Genome Mining Reveals the Biosynthesis of Sativene and Its Oxidative Conversion to seco-Sativene

Bioinformatics assisted construction of the link between biosynthetic gene clusters and secondary metabolites in fungi

Fungal secondary metabolites are considered as important resources for drug discovery. Despite various methods being employed to facilitate the discovery of new fungal secondary metabolites, the trend of identifying novel secondary metabolites from fungi is inevitably slowing down. Under laboratory conditions, the majority of biosynthetic gene clusters, which store information for secondary metabolites, remain inactive. Therefore, establishing the link between biosynthetic gene clusters and secondary metabolites would contribute to understanding the genetic logic underlying secondary metabolite biosynthesis and alleviating the current challenges in discovering novel natural products. Bioinformatics methods have garnered significant attention due to their powerful capabilities in data mining and analysis, playing a crucial role in various aspects. Thus, we have summarized successful cases since 2016 in which bioinformatics methods were utilized to establish the link between fungal biosynthetic gene clusters and secondary metabolites, focusing on their biosynthetic gene clusters and associated secondary metabolites, with the goal of aiding the field of natural product discovery.

New sesquiterpenoids with anti-inflammatory effects from phytopathogenic fungus Bipolaris sorokiniana 11134

Sesquiterpenoids represent a structurally diverse class of natural products widely recognized for their ecological significance and pharmacological potential, including antimicrobial, anti-inflammatory, and anticancer properties. As part of our efforts to explore bioactive secondary metabolites from phytopathogenic fungi, we conducted a molecular networking-based analysis of Bipolaris sorokiniana isolate BS11134, which was fermented on a rice medium. This analysis led to the identification of three new seco-sativene-type sesquiterpenoids (1-3) and seven known analogues (4-10), with the NMR data of compound 4 being reported for the first time. The structures of these compounds were elucidated using HR-ESI-MS and extensive spectroscopic data analysis. Notably, compound 9 significantly inhibited nitrous oxide expression in lipopolysaccharide (LPS)-treated RAW264.7 cells in vitro (inhibition rate: 84.7 ± 1.7% at 10 μM), while compound 1 (10 μM) showed a weak inhibitory effect (inhibition rate = 28.0 ± 2.4%). Additionally, we proposed a biosynthetic pathway for these compounds. This study not only expands the chemical space of the helminthoporene class of molecules but also underscores the untapped potential of phytopathogenic fungi as promising sources of structurally unique and biologically active natural products.

Genome Mining and Biosynthesis of Fungal Africane-Type Sesquiterpenes

Africane-type sesquiterpenes are a growing family of natural products featuring a stereochemically complex 5/7/3 tricyclic skeleton, and their biosynthesis has not been well-investigated in fungi. Here, (1) an africanol (1) sesquiterpene cyclase was discovered by genome mining; (2) two cytochrome P450s were identified for conversion of compound 1 to ophioceric acid (3) via formation of α,β-unsaturated ketone cyclopentane and a C14-carboxyl group; and (3) compound 3 is a phytotoxin that inhibits root growth of Arabidopsis thaliana.

Innovative approaches in the discovery of terpenoid natural products

As a class of natural compounds ubiquitous in nature, diverse terpenoids exhibit a broad spectrum of applications in human endeavors. The efficient discovery of novel terpenoids and the establishment of a terpene library for broad utilization represent pressing challenges in terpenoid natural product research. Various microbial platforms offer abundant precursors for terpene biosynthesis from diverse sources. Leveraging artificial intelligence for enzyme function prediction and screening can facilitate the identification of terpenoid synthesis components with innovative mechanisms. Automated high-throughput bio-foundry workstations can expedite the construction of terpenoid libraries, providing substantial time and labor savings. The integration of multiple strategies promises to yield substantial advancements in the exploration of valuable terpenoids.

Biosynthesis of (-)-Vinigrol

(-)-Vinigrol is one of the most complex and challenging molecules in total synthesis; however, the parallel biosynthetic strategy employed by nature for the synthesis of this compound has not yet been identified. In this study, we identified a minimal gene cluster encoding a diterpene cyclase (VniA) and a cytochrome P450 (VniB) which enables the synthesis of (-)-vinigrol through three steps. VniA first cyclizes geranylgeranyl diphosphate to generate an unusual vinigrol-type diterpene skeleton, and then VniB catalyzes the allylic C(sp3)-H iterative oxidation. Further genome mining investigation provides new fungal sources for this rare and valuable vinigrol-type diterpene skeleton.

