Agrocybe aegerita Serves As a Gateway for Identifying Sesquiterpene Biosynthetic Enzymes in Higher Fungi

Integrative Transcriptome and Metabolome Analysis Reveals Candidate Genes Related to Terpenoid Synthesis in Amylostereum areolatum (Russulales: Amylostereaceae)

Amylostereum areolatum (Chaillet ex Fr.) Boidin (Russulales: Amylostereaceae) is a symbiotic fungus of Sirex noctilio Fabricius that has ecological significance. Terpenoids are key mediators in fungal-insect interactions, yet the biosynthetic mechanisms of terpenoids in this species remain unclear. Under nutritional conditions that mimic natural growth, A. areolatum was sampled during the lag phase (day 7), exponential phase (day 14), and stationary phase (day 21). Metabolome (solid-phase microextraction (SPME) combined with gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS)) and transcriptome (Illumina NovaSeq) profiles were integrated to investigate terpenoid-gene correlations. This analysis identified 103 terpenoids in A. areolatum, substantially expanding the known repertoire of terpenoid compounds in this species. Total terpenoid abundance progressively increased across three developmental stages, with triterpenoids and sesquiterpenoids demonstrating the highest diversity and abundance levels. Transcriptomic profiling (61.66 Gb clean data) revealed 26 terpenoid biosynthesis-associated genes, establishing a comprehensive transcriptional framework for fungal terpenoid metabolism. Among 11 differentially expressed genes (DEGs) (|log2Fold Change| ≥ 1, adjusted p < 0.05), HMGS1, HMGR2, and AaTPS1-3 emerged as key regulators potentially governing terpenoid biosynthesis. These findings provide foundational insights into the molecular mechanisms underlying terpenoid production in A. areolatum and related basidiomycetes.

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.

Cloning and functional characterization of sesquiterpene synthase genes from Inonotus obliquus using a Saccharomyces cerevisiae expression system

Inonotus obliquus (Chaga mushroom) is a large medicinal and edible fungus that contains a wealth of bioactive terpenoids. However, the detection of certain low-abundance sesquiterpenoids remains a challenge due to limitations in extraction and analytical techniques. Furthermore, the synthase genes responsible for the biosynthesis of the identified terpenoids have not yet been clearly elucidated. To address this, our study combined transcriptome mining with yeast heterologous expression to investigate the synthase genes involved in sesquiterpenoid production in I. obliquus. We successfully identified eight sesquiterpene synthase genes and one farnesyltransferase. Among these, only cis-β-farnesene, synthesized by IoTPS2, had been previously detected before in the sclerotium of I. obliquus, while the other nine sesquiterpenoids-including neoisolongifolene-8-ol, β-longipinene, vetiselinenol, isolongifolene, 7,8-dehydro-8a-hydroxy-, 4a,8b,10b,11a-tetramethylbicyclo[6.3.0]undec-1-en-5-one, 6,11-oxido-acor-4-ene, β-maaliene, neointermedeol, and longifolenaldehyde-were discovered for the first time. This research provides a critical scientific foundation for expanding the known repertoire of sesquiterpenoids and their corresponding synthase genes in I. obliquus.

Unravelling the aromatic symphony: redirecting bifunctional mushroom synthases towards linalool monofunctionality

Enzymes are the cornerstone of biocatalysis, biosynthesis and synthetic biology. However, their applicability is often limited by low substrate selectivity. A prime example is the bifunctional linalool/nerolidol synthase (LNS) that can use both geranyl diphosphate (GPP) and farnesyl diphosphate (FPP) to produce linalool and nerolidol, respectively. This bifunctionality can lead to undesired byproducts in synthetic biology applications. To enhance enzyme specificity and create monofunctional linalool synthases, we modified amino acids in the loop between helices C and D of four bifunctional mushroom LNSs. Through these modifications, we successfully shifted the substrate preference of two LNSs (ApLNS from Agrocybe pediades and HsLNS from Hypholoma sublateritium) from FPP towards GPP. Although complete monofunctionality was not achieved, we significantly increased linalool yield by 13 times while minimizing nerolidol production to 1% of the wildtype HsLNS. Docking simulations revealed a substantial reduction in the FPP binding score compared to that of the wildtype. Molecular dynamics simulations suggested that Tyr300 in the apo HsLNS mutant has a greater tendency to adopt an inward orientation. Together with Met77, the inward-facing Tyr300 creates a steric barrier that prevents the longer FPP molecule from entering the substrate binding pocket, thereby greatly reducing its activity towards FPP. This study demonstrates the potential of enzyme engineering to design substrate-specific terpene synthases, which is a challenging task and few successful examples are available. The insights gained can inform future enzyme design efforts, including the development of artificial intelligence models.

Bifunctional Sesquiterpene/Diterpene Synthase Agr2 from Cyclocybe aegerita Gives Rise to the Novel Diterpene Cyclocybene

Cyclocybe aegerita is a model mushroom belonging to the fungal phylum Basidiomycota. Among others, C. aegerita is known for its diverse terpenome, containing various volatile and nonvolatile terpenes and terpenoids. Here, we deepen the knowledge on their biosynthetic pathways by studying the terpene synthase Agr2 in detail. In contrast to previous studies, the heterologous production of Agr2 in the agaric host Coprinopsis cinerea revealed the production of two terpenes, one of which was the already known sesquiterpene viridiflorene. The other one was a so far unknown diterpene that had to be isolated and purified by means of preparative RP-HPLC for structure elucidation. 1D- and 2D-NMR experiments revealed the compound as the novel diterpene cyclocybene, pointing to the bifunctionality of Agr2 to produce both a sesquiterpene and a diterpene.

The Recent Progress of Tricyclic Aromadendrene-Type Sesquiterpenoids: Biological Activities and Biosynthesis

The tricyclic-aromadendrene-type sesquiterpenes are widely distributed and exhibit a range of biological activities, including anti-inflammatory, analgesic, antioxidant, antibacterial, insecticidal and cytotoxic properties. Several key sesquiterpene synthases (STSs) of this type have been identified, of which, viridiflorol synthase has been engineered for efficiently biosynthesizing viridiflorol in an Escherichia coli strain. This paper comprehensively summarizes the distribution and biological activity of aromadendrene-type sesquiterpenes in plant essential oils and microorganisms. The progress in aromadendrene-type sesquiterpene biosynthesis research, including the modifications of key STSs and the optimization of synthetic pathways, is reviewed. Finally, the prospects and associated challenges for the application and biosynthesis of these natural products are also discussed.

