Identification of cyclosporin C from Amphichorda felina using a Cryptococcus neoformans differential temperature sensitivity assay

Cyclic natural product oligomers: diversity and (bio)synthesis of macrocycles

Cyclic compounds are generally preferred over linear compounds for functional studies due to their enhanced bioavailability, stability towards metabolic degradation, and selective receptor binding. This has led to a need for effective cyclization strategies for compound synthesis and hence increased interest in macrocyclization mediated by thioesterase (TE) domains, which naturally boost the chemical diversity and bioactivities of cyclic natural products. Many non-ribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) derived natural products are assembled to form cyclodimeric compounds, with these molecules possessing diverse structures and biological activities. There is significant interest in identifying the biosynthetic pathways that produce such molecules given the challenge that cyclodimerization represents from a biosynthetic perspective. In the last decade, many groups have pursued the characterization of TE domains and have provided new insights into this biocatalytic machinery: however, the enzymes involved in formation of cyclodimeric compounds have proven far more elusive. In this review we focus on natural products that involve macrocyclization in their biosynthesis and chemical synthesis, with an emphasis on the function and biosynthetic investigation on the special family of TE domains responsible for forming cyclodimeric natural products. We also introduce additional macrocyclization catalysts, including butelase and the CT-mediated cyclization of peptides, alongside the formation of cyclodipeptides mediated by cyclodipeptide synthases (CDPS) and single-module NRPSs. Due to the interdisciplinary nature of biosynthetic research, we anticipate that this review will prove valuable to synthetic chemists, drug discovery groups, enzymologists, and the biosynthetic community in general, and inspire further efforts to identify and exploit these biocatalysts for the formation of novel bioactive molecules.

Multi-locus molecular phylogenetic analysis reveals two new species of Amphichorda (Bionectriaceae, Hypocreales)

Amphichorda has been previously accepted as a member of the Cordycipitaceae and currently it is considered a member of the Bionectriaceae. The substrates of Amphichorda were complex and varied, being mainly animal faeces. This study reports two new species of Amphichorda from Yunnan Province in south-western China. Based on the five-gene (nrSSU, nrLSU, tef-1α, rpb1 and rpb2) sequence and ITS data phylogenetic analysis, two new species, namely A.excrementa and A.kunmingensis, are proposed and a detailed description of the new species is provided. Amphichordaexcrementa and A.kunmingensis were isolated from animal faeces in the park. The morphological characteristics of two novel species and seven known species in Amphichorda are also compared.

Amphichorda monjolensis sp. nov., a new fungal species isolated from a Brazilian limestone cave, with an update on acremonium-like species in Bionectriaceae

Caves are unique environments characterized by spatial limitations, partial or total absence of direct light, and scarcity of organic carbon and nutrients. Caves are shelters for a variety of adapted animals and microorganisms such as fungi, many of which are still unknown. Amphichorda is a fungal genus belonging to the family Bionectriaceae, which includes cave-dwelling and entomopathogenic species with biotechnological applications. In this study, a new fungal species was identified using morphological and multi-locus phylogenetic analyses of the ITS, LSU, and TEF loci, in the Gruta Velha Nova limestone cave located in the Southern Espinhaço Range, Monjolos, Minas Gerais, Brazil. During the exposure of potato dextrose agar plates to the cave environment, an insect from the family Rhaphidophoridae passed by and fed on the culture medium, resulting in three fungal isolates. Phylogenetic analyses showed that these isolates formed a clade distinct from all known species, leading us to introduce a new species, Amphichorda monjolensis, which may be associated with this insect. Here, we also proposed two new combinations for species of acremonium-like fungi in the Bionectriaceae: Bulbithecium globosisporum (synonym: Acremonium globosisporum) and Hapsidospora curva (synonym: Acremonium curvum). The discovery of A. monjolensis highlights the potential of caves as shelters for new species with significant biotechnological importance.

