Secondary Metabolome Research Articles

Iron limitation triggers roseoceramide biosynthesis and membrane remodeling in marine roseobacter

Chemical communication between marine bacteria and their algal hosts drives population dynamics and ultimately determines the fate of major biogeochemical cycles in the ocean. To gain deeper insights into this small molecule exchange, we screened niche-specific metabolites as potential modulators of the secondary metabolome of the roseobacter, Roseovarius tolerans. Metabolomic analysis led to the identification of a group of cryptic lipids that we have termed roseoceramides. The roseoceramides are elicited by iron-binding algal flavonoids, which are produced by macroalgae that Roseovarius species associate with. Investigations into the mechanism of elicitation show that iron limitation in R. tolerans initiates a stress response that results in lowered oxidative phosphorylation, increased import and catabolism of algal exudates, and reconfiguration of lipid ynthesis to prioritize production of roseoceramides over phospholipids, likely to fortify membrane integrity as well as promote a sessile and symbiotic lifestyle. Our findings add new small molecule words and their "meanings" to the algal-bacterial lexicon and have implications for the initiation of these interactions.

Two pathogen-inducible UDP-glycosyltransferases, UGT73C3 and UGT73C4, catalyze the glycosylation of pinoresinol to promote plant immunity in Arabidopsis.

UDP-glycosyltransferases (UGTs) constitute the largest glycosyltransferase family in the plant kingdom. They are responsible for transferring sugar moieties onto various small molecules to control many metabolic processes. However, their physiological significance in plants is largely unknown. Here, we revealed the function and mechanism of two Arabidopsis UGT genes, UGT73C3 and UGT73C4, which can be strongly induced by Pseudomonas syringae pv. tomato DC3000. Their overexpression significantly enhanced plant immune response, while the loss of their functions in double mutants resulted in the more sensitive phenotype to pathogen infection, although their single mutants had no obvious alteration in pathogen resistance. To understand the regulatory mechanism of UGT3C3/C4 in plant immunity, a completely secondary metabolome analysis and glycoside quantification were conducted. More accumulation of pinoresinol diglucosides was revealed in the UGT73C3 and UGT73C4 overexpression lines than that in wild-type plants whether before or after Pst DC3000 treatment, whereas the double mutants accumulated less pinoresinol diglucosides. Further, the in vitro and in vivo experiments demonstrated that UGT73C3 and UGT73C4 were capable of glycosylating pinoresinol to form pinoresinol monoglucoside and diglucoside. Moreover, we found that pinoresinol glycosylation promoted plant immune response by enhancing ROS production and callose deposition. Additionally, the transcriptional factor HB34 was identified to be responsible for the activation of UGT73C3 and UGT73C4 transcription and play a key role in plant immune responses. Overall, this study revealed a new pathway of plant immune responses via UGT73C3/C4 mediated pinoresinol glycosylation under the HB34 regulation.

Combatting melioidosis with chemical synthetic lethality

Burkholderia thailandensis has emerged as a nonpathogenic surrogate for Burkholderia pseudomallei, the causative agent of melioidosis, and an important Gram-negative model bacterium for studying the biosynthesis and regulation of secondary metabolism. We recently reported that subinhibitory concentrations of trimethoprim induce vast changes in both the primary and secondary metabolome of B. thailandensis. In the current work, we show that the folate biosynthetic enzyme FolE2 is permissive under standard growth conditions but essential for B. thailandensis in the presence of subinhibitory doses of trimethoprim. Reasoning that FolE2 may serve as an attractive drug target, we screened for and identified ten inhibitors, including dehydrocostus lactone (DHL), parthenolide, and β-lapachone, all of which are innocuous individually but form a chemical-synthetic lethal combination with subinhibitory doses of trimethoprim. We show that DHL is a mechanism-based inhibitor of FolE2 and capture the structure of the covalently inhibited enzyme using X-ray crystallography. In vitro, the combination of subinhibitory trimethoprim and DHL is more potent than Bactrim, the current standard of care against melioidosis. Moreover, unlike Bactrim, this combination does not affect the growth of most commensal and beneficial gut bacteria tested, thereby providing a degree of specificity against B. pseudomallei. Our work provides a path for identifying antimicrobial drug targets and for utilizing binary combinations of molecules that form a toxic cocktail based on metabolic idiosyncrasies of specific pathogens.