Telomere-to-Telomere Haplotype-Resolved Genomes of Agrocybe chaxingu Reveals Unique Genetic Features and Developmental Insights

Agrocybe chaxingu is a widely cultivated edible fungus in China, which is rich in nutrients and medicinal compounds. However, the lack of a high-quality genome hinders further research. In this study, we assembled the telomere-to-telomere genomes of two sexually compatible monokaryons (CchA and CchB) derived from a primarily cultivated strain AS-5. The genomes of CchA and CchB were 50.60 Mb and 51.66 Mb with contig N50 values of 3.95 Mb and 3.97 Mb, respectively. Each contained 13 complete chromosomes with telomeres at both ends. The high mapping rate, uniform genome coverage, high LAI score, all BUSCOs with 98.5%, and all base accuracy exceeding 99.999% indicated the high level of integrity and quality of these two assembled genomes. Comparison of the two genomes revealed that approximately 30% of the nucleotide sequences between homologous chromosomes were non-syntenic, including 19 translocations, 36 inversions, and 15 duplications. An additional gene CchA_000467 was identified at the Mat A locus of CchA, which was observed exclusively in the Cyclocybe cylindracea species complex. A total of 613 (4.26%) and 483 (3.4%) unique genes were identified in CchA and CchB, respectively, with over 80% of these being hypothetical proteins. Transcriptomic analysis revealed that the expression levels of unique genes in CchB were significantly higher than those in CchA, and both CchA and CchB had unique genes specifically expressed at stages of mycelium and fruiting body. It was indicated that the growth and development of the A. chaxingu strain AS-5 required the coordinated action of two different nuclei, with CchB potentially playing a more significant role. These findings contributed to a more profound comprehension of the growth and developmental processes of basidiomycetes.

Mechanistic characterisation of the diterpene synthase for clitopilene and identification of isopentalenene synthase from the fungus Clitopilus passeckerianus

Two terpene synthases from the pleuromutilin producing fungus Clitopilus passeckerianus were functionally characterised. The first enzyme CpTS1 produces the new diterpene clitopilene with a novel 6-6-5-5 tetracyclic skeleton, while the second enzyme CpTS2 makes the new sesquiterpene isopentalenene. The CpTS1 reaction mechanism was studied in depth using experimental and theoretical approaches.

Biosynthesis of fungal terpenoids

Covering: up to August 2023Terpenoids, which are widely distributed in animals, plants, and microorganisms, are a large group of natural products with diverse structures and various biological activities. They have made great contributions to human health as therapeutic agents, such as the anti-cancer drug paclitaxel and anti-malarial agent artemisinin. Accordingly, the biosynthesis of this important class of natural products has been extensively studied, which generally involves two major steps: hydrocarbon skeleton construction by terpenoid cyclases and skeleton modification by tailoring enzymes. Additionally, fungi (Ascomycota and Basidiomycota) serve as an important source for the discovery of terpenoids. With the rapid development of sequencing technology and bioinformatics approaches, genome mining has emerged as one of the most effective strategies to discover novel terpenoids from fungi. To date, numerous terpenoid cyclases, including typical class I and class II terpenoid cyclases as well as emerging UbiA-type terpenoid cyclases, have been identified, together with a variety of tailoring enzymes, including cytochrome P450 enzymes, flavin-dependent monooxygenases, and acyltransferases. In this review, our aim is to comprehensively present all fungal terpenoid cyclases identified up to August 2023, with a focus on newly discovered terpenoid cyclases, especially the emerging UbiA-type terpenoid cyclases, and their related tailoring enzymes from 2015 to August 2023.

Genome Mining of Fungal Unique Trichodiene Synthase-like Sesquiterpene Synthases

Sesquiterpenoids served as an important source for natural product drug discovery. Although genome mining approaches have revealed numerous novel sesquiterpenoids and biosynthetic enzymes, the comprehensive landscape of fungal sesquiterpene synthases (STSs) remains elusive. In this study, 123 previously reported fungal STSs were subjected to phylogenetic analysis, resulting in the identification of a fungi-specific STS family known as trichodiene synthase-like sesquiterpene synthases (TDTSs). Subsequently, the application of hidden Markov models allowed the discovery of 517 TDTSs from our in-house fungi genome library of over 400 sequenced genomes, and these TDTSs were defined into 79 families based on a sequence similarity network. Based on the novelty of protein sequences and the completeness of their biosynthetic gene clusters, 23 TDTS genes were selected for heterologous expression in Aspergillus oryzae. In total, 10 TDTSs were active and collectively produced 12 mono- and sesquiterpenes, resulting in the identification of the first chamipinene synthase, as well as the first fungi-derived cedrene, sabinene, and camphene synthases. Additionally, with the guidance of functionally characterized TDTSs, we found that TDTSs in Family 1 could produce bridged-cyclic sesquiterpenes, while those in Family 2 could synthesize spiro- and bridged-cyclic sesquiterpenes. Our research presents a new avenue for the genome mining of fungal sesquiterpenoids.

Unravelling the Function of the Sesquiterpene Cyclase STC3 in the Lifecycle of Botrytis cinerea

The genome sequencing of Botrytis cinerea supplies a general overview of the map of genes involved in secondary metabolite synthesis. B. cinerea genomic data reveals that this phytopathogenic fungus has seven sesquiterpene cyclase (Bcstc) genes that encode proteins involved in the farnesyl diphosphate cyclization. Three sesquiterpene cyclases (BcStc1, BcStc5 and BcStc7) are characterized, related to the biosynthesis of botrydial, abscisic acid and (+)-4-epi-eremophilenol, respectively. However, the role of the other four sesquiterpene cyclases (BcStc2, BcStc3, BcStc4 and BcStc6) remains unknown. BcStc3 is a well-conserved protein with homologues in many fungal species, and here, we undertake its functional characterization in the lifecycle of the fungus. A null mutant ΔBcstc3 and an overexpressed-Bcstc3 transformant (OvBcstc3) are generated, and both strains show the deregulation of those other sesquiterpene cyclase-encoding genes (Bcstc1, Bcstc5 and Bcstc7). These results suggest a co-regulation of the expression of the sesquiterpene cyclase gene family in B. cinerea. The phenotypic characterization of both transformants reveals that BcStc3 is involved in oxidative stress tolerance, the production of reactive oxygen species and virulence. The metabolomic analysis allows the isolation of characteristic polyketides and eremophilenols from the secondary metabolism of B. cinerea, although no sesquiterpenes different from those already described are identified.