The biosynthetic logic and enzymatic machinery of approved fungi-derived pharmaceuticals and agricultural biopesticides

Covering: 2000 to 2023The kingdom Fungi has become a remarkably valuable source of structurally complex natural products (NPs) with diverse bioactivities. Since the revolutionary discovery and application of the antibiotic penicillin from Penicillium, a number of fungi-derived NPs have been developed and approved into pharmaceuticals and pesticide agents using traditional "activity-guided" approaches. Although emerging genome mining algorithms and surrogate expression hosts have brought revolutionary approaches to NP discovery, the time and costs involved in developing these into new drugs can still be prohibitively high. Therefore, it is essential to maximize the utility of existing drugs by rational design and systematic production of new chemical structures based on these drugs by synthetic biology. To this purpose, there have been great advances in characterizing the diversified biosynthetic gene clusters associated with the well-known drugs and in understanding the biosynthesis logic mechanisms and enzymatic transformation processes involved in their production. We describe advances made in the heterogeneous reconstruction of complex NP scaffolds using fungal polyketide synthases (PKSs), non-ribosomal peptide synthetases (NRPSs), PKS/NRPS hybrids, terpenoids, and indole alkaloids and also discuss mechanistic insights into metabolic engineering, pathway reprogramming, and cell factory development. Moreover, we suggest pathways for expanding access to the fungal chemical repertoire by biosynthesis of representative family members via common platform intermediates and through the rational manipulation of natural biosynthetic machineries for drug discovery.

New Anti-Hypoxic Metabolites from Co-Culture of Marine-Derived Fungi Aspergillus carneus KMM 4638 and Amphichorda sp. KMM 4639

The KMM 4639 strain was identified as Amphichorda sp. based on two molecular genetic markers: ITS and β-tubulin regions. Chemical investigation of co-culture marine-derived fungi Amphichorda sp. KMM 4639 and Aspergillus carneus KMM 4638 led to the identification of five new quinazolinone alkaloids felicarnezolines A-E (1-5), a new highly oxygenated chromene derivative oxirapentyn M (6) and five previously reported related compounds. Their structures were established using spectroscopic methods and by comparison with related known compounds. The isolated compounds showed low cytotoxicity against human prostate and breast cancer cells but felicarnezoline B (2) protected rat cardiomyocytes H9c2 and human neuroblastoma SH-SY5Y cells against CoCl₂-induced damage.

Genome Features and AntiSMASH Analysis of an Endophytic Strain Fusarium sp. R1

Endophytic fungi are one of the most prolific sources of functional biomolecules with therapeutic potential. Besides playing an important role in serious plant diseases, Fusarium strains possess the powerful capability to produce a diverse array of bioactive secondary metabolites (SMs). In order to in-depth mine gene clusters for SM biosynthesis of the genus Fusarium, an endophytic strain Fusarium sp. R1 isolated from Rumex madaio Makino was extensively investigated by whole-genome sequencing and in-depth bioinformatic analysis, as well as antiSMASH annotation. The results displayed that strain R1 harbors a total of 51.8 Mb genome, which consists of 542 contigs with an N50 scaffold length of 3.21 Mb and 50.4% GC content. Meanwhile, 19,333 functional protein-coding genes, 338 tRNA and 111 rRNA were comprehensively predicted and highly annotated using various BLAST databases including non-redundant (Nr) protein sequence, nucleotide (Nt) sequence, Swiss-Prot, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Clusters of Orthologous Groups (COG), as well as Pathogen Host Interactions (PHI) and Carbohydrate-Active enzymes (CAZy) databases. Antibiotics and Secondary Metabolites Analysis Shell (AntiSMASH) results showed that strain R1 has 37 SM biosynthetic gene clusters (BGCs), including 17 nonribosomal peptide synthetases (NRPSs), 13 polyketide synthetases (PKSs), 3 terpene synthases (Ts), 3 hybrid NRPS + PKS and 1 hybrid indole + NRPS. These findings improve our knowledge of the molecular biology of the genus Fusarium and would promote the discovery of new bioactive SMs from strain R1 using gene mining strategies including gene knockout and heteroexpression.

Genomics-driven discovery of a new cyclodepsipeptide from the guanophilic fungus Amphichorda guana

Two potential non-ribosomal peptide synthetases (NRPSs) were identified in the genome of a guanophilic fungus Amphichorda guana by bioinformatics analysis and gene knockout experiments. Liquid chromatography coupled with mass spectrometry (LC-MS) guided isolation led to the discovery of a new cyclodepsipeptide isaridin H (1) and seven known analogs, desmethylisaridin E (2), isaridin E (3), isariin A (4), iso-isariin B (5), iso-isariin D (6), isariin E (7), and nodupetide (8). The absolute configuration of isaridin H (1) was achieved by Marfey's method. Isaridin H (1) showed significant antifungal activity against Botrytis cinerea and Alternaria solani.