Co-existence of two antibiotic-producing marine bacteria: Pseudoalteromonas piscicida reduce gene expression and production of the antibacterial compound, tropodithietic acid, in Phaeobacter sp.

Many bacteria co-exist and produce antibiotics, yet we know little about how they cope and occupy the same niche. The purpose of the present study was to determine if and how two potent antibiotic-producing marine bacteria influence the secondary metabolome of each other. We established an agar- and broth-based system allowing co-existence of a Phaeobacter species and Pseudoalteromonas piscicida that, respectively, produce tropodithietic acid (TDA) and bromoalterochromides (BACs). Co-culturing of Phaeobacter sp. strain A36a-5a on Marine Agar with P. piscicida strain B39bio caused a reduction of TDA production in the Phaeobacter colony. We constructed a transcriptional gene reporter fusion in the tdaC gene in the TDA biosynthetic pathway in Phaeobacter and demonstrated that the reduction of TDA by P. piscicida was due to the suppression of the TDA biosynthesis. A stable liquid co-cultivation system was developed, and the expression of tdaC in Phaeobacter was reduced eightfold lower (per cell) in the co-culture compared to the monoculture. Mass spectrometry imaging of co-cultured colonies revealed a reduction of TDA and indicated that BACs diffused into the Phaeobacter colony. BACs were purified from Pseudoalteromonas; however, when added as pure compounds or a mixture they did not influence TDA production. In co-culture, the metabolome was dominated by Pseudoalteromonas features indicating that production of other Phaeobacter compounds besides TDA was reduced. In conclusion, co-existence of two antibiotic-producing bacteria may be allowed by one causing reduction in the antagonistic potential of the other. The reduction (here of TDA) was not caused by degradation but by a yet uncharacterized mechanism allowing Pseudoalteromonas to reduce expression of the TDA biosynthetic pathway.IMPORTANCEThe drug potential of antimicrobial secondary metabolites has been the main driver of research into these compounds. However, in recent years, their natural role in microbial systems and microbiomes has become important to determine the assembly and development of microbiomes. Herein, we demonstrate that two potent antibiotic-producing bacteria can co-exist, and one mechanism allowing the co-existence is the specific reduction of antibiotic production in one bacterium by the other. Understanding the molecular mechanisms in complex interactions provides insights for applied uses, such as when developing TDA-producing bacteria for use as biocontrol in aquaculture.

Traditional Processing Can Enhance the Medicinal Effects of Polygonatum cyrtonema by Inducing Significant Chemical Changes in the Functional Components in Its Rhizomes.

The aims of this study were to explore the significant chemical changes in functional components induced by the traditional processing method and evaluate whether this method based on nine cycles of steaming and drying can effectively enhance the medicinal effects of Polygonatum cyrtonema rhizome. A global analysis on dynamic changes in secondary metabolites during nine processing cycles was performed, and the significantly differentially accumulated secondary metabolites were initially identified based on the secondary metabolome. Unsupervised principal component analysis (PCA), hierarchical clustering analysis (HCA), and orthogonal partial least squares discriminant analysis (OPLA-DA) on secondary metabolites clearly showed that processing significantly increased the global accumulation of secondary metabolites in processed P. cyrtonema rhizomes compared to unprocessed crude rhizomes. The first six processing cycles induced drastic changes in the accumulation of functional components, while the last three did not induce further changes. The accumulations of most functional components were significantly enhanced after the first three cycles and stabilized after six cycles; meanwhile, the first three cycles also led to numerous new components. However, the enhancing effects were unavoidably reversed or weakened under continued processing lasting 6-9 cycles. Furthermore, continued processing also reduced the contents of a small number of original components to undetectable levels. Processing induced some significantly enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, among which the first three processing cycles enhanced the synthesis of various secondary metabolites and significantly affected the metabolisms of amino acids. In conclusion, this study not only reveals that processing can effectively enhance the medicinal effects, by two main mechanisms including enhancing chemical synthesis and inducing structural transformation of functional components, but also provides theoretical guidance for the optimization of the traditional processing method based on nine cycles of steaming and drying for achieving optimal effects on enhancing the medicinal effects of P. cyrtonema rhizome.