Functional Characterization of Sesquiterpene Synthases and P450 Enzymes in Flammulina velutipes for Biosynthesis of Spiro [4.5] Decane Terpene

Flammulina velutipes, a popular edible mushroom, contains sesquiterpenes with potential health benefits. We characterized 12 sesquiterpene synthases and one P450 enzyme in F. velutipes using Aspergillus oryzae as a heterologous expression system, culminating in the biosynthesis of 16 distinct sesquiterpene compounds. An enzyme encoded by the axeB gene responsible for the synthesis of the spiro [4.5] decane compound axenol was discovered, and the mechanism of spirocycle formation was elucidated through quantum mechanical calculations. Furthermore, we delineated the role of a P450 enzyme colocated with AxeB in producing the novel compound 3-oxo-axenol. Our findings highlight the diverse array of sesquiterpene skeletons and functional groups biosynthesized by these enzymes in F. velutipes and underscore the effectiveness of the A. oryzae system as a heterologous host for expressing genes in the Basidiomycota genome. These insights into the biosynthesis of bioactive compounds in F. velutipes have significant implications for functional food and drug development.

Sequence-Structure Analysis Unlocking the Potential Functional Application of the Local 3D Motifs of Plant-Derived Diterpene Synthases

Plant-derived diterpene synthases (PdiTPSs) play a critical role in the formation of structurally and functionally diverse diterpenoids. However, the specificity or functional-related features of PdiTPSs are not well understood. For a more profound insight, we collected, constructed, and curated 199 functionally characterized PdiTPSs and their corresponding 3D structures. The complex correlations among their sequences, domains, structures, and corresponding products were comprehensively analyzed. Ultimately, our focus narrowed to the geometric arrangement of local structures. We found that local structural alignment can rapidly localize product-specific residues that have been validated by mutagenesis experiments. Based on the 3D motifs derived from the residues around the substrate, we successfully searched diterpene synthases (diTPSs) from the predicted terpene synthases and newly characterized PdiTPSs, suggesting that the identified 3D motifs can serve as distinctive signatures in diTPSs (I and II class). Local structural analysis revealed the PdiTPSs with more conserved amino acid residues show features unique to class I and class II, whereas those with fewer conserved amino acid residues typically exhibit product diversity and specificity. These results provide an attractive method for discovering novel or functionally equivalent enzymes and probing the product specificity in cases where enzyme characterization is limited.

A comprehensive review of secondary metabolites from the genus Agrocybe: Biological activities and pharmacological implications

The genus Agrocybe, situated within the Strophariaceae family, class Agaricomycetes, and phylum Basidiomycota, encompasses a myriad of species exhibiting significant biological activities. This review presents an integrative overview of the secondary metabolites derived from Agrocybe species, elucidating their respective biological activities and potential pharmacological applications. The metabolites under scrutiny encompass a diverse array of biological macromolecules, specifically polysaccharides and lectins, as well as a diverse group of 80 documented small molecular chemical constituents, classified into sterols, sesquiterpenes, volatile compounds, polyenes, and other compounds, their manifesting anti-inflammatory, anticancer, antioxidant, hepatoprotective, antimicrobial, and antidiabetic activities, these metabolites, in which polysaccharides exhibit abundant activities, underscore the potential of the Agrocybe genus as a valuable source of biologically active natural products. The present review emphasises the need for escalated research into Agrocybe, including investigations into the biosynthetic pathways of these metabolites, which could foster the development of novel pharmaceutical therapies to address various health challenges.

A "Magic Mushroom" Multi-Product Sesquiterpene Synthase

Psilocybe "magic mushrooms" are chemically well understood for their psychotropic tryptamines. However, the diversity of their other specialized metabolites, in particular terpenoids, has largely remained an open question. Yet, knowledge on the natural product background is critical to understand if other compounds modulate the psychotropic pharmacological effects. CubA, the single clade II sesquiterpene synthase of P. cubensis, was heterologously produced in Escherichia coli and characterized in vitro, complemented by in vivo product formation assays in Aspergillus niger as a heterologous host. Extensive GC-MS analyses proved a function as multi-product synthase and, depending on the reaction conditions, cubebol, β-copaene, δ-cadinene, and germacrene D were detected as the major products of CubA. In addition, mature P. cubensis carpophores were analysed chromatographically which led to the detection of β-copaene and δ-cadinene. Enzymes closely related to CubA are encoded in the genomes of various Psilocybe species. Therefore, our results provide insight into the metabolic capacity of the entire genus.

Identification of a (+)-cubenene synthase from filamentous fungi Acremonium chrysogenum

Sesquiterpene synthases convert farnesyl diphosphate into various sesquiterpenes, which find wide applications in the food, cosmetics and pharmaceutical industries. Although numerous putative sesquiterpene synthases have been identified in fungal genomes, many lack biochemical characterization. In this study, we identified a putative terpene synthase AcTPS3 from Acremonium chrysogenum. Through sequence analysis and in vitro enzyme assay, AcTPS3 was identified as a sesquiterpene synthase. To obtain sufficient product for NMR testing, a metabolic engineered Saccharomyces cerevisiae was constructed to overproduce the product of AcTPS3. The major product of AcTPS3 was identified as (+)-cubenene (55.46%) by GC-MS and NMR. Thus, AcTPS3 was confirmed as (+)-cubenene synthase, which is the first report of (+)-cubenene synthase. The optimized S. cerevisiae strain achieved a biosynthesis titer of 597.3 mg/L, the highest reported for (+)-cubenene synthesis.

Molecular and Functional Analyses of Characterized Sesquiterpene Synthases in Mushroom-Forming Fungi

Sesquiterpenes are a type of abundant natural product with widespread applications in several industries. They are biosynthesized by sesquiterpene synthases (STSs). As valuable and abundant biological resources, mushroom-forming fungi are rich in new sesquiterpenes and STSs, which remain largely unexploited. In the present study, we collected information on 172 STSs from mushroom-forming fungi with experimentally characterized products from the literature and sorted them to develop a dataset. Furthermore, we analyzed and discussed the phylogenetic tree, catalytic products, and conserved motifs of STSs. Phylogenetic analysis revealed that the STSs were clustered into four clades. Furthermore, their cyclization reaction mechanism was divided into four corresponding categories. This database was used to predict 12 putative STS genes from the edible fungi Flammulina velutipes. Finally, three FvSTSs were selected to experimentally characterize their functions. FvSTS03 predominantly produced Δ-cadinol and FvSTS08 synthesized β-barbatene as the main product; these findings were consistent with those of the functional prediction analysis. A product titer of 78.8 mg/L β-barbatene was achieved in Saccharomyces cerevisiae via metabolic engineering. Our study findings will help screen or design STSs from fungi with specific product profiles as functional elements for applications in synthetic biology.

Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes

Fruiting bodies (sporocarps, sporophores or basidiomata) of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates their growth, tissue differentiation and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is still limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim at a comprehensive identification of conserved genes related to fruiting body morphogenesis and distil novel functional hypotheses for functionally poorly characterised ones. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported to be involved in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defence, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1 480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for ~10 % of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. Citation: Nagy LG, Vonk PJ, Künzler M, Földi C, Virágh M, Ohm RA, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu XB, Nan S, M. Pareek M, Sahu N, Szathmári B, Varga T, Wu W, Yang X, Merényi Z (2023). Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Studies in Mycology 104: 1-85. doi: 10.3114/sim.2022.104.01.

Recent advances on Pestalotiopsis genus: chemistry, biological activities, structure-activity relationship, and biosynthesis

Strains of the fungal genus Pestalotiopsis are reported as large promising sources of structurally varied biologically active metabolites. Many bioactive secondary metabolites with diverse structural features have been derived from Pestalotiopsis. Moreover, some of these compounds can potentially be developed into lead compounds. Herein, we have systematically reviewed the chemical constituents and bioactivities of the fungal genus Pestalotiopsis, covering a period ranging from January 2016 to December 2022. As many as 307 compounds, including terpenoids, coumarins, lactones, polyketides, and alkaloids, were isolated during this period. Furthermore, for the benefit of readers, the biosynthesis and potential medicinal value of these new compounds are also discussed in this review. Finally, the perspectives and directions for future research and the potential applications of the new compounds are summarized in various tables.

Genomic and Transcriptomic Approaches Provide a Predictive Framework for Sesquiterpenes Biosynthesis in Desarmillaria tabescens CPCC 401429

Terpenoids constitute a structurally diverse class of secondary metabolites with wide applications in the pharmaceutical, fragrance and flavor industries. Desarmillaria tabescens CPCC 401429 is a basidiomycetous mushroom that could produce anti-tumor melleolides. To date, no studies have been conducted to thoroughly investigate the sesquiterpenes biosynthetic potential in Desarmillaria or related genus. This study aims to unravel the phylogeny, terpenome, and functional characterization of unique sesquiterpene biosynthetic genes of the strain CPCC 401429. Herein, we report the genome of the fungus containing 15,145 protein-encoding genes. MLST-based phylogeny and comparative genomic analyses shed light on the precise reclassification of D. tabescens suggesting that it belongs to the genus Desarmillaria. Gene ontology enrichment and pathway analyses uncover the hidden capacity for producing polyketides and terpenoids. Genome mining directed predictive framework reveals a diverse network of sesquiterpene synthases (STSs). Among twelve putative STSs encoded in the genome, six ones are belonging to the novel minor group: diverse Clade IV. In addition, RNA-sequencing based transcriptomic profiling revealed differentially expressed genes (DEGs) of the fungus CPCC 401429 in three different fermentation conditions, that of which enable us to identify noteworthy genes exemplified as STSs coding genes. Among the ten sesquiterpene biosynthetic DEGs, two genes including DtSTS9 and DtSTS10 were selected for functional characterization. Yeast cells expressing DtSTS9 and DtSTS10 could produce diverse sesquiterpene compounds, reinforced that STSs in the group Clade IV might be highly promiscuous producers. This highlights the potential of Desarmillaria in generating novel terpenoids. To summarize, our analyses will facilitate our understanding of phylogeny, STSs diversity and functional significance of Desarmillaria species. These results will encourage the scientific community for further research on uncharacterized STSs of Basidiomycota phylum, biological functions, and potential application of this vast source of secondary metabolites.

Structural Understanding of Fungal Terpene Synthases for the Formation of Linear or Cyclic Terpene Products

Terpene synthases (TPSs), known gatekeepers of terpenoid diversity, are the main targets for enzyme engineering attempts. To this end, we have determined the crystal structure of Agrocybe pediades linalool synthase (Ap.LS), which has been recently reported to be 44-fold and 287-fold more efficient than bacterial and plant counterparts, respectively. Structure-based molecular modeling followed by in vivo as well as in vitro tests confirmed that the region of 60-69aa and Tyr299 (adjacent to the motif "WxxxxxRY") are essential for maintaining Ap.LS specificity toward a short-chain (C10) acyclic product. Ap.LS Y299 mutants (Y299A, Y299C, Y299G, Y299Q, and Y299S) yielded long-chain (C15) linear or cyclic products. Molecular modeling based on the Ap.LS crystal structure indicated that farnesyl pyrophosphate in the binding pocket of Ap.LS Y299A has less torsion strain energy compared to the wild-type Ap.LS, which can be partially attributed to the larger space in Ap.LS Y299A for better accommodation of the longer chain (C15). Linalool/nerolidol synthase Y298 and humulene synthase Y302 mutations also produced C15 cyclic products similar to Ap.LS Y299 mutants. Beyond the three enzymes, our analysis confirmed that most microbial TPSs have asparagine at the position and produce mainly cyclized products (δ-cadinene, 1,8-cineole, epi-cubebol, germacrene D, β-barbatene, etc.). In contrast, those producing linear products (linalool and nerolidol) typically have a bulky tyrosine. The structural and functional analysis of an exceptionally selective linalool synthase, Ap.LS, presented in this work provides insights into factors that govern chain length (C10 or C15), water incorporation, and cyclization (cyclic vs acyclic) of terpenoid biosynthesis.

Predicting functions of putative fungal sesquiterpene synthase genes based on multiomics data analysis

Sesquiterpenes (STs) are secondary metabolites, which mediate biotic interactions between different organisms. Predicting the species-specific ST repertoires can contribute to deciphering the language of communication between organisms of the same or different species. High biochemical plasticity and catalytic promiscuity of sesquiterpene synthases (STSs), however, challenge the homology-based prediction of the STS functions. Using integrated analyses of genomic, transcriptomic, volatilomic, and metabolomic data, we predict product profiles for 116 out of 146 putative STS genes identified in the genomes of 30 fungal species from different trophic groups. Our prediction method is based on the observation that STSs encoded by genes closely related phylogenetically are likely to share the initial enzymatic reactions of the ST biosynthesis pathways and, therefore, produce STs via the same reaction route. The classification by reaction routes allows to assign STs known to be emitted by a particular species to the putative STS genes from this species. Gene expression information helps to further specify these ST-to-STS assignments. Validation of the computational predictions of the STS functions using both in silico and experimental approaches shows that integrated multiomic analyses are able to correctly link cyclic STs of non-cadalane type to genes. In the process of the experimental validation, we characterized catalytic properties of several putative STS genes from the mycorrhizal fungus Laccaria bicolor. We show that the STSs encoded by the L.bicolor mycorrhiza-induced genes emit either nerolidol or α-cuprenene and α-cuparene, and discuss the possible roles of these STs in the mycorrhiza formation.

