysis indicated involvement in numerous biological processes, including growth, development, hormone responses, abiotic stress resistance, and secondary metabolite biosynthesis. Protein interaction network analysis identified extensive interactions between HbbHLH genes and other functional genes, forming key clusters related to iron homeostasis, plant growth, and stomatal development. Expression profiling of HbbHLH genes have demonstrated varied responses to endogenous and environmental changes. RT-qPCR of eleven HbbHLH genes in different tissues and under ethylene, jasmonic acid, and cold treatments revealed tissue-specific expression patterns and significant responses to these stimuli, highlighting the roles of these genes in hormone and cold stress responses. These findings establish a framework for exploring the molecular functions of bHLH transcription factors in rubber trees.

Preparation of Multifunctional Nano-Protectants for High-Efficiency Green Control of Anthracnose.

Nanomaterials cannot only act as active ingredients (AIs), but also adjuvants to encapsulate or attach AIs to improve their fungicidal activity. Herein, a hydrophilic and lipophilic diblock polymer (HLDP) is designed and synthesized to prepare a series of HLDP nano-protectants to explore the best HLDP nano-protectant for anthracnose management. These results demonstrate that the HLDP-CS nano-protectant displays the best control effects on mango anthracnose via the direct pathogen inhibition and amplified plant immune responses. The HLDP can be spontaneously conjugated with CS into nanoscale spherical particles through hydrophobic interaction. The complexation of CS with HLDP remarkably improves the deposition and adhesion of CS droplets on mango leaves. The HLDP can interact with mycelium via electrostatic interaction to damage the cell wall/membrane, which can act as an AI to directly suppress the spore germination and mycelial growth. Meanwhile, HLDP can be applied as an adjuvant for CS to amplify the plant immune responses via accelerating the biosynthesis of secondary metabolites and plant hormones. This work reports the multiple missions for nanomaterials in pathogen control, which proposes a novel strategy for designing nano-protectant with dual-synergistic mechanism.

Nutrients, Phytochemicals, and Antioxidant Capacity of Red Raspberry Nectar Fermented with Lacticaseibacillus paracasei.

Fresh raspberries are highly perishable, but lactic acid bacteria fermentation offers a favourable method for developing healthy products. This study investigated the effects of Lacticaseibacillus paracasei fermentation on the nutrients and phytochemicals of red raspberry nectar using widely targeted metabolomics, as well as its antioxidant activity. The fermentation notably disrupted the raspberry tissue structure, reshaped its non-volatile composition, and increased its DPPH and hydroxyl free radical scavenging abilities. A total of 261 compounds showed significant differences, with 198 upregulated and 63 downregulated. Among these, certain flavonoid glucosides (e.g., pelargonid-in-3-O-rutinoside, delphinidin-3-O-rutinoside-7-O-glucoside, and kaempferol-3-O-glucoside) were significantly downregulated, while some bioactive phenolic acids (e.g., 3-(4-Hydroxyphenyl)-propionic acid and DL-3-phenyllactic acid), alkaloids (e.g., deoxymutaaspergillic acid and indole-3-lactic acid), amino acids (e.g., L-phenylalanine and L-glutamine), and B vitamins (e.g., VB6, VB7, and VB3) were substantially upregulated. Furthermore, the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation and enrichment analysis revealed that metabolic pathways and the biosynthesis of secondary metabolites contributed significantly to the new profile of fermented red raspberry nectar. These findings provide valuable insights for developing fermented raspberry products using Lacticaseibacillus paracasei, which can help minimise fresh raspberry loss and enhance their valorisation.