Sativene-Related Sesquiterpenoids with Phytotoxic and Plant-Promoting Activities from the Plant Pathogenic Fungus Bipolaris sorokiniana Based on a Molecular Networking Strategy

Sativene-related sesquiterpenoids including seco-sativene analogs are a large member of fungal secondary metabolites with phytotoxic and growth-promoting effects on different plants. In this report, a series of sativene-related sesquiterpenoids with diverse carbon skeletons (1-9, sativene/isosativene/seco-sativene/cyclosativene/seco-isosativene ring systems) were isolated from the plant pathogenic fungus Bipolaris sorokiniana based on a molecular networking strategy. The undescribed structures were elucidated based on NMR spectra, X-ray diffraction analysis, chemical derivation, and calculated electronic circular dichroism calculations. Bipolaric acid (1) has a bicyclo[3.2.1] nonane skeleton (seco-sativene), bipolarone (2) is a unique cage-like cyclosativene sesquiterpenoid first isolated from fungi, and bipolariols A (3) and B (4) contain a novel octahydro-1,4-ethano isobenzofuran ring system (seco-isosativene). The possible biosynthetic pathways of these sesquiterpenoids (1-9) were proposed based on their structural features. Drechslerine B (8) exhibited phytotoxic activities to green foxtails, and compounds 5-7 and 9 showed growth-promoting effects with varying degrees on seedling growth of Arabidopsis thaliana.

Identifying sesterterpenoids via feature-based molecular networking and small-scale fermentation

Terpenoids are known for their diverse structures and broad bioactivities with significant potential in pharmaceutical applications. However, natural products with low yields are usually ignored in traditional chemical analysis. Feature-based molecular networking (FBMN) was developed recently to cluster compounds with similar skeletons, which can highlight trace amounts of unknown compounds. Fusoxypene A is a sesterterpene synthesized by Fusarium oxysporum fusoxypene synthase (FoFS) with a unique 5/6/7/3/5 ring system. In this study, the FoFS-containing biosynthetic gene cluster was identified from F. oxysporum FO14005, and an efficient FBMN-based strategy was established to characterize four new sesterterpenoids, fusoxyordienoid A-D (1-4), based on a small-scale fermentation strategy. A cytochrome P450 monooxygenase, FusB, was found to be involved in the functionalization of fusoxypene A at C-17 and C-24 and responsible for the hydroxylation of fusoxyordienoid A at C-1 and C-8. This study highlights the potential of FBMN as a powerful tool for the discovery and characterization of natural compounds with low abundance. KEY POINTS: Combined small-scale fermentation and FBMN for rapid discovery of fusoxyordienoids Characterization of four new fusoxyordienoids with 5/6/7/3/5 ring system Biosynthetic pathway elucidation via tandem expression and substrate feeding.

Discovery of a polyketide carboxylate phytotoxin from a polyketide glycoside hybrid by β-glucosidase mediated ester bond hydrolysis

Fungal phytotoxins cause significant harm to agricultural production or lead to plant diseases. Discovering new phytotoxins, dissecting their formation mechanism and understanding their action mode are important for controlling the harmful effects of fungal phytopathogens. In this study, a long-term unsolved cluster (polyketide synthase 16, PKS16 cluster) from Fusarium species was thoroughly investigated and a series of new metabolites including both complex α-pyrone-polyketide glycosides and simple polyketide carboxylates were identified from F. proliferatum. The whole pathway reveals an unusual assembly and inactivation process for phytotoxin biosynthesis, with key points as follows: (1) a flavin dependent monooxygenase catalyzes Baeyer-Villiger oxidation on the linear polyketide side chain of α-pyrone-polyketide glycoside 8 to form ester bond compound 1; (2) a β-glucosidase unexpectedly mediates the ester bond hydrolysis of 1 to generate polyketide carboxylate phytotoxin 2; (3) oxidation occurring on the terminal inert carbons of 2 by intracellular oxidase(s) eliminates its phytotoxicity. Our work identifies the chemical basis of the PKS16 cluster in phytotoxicity, shows that polyketide carboxylate is a new structural type of phytotoxin in Fusarium and importantly uncovers a rare ester bond hydrolysis function of β-glucosidase family enzymes.

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