CusProSe: a customizable protein annotation software with an application to the prediction of fungal secondary metabolism genes

We report here a new application, CustomProteinSearch (CusProSe), whose purpose is to help users to search for proteins of interest based on their domain composition. The application is customizable. It consists of two independent tools, IterHMMBuild and ProSeCDA. IterHMMBuild allows the iterative construction of Hidden Markov Model (HMM) profiles for conserved domains of selected protein sequences, while ProSeCDA scans a proteome of interest against an HMM profile database, and annotates identified proteins using user-defined rules. CusProSe was successfully used to identify, in fungal genomes, genes encoding key enzyme families involved in secondary metabolism, such as polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), hybrid PKS-NRPS and dimethylallyl tryptophan synthases (DMATS), as well as to characterize distinct terpene synthases (TS) sub-families. The highly configurable characteristics of this application makes it a generic tool, which allows the user to refine the function of predicted proteins, to extend detection to new enzymes families, and may also be applied to biological systems other than fungi and to other proteins than those involved in secondary metabolism.

A Spirobicyclo[3.1.0]Terpene from the Investigation of Sesquiterpene Synthases from Lactarius deliciosus

Milk cap mushrooms in the genus Lactarius are known to produce a wide variety of terpene natural products. However, their repertoire of terpene biosynthetic enzymes has not been fully explored. In this study, several candidate sesquiterpene synthases were identified from the genome of the saffron milk cap mushroom L. deliciosus and expressed in a sesquiterpene-overproducing Escherichia coli strain. In addition to enzymes that produce several known terpenes, we identified an enzyme belonging to a previously unknown clade of sesquiterpene synthases that produces a terpene with a unique spiro-tricyclic scaffold. These findings add to the rich diversity of terpene scaffolds and mushroom terpene synthases and are valuable for biotechnological applications in producing these terpenoids.

Challenges to Ensure a Better Translation of Metabolic Engineering for Industrial Applications

Metabolic engineering has evolved towards creating cell factories with increasingly complex pathways as economic criteria push biotechnology to higher value products to provide a sustainable source of speciality chemicals. Optimization of such pathways often requires high combinatory exploration of best pathway balance, and this has led to increasing use of high-throughput automated strain construction platforms or novel optimization techniques. In addition, the low catalytic efficiency of such pathways has shifted emphasis from gene expression strategies towards novel protein engineering to increase specific activity of the enzymes involved so as to limit the metabolic burden associated with excessively high pressure on ribosomal machinery when using massive overexpression systems. Metabolic burden is now generally recognized as a major hurdle to be overcome with consequences on genetic stability but also on the intensified performance needed industrially to attain the economic targets for successful product launch. Increasing awareness of the need to integrate novel genetic information into specific sites within the genome which not only enhance genetic stability (safe harbors) but also enable maximum expression profiles has led to genome-wide assessment of best integration sites, and bioinformatics will facilitate the identification of most probable landing pads within the genome.To facilitate the transfer of novel biotechnological potential to industrial-scale production, more attention, however, has to be paid to engineering metabolic fitness adapted to the specific stress conditions inherent to large-scale fermentation and the inevitable heterogeneity that will occur due to mass transfer limitations and the resulting deviation away from ideal conditions as seen in laboratory-scale validation of the engineered cells. To ensure smooth and rapid transfer of novel cell lines to industry with an accelerated passage through scale-up, better coordination is required form the onset between the biochemical engineers involved in process technology and the genetic engineers building the new strain so as to have an overall strategy able to maximize innovation at all levels. This should be one of our key objectives when building fermentation-friendly chassis organisms.

A Combination of Genome Mining with an OSMAC Approach Facilitates the Discovery of and Contributions to the Biosynthesis of Melleolides from the Basidiomycete Armillaria tabescens

Genome mining revealed that the genomes of basidiomycetes may include a considerable number of biosynthetic gene clusters (BGCs), yet numerous clusters remain unidentified. Herein, we report a combination of genome mining with an OSMAC (one strain, many compounds) approach to characterize the spectrum of melleolides produced by Armillaria tabescens CPCC 401429. Using F1 fermentation medium, the metabolic pathway of the gene cluster mel was successfully upregulated. From the extracts of the wild-type strain, two new melleolides (1 and 2), along with five new orsellinic acid-derived lactams (10-14), were isolated, and their structures were elucidated by LC-HR-ESIMS/MS and 2D-NMR. Several melleolides exhibited moderate anti-carcinoma (A549, NCI-H520, and H1299) effects with IC₅₀ values of 4.0-48.8 μM. RNA-sequencing based transcriptomic profiling broadened our knowledge of the genetic background, regulation, and mechanisms of melleolide biosynthesis. These results may promote downstream metabolic engineering studies of melleolides. Our study demonstrates the approach is effective for discovering new secondary metabolites from Armillaria sp. and will facilitate the mining of the unexploited biosynthetic potential in other basidiomycetes.

Biosynthesis of Sesquiterpenes in Basidiomycetes: A Review

Sesquiterpenes are common small-molecule natural products with a wide range of promising applications and are biosynthesized by sesquiterpene synthase (STS). Basidiomycetes are valuable and important biological resources. To date, hundreds of related sesquiterpenoids have been discovered in basidiomycetes, and the biosynthetic pathways of some of these compounds have been elucidated. This review summarizes 122 STSs and 2 fusion enzymes STSs identified from 26 species of basidiomycetes over the past 20 years. The biological functions of enzymes and compound structures are described, and related research is discussed.

Diverse Metabolites and Pharmacological Effects from the Basidiomycetes Inonotus hispidus

Inonotus hispidus mushroom is a popular edible and medicinal mushroom with a long history of use. It is well known as a medicinal fungus with various health benefits for its significant anticancer and immunomodulatory activities. Over the last 60 years, secondary metabolites derived from I. hispidus and their biological activities have been discovered and investigated. Structurally, these compounds are mainly polyphenols and triterpenoids, which have anticancer, anti-inflammatory, antioxidant, antimicrobial, and enzyme inhibitor activities. Here, the secondary metabolites derived from I. hispidus and their activities were systematically and comprehensively classified and summarized, and the biosynthetic pathway of stylylpyrones was deduced and analyzed further. This review contributes to our understanding of I. hispidus and will help with research into natural product chemistry, pharmacology, and the biosynthesis of I. hispidus metabolites. According to this review, I. hispidus could be a promising source of bioactive compounds for health promotion and the development of functional foods.

