Basidiomycete non-reducing polyketide synthases function independently of SAT domains

Mechanism of Unexpected In-Trans Post-PKS Polyketide Reduction in Cochliodone Biosynthesis

Cochliodone A, a dimeric azaphilone-type compound, is the major product and one of many natural products produced by Chaetomium globosum, a filamentous fungus. Cochliodone A exerts antimalarial and antimycobacterial activities in addition to being cytotoxic against KB, BC1, and NCI-H187 human cancer cell lines. The potential of cochliodone A and its analogues as effective therapeutics against cancer, tuberculosis, and malaria, together with its complex dimeric chemical structure, are reasons enough for continued investigation. Here, sequence analyses of the open reading frames found in the previously identified cochliodone A biosynthetic gene cluster, together with a series of gene-knockout experiments, heterologous in vivo production of pathway intermediates in Aspergillus nidulans and in vitro assays of key enzymes allowed us to propose a biosynthetic pathway and detailed mechanisms leading to the production of cochliodones. In addition, we identified that the elimination of the dimerizing multicopper oxidase CcdJ from the ccd pathway led to pathway crosstalk between the ccd pathway and an unrelated benzaldehyde-producing biosynthetic pathway formation to generate new secondary metabolites. Most interestingly, however, through the in vitro study, we established that the sequential actions of an acetyltransferase, an acetate lyase, and an enoyl reductase achieve a full reduction of the unsaturated backbone of the polyketide (PKs) product generated by the nonreducing polyketide synthase (PKS) CcdL. This alternative mode of reducing a polyketomethylene chain could be engineered further to develop a facile chemoenzymatic modification of the polyketide backbone saturation level postpolyketide synthesis in trans.

Discovery of Cortinarius O-methyltransferases for the heterologous production of dermolutein and physcion

BACKGROUND

Anthraquinones in the emodin family are produced by bacteria, fungi, and plants. They display various biological activities exploited, e.g., for crop protection, and may also be utilized as sustainable, bio-based colorants for the textile, paints, electronics, and cosmetic industries. Anthraquinone pigments from Cortinarius mushrooms have been used for artisan dyeing because they are stable, colorfast, and compatible with various dyeing methods. However, their chemical synthesis is complex and uneconomical, and harvesting wild mushrooms from forests in commercial quantities is not feasible.

RESULTS

Here, we use genomics, transcriptomics, and synthetic biology to uncover the biosynthesis of the anthraquinone scaffold compounds emodin and endocrocin, and their methylation to the yellow pigments physcion and dermolutein in Cortinarius semisanguineus and C. sp. KIS-3. Both the nonreducing polyketide synthases (nrPKSs), and the regiospecific, fastidious O-methyltransferases (OMTs) are non-orthologous to their Ascomycete counterparts, suggesting a parallel evolutionary origin for the pathway in Basidiomycetes. The genes for the nrPKS and the OMTs are not all clustered in Cortinarius, revealing metabolic crosstalk among paralogous nrPKS biosynthetic gene clusters.

CONCLUSIONS

Heterologous biosynthesis of physcion and dermolutein in Saccharomyces cerevisiae opens the way to produce specific Cortinarius anthraquinones, and to modify these scaffolds to tune their chemistry towards their various applications.

Haplotype-Phased Chromosome-Level Genome Assembly of Cryptoporus qinlingensis, a Typical Traditional Chinese Medicine Fungus

This study presents the first comprehensive genomic analysis of Cryptoporus qinlingensis, a classical folk medicine and newly identified macrofungus from the Qinling Mountains. Utilizing advanced sequencing technologies, including PacBio HiFi and Hi-C, we achieved a high-quality chromosome-level genome assembly. The genome, sized at 39.1 Mb, exhibits a heterozygosity of 0.21% and contains 21.2% repetitive sequences. Phylogenetic analysis revealed a recent divergence of C. qinlingensis from Dichomitus squalens approximately 212.26 million years ago (MYA), highlighting the rapid diversification within the Polyporaceae family. Comparative genomic studies indicate significant gene family contraction in C. qinlingensis, suggesting evolutionary adaptations. The identification of a tetrapolar mating system, along with the analysis of CAZymes and P450 genes, underscores the genomic complexity and ecological adaptability of this species. Furthermore, the discovery of 30 biosynthetic gene clusters (BGCs) related to secondary metabolites, including polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS), and terpene synthesis enzymes, opens new avenues for exploring bioactive compounds with potential medicinal applications. This research not only enriches our understanding of the Cryptoporus genus but also provides a valuable foundation for future studies aiming to harness the therapeutic potential of C. qinlingensis and to further explore its ecological and evolutionary significance.