Establishment of a Genetic Transformation System in Guanophilic Fungus Amphichorda guana

Fungi from unique environments exhibit special physiological characters and plenty of bioactive natural products. However, the recalcitrant genetics or poor transformation efficiencies prevent scientists from systematically studying molecular biological mechanisms and exploiting their metabolites. In this study, we targeted a guanophilic fungus Amphichorda guana LC5815 and developed a genetic transformation system. We firstly established an efficient protoplast preparing method by conditional optimization of sporulation and protoplast regeneration. The regeneration rate of the protoplast is up to about 34.6% with 0.8 M sucrose as the osmotic pressure stabilizer. To develop the genetic transformation, we used the polyethylene glycol-mediated protoplast transformation, and the testing gene AG04914 encoding a major facilitator superfamily transporter was deleted in strain LC5815, which proves the feasibility of this genetic manipulation system. Furthermore, a uridine/uracil auxotrophic strain was created by using a positive screening protocol with 5-fluoroorotic acid as a selective reagent. Finally, the genetic transformation system was successfully established in the guanophilic fungus strain LC5815, which lays the foundation for the molecular genetics research and will facilitate the exploitation of bioactive secondary metabolites in fungi.

Purification and biochemical characterization of an extracellular fructosyltransferase enzyme from Aspergillus niger sp. XOBP48: implication in fructooligosaccharide production

An extracellular fructosyltransferase (Ftase) enzyme with a molar mass of ≈70 kDa from a newly isolated indigenous coprophilous fungus Aspergillus niger sp. XOBP48 is purified to homogeneity and characterized in this study. The enzyme was purified to 4.66-fold with a total yield of 15.53% and specific activity of 1219.17 U mg^-1 of protein after a three-step procedure involving (NH₄)₂SO₄ fractionation, dialysis and anion exchange chromatography. Ftase showed optimum activity at pH 6.0 and temperature 50 °C. Ftase exhibited over 80% residual activity at pH range of 4.0-10.0 and ≈90% residual activity at temperature range of 40-60 °C for 6 h. Metal ion inhibitors Hg²⁺ and Ag⁺ significantly inhibited Ftase activity at 1 mmol concentration. Ftase showed K _m, v _max and k _cat values of 79.51 mmol, 45.04 µmol min^-1 and 31.5 min^-1, respectively, with a catalytic efficiency (k _cat/K _m) of 396 µmol^-1 min^-1 for the substrate sucrose. HPLC-RI experiments identified the end products of fructosyltransferase activity as monomeric glucose, 1-kestose (GF₂), and 1,1-kestotetraose (GF₃). This study evaluates the feasibility of using this purified extracellular Ftase for the enzymatic synthesis of biofunctional fructooligosaccharides.

Sphaerostilbellins, New Antimicrobial Aminolipopeptide Peptaibiotics from Sphaerostilbella toxica

Sphaerostilbella toxica is a mycoparasitic fungus that can be found parasitizing wood-decay basidiomycetes in the southern USA. Organic solvent extracts of fermented strains of S. toxica exhibited potent antimicrobial activity, including potent growth inhibition of human pathogenic yeasts Candida albicans and Cryptococcus neoformans, the respiratory pathogenic fungus Aspergillus fumigatus, and the Gram-positive bacterium Staphylococcus aureus. Bioassay-guided separations led to the purification and structure elucidation of new peptaibiotics designated as sphaerostilbellins A and B. Their structures were established mainly by analysis of NMR and HRMS data, verification of amino acid composition by Marfey's method, and by comparison with published data of known compounds. They incorporate intriguing structural features, including an N-terminal 2-methyl-3-oxo-tetradecanoyl (MOTDA) residue and a C-terminal putrescine residue. The minimal inhibitory concentrations for sphaerostilbellins A and B were measured as 2 μM each for C. neoformans, 1 μM each for A. fumigatus, and 4 and 2 μM, respectively, for C. albicans. Murine macrophage cells were unaffected at these concentrations.

Identification of the Antifungal Metabolite Chaetoglobosin P From Discosia rubi Using a Cryptococcus neoformans Inhibition Assay: Insights Into Mode of Action and Biosynthesis

Cryptococcus neoformans is an important human pathogen with limited options for treatments. We have interrogated extracts from fungal fermentations to find Cryptococcus-inhibiting natural products using assays for growth inhibition, differential thermosensitivity, and synergy with existing antifungal drugs. Extracts from fermentations of strains of Discosia rubi from eastern Texas showed anticryptococcal bioactivity with preferential activity in agar zone of inhibition assays against C. neoformans at 37°C versus 25°C. Assay-guided fractionation led to the purification and identification of chaetoglobosin P as the active component of these extracts. Genome sequencing of these strains revealed a biosynthetic gene cluster consistent with chaetoglobosin biosynthesis and β-methylation of the tryptophan residue. Proximity of genes of the actin-binding protein twinfilin-1 to the chaetoglobosin P and K gene clusters suggested a possible self-resistance mechanism involving twinfilin-1 which is consistent with the predicted mechanism of action involving interference with the polymerization of the capping process of filamentous actin. A C. neoformans mutant lacking twinfilin-1 was hypersensitive to chaetoglobosin P. Chaetoglobosins also potentiated the effects of amphotericin B and caspofungin on C. neoformans.

Fusarium: a treasure trove of bioactive secondary metabolites

Covering up to December 2019Fusarium, one of the most common fungal genera, has received considerable attention because of its biosynthetic exuberance, the result of many unique gene clusters involved in the production of secondary metabolites. This review provides the first comprehensive analysis of the secondary metabolites unique to the genus Fusarium, describing their occurrence, bioactivity, and genome features.

Cyclodepsipeptide Biosynthesis in Hypocreales Fungi and Sequence Divergence of The

Fungi from the Hypocreales order synthesize a range of toxic non-ribosomal cyclic peptides with antimicrobial, insecticidal and cytotoxic activities. Entomopathogenic Beauveria, Isaria and Cordyceps as well as phytopathogenic Fusarium spp. are known producers of beauvericins (BEAs), beauvenniatins (BEAEs) or enniatins (ENNs). The compounds are synthesized by beauvericin/enniatin synthase (BEAS/ESYN1), which shows significant sequence divergence among Hypocreales members. We investigated ENN, BEA and BEAE production among entomopathogenic (Beauveria, Cordyceps, Isaria) and phytopathogenic (Fusarium) fungi; BEA and ENNs were quantified using an LC-MS/MS method. Phylogenetic analysis of partial sequences of putative BEAS/ESYN1 amplicons was also made. Nineteen fungal strains were identified based on sequence analysis of amplified ITS and tef-1α regions. BEA was produced by all investigated fungi, with F. proliferatum and F. concentricum being the most efficient producers. ENNs were synthesized mostly by F. acuminatum, F. avenaceum and C. confragosa. The phylogeny reconstruction suggests that ancestral BEA biosynthesis independently diverged into biosynthesis of other compounds. The divergent positioning of three Fusarium isolates raises the possibility of parallel acquisition of cyclic depsipeptide synthases in ancient complexes within Fusarium genus. Different fungi have independently evolved NRPS genes involved in depsipeptide biosynthesis, with functional adaptation towards biosynthesis of overlapping yet diversified metabolite profiles.

Wortmannin and Wortmannine Analogues from an Undescribed Niesslia sp

In the course of our studies of coprophilous fungi as sources of antifungal agents, a strain of an undescribed species in the genus Niesslia (TTI-0426) was isolated from horse dung collected in Texas. An extract from fermentation cultures of this strain afforded two new antifungal wortmannin derivatives, wortmannins C and D (1 and 2), as well as four additional new related compounds, wortmannines B1-B4 (3-6), containing an unusual ring system. The structures of these metabolites were established mainly by analysis of HRESIMS and 2D NMR data. Relative configurations were assigned using NOESY data, and the structure assignments were supported by NMR comparison with similar compounds. Wortmannins C and D showed activity against Cryptococcus neoformans and Candida albicans in disk assays, but low MIC potency observed for 1 was suggested to be due in part to efflux processes on the basis of assay results for a Schizosaccharomyces pombe efflux mutant in comparison to wild-type.