Ectomycorrhizal Influence on the Dynamics of Sesquiterpene Release by Tricholoma vaccinum

Tricholoma vaccinum is an ectomycorrhizal basidiomycete with high host specificity. The slow-growing fungus is able to produce twenty sesquiterpenes, including α-barbatene, sativene, isocaryophyllene, α-cuprenene, β-cedrene, ß-copaene, 4-epi-α-acoradiene, and chamigrene in axenic culture. For the three major compounds, Δ6-protoilludene, β-barbatene, and an unidentified oxygenated sesquiterpene (m/z 218.18), changed production during co-cultivation with the ectomycorrhizal partner tree, Picea abies, could be shown with distinct dynamics. During the mycorrhizal growth of T. vaccinum-P. abies, Δ6-protoilludene and the oxygenated sesquiterpene appeared at similar times, which warranted further studies of potential biosynthesis genes. In silico analyses identified a putative protoilludene synthesis gene, pie1, as being up-regulated in the mycorrhizal stage, in addition to the previously identified, co-regulated geosmin synthase, ges1. We therefore hypothesize that the sesquiterpene synthase pie1 has an important role during mycorrhization, through Δ6-protoilludene and/or its accompanied oxygenated sesquiterpene production.

Unusual (2R,6R)-bicyclo[3.1.1]heptane ring construction in fungal α-trans-bergamotene biosynthesis

Bergamotenes are bicyclo[3.1.1]heptane sesquiterpenes found abundantly in plants and fungi. Known bergamotene derivatives all possess (2S,6S)-bergamotene backbone. In this study, two (+)-α-trans-bergamotene derivatives (1 and 2) with unusual (2R,6R) configuration were isolated and elucidated from marine fungus Nectria sp. HLS206. The first (+)-α-trans-bergamotene synthase NsBERS was characterized using genome mining and heterologous expression-based strategies. Based on homology search, we characterized another (+)-α-trans-bergamotene synthase LsBERS from Lachnellula suecica and an (+)-α-bisabolol synthase BcBOS from Botrytis cinerea. We proposed that the cyclization mechanism of (+)-α-trans-bergamotene involved endo-anti cyclization of left-handed helix farnesyl pyrophosphate by (6R)-bisabolyl cation, which was supported by molecular docking. The biosynthesis-based volatiles (3-6) produced by heterologous fungal expression systems elicited significant electroantennographic responses of Helicoverpa armigera and Spodoptera frugiperda, respectively, suggesting their potential in biocontrol of these pests. This work enriches diversity of sesquiterpenoids and fungal sesquiterpene synthases, providing insight into the enzymatic mechanism of formation of enantiomeric sesquiterpenes.

Improved Foods Using Enzymes from Basidiomycetes

Within the kingdom of fungi, the division Basidiomycota represents more than 30,000 species, some with huge genomes indicating great metabolic potential. The fruiting bodies of many basidiomycetes are appreciated as food (“mushrooms”). Solid-state and submerged cultivation processes have been established for many species. Specifically, xylophilic fungi secrete numerous enzymes but also form smaller metabolites along unique pathways; both groups of compounds may be of interest to the food processing industry. To stimulate further research and not aim at comprehensiveness in the broad field, this review describes some recent progress in fermentation processes and the knowledge of fungal genetics. Processes with potential for food applications based on lipases, esterases, glycosidases, peptidases and oxidoreductases are presented. The formation and degradation of colourants, the degradation of harmful food components, the formation of food ingredients and particularly of volatile and non-volatile flavours serve as examples. In summary, edible basidiomycetes are foods—and catalysts—for food applications and rich donors of genes to construct heterologous cell factories for fermentation processes. Options arise to support the worldwide trend toward greener, more eco-friendly and sustainable processes.

Influence of Association Network Properties and Ecological Assembly of the Foliar Fugal Community on Crop Quality

Revealing community assembly and their impacts on ecosystem service is a core issue in microbial ecology. However, what ecological factors play dominant roles in phyllosphere fungal community assembly and how they link to crop quality are largely unknown. Here, we applied internal transcriptional spacer high-throughput sequencing to investigate foliar fungal community assembly across three cultivars of a Solanaceae crop (tobacco) and two planting regions with different climatic conditions. Network analyses were used to reveal the pattern in foliar fungal co-occurrence, and phylogenetic null model analysis was used to elucidate the ecological assembly of foliar fungal communities. We found that the sensory quality of crop leaves and the composition of foliar fungal community varied significantly across planting regions and cultivars. In Guangcun (GC), a region with relatively high humidity and low precipitation, there was a higher diversity and more unique fungal species than the region of Wuzhishan (WZS). Further, we found that the association network of foliar fungal communities in GC was more complex than that in WZS, and the network properties were closely related to the sensory quality of crop. Finally, the results of the phylogenetic analyses show that the stochastic processes played important roles in the foliar fungal community assembly, and their relative importance was significantly correlated with the sensory quality of crop leaves, which implies that ecological assembly processes could affect crop quality. Taken together, our results highlight that climatic conditions, and plant cultivars play key roles in the assembly of foliar fungal communities and crop quality, which enhances our understanding of the connections between the phyllosphere microbiome and ecosystem services, especially in agricultural production.

Identification of volatile producing enzymes in higher fungi: Combining analytical and bioinformatic methods

Filamentous fungi harbor the genetic potential for the biosynthesis of several secondary metabolites including various volatile organic compounds (VOCs). Nonetheless, under standard laboratory conditions, many of these VOCs are not formed. Furthermore, little is known about enzymes involved in the production of fungal VOCs. To tap these interesting topics, we developed an approach to identify enzymes putatively involved in the fungal VOC biosynthesis. In this chapter, we highlight different fungal cultivation methods and techniques for the extraction of VOCs, including a method that allows the noninvasive analysis of VOCs. In addition using terpene synthases as an example, it is depicted how enzymes putatively involved in VOC synthesis can be identified by means of bioinformatic approaches. Transcriptomic data of chosen genes combined with volatilome data obtained during different developmental stages is demonstrated as a powerful tool to identify enzymes putatively involved in fungal VOC biosynthesis. Especially with regard to subsequent enzyme characterization, this procedure is a target-oriented way to save time and efforts by considering only the most important enzymes.

Progress in biological activities and biosynthesis of edible fungi terpenoids

The edible fungi have both edible and medicinal functions, in which terpenoids are one of the most important active ingredients. Terpenoids possess a wide range of biological activities and show great potential in the pharmaceutical and healthcare industries. In this review, the diverse biological activities of edible fungi terpenoids were summarized with emphasis on the mechanism of anti-cancer and anti-inflammation. Subsequently, this review focuses on advances in knowledge and understanding of the biosynthesis of terpenoids in edible fungi, especially in the generation of sesquiterpenes, diterpenes, and triterpenes. This paper is aim to provide an overview of biological functions and biosynthesis developed for utilizing the terpenoids in edible fungi.

