Efficient gene editing in the slow-growing, non-sporulating, melanized, endophytic fungus Berkleasmium sp. Dzf12 using a CRISPR/Cas9 system.

The endophytic fungus Berkleasmium sp. Dzf12 that was isolated from Dioscorea zingiberensis, is a proficient producer of palmarumycins, which are intriguing polyketides of the spirobisnaphthalene class. These compounds displayed a wide range of bioactivities, including antibacterial, antifungal, and cytotoxic activities. However, conventional genetic manipulation of Berkleasmium sp. Dzf12 is difficult and inefficient, partially due to the slow-growing, non-sporulating, and highly pigmented behavior of this fungus. Herein, we developed a CRISPR/Cas9 system suitable for gene editing in Berkleasmium sp. Dzf12. The protoplast preparation was optimized, and the expression of Cas9 in Berkleasmium sp. Dzf12 was validated. To assess the gene disruption efficiency, a putative 1, 3, 6, 8-tetrahydroxynaphthalene synthase encoding gene, bdpks, involved in 1,8-dihydroxynaphthalene (DHN)-melanin biosynthesis, was selected as the target for gene disruption. Various endogenous sgRNA promoters were tested, and different strategies to express sgRNA were compared, resulting in the construction of an optimal system using the U6 snRNA-1 promoter as the sgRNA promoter. Successful disruption of bdpks led to a complete abolishment of the production of spirobisnaphthalenes and melanin. This work establishes a useful gene targeting disruption system for exploration of gene functions in Berkleasmium sp. Dzf12, and also provides an example for developing an efficient CRISPR/Cas9 system to the fungi that are difficult to manipulate using conventional genetic tools.

Elucidation of Palmarumycin Spirobisnaphthalene Biosynthesis Reveals a Set of Previously Unrecognized Oxidases and Reductases.

Spirobisnaphthalenes (SBNs) are a class of highly oxygenated, fungal bisnaphthalenes containing a unique spiroketal bridge, that displayed diverse bioactivities. Among the reported SBNs, palmarumycins are the major type, which are precursors for the other type of SBNs structurally. However, the biosynthesis of SBNs is unclear. In this study, we elucidated the biosynthesis of palmarumycins, using gene disruption, heterologous expression, and substrate feeding experiments. The biosynthetic gene cluster for palmarumycins was identified to be distant from the polyketide synthase gene cluster, and included two cytochrome P450s (PalA and PalB), and one short chain dehydrogenase/reductase (PalC) encoding genes as key structural genes. PalA is an unusual, multifunctional P450 that catalyzes the oxidative dimerization of 1,8-dihydroxynaphthalene to generate the spiroketal linkage and 2,3-epoxy group. Chemical synthesis of key intermediate and in vitro biochemical assays proved that the oxidative dimerization proceeded via a binaphthyl ether. PalB installs the C-5 hydroxy group, widely found in SBNs. PalC catalyzes 1-keto reduction, the reverse 1-dehydrogenation, and 2,3-epoxide reduction. Moreover, an FAD-dependent oxidoreductase, encoded by palD, which locates outside the cluster, functions as a 1-dehydrogenase. These results provided the first genetic and biochemical evidence for the biosynthesis of palmarumycin SBNs.

A Genome-Wide Comparison of Rice False Smut Fungus Villosiclava virens Albino Strain LN02 Reveals the Genetic Diversity of Secondary Metabolites and the Cause of Albinism.

Rice false smut (RFS) caused by Villosiclava virens (anamorph: Ustilaginoidea virens) has become one of the most destructive fungal diseases to decrease the yield and quality of rice grains. An albino strain LN02 was isolated from the white RFS balls collected in the Liaoning Province of China in 2019. The strain LN02 was considered as a natural albino mutant of V. virens by analyzing its phenotypes, internal transcribed spacer (ITS) conserved sequence, and biosynthesis gene clusters (BGCs) for secondary metabolites. The total assembled genome of strain LN02 was 38.81 Mb, which was comprised of seven nuclear chromosomes and one mitochondrial genome with an N50 value of 6,326,845 bp and 9339 protein-encoding genes. In addition, the genome of strain LN02 encoded 19 gene clusters for biosynthesis of secondary metabolites mainly including polyketides, terpenoids and non-ribosomal peptides (NRPs). Four sorbicillinoid metabolites were isolated from the cultures of strain LN02. It was found that the polyketide synthase (PKS)-encoding gene uspks1 for ustilaginoidin biosynthesis in strain LN02 was inactivated due to the deletion of four bases in the promoter sequence of uvpks1. The normal uvpks1 complementary mutant of strain LN02 could restore the ability to synthesize ustilaginoidins. It demonstrated that deficiency of ustilaginoidin biosynthesis is the cause of albinism for RFS albino strain LN02, and V. virens should be a non-melanin-producing fungus. This study further confirmed strain LN02 as a white phenotype mutant of V. virens. The albino strain LN02 will have a great potential in the development and application of secondary metabolites. The physiological and ecological functions of ustilaginoidins in RFS fungus are needed for further investigation.

Elucidation of ustilaginoidin biosynthesis reveals a previously unrecognised class of ene-reductases.

