Epigenetic manipulation for secondary metabolite activation in endophytic fungi: current progress and future directions

Genome-wide identification and expression analysis of epigenetic regulator gene families in the medicinal mushroom Ganoderma lucidum

Epigenetic regulator (ER) genes, crucial for fungal growth and development, remain largely unexplored in Ganoderma lucidum, a medicinal mushroom valued for its bioactive compounds. This study identified 81 ER genes in G. lucidum, distributed across 12 chromosomes and classified into six families: 3 chromatin remodelers, 4 DNA methyltransferases, 7 histone acetyltransferases, 22 histone deacetylases, 23 histone methyltransferases, and 22 histone demethyltransferases. Comparative and phylogenetic analyses with other species revealed conserved orthologs and species-specific clusters. Gene duplication analysis suggested whole-genome duplication expanded ER gene families, primarily histone demethyltransferases under purifying selection. Additionally, gene structure, motif, and domain analyses revealed family-specific intron/exon organization and conserved domains. Transcriptome profiling across four developmental stages (mycelium, primordia, young and mature fruiting body) revealed dynamic stage-specific expression patterns, suggesting their developmental significance. The result of qRT-PCR validated the expression patterns for 18 ER genes, laying foundation for future research exploring epigenetic regulation in fungal development and bioactive compound production.

The Effect of Endophytic Fungus CA3-A with Biotransformation or Catalysis Activity on the Metabolite Formation of Traditional Chinese Medicinal Astragalus Membranaceus var. Mongholicus (Bunge) P. K. Hsiao

The effect of endophytic fungal biotransformation on the formation of metabolic substances has become a non-negligible factor in assessing the quality of medicinal plants. However, the relevant evidences are still particularly lacking. In this study, an endophytic fungus CA3-A with biotransformation activity was screened and identified as Talaromyces coprophilus from root of Astragalus mongholicus. Its biotransformation effect on host metabolism was studied by co-culture with fungus and host root. The results showed that in addition to the significant changes in primary metabolites, secondary metabolite conversions are mainly focused on compounds such as terpenoids, phenols and flavonoids. The transformed metabolic pathways are mainly enriched in glycerophospholipid metabolism, ubiquinone and terpenoid quinones biosynthesis, and tyrosine metabolism. A total of 38 signature differential metabolites are found through multivariate statistical analysis. In addition to eleven primary metabolites including glycerides and glycerophospholipids, twenty-eight secondary metabolites distribute in terpenes, sterols, phenols, flavonoids, benzene, lipids and other classes of compounds, respectively. In conclusion, this study aims to quickly focus on the signature differentially metabolites from a large amount of information, narrow the possible range of potential transformation products, and provide help for understanding of influence of endophytes on host metabolism and the search for new natural products.

Developing filamentous fungal chassis for natural product production

The growing demand for green and sustainable production of high-value chemicals has driven the interest in microbial chassis. Recent advances in synthetic biology and metabolic engineering have reinforced filamentous fungi as promising chassis cells to produce bioactive natural products. Compared to the most used model organisms, Escherichia coli and Saccharomyces cerevisiae, most filamentous fungi are natural producers of secondary metabolites and possess an inherent pre-mRNA splicing system and abundant biosynthetic precursors. In this review, we summarize recent advances in the application of filamentous fungi as chassis cells. Emphasis is placed on strategies for developing a filamentous fungal chassis, including the establishment of mature genetic manipulation and efficient genetic tools, the catalogue of regulatory elements, and the optimization of endogenous metabolism. Furthermore, we provide an outlook on the advanced techniques for further engineering and application of filamentous fungal chassis.

Regulation of Histone Acetylation Modification on Biosynthesis of Secondary Metabolites in Fungi

The histone acetylation modification is a conservative post-translational epigenetic regulation in fungi. It includes acetylation and deacetylation at the lysine residues of histone, which are catalyzed by histone acetyltransferase (HAT) and deacetylase (HDAC), respectively. The histone acetylation modification plays crucial roles in fungal growth and development, environmental stress response, secondary metabolite (SM) biosynthesis, and pathogenicity. One of the most important roles is to regulate the gene expression that is responsible for SM biosynthesis in fungi. This mini-review summarized the regulation of histone acetylation modification by HATs and HDACs on the biosynthesis of SMs in fungi. In most cases, histone acetylation by HATs positively regulated the biosynthesis of fungal SMs, while HDACs had their negative regulations. Some HATs and HDACs were revealed to regulate fungal SM biosynthesis. Hda1 was found to be the most efficient regulator to affect the biosynthesis of SMs in fungi. The regulated fungal species were mainly from the genera of Aspergillus, Calcarisporium, Cladosporium, Fusarium, Monascus, Penicillium, and Pestalotiopsis. With the strategy of histone acetylation modification, the biosynthesis of some harmful SMs will be inhibited, while the production of useful bioactive SMs will be promoted in fungi. The subsequent research should focus on the study of regulatory mechanisms.

A review of the pharmaceutical applications of endophytic fungal secondary metabolites

A major challenge to human health is the emergence of drug-resistant pathogenic strains of organisms. Studies have found ecologically friendly, cost-effective, and innocuous alternative sources of bioactive compounds capable of managing drug-resistant menace. This review x-rays the endophytic fungal community and the pharmaceutical applications of their secondary metabolites. Endophytic fungi house biologically active compounds, which makes them a good pharmaceutical alternative. Also, their intrinsic ability to produce such an avalanche of bioactive compounds could be attributed to their mutualistic interaction with the plant's host. Secondary metabolites harvested from endophytic fungi have been identified and categorised: steroids, xanthones, terpenoids, isocoumarins, phenols, tetralones, benzopyranones, and enniatrines. This review also highlights optimisation strategy, co-culture method, chemical epigenetic remodelling, and molecular method as approaches adopted to boost the production of bioactive compounds. The numerous applications of endophytic fungal secondary metabolites were equally presented, which include their bioactive properties, as well as their use in industries.

[Using metabolomics to explore the effects of epigenetic-modification strategies on the metabolites of Acanthus ilicifolius L. endophytic fungi against ovarian cancer]

Ovarian cancer is a serious threat to women's health and safety. So far, people have discovered more than 130 small molecule compounds of natural origin for anti-tumor, of which approximately 50% are of microbial origin. The Acanthus ilicifolius L. species is primarily distributed in the Guangdong, Hainan, and Guangxi regions of China and grows in tidally accessible coastal areas. Recent studies have revealed that Acanthus ilicifolius L. extracts are endowed with a range of pharmacological properties, including anti-inflammatory, hepatoprotective, antioxidant, and antitumor activities. Endophytic fungi are commonly found in the healthy tissue and organs of medicinal plants. These fungi and the plants they inhabit form mutually beneficial symbiotic relationships. Endophytic fungi produce a series of secondary metabolites, with active substances having shown great economic value and applications prospects in drug research and development as well as for the biological control of plant diseases. Secondary metabolites production by endophytic fungi is regulated by specific gene clusters, and several techniques have been used to stimulate the secondary metabolic processes of fungi, including epigenetic-modification and OSMAC (one strain many compounds) strategies, co-culturing, and gene modification. Among these, epigenetic modification has been shown to be effective; this strategy involves the addition of small-molecule epigenetic modifiers to the culture medium, thereby activating silenced biosynthetic gene clusters without altering the DNA sequences of the fungi. This approach facilitates the expression of silenced genes in endophytic fungi, thereby increasing the number and diversity of secondary metabolites. Furthermore, it assists in overcoming the inhibition of microbial secondary-metabolite synthesis under laboratory conditions, and enhances silenced-gene expressions. The advent of novel analytical techniques and bioinformatics has provided a comprehensive, multifaceted, and holistic understanding of fungal metabolism through the development of metabolomics as a research platform. However, few studies have combined anti-ovarian cancer-activity screening with metabolomic approaches in the search for activity-differentiating metabolites from endophytic fungi under the intervention of epigenetic modifiers. Herein, we investigated the impact of epigenetic modifiers on the secondary metabolites of the endophytic Diaporthe goulteri fungus from Acanthus ilicifolius L. to determine their potential anti-ovarian cancer activities. Crude extracts were obtained by controlling three variables: the number of fermentation days, the type of epigenetic modifier, and its concentration, with activities screened using the CCK-8 (cell counting kit-8) method. Ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was subsequently employed for non-targeted metabolomic analysis. A multivariate statistical analysis model was constructed using principal component analysis and orthogonal partial least squares-discriminant analysis, which combines model and variable importance projection, with qualitative screening performed and significant changes (variable importance in the projection (VIP)≥1; P<0. 05) determined. Fifteen differential metabolites were identified in the fungal and epigenetic modification group, primarily comprising polyketides, amino acids, derivatives, alkaloids, and organic acids, including prenderol, glycine, valine, 2-ethylcaproic acid, rubratoxin B, finasteride, 6-silaspiro[5.5]undecane, 1-(2-nitrophenoxy)octane, heptadecene, 1-pentadecene, 11-ketoetiocholanolone, 3-(1-ethyl-1,3,3-trimethyl-2,3-dihydro-1H-inden-5-yl)butanal, N2-benzoylarginine, tabutrex, (3aR,6S,6aS)-6-(4-hydroxy-2-methoxy-2-butanyl)-4,4-dimethylhexahydro-1(2H)-pentalenone, and 8-aminoquinoline. The expressions of prenderol, 1-(2-nitrophenoxy)octane, 3-(1-ethyl-1,3,3-trimethyl-2,3-dihydro-1H-inden-5-yl)butanal, N2-benzoylarginine, and 8-aminoquinoline were downregulated, whereas the expressions of the remaining 10 substances were upregulated. Polyketides were the main components that exhibited higher expressions. This study showed that latent active differential metabolites can be searched by combining anti-ovarian cancer-activity screening with metabolomics analysis, thereby providing a reference for the further development of Acanthus ilicifolius L. resources and the subsequent targeted isolation of active compounds.

Myco-nanotechnological approach to synthesize gold nanoparticles using a fungal endophyte,Penicillium oxalicum, and unravelling its antibacterial activity and anti-breast cancer role via metabolic reprogramming

The present study has been designed to fabricate fungal endophyte-assisted gold nanoparticles (AuNPs) and elucidate their anti-breast cancer potential. The aqueous extract of fungal endophytePenicillium oxalicum(PO), associated with the medicinal plantAmoora rohituka, was used for the fabrication of AuNPs (POAuNPs). Physico-chemical characterization using Ultraviolet-visible spectroscopy, Fourier transform infrared, X-ray diffraction, Dynamic light scattering, Zeta potential, Transmission electron microscopy and Field emission scanning electron microscopy analysis revealed stable, uniform distribution, spherical shape and crystalline nature of POAuNPs with a size range of 3-46 nm. Furthermore, the POAuNPs potentially inhibited the growth of pathogenic bacterial strainsEscherichia coliandStaphylococcus aureus. The synthesized POAuNPs have shown potential antioxidant effects against 2,2-diphenyl-1-picrylhydrazyl (DPPH), superoxide and nitric oxide (NO) radical scavenging assays with an EC50value of 8.875 ± 0.082, 52.593 ± 2.506 and 43.717 ± 1.449 µg mL-1, respectively. Moreover, the value of EC50for the total antioxidant capacity of POAuNPs was found to be 23.667 ± 1.361 µg mL-1. The cell viability of human breast cancer cells, MDA-MB-231 and MCF-7, was found to be reduced after treatment with POAuNPs, and IC50values were found to be 19.753 ± 0.640 and 35.035 ± 0.439 µg mL-1, respectively. Further,in vitrobiochemical assays revealed that POAuNPs induces metabolic reprogramming in terms of reduced glucose uptake, increased lactate dehydrogenase (LDH) release and, disruption of oxidative balance through depletion of glutathione levels, increased nitric oxide (NO) and lipid peroxidation levels as a possible pathway to suppress human breast cancer cell proliferation. Apoptosis-specific nuclear modulations induced by POAuNPs in human breast cancer cells were validated through 4',6-diamidino-2-phenylindole (DAPI) nuclear staining. The present investigation thus attempts to show the first ever fabrication of AuNPs using an aqueous extract ofP. oxalicumassociated withA. rohituka. The results revealed unique physico-chemical characteristics of mycogenic AuNPs, and screening their effect against breast cancer via metabolic reprogramming and induction of apoptosis thus adds great significance for cancer therapeutics, suggesting further exploration to develop nanotherapeutic drugs.

Stimulating Novel and Bioactive Metabolite Production by Cocultivation of Two Fungi─Aspergillus oryzae and Epicoccum dendrobii

Fungi produce various bioactive secondary metabolites (SMs) as protective and weaponized tools to enhance survival in shared ecological niches. By mimicking a competitive ecosystem, cocultivation has been proven to be particularly successful in stimulating SM discovery. Here, we reported the identification of four novel metabolites, epiclactones A and B, epioxochromane and aoergostane, from the coculture of two biotechnologically important strains, Aspergillus oryzae and Epicoccum dendrobii. Transcriptome and metabolome analyses revealed widespread silent gene activation during fungal-fungal interaction. The majority of differentially expressed gene clusters were summarized for both strains. Based on these highly activated biosynthetic pathways, we suggested that a bidirectional chemical defense occurred under cocultivation. E. dendrobii enhanced the production of the spore inhibitor, fumigermin. Moreover, A. oryzae highly accumulated the antifungal agent kojic acid with a yield of up to 1.10 g/L. This study provides an excellent example for the discovery of hidden natural products by cocultivation.

Epigenetic modifiers as inducer of bioactive secondary metabolites in fungi

Scientists are making efforts to search for new metabolites as they are essential lead molecules for the drug discovery, much required due to the evolution of multi drug resistance and new diseases. Moreover, higher production of known drugs is required because of the ever growing population. Microorganisms offer a vast collection of chemically distinct compounds that exhibit various biological functions. They play a crucial role in safeguarding crops, agriculture, and combating several infectious ailments and cancer. Research on fungi have grabbed a lot of attention after the discovery of penicillin, most of the compounds produced by fungi under normal cultivation conditions are discovered and now rarely new compounds are discovered. Treatment of fungi with the epigenetic modifiers has been becoming very popular since the last few years to boost the discovery of new molecules and enhance the production of already known molecules. Epigenetic literally means above genetics that actually does not alter the genome but alter its expression by altering the state of chromatin from heterochromatin to euchromatin. Chromatin in heterochromatin state usually doesn't express because it is closely packed by histones in this state. Epigenetic modifiers loosen the packing of chromatin by inhibiting DNA methylation and histone deacetylation and thus permit the expression of genes that usually remain dormant. This study delves into the possibility of utilizing epigenetic modifying agents to generate pharmacologically significant secondary metabolites from fungi.