Characterization of γ-Cadinene Enzymes in Ganoderma lucidum and Ganoderma sinensis from Basidiomycetes Provides Insight into the Identification of Terpenoid Synthases

Enzymes boost protein engineering, directed evolution, and the biochemical industry and are also the cornerstone of metabolic engineering. Basidiomycetes are known to produce a large variety of terpenoids with unique structures. However, basidiomycetous terpene synthases remain largely untapped. Therefore, we provide a modeling method to obtain specific terpene synthases. Aided by bioinformatics analysis, three γ-cadinene enzymes from Ganoderma lucidum and Ganoderma sinensis were accurately predicted and identified experimentally. Based on the highly conserved amino motifs of the characterized γ-cadinene enzymes, the enzyme was reassembled as model 1. Using this model as a template, 67 homologous sequences of the γ-cadinene enzyme were screened from the National Center for Biotechnology Information (NCBI). According to the 67 sequences, the same gene structure, and similar conserved motifs to model 1, the γ-cadinene enzyme model was further improved by the same construction method and renamed as model 2. The results of bioinformatics analysis show that the conservative regions of models 1 and 2 are highly similar. In addition, five of these sequences were verified, 100% of which were γ-cadinene enzymes. The accuracy of the prediction ability of the γ-cadinene enzyme model was proven. In the same way, we also reanalyzed the identified Δ6-protoilludene enzymes in fungi and (-)-α-bisabolol enzymes in plants, all of which have their own unique conserved motifs. Our research method is expected to be used to study other terpenoid synthases with a similar or the same function in basidiomycetes, ascomycetes, bacteria, and plants and to provide rich enzyme resources.

Comparative Genomic and Metabolomic Analysis of Termitomyces Species Provides Insights into the Terpenome of the Fungal Cultivar and the Characteristic Odor of the Fungus Garden of Macrotermes natalensis Termites

Macrotermitinae termites have domesticated fungi of the genus Termitomyces as food for their colony, analogously to human farmers growing crops. Termites propagate the fungus by continuously blending foraged and predigested plant material with fungal mycelium and spores (fungus comb) within designated subterranean chambers. To test the hypothesis that the obligate fungal symbiont emits specific volatiles (odor) to orchestrate its life cycle and symbiotic relations, we determined the typical volatile emission of fungus comb biomass and Termitomyces nodules, revealing α-pinene, camphene, and d-limonene as the most abundant terpenes. Genome mining of Termitomyces followed by gene expression studies and phylogenetic analysis of putative enzymes related to secondary metabolite production encoded by the genomes uncovered a conserved and specific biosynthetic repertoire across strains. Finally, we proved by heterologous expression and in vitro enzymatic assays that a highly expressed gene sequence encodes a rare bifunctional mono-/sesquiterpene cyclase able to produce the abundant comb volatiles camphene and d-limonene.

IMPORTANCE The symbiosis between macrotermitinae termites and Termitomyces is obligate for both partners and is one of the most important contributors to biomass conversion in the Old World tropic’s ecosystems. To date, research efforts have dominantly focused on acquiring a better understanding of the degradative capabilities of Termitomyces to sustain the obligate nutritional symbiosis, but our knowledge of the small-molecule repertoire of the fungal cultivar mediating interspecies and interkingdom interactions has remained fragmented. Our omics-driven chemical, genomic, and phylogenetic study provides new insights into the volatilome and biosynthetic capabilities of the evolutionarily conserved fungal genus Termitomyces, which allows matching metabolites to genes and enzymes and, thus, opens a new source of unique and rare enzymatic transformations.

Biosynthesis and regulation of terpenoids from basidiomycetes: exploration of new research

Basidiomycetes, also known as club fungi, consist of a specific group of fungi. Basidiomycetes produce a large number of secondary metabolites, of which sesquiterpenoids, diterpenoids and triterpenoids are the primary components. However, these terpenoids tend to be present in low amounts, which makes it difficult to meet application requirements. Terpenoid biosynthesis improves the quantity of these secondary metabolites. However, current understanding of the biosynthetic mechanism of terpenoids in basidiomycetes is insufficient. Therefore, this article reviews the latest research on the biosynthesis of terpenoids in basidiomycetes and summarizes the CYP450 involved in the biosynthesis of terpenoids in basidiomycetes. We also propose opportunities and challenges for chassis microbial heterologous production of terpenoids in basidiomycetes and provide a reference basis for the better development of basidiomycete engineering.

Sesquiterpene Cyclases from the Basidiomycete Cerrena unicolor

Hundreds of terpenoids have been isolated from Basidiomycota, among them are volatile mono- and sesquiterpenes with amazing sensory qualities, representing a promising alternative to essential oils from endangered plant species. Sesquiterpene synthases (STS) appear to be an abundant class of enzymes in these fungi. The basidiomycete Cerrena unicolor, a known sesquiterpene producer, was in silico screened for sesquiterpene cyclases via homology Basic Local Alignment Search Tool searches. Cyclase genes identified were cloned and heterologously expressed in Escherichia coli Bl21 using pCOLD I as the expression vector. Ten cyclases were successfully produced and purified, and their identity was confirmed using amino acid sequencing of tryptic peptides by nano-liquid chromatography-high resolution-electrospray ionization-tandem mass spectrometry. Gas chromatography/mass spectrometry analysis was applied to characterize these cyclases according to the formation of sesquiterpene hydrocarbons and oxidized terpenoids. Bioinformatic characterization and phylogenetic determination allowed for the classification of these diverse fungal enzymes. A representative single and a multi-product STS, respectively, were further analyzed for their dependency from divalent metal cations as a cofactor for the catalytic activity.

Microbes as a production host to produce natural activecompounds from mushrooms: biosynthetic pathway elucidationand metabolic engineering

Mushrooms are abundant in bioactive natural compounds. Due to strict growth conditions and long fermentation-time, microbe as a production host is an alternative and sustainable approach for the production of natural compounds. This review focuses on the biosynthetic pathways of mushroom originated natural compounds and microbes as the production host for the production of the above natural compounds.

