Systematic mining of fungal chimeric terpene synthases using an efficient precursor-providing yeast chassis

Emerindanols A and B: Two Bipolyhydroindenol Sesterterpenes with 5/6-6/5 Coupled Ring System Discovered by Genome Mining

Genome mining of Emericella sp. XL-029 achieved a new type E sesterterpene synthase, EmES, which affored a novel bipolyhydroindenol sesterterpene, emerindanol A. Heterologous coexpression with the upstream P450 oxidase revealed C-4 hydroxylated product, emerindanol B. Notably, emerindanols A and B represented the first sesterterpenes featuring a unique 5/6-6/5 coupled ring system. EmES was postulated to initiate through C1-IV-V pathway and convert the fused ring intermediate into the final coupled ring product through a spiro skeleton.

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.

Sesquiterpenes of the ectomycorrhizal fungus Pisolithus microcarpus alter root growth and promote host colonization

Trees form symbioses with ectomycorrhizal (ECM) fungi, maintained in part through mutual benefit to both organisms. Our understanding of the signaling events leading to the successful interaction between the two partners requires further study. This is especially true for understanding the role of volatile signals produced by ECM fungi. Terpenoids are a predominant class of volatiles produced by ECM fungi. While several ECM genomes are enriched in the enzymes responsible for the production of these volatiles (i.e., terpene synthases (TPSs)) when compared to other fungi, we have limited understanding of the biochemical products associated with each enzyme and the physiological impact of specific terpenes on plant growth. Using a combination of phylogenetic analyses, RNA sequencing, and functional characterization of five TPSs from two distantly related ECM fungi (Laccaria bicolor and Pisolithus microcarpus), we investigated the role of these secondary metabolites during the establishment of symbiosis. We found that despite phylogenetic divergence, these TPSs produced very similar terpene profiles. We focused on the role of P. microcarpus terpenes and found that the fungus expressed a diverse array of mono-, di-, and sesquiterpenes prior to contact with the host. However, these metabolites were repressed following physical contact with the host Eucalyptus grandis. Exposure of E. grandis to heterologously produced terpenes (enriched primarily in γ -cadinene) led to a reduction in the root growth rate and an increase in P. microcarpus-colonized root tips. These results support a very early putative role of fungal-produced terpenes in the establishment of symbiosis between mycorrhizal fungi and their hosts.

The microbial biosynthesis of noncanonical terpenoids

Terpenoids are a class of structurally complex, naturally occurring compounds found predominantly in plant, animal, and microorganism secondary metabolites. Classical terpenoids typically have carbon atoms in multiples of five and follow well-defined carbon skeletons, whereas noncanonical terpenoids deviate from these patterns. These noncanonical terpenoids often result from the methyltransferase-catalyzed methylation modification of substrate units, leading to irregular carbon skeletons. In this comprehensive review, various activities and applications of these noncanonical terpenes have been summarized. Importantly, the review delves into the biosynthetic pathways of noncanonical terpenes, including those with C6, C7, C11, C12, and C16 carbon skeletons, in bacteria and fungi host. It also covers noncanonical triterpenes synthesized from non-squalene substrates and nortriterpenes in Ganoderma lucidum, providing detailed examples to elucidate the intricate biosynthetic processes involved. Finally, the review outlines the potential future applications of noncanonical terpenoids. In conclusion, the insights gathered from this review provide a reference for understanding the biosynthesis of these noncanonical terpenes and pave the way for the discovery of additional unique and novel noncanonical terpenes. KEY POINTS: •The activities and applications of noncanonical terpenoids are introduced. •The noncanonical terpenoids with irregular carbon skeletons are presented. •The microbial biosynthesis of noncanonical terpenoids is summarized.

Molecular insights into the catalytic promiscuity of a bacterial diterpene synthase

Diterpene synthase VenA is responsible for assembling venezuelaene A with a unique 5-5-6-7 tetracyclic skeleton from geranylgeranyl pyrophosphate. VenA also demonstrates substrate promiscuity by accepting geranyl pyrophosphate and farnesyl pyrophosphate as alternative substrates. Herein, we report the crystal structures of VenA in both apo form and holo form in complex with a trinuclear magnesium cluster and pyrophosphate group. Functional and structural investigations on the atypical 115DSFVSD120 motif of VenA, versus the canonical Asp-rich motif of DDXX(X)D/E, reveal that the absent second Asp of canonical motif is functionally replaced by Ser116 and Gln83, together with bioinformatics analysis identifying a hidden subclass of type I microbial terpene synthases. Further structural analysis, multiscale computational simulations, and structure-directed mutagenesis provide significant mechanistic insights into the substrate selectivity and catalytic promiscuity of VenA. Finally, VenA is semi-rationally engineered into a sesterterpene synthase to recognize the larger substrate geranylfarnesyl pyrophosphate.

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.