Ustilaginoidins are a type of mycotoxin featuring a dimeric naphtho-γ-pyrone skeleton, produced by the rice false smut pathogen Ustilaginoidea virens. Here we used gene disruption, heterologous expression in Aspergillus oryzae, feeding experiments, and in vitro experiments to fully elucidate the biosynthesis of ustilaginoidins. A new route to dimeric 2,3-unsaturated naphtho-γ-pyrones via dimerization of YWA1 (and 3-methyl YWA1) followed by dehydration was discovered. Intriguingly, the reduction of the 2,3-double bond of the pyrenone ring was catalyzed by a phospholipid methyltransferase-like enzyme (UsgR). The reductase was specific for reduction of monomeric, linear naphtho-γ-pyrenones, but not for the dimers. Atroposelective coupling of various monomers by the laccase (UsgL) led to diverse ustilaginoidins. Moreover, 3-epimerism of the 3-methyl-2,3-dihydro-naphtho-γ-pyrones adds additional complexity to the biosynthesis.

Chromone and isocoumarin derivatives from the endophytic fungus Xylomelasma sp. Samif07, and their antibacterial and antioxidant activities.

Five chromone derivatives, including 2,6-dimethyl-5-methoxyl-7-hydroxylchromone (1), 6-hydroxymethyleugenin (2), 6-methoxymethyleugenin (3), chaetoquadrin D (4), and isoeugenitol (5), and three isocoumarin congeners, namely diaporthin (6), 8-hydroxy-6-methoxy-3-methylisocoumarin (7), and 6-methoxymellein (8), were isolated from the culture of the endophytic fungus Xylomelasma sp. Samif07 derived from the medicinal plant Salvia miltiorrhiza Bunge. Among them, compound 1 was a new natural product. Their structures were determined by spectroscopic methods and comparison with the literature. The isolated compounds were evaluated for their antibacterial and antioxidant activities. Compound 5 showed notable antitubercular activity against Mycobacterium tuberculosis with MIC value of 10.31 µg/mL, while compounds 1-3, and 5-7 displayed inhibitory activities against the other bacteria with MIC range of 25 ∼ 100 µg/mL. Meanwhile, compound 6 showed potent hydroxyl radical-scavenging activity with EC50 value of 15.1 µg/mL, while compounds 5-7 showed certain ferric reducing ability.

Ustilaginoidin M1, a new bis-naphtho-γ-pyrone from the fungus Villosiclava virens.

Ustilaginoidin M1 (1), a novel bis-naphtho-γ-pyrone, was isolated from the cultures of the fungus Villosiclava virens which was the pathogen of rice false smut disease. Its structure was elucidated by spectroscopic analysis and by comparison of its physical and spectroscopic data with the literature. Compound 1 was tested for its cytotoxicity against five human cancer cell lines.

New chlamydosporol derivatives from the endophytic fungus Pleosporales sp. Sigrf05 and their cytotoxic and antimicrobial activities.

Five new chlamydosporol derivatives, named pleospyrones A-E (1-5), together with one known congener (6), were isolated from the culture of the endophytic fungus Pleosporales sp. Sigrf05, obtained from the medicinal plant Siraitia grosvenorii. The structures of the new compounds were elucidated mainly by analysis of the HRESIMS, and (1D, 2D) NMR data, while ECD and optical rotation calculations were used to assign the absolute configurations. The plausible biosynthetic pathway of these compounds were proposed. The isolated compounds were evaluated for their cytotoxicity, antifungal and antibacterial activities. Compounds 1, and 4-6 were cytotoxic against the tested cancer cells with IC50 values of 1.26~47.5 µM. Compounds 1-3 showed moderate antifungal activities against Magnaporthe oryzae, while compound 5 displayed weak antibacterial activity.

Rhizovagine A, an unusual dibenzo-α-pyrone alkaloid from the endophytic fungus Rhizopycnis vagum Nitaf22.

Rhizovagine A (1), a novel dibenzo-α-pyrone alkaloid with an unprecedented 5/5/6/6/6 fused pentacyclic skeleton, was isolated from the endophytic fungus Rhizopycnis vagum Nitaf22. The structure was elucidated by comprehensive spectroscopic analysis, in combination with quantum chemical 13C NMR and electronic circular dichroism (ECD) calculations for configurational assignment. A plausible biosynthetic pathway for 1 was proposed. Compound 1 displayed acetylcholinesterase inhibitory activity.

Rice Secondary Metabolites: Structures, Roles, Biosynthesis, and Metabolic Regulation.

Rice (Oryza sativa L.) is an important food crop providing energy and nutrients for more than half of the world population. It produces vast amounts of secondary metabolites. At least 276 secondary metabolites from rice have been identified in the past 50 years. They mainly include phenolic acids, flavonoids, terpenoids, steroids, alkaloids, and their derivatives. These metabolites exhibit many physiological functions, such as regulatory effects on rice growth and development, disease-resistance promotion, anti-insect activity, and allelopathic effects, as well as various kinds of biological activities such as antimicrobial, antioxidant, cytotoxic, and anti-inflammatory properties. This review focuses on our knowledge of the structures, biological functions and activities, biosynthesis, and metabolic regulation of rice secondary metabolites. Some considerations about cheminformatics, metabolomics, genetic transformation, production, and applications related to the secondary metabolites from rice are also discussed.