Regioselective Oxidative Phenol Coupling by a Mushroom Unspecific Peroxygenase

Bioactive dimeric (pre-)anthraquinones are ubiquitous in nature and are found in bacteria, fungi, insects, and plants. Their biosynthesis via oxidative phenol coupling (OPC) is catalyzed by cytochrome P450 enzymes, peroxidases, or laccases. While the biocatalysis of OPC in molds (Ascomycota) is well-known, the respective enzymes in mushroom-forming fungi (Basidiomycota) are unknown. Here, we report on the biosynthesis of the atropisomers phlegmacin A1 and B1 of the mushroom Cortinarius odorifer. The biosynthesis of these unsymmetrically 7,10'-homo-coupled dihydroanthracenones was heterologously reconstituted in the mold Aspergillus niger. Methylation of the parental monomer atrochrysone to its 6-O-methyl ether torosachrysone by the O-methyltransferase CoOMT1 precedes the regioselective homocoupling to phlegmacin, catalyzed by the enzyme CoUPO1 annotated as an "unspecific peroxygenase" (UPO). Our results reveal an unprecedented UPO reaction, thereby expanding the biocatalytic portfolio of oxidative phenol coupling beyond the commonly reported enzymes. The results show that Basidiomycota use peroxygenases to selectively couple aryls independently of and convergently to any other group of organisms, emphasizing the central role of OPC in natural processes.

From the forest floor to the lab: Insights into the diversity and complexity of mushroom polyketide synthases

Mushroom-forming fungi exhibit a distinctive ecology, which is unsurprisingly also reflected in unique and divergent biosynthetic pathways. We review this phenomenon through the lens of the polyketide metabolism, where mushrooms often deviate from established principles and challenge conventional paradigms. This is evident not only by non-canonical enzyme architectures and functions but also by their propensity for multi-product synthases rather than single-product pathways. Nevertheless, mushrooms also feature many polyketides familiar from plants, bacteria, and fungi of their sister division Ascomycota, which, however, are the result of an independent evolution. In this regard, the captivating biosynthetic pathways of mushrooms might even help us understand the biological pressures that led to the simultaneous production of the same natural products (via convergent evolution, co-evolution, and/or metaevolution) and thus address the question of their raison d'être.

Activation of cryptic biosynthetic gene clusters by fungal artificial chromosomes to produce novel secondary metabolites

In 2017, we reported the discovery of Berkeleylactone A (BPLA), a novel, potent antibiotic produced exclusively in co-culture by two extremophilic fungi, Penicillium fuscum and P. camembertii/clavigerum, which were isolated from the Berkeley Pit, an acid mine waste lake, in Butte, Montana. Neither fungus synthesized BPLA when grown in axenic culture. Recent studies suggest that secondary metabolites (SMs) are often synthesized by enzymes encoded by co-localized genes that form "biosynthetic gene clusters" (BGCs), which might remain silent (inactive) under various fermentation conditions. Fungi may also harbor cryptic BGCs that are not associated with previously characterized molecules. We turned to the tools of Fungal Artificial Chromosomes (FAC)-Next-Gen-Sequencing (NGS) to understand how co-culture activated cryptic biosynthesis of BPLA and several related berkeleylactones and to further investigate the true biosynthetic potential of these two fungi. FAC-NGS enables the capture of BGCs as individual FACs for heterologous expression in a modified strain of Aspergillus nidulans (heterologous host, FAC-AnHH). With this methodology, we created ten BGC-FACs that yielded fourteen different SMs, including strobilurin, which was previously isolated exclusively from basidiomycetes. Eleven of these compounds were not detected in the extracts of the FAC-AnHH. Of this discrete set, only the novel compound citreohybriddional had been isolated from either Penicillium sp. before and only at very low yield. We propose that through heterologous expression, FACs activated these silent BGCs, resulting in the synthesis of new natural products (NPs) with yields as high as 50%-60% of the crude organic extracts.