Multifunctional Enzymes in Microbial Secondary Metabolic Processes

Microorganisms possess a strong capacity for secondary metabolite synthesis, which is represented by tightly controlled networks. The absence of any enzymes leads to a change in the original metabolic pathway, with a decrease in or even elimination of a synthetic product, which is not permissible under conditions of normal life activities of microorganisms. In order to improve the efficiency of secondary metabolism, organisms have evolved multifunctional enzymes (MFEs) that can catalyze two or more kinds of reactions via multiple active sites. However, instead of interfering, the multifunctional catalytic properties of MFEs facilitate the biosynthetic process. Among the numerous MFEs considered of vital importance in the life activities of living organisms are the synthases involved in assembling the backbone of compounds using different substrates and modifying enzymes that confer the final activity of compounds. In this paper, we review MFEs in terms of both synthetic and post-modifying enzymes involved in secondary metabolic biosynthesis, focusing on polyketides, non-ribosomal peptides, terpenoids, and a wide range of cytochrome P450s(CYP450s), and provide an overview and describe the recent progress in the research on MFEs.

Engineering fungal terpene biosynthesis

Covering: 2015 to 2022Fungal terpenoids are of large structural diversity and often exhibit interesting biological activities. Recent work has focused on two main aspects: (1) the discovery and understanding of unknown biosynthetic genes and pathways, and (2) the usage of already known biosynthetic genes in the construction of high yielding production strains. Both aspects will be covered in this review article that aims to summarise the most important work of the past few years.

Biosynthesis of mushroom-derived type II ganoderic acids by engineered yeast

Type II ganoderic acids (GAs) produced by the traditional medicinal mushroom Ganoderma are a group of triterpenoids with superior biological activities. However, challenges in the genetic manipulation of the native producer, low level of accumulation in the farmed mushroom, the vulnerabilities of the farming-based supply chain, and the elusive biosynthetic pathway have hindered the efficient production of type II GAs. Here, we assemble the genome of type II GAs accumulating G. lucidum accession, screen cytochrome P450 enzymes (CYPs) identified from G. lucidum in baker's yeast, identify key missing CYPs involved in type II GAs biosynthesis, and investigate the catalytic reaction sequence of a promiscuous CYP. Then, we engineer baker's yeast for bioproduciton of GA-Y (3) and GA-Jb (4) and achieve their production at higher level than those from the farmed mushroom. Our findings facilitate the further deconvolution of the complex GA biosynthetic network and the development of microbial cell factories for producing GAs at commercial scale.

Research Progress on Fungal Sesterterpenoids Biosynthesis

Sesterterpenes are 25-carbon terpenoids formed by the cyclization of dimethyl allyl diphosphate (DMAPP) and isopentenyl diphosphate (IPP) as structural units by sesterterpenes synthases. Some (not all) sesterterpenoids are modified by cytochrome P450s (CYP450s), resulting in more intricate structures. These compounds have significant physiological activities and pharmacological effects in anti-inflammatory, antibacterial, antitumour, and hypolipidemic communities. Despite being a rare class of terpenoids, sesterterpenoids derived from fungi show a wide range of structural variations. The discovered fungal sesterterpenoid synthases are composed of C-terminal prenyltransferase (PT) and N-terminal terpene synthase (TS) domains, which were given the name PTTSs. PTTSs have the capacities to catalyze chain lengthening and cyclization concurrently. This review summarizes all 52 fungal PTTSs synthases and their biosynthetic pathways involving 100 sesterterpenoids since the discovery of the first PTTSs synthase from fungi in 2013.

Identification and Characterization of a Cryptic Bifunctional Type I Diterpene Synthase Involved in Talaronoid Biosynthesis from a Marine-Derived Fungus

We report the identification of the tnd biosynthetic cluster from the marine-derived fungus Aspergillus flavipes and the in vivo characterization of a cryptic type I diterpene synthase. The heterologous expression of the bifunctional terpene synthase led to the discovery of a diterpene backbone, talarodiene, harboring a benzo[a]cyclopenta[d]cyclooctane tricyclic fused ring system. The conversion of geranylgeranyl diphosphate to talarodiene was investigated using ¹³C-labeling studies, and stable isotope tracer experiments showed the biotransformation of talarodiene into talaronoid C.

Schultriene and nigtetraene: two sesterterpenes characterized from pathogenetic fungi via genome mining approach

Fungal bifunctional terpene synthases (BFTSs) have been reported to contribute to the biosynthesis of a variety of di/sesterterpenes via different carbocation transportation pathways. Genome mining of new BFTSs from unique fungal resources will, theoretically, allow for the identification of new terpenes. In this study, we surveyed the distribution of BFTSs in our in-house collection of 430 pathogenetic fungi and preferred two BFTSs (CsSS and NnNS), long distance from previously characterized BFTSs and located in relatively independent branches, based on the established phylogenetic tree. The heterologous expression of the two BFTSs in Aspergillus oryzae and Saccharomyces cerevisiae led to the identification of two new sesterterpenes separately, 5/12/5 tricyclic type-A sesterterpene (schultriene, 1) for CsSS and 5/11 bicyclic type-B sesterterpene (nigtetraene, 2) for NnNS. In addition, to the best of our knowledge, 2 is the first 5/11 bicyclic type-B characterized sesterterpene to date. On the basis of this, the plausible cyclization mechanisms of 1 and 2 were proposed based on density functional theory calculations. These new enzymes and their corresponding terpenes suggest that the chemical spaces produced by BFTSs remain large and also provide important evidences for further protein engineering for new terpenes and for understanding of cyclization mechanism catalyzed by BFTSs. KEY POINTS: • Genome mining of two BFTSs yields two new sesterterpenoids correspondingly. • Identification of the first 5/11 ring system type-B product. • Parse out the rational cyclization mechanism of isolated sesterