Secondary metabolites produced by Macrophomina phaseolina, a fungal root endophyte of Brugmansia aurea, using classical and epigenetic manipulation approach

Exploring the modern approaches to enhance fungal endophyte-derived bioactive secondary metabolites

Over the past few decades, microbial-derived bioactive compounds have been tested for antiviral, antimicrobial, and anticancer properties. In addition, fungal-derived bioactive secondary metabolites (SMs) are increasingly being suggested as suitable alternative sources of potent bioactive compounds. The development of suitable, precise in vitro and in vivo screening techniques may contribute to identifying the biochemical and physiological effects of compounds. This advancement in bioassay evaluation techniques helps identify potential bioactive microbes rapidly. The main obstacles, however, have been the production of insufficient amounts of chemicals, endophytes' attenuation or loss of ability to produce the molecule of interest when grown in cultures, and fungal endophytes' failure to exhibit their full biosynthetic potential in lab conditions. These have led to the use of small chemical elicitors that activate the silent biosynthetic gene clusters (BGCs) in fungi, causing epigenetic alterations that increase the amount of desired metabolites or trigger the synthesis of hitherto unknown compounds. The silent BGCs were activated to maximize production of bioactive secondary metabolites, thereby increasing the yield of desired compounds or triggering the synthesis of novel metabolites. Other strategies include gene knocking, inducing mutations, heterologous expression, one strain-many compounds (OSMAC), epigenetic modifications, etc. This review is focused on the mechanism of plant-microbe interaction in enhancing the biosynthesis of fungal metabolites along with the BGCs for the biosynthesis of the bioactive fungal metabolites. Furthermore, we also discuss the genomic mining approaches for BGCs, the role of ribosomal engineering, precursor feeding, and various elicitors to explore the structural diversity of novel bioactive compounds.

Chae-type cytochalasans from coculture of Aspergillus flavipes and Chaetomium globosum

Cocultivation of the high cytochalasan-producing fungi Aspergillus flavipes and Chaetomium globosum resulted in the isolation of 11 undescribed Chae-type cytochalasans. Their structures were determined by spectroscopic data and NMR data calculations. Asperchaetoglobin A (1) was the first Chae-type cytochalasan possessing an unprecedented nitrogen bridge between C-17 and C-20 to generate a surprising 5/6/12/5 multiple ring system; asperchaetoglobins B and C (2 and 3) displayed higher oxidation with an additional epoxide at the thirteen-member ring; asperchaetoglobin D (4) was the second Chae-type cytochalasin featuring a 5/6/12 tricyclic ring system. The cytotoxic activities against five human cancer cell lines and antibacterial activities against Staphylococcus aureus and Colon bacillus of selected compounds were evaluated in vitro.

Structural diversity of microbial secondary metabolites based on chemical epigenetic manipulation

Fungi are microorganisms with biosynthetic potential that are capable of producing a wide range of chemically diverse and biologically interesting small molecules. Chemical epigenetic manipulation has been increasingly explored as a simple and powerful tool to induce the production of additional microbial secondary metabolites in fungi. This review focuses on chemical epigenetic manipulation in fungi and summarizes 379 epigenetic manipulation products discovered from 2008 to 2022 to promote the discovery of their medicinal value.

Xylarcurcosides A-C, three novel isopimarane-type diterpene glycosides from Xylaria curta YSJ-5

Three previously undescribed isopimarane-type diterpene glycosides named as xylarcurcosides A-C (1-3) along with two known ones 16-α-d-mannopyranosyloxyisopimar-7-en-19-oic acid (4) and hypoxylonoid A (5) were successfully isolated from an ethyl acetate extract of the endophytic fungus Xylaria curta YSJ-5 growing in leaves of Alpinia zerumbet. The spectroscopic methods, electronic circular dichroism (ECD) calculations, and X-ray diffraction experiments were conducted to identify their absolute chemical structures. All these compounds were tested for in vitro cytotoxic, anti-inflammatory, α-glucosidase inhibitory, and antibacterial activities. As a result, these novel compounds demonstrated no obvious cytotoxic and antibacterial activity.

Metabolomic and microbiomic insights into color changes during the sweating process in Dipsacus asper

Sweating is one of the most important primary processing methods of Chinese medicinal materials. Dipsacus asper is a typical representative of sweating treatment that is recommended by the Chinese Pharmacopoeia. The color change of the fracture surface of the root is the prominent feature of sweating treatment. However, few studies have focused on the mechanism of color change during sweating treatment. In this study, widely targeted metabolomics and ITS high-throughput sequencing technologies were applied to detect metabolites and microbial structure and diversity in the root of D. asper during sweating treatment. A total of 667 metabolites, including 36 downregulated and 78 upregulated metabolites, were identified in D. asper following sweating treatment. The significantly differential metabolites were divided into 12 classes, including terpenoids and phenolic acids. Moreover, all the differential terpenoids were upregulated and 20 phenolic acids showed a significant change after sweating treatment. In addition, microbial community diversity and richness increased following sweating treatment. The composition of microbial communities revealed that the relative abundances of Ascomycota and Basidiomycota significantly changed after sweating treatment. Correlation analysis revealed that Ascomycota (Fusarium sp., Macrophomina sp., Ilyonectria sp., Memnoniella sp., Penicillium sp., Cyphellophora sp., Neocosmospora sp., unclassified_f_Nectriaceae, and unclassified_o_Saccharomycetales) and Basidiomycota (Armillaria sp.) were associated with the content of terpenoids (6-deoxycatalpol and laciniatoside III) and phenolic acids (3-(4-hydroxyphenyl)-propionic acid, ethyl caffeate, 4-O-glucosyl-4-hydroxybenzoic acid, 2-acetyl-3-hydroxyphenyl-1-O-glucoside, 4-O-glucosyl-3,4-dihydroxybenzyl alcohol, 3-O-feruloylquinic acid, 3,4-O-dicaffeoylquinic acid methyl ester, O-anisic acid, and coniferyl alcohol). We speculate that the Ascomycota and Basidiomycota affect the content of terpenoids and phenolic acids, resulting in color change during sweating treatment in D. asper. This study provides a foundation for analyzing the mechanism involved in the processing of Chinese medicinal materials.

Recent Advances in Search of Bioactive Secondary Metabolites from Fungi Triggered by Chemical Epigenetic Modifiers

Genomic analysis has demonstrated that many fungi possess essential gene clusters for the production of previously unobserved secondary metabolites; however, these genes are normally reduced or silenced under most conditions. These cryptic biosynthetic gene clusters have become treasures of new bioactive secondary metabolites. The induction of these biosynthetic gene clusters under stress or special conditions can improve the titers of known compounds or the production of novel compounds. Among the inducing strategies, chemical-epigenetic regulation is considered a powerful approach, and it uses small-molecule epigenetic modifiers, which mainly act as the inhibitors of DNA methyltransferase, histone deacetylase, and histone acetyltransferase, to promote changes in the structure of DNA, histones, and proteasomes and to further activate cryptic biosynthetic gene clusters for the production of a wide variety of bioactive secondary metabolites. These epigenetic modifiers mainly include 5-azacytidine, suberoylanilide hydroxamic acid, suberoyl bishydroxamic acid, sodium butyrate, and nicotinamide. This review gives an overview on the method of chemical epigenetic modifiers to trigger silent or low-expressed biosynthetic pathways to yield bioactive natural products through external cues of fungi, mainly based on the research progress in the period from 2007 to 2022. The production of about 540 fungal secondary metabolites was found to be induced or enhanced by chemical epigenetic modifiers. Some of them exhibited significant biological activities such as cytotoxic, antimicrobial, anti-inflammatory, and antioxidant activity.