Unravelling the secondary metabolome and biocontrol potential of the recently described species Bacillus nakamurai

In the prospect of novel potential biocontrol agents, a new strain BDI-IS1 belonging to the recently described Bacillus nakamurai was selected for its strong in vitro antimicrobial activities against a range of bacterial and fungal phytopathogens. Genome mining coupled with metabolomics revealed that BDI-IS1 produces multiple non-ribosomal secondary metabolites including surfactin, iturin A, bacillaene, bacillibactin and bacilysin, together with some some ribosomally-synthesized and post-translationally modified peptides (RiPPs) such as plantazolicin, and potentially amylocyclicin, bacinapeptin and LCI. Reverse genetics further showed the specific involvement of some of these compounds in the antagonistic activity of the strain. Comparative genomics between the five already sequenced B. nakamurai strains showed that non-ribosomal products constitute the core metabolome of the species while RiPPs are more strain-specific. Although the secondary metabolome lacks some key bioactive metabolites found in B. velezensis, greenhouse experiments show that B. nakamurai BDI-IS1 is able to protect tomato and maize plants against early blight and northern leaf blight caused by Alternaria solani and Exserohilum turcicum, respectively, at levels similar to or better than B. velezensis QST713. The reduction of these foliar diseases, following root or leaf application of the bacterial suspension demonstrates that BDI-IS1 can act by direct antibiosis and by inducing plant defence mechanisms. These findings indicate that B. nakamurai BDI-IS1 can be considered as a good candidate for biocontrol of plant diseases prevailing in tropical regions, and encourage further research into its spectrum of activity, its requirements and the conditions needed to ensure its efficacy.

Identification by Synthesis: Imidacins, Urocanate-Derived Alkaloids from the Myxobacterium Stigmatella aurantiaca.

Innovative discovery approaches such as genome-mining and metabolomics-inspired methods have reshaped the natural product research field, complementing traditional bioactivity-based screens and allowing hitherto unseen compounds to be uncovered from previously investigated producers. In line with these trends, we report here imidacins, a novel class of secondary metabolites specific to the myxobacterial genus Stigmatella. A combination of secondary metabolome analysis, genome-mining techniques, spectroscopic analysis, and finally total synthesis was used to allow structure elucidation. Imidacins are urocanate-derived aliphatic acids with an adjacent cyclopropane moiety, structural features unprecedented in natural products to date.

Deletions of conserved extracytoplasmic function sigma factors-encoding genes in Streptomyces have a major impact on secondary metabolism

BackgroundEthanol shock significantly affects expression of over 1200 genes in Streptomyces venezuelae NRRL B-65,442, including those involved in secondary metabolite biosynthesis and a cryptic gene pepX, which encodes a 19-amino acid peptide with an unknown function.ResultsTo establish a possible correlation between the PepX peptide and secondary metabolism in S. venezuelae, its gene was deleted, followed by analyses of the transcriptome and secondary metabolome of the mutant. Although the secondary metabolome of the pepX mutant was not strongly affected, pepX deletion, similar to ethanol shock, mostly resulted in downregulated expression of secondary metabolite biosynthesis gene clusters (BGCs). At the same time, there was a reverse correlation between the expression of certain extracytoplasmic function sigma factors (ECFs) and several BGCs. Individual deletions of three selected ECF-coding genes conserved in Streptomyces that were upregulated upon both pepX deletion and ethanol shock, had a profound positive effect on the expression of BGCs, which also correlated with the overproduction of specific secondary metabolites. Deletion of one such ECF-coding gene in a marine sponge-derived Streptomyces sp. also significantly altered the secondary metabolite profile, suggesting an important role of this ECF in the regulation of secondary metabolism.ConclusionsThese findings pave the way for the activation or upregulation of BGCs in Streptomyces bacteria harboring genes for ECFs homologous to those identified in this study, hereby assisting in the discovery of novel bioactive secondary metabolites.

Molecular Networking‐Guided Discovery of Kyonggic Acids in Massilia spp.

AbstractIn recent years, bacteria of the genus Massilia have been identified as promising sources of bioactive natural products. In this study, we used mass spectrometry (MS)‐based molecular networking for the first comprehensive analysis of the secondary metabolome of these microorganisms. Annotation of the detected metabolite clusters with a mass fragmentation database revealed several compounds not previously known to be produced by Massilia species. To secure sufficient material for further structural analyses as well as biological testing, we selected the most promising producer strains from our molecular networking analysis and subjected them to larger‐scale cultivation. Following extraction and UV‐directed isolation, we obtained five metabolites in milligram quantities. In addition to a cyclic dipeptide, we elucidated the structures of four acyl amino acids that are related to thalassotalic acid C from the marine bacterium Thalassotalea sp. The Massilia‐derived kyonggic acids were found to inhibit the enzyme tyrosinase, which is involved in melanin biosynthesis influencing skin and hair pigmentation. This study illustrates the value of combining spectroscopic and computational tools in natural product discovery in order to detect and guide the isolation of previously overlooked bioactive compounds.

Impacts of Arbuscular Mycorrhizal Fungi on Metabolites of an Invasive Weed Wedelia trilobata.

The invasive plant Wedelia trilobata benefits in various aspects, such as nutrient absorption and environmental adaptability, by establishing a close symbiotic relationship with arbuscular mycorrhizal fungi (AMF). However, our understanding of whether AMF can benefit W. trilobata by influencing its metabolic profile remains limited. In this study, Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was conducted to analyze the metabolites of W. trilobata under AMF inoculation. Metabolomic analysis identified 119 differentially expressed metabolites (DEMs) between the groups inoculated with AMF and those not inoculated with AMF. Compared to plants with no AMF inoculation, plants inoculated with AMF showed upregulation in the relative expression of 69 metabolites and downregulation in the relative expression of 50 metabolites. AMF significantly increased levels of various primary and secondary metabolites in plants, including amino acids, organic acids, plant hormones, flavonoids, and others, with amino acids being the most abundant among the identified substances. The identified DEMs mapped 53 metabolic pathways, with 7 pathways strongly influenced by AMF, particularly the phenylalanine metabolism pathway. Moreover, we also observed a high colonization level of AMF in the roots of W. trilobata, significantly promoting the shoot growth of this plant. These changes in metabolites and metabolic pathways significantly affect multiple physiological and biochemical processes in plants, such as free radical scavenging, osmotic regulation, cell structure stability, and material synthesis. In summary, AMF reprogrammed the metabolic pathways of W. trilobata, leading to changes in both primary and secondary metabolomes, thereby benefiting the growth of W. trilobata and enhancing its ability to respond to various biotic and abiotic stressors. These findings elucidate the molecular regulatory role of AMF in the invasive plant W. trilobata and provide new insights into the study of its competitive and stress resistance mechanisms.

Leaf rust (Puccinia recondita f. sp. secalis) triggers substantial changes in rye (Secale cereale L.) at the transcriptome and metabolome levels

BackgroundRye (Secale cereale L.) is a cereal crop highly tolerant to environmental stresses, including abiotic and biotic stresses (e.g., fungal diseases). Among these fungal diseases, leaf rust (LR) is a major threat to rye production. Despite extensive research, the genetic basis of the rye immune response to LR remains unclear.ResultsAn RNA-seq analysis was conducted to examine the immune response of three unrelated rye inbred lines (D33, D39, and L318) infected with compatible and incompatible Puccinia recondita f. sp. secalis (Prs) isolates. In total, 877 unique differentially expressed genes (DEGs) were identified at 20 and 36 h post-treatment (hpt). Most of the DEGs were up-regulated. Two lines (D39 and L318) had more up-regulated genes than down-regulated genes, whereas the opposite trend was observed for line D33. The functional classification of the DEGs helped identify the largest gene groups regulated by LR. Notably, these groups included several DEGs encoding cytochrome P450, receptor-like kinases, methylesterases, pathogenesis-related protein-1, xyloglucan endotransglucosylases/hydrolases, and peroxidases.The metabolomic response was highly conserved among the genotypes, with line D33 displaying the most genotype-specific changes in secondary metabolites. The effect of pathogen compatibility on metabolomic changes was less than the effects of the time-points and genotypes. Accordingly, the secondary metabolome of rye is altered by the recognition of the pathogen rather than by a successful infection. The results of the enrichment analysis of the DEGs and differentially accumulated metabolites (DAMs) reflected the involvement of phenylpropanoid and diterpenoid biosynthesis as well as thiamine metabolism in the rye immune response.ConclusionOur work provides novel insights into the genetic and metabolic responses of rye to LR. Numerous immune response-related DEGs and DAMs were identified, thereby clarifying the mechanisms underlying the rye response to compatible and incompatible Prs isolates during the early stages of LR development. The integration of transcriptomic and metabolomic analyses elucidated the contributions of phenylpropanoid biosynthesis and flavonoid pathways to the rye immune response to Prs. This combined analysis of omics data provides valuable insights relevant for future research conducted to enhance rye resistance to LR.