Genetic engineering of yeast, filamentous fungi and bacteria for terpene production and applications in food industry

Terpenes are a major class of natural aromatic compounds in grapes and wines to offer the characteristic flavor and aroma, serving as important quality traits of wine products. Saccharomyces cerevisiae represents an excellent cell factory platform for large-scale bio-based terpene production. This review describes the biosynthetic pathways of terpenes in different organisms. The metabolic engineering of S. cerevisiae for promoting terpene biosynthesis and the alternative microbial engineering platforms including filamentous fungi and Escherichia coli are also elaborated. Additionally, the potential applications of the terpene products from engineered microorganisms in food and beverage industries are also discussed. This review provides comprehensive information for an innovative supply way of terpene via microbial cell factory, which could facilitate the development and application of this technique at the industrial scale.

Transcriptome of different fruiting stages in the cultivated mushroom Cyclocybe aegerita suggests a complex regulation of fruiting and reveals enzymes putatively involved in fungal oxylipin biosynthesis

BACKGROUND

Cyclocybe aegerita (syn. Agrocybe aegerita) is a commercially cultivated mushroom. Its archetypal agaric morphology and its ability to undergo its whole life cycle under laboratory conditions makes this fungus a well-suited model for studying fruiting body (basidiome, basidiocarp) development. To elucidate the so far barely understood biosynthesis of fungal volatiles, alterations in the transcriptome during different developmental stages of C. aegerita were analyzed and combined with changes in the volatile profile during its different fruiting stages.

RESULTS

A transcriptomic study at seven points in time during fruiting body development of C. aegerita with seven mycelial and five fruiting body stages was conducted. Differential gene expression was observed for genes involved in fungal fruiting body formation showing interesting transcriptional patterns and correlations of these fruiting-related genes with the developmental stages. Combining transcriptome and volatilome data, enzymes putatively involved in the biosynthesis of C8 oxylipins in C. aegerita including lipoxygenases (LOXs), dioxygenases (DOXs), hydroperoxide lyases (HPLs), alcohol dehydrogenases (ADHs) and ene-reductases could be identified. Furthermore, we were able to localize the mycelium as the main source for sesquiterpenes predominant during sporulation in the headspace of C. aegerita cultures. In contrast, changes in the C8 profile detected in late stages of development are probably due to the activity of enzymes located in the fruiting bodies.

CONCLUSIONS

In this study, the combination of volatilome and transcriptome data of C. aegerita revealed interesting candidates both for functional genetics-based analysis of fruiting-related genes and for prospective enzyme characterization studies to further elucidate the so far barely understood biosynthesis of fungal C8 oxylipins.

Bioinformatics-aided identification, characterization and applications of mushroom linalool synthases

Enzymes empower chemical industries and are the keystone for metabolic engineering. For example, linalool synthases are indispensable for the biosynthesis of linalool, an important fragrance used in 60-80% cosmetic and personal care products. However, plant linalool synthases have low activities while expressed in microbes. Aided by bioinformatics analysis, four linalool/nerolidol synthases (LNSs) from various Agaricomycetes were accurately predicted and validated experimentally. Furthermore, we discovered a linalool synthase (Ap.LS) with exceptionally high levels of selectivity and activity from Agrocybe pediades, ideal for linalool bioproduction. It effectively converted glucose into enantiopure (R)-linalool in Escherichia coli, 44-fold and 287-fold more efficient than its bacterial and plant counterparts, respectively. Phylogenetic analysis indicated the divergent evolution paths for plant, bacterial and fungal linalool synthases. More critically, structural comparison provided catalytic insights into Ap.LS superior specificity and activity, and mutational experiments validated the key residues responsible for the specificity.

Mind the mushroom: natural product biosynthetic genes and enzymes of Basidiomycota

Covering: up to September 2020 Mushroom-forming fungi of the division Basidiomycota have traditionally been recognised as prolific producers of structurally diverse and often bioactive secondary metabolites, using the methods of chemistry for research. Over the past decade, -omics technologies were applied on these fungi, and sophisticated heterologous gene expression platforms emerged, which have boosted research into the genetic and biochemical basis of the biosyntheses. This review provides an overview on experimentally confirmed natural product biosyntheses of basidiomycete polyketides, amino acid-derived products, terpenoids, and volatiles. We also present challenges and solutions particular to natural product research with these fungi. 222 references are cited.

Systems biology approaches integrated with artificial intelligence for optimized metabolic engineering

Metabolic engineering aims to maximize the production of bio-economically important substances (compounds, enzymes, or other proteins) through the optimization of the genetics, cellular processes and growth conditions of microorganisms. This requires detailed understanding of underlying metabolic pathways involved in the production of the targeted substances, and how the cellular processes or growth conditions are regulated by the engineering. To achieve this goal, a large system of experimental techniques, compound libraries, computational methods and data resources, including multi-omics data, are used. The recent advent of multi-omics systems biology approaches significantly impacted the field by opening new avenues to perform dynamic and large-scale analyses that deepen our knowledge on the manipulations. However, with the enormous transcriptomics, proteomics and metabolomics available, it is a daunting task to integrate the data for a more holistic understanding. Novel data mining and analytics approaches, including Artificial Intelligence (AI), can provide breakthroughs where traditional low-throughput experiment-alone methods cannot easily achieve. Here, we review the latest attempts of combining systems biology and AI in metabolic engineering research, and highlight how this alliance can help overcome the current challenges facing industrial biotechnology, especially for food-related substances and compounds using microorganisms.

Highly Oxygenated Caryophyllene-Type Sesquiterpenes from a Plant-Associated Fungus, Pestalotiopsis hainanensis, and Their Biosynthetic Gene Cluster

Seven new β-caryophyllene derivatives, pestalotiphains A-G (1-7), along with six known analogues (8-13), were isolated from the plant-associated Pestalotiopsis hainanensis. Compound 1 represents the first example of a caryophyllene-adenine hybrid, and 2 contains a novel oxatricyclo[4.3.1.0] system. Their structures and absolute configurations were assigned by interpretation of a combination of spectroscopic data and electronic circular dichroism calculations. Compound 8 exhibited moderate inhibition of HL-60 and THP-1 cell lines (IC₅₀, 6.2 and 2.0 μM, respectively). A candidate biosynthetic gene cluster responsible for these compounds was uncovered by bioinformatics analyses and confirmed by a biochemical approach.

Natural Products from Endophytic Fungi Associated with Rubiaceae Species

This review presents the chemical diversity and pharmacological properties of secondary metabolites produced by endophytic fungi associated with various genera of Rubiaceae. Several classes of natural products are described for these endophytes, although, this study highlights the importance of some metabolites, which are involved in antifungal, antibacterial, anti-protozoal activities; neurodegenerative diseases; cytotoxic activity; anti-inflammatory and antioxidant activity; and hyperglycemic control.