A multiplex metabolomic approach for quality control of Spirulina supplement and its allied microalgae (Amphora & Chlorella) assisted by chemometrics and molecular networking

Microalgae species are of economic importance regarded as “green gold” being rich in bioactive compounds. Spirulina and Chlorella are the most popular microalgal species and are marketed as healthy food supplements. At the same time, Amphora holds potential as a source of healthy lipids and essential fatty acids. Yet, there are considerable variations in their reported chemical composition, and less is known about their compositional differences. A multiplexed metabolomic approach was adopted for the quality control (QC) of Spirulina supplements and to compare its constitutive metabolome to Chlorella and Amphora. The adopted protocol comprised gas chromatography-mass spectrometry (GC–MS), ultra-high performance liquid chromatography coupled with high-resolution tandem mass spectrometry (UPLC-HRMS/MS), and ultraviolet–visible spectrophotometry (UV/Vis) for mapping their primary and secondary metabolome. Interestingly, UPLC-HRMS/MS analysis delineated the abundance of fatty acids in Amphora versus glycolipids enrichment in Spirulina, and porphyrins were the main pigments identified in Spirulina, with scarce occurrence in Chlorella. Orthogonal projections to latent structures discriminant analysis (OPLS-DA) analysis of GC–MS data set revealed palmitic acid, 3-mannobiose, and glyceryl-glycoside as being most enriched in Spirulina, versus sucrose and leucine in Chlorella and Amphora, respectively. Despite being of low discriminatory potential, UV/Vis OPLS-DA modeling showed that Spirulina was distinguished with the UV absorbances of carotenoids and chlorophyll pigments, as indicated by its OPLS-DA derived S-plot. Our study provides a QC approach for the analysis of the microalgal species and poses alternative spectral and compositional markers for their discrimination.

Genomes and secondary metabolomes of Streptomyces spp. isolated from Leontopodium nivale ssp. alpinum.

Bacterial endophytes dwelling in medicinal plants represent an as yet underexplored source of bioactive natural products with the potential to be developed into drugs against various human diseases. For the first time, several Streptomyces spp. were isolated from the rare and endangered traditional medicinal plant Leontopodium nivale ssp. alpinum, also known as Edelweiss. In the search for novel natural products, nine endophytic Streptomyces spp. from Edelweiss were investigated via genome sequencing and analysis, followed by fermentation in different media and investigation of secondary metabolomes. A total of 214 secondary metabolite biosynthetic gene clusters (BGCs), of which 35 are presumably unique, were identified by the bioinformatics tool antiSMASH in the genomes of these isolates. LC-MS analyses of the secondary metabolomes of these isolates revealed their potential to produce both known and presumably novel secondary metabolites, whereby most of the identified molecules could be linked to their cognate BGCs. This work sets the stage for further investigation of endophytic streptomycetes from Edelweiss aimed at the discovery and characterization of novel bioactive natural products.

Molecular networking-guided investigation of the secondary metabolome of four Morus species and their in vivo neuroprotective potential for the mitigation of Alzheimer's disease.

Alzheimer's Disease (AD) is a fatal age-related neurodegenerative condition with a multifactorial etiology contributing to 70% of dementia globally. The search for a multi-target agent to hit different targets involved in the pathogenesis of AD is crucial. In the present study, the neuroprotective effects of four Morus extracts were assessed in LPS-induced AD in mice. Among the studied species, M. macroura exhibited a profound effect on alleviating the loss of cognitive function, improved the learning ability, restored the acetylcholine esterase (AChE) levels to normal, and significantly reduced the tumor necrosis factor alpha (TNF-α) brain content in LPS-treated mice. To investigate the secondary metabolome of the studied Morus species, ultra-performance liquid chromatography coupled to tandem mass spectrometry (UPLC-HRMS/MS), aided with feature-based molecular networking, was employed. Among the annotated features, aryl benzofurans and prenylated flavonoids were suggested as being responsible for the observed neuroprotective effect. Furthermore, some of the detected metabolites were proposed as new natural products such as moranoline di-O-hexoside (1), isomers of trimethoxy-dihydrochalcone-O-dihexoside (59 & 76), (hydroxy-dimethoxyphenyl)butenone-O-hexoside (82), and O-methylpreglabridin-O-sulphate (105). In conclusion, our findings advocate the potential usage of M. macroura leaves for the management of AD, yet after considering further clinical trials.

Beyond Penicillin: The Potential of Filamentous Fungi for Drug Discovery in the Age of Antibiotic Resistance.

Antibiotics are a staple in current medicine for the therapy of infectious diseases. However, their extensive use and misuse, combined with the high adaptability of bacteria, has dangerously increased the incidence of multi-drug-resistant (MDR) bacteria. This makes the treatment of infections challenging, especially when MDR bacteria form biofilms. The most recent antibiotics entering the market have very similar modes of action to the existing ones, so bacteria rapidly catch up to those as well. As such, it is very important to adopt effective measures to avoid the development of antibiotic resistance by pathogenic bacteria, but also to perform bioprospecting of new molecules from diverse sources to expand the arsenal of drugs that are available to fight these infectious bacteria. Filamentous fungi have a large and vastly unexplored secondary metabolome and are rich in bioactive molecules that can be potential novel antimicrobial drugs. Their production can be challenging, as the associated biosynthetic pathways may not be active under standard culture conditions. New techniques involving metabolic and genetic engineering can help boost antibiotic production. This study aims to review the bioprospection of fungi to produce new drugs to face the growing problem of MDR bacteria and biofilm-associated infections.

Comparing steamed and wine-stewed Rehmanniae Radix in terms of Yin-nourishing effects via metabolomics and microbiome analysis.

Rehmanniae Radix Praeparata (RRP), the processed root of Rehmannia glutinosa, has been widely used to treat Yin deficiency syndrome in traditional Chinese medicine. RRP is available in two forms: processed by steaming with water (SRR) or processed by stewing with yellow rice wine (WRR). Previous work has documented chemical differences in the secondary metabolomes and glycomes of SRR and WRR. This study aimed to compare SRR and WRR in terms of Yin-nourishing effects via metabolomics and microbiome analysis. ICR mice were orally administered with thyroxine for 14d to induce Yin deficiency. Changes in biochemical indices and histopathology were detected. Serum metabolomics analysis and microbial 16S rRNA sequencing were performed to compare the therapeutic effects and mechanisms between SRR and WRR in treating thyroxine-induced Yin deficiency. Both SRR and WRR decreased serum T3, T4 and MDA levels, and increased SOD activity. SRR more effectively decreased serum Cr, and ameliorated kidney injury, while WRR showed better regulation on ratio of cAMP/cGMP and serum TSH, and relieved thyroid injury. Both SRR and WRR regulated tyrosine, glycerophospholipid, and linoleic acid metabolism and the citric acid cycle. Additionally, SRR regulated fatty acid metabolism, while WRR influenced alanine, aspartate and glutamate metabolism, and bile acid biosynthesis. SRR significantly enriched the genera Staphylococcus and Bifidobacterium in the gut microbiome, while WRR significantly enriched the genera Akkermansia, Bacteroides and Parabacteroides, and decreased the abundance of Lactobacillus. SRR displayed better protective effects on kidney, while WRR showed stronger effects on thyroid in thyroxine-induced Yin deficient mice. These differences might be due to different regulating effects of SRR and WRR on the metabolome and gut microbiota.

The resilient cotton plant: uncovering the effects of stresses on secondary metabolomics and its underlying molecular mechanisms

Cotton is an important fiber crop cultivated around the world under diverse climate conditions and generates billions of dollars in annual revenue globally. Biotic and abiotic stresses have caused reduction in yield and productivity of cotton crops. In this review, we comprehensively analyzed and summarized the effect of biotic and abiotic stress on secondary metabolite production in cotton. The development of cotton varieties with improved tolerance against abiotic and biotic stress can play an important role in sustainable cotton production. Under stress conditions, plants develop a variety of defense mechanisms such as initiating signaling functions to upregulate defense responsive genes and accumulation of secondary metabolites. Understanding the impact of stress on secondary metabolite production in cotton is crucial for developing strategies to alleviate the negative effects of stress on crop yield and quality. Further, the potential industrial applications of these secondary metabolites in cotton, such as gossypol, could provide new opportunities for sustainable cotton production and the development of value-added products. Additionally, transgenic and genome-edited cotton cultivars can be developed to provide tolerance to both abiotic and biotic stress in cotton production.

Strategies for Natural Product Discovery by Unlocking Cryptic Biosynthetic Gene Clusters in Fungi

Recent advancements in genome sequencing and bioinformatic analysis of fungal genomes have revealed that fungi possess cryptic or silent biosynthetic gene clusters (BGCs). This discovery suggests that our understanding of the universe of fungal secondary metabolomes is limited. In this review, we summarize recent strategies for activating cryptic BGCs in fungi, identify fungal secondary metabolites, and highlight their biological activities. We also briefly discuss the isolation and purification methods for these compounds. Our focus is on genetics-dependent and genetics-independent approaches for activating cryptic BGCs in fungi. Using the strategies discussed here, cryptic fungal natural products hold significant potential as a source for the discovery of new drug candidates.

Amesia hispanica sp. nov., Producer of the Antifungal Class of Antibiotics Dactylfungins.

During a study of the diversity of soilborne fungi from Spain, a strain belonging to the family Chaetomiaceae (Sordariales) was isolated. The multigene phylogenetic inference using five DNA loci showed that this strain represents an undescribed species of the genus Amesia, herein introduced as A. hispanica sp. nov. Investigation of its secondary metabolome led to the isolation of two new derivatives (2 and 3) of the known antifungal antibiotic dactylfungin A (1), together with the known compound cochliodinol (4). The planar structures of 1-4 were determined by ultrahigh performance liquid chromatography coupled with diode array detection and ion mobility tandem mass spectrometry (UHPLC-DAD-IM-MS/MS) and extensive 1D and 2D nuclear magnetic resonance (NMR) spectroscopy after isolation by HPLC. All isolated secondary metabolites were tested for their antimicrobial and cytotoxic activities. Dactylfungin A (1) showed selective and strong antifungal activity against some of the tested human pathogens (Aspergillus fumigatus and Cryptococcus neoformans). The additional hydroxyl group in 2 resulted in the loss of activity against C. neoformans but still retained the inhibition of As. fumigatus in a lower concentration than that of the respective control, without showing any cytotoxic effects. In contrast, 25″-dehydroxy-dactylfungin A (3) exhibited improved activity against yeasts (Schizosaccharomyces pombe and Rhodotorula glutinis) than 1 and 2, but resulted in the appearance of slight cytotoxicity. The present study exemplifies how even in a well-studied taxonomic group such as the Chaetomiaceae, the investigation of novel taxa still brings chemistry novelty, as demonstrated in this first report of this antibiotic class for chaetomiaceous and sordarialean taxa.

Structure Elucidation and Biosynthesis of Nannosterols A and B, Myxobacterial Sterols from Nannocystis sp. MNa10993.

Myxobacteria represent an underinvestigated source of chemically diverse and biologically active secondary metabolites. Here, we report the discovery, isolation, structure elucidation, and biological evaluation of two new bacterial sterols, termed nannosterols A and B (1, 2), from the terrestrial myxobacterium Nannocystis sp. (MNa10993). Nannosterols feature a cholestanol core with numerous modifications including a secondary alcohol at position C-15, a terminal vicinal diol side chain at C-24-C-25 (1, 2), and a hydroxy group at the angular methyl group at C-18 (2), which is unprecedented for bacterial sterols. Another rare chemical feature of bacterial triterpenoids is a ketone group at position C-7, which is also displayed by 1 and 2. The combined exploration based on myxobacterial high-resolution secondary metabolome data and genomic in silico investigations exposed the nannosterols as frequently produced sterols within the myxobacterial suborder of Nannocystineae. The discovery of the nannosterols provides insights into the biosynthesis of these new myxobacterial sterols, with implications in understanding the evolution of sterol production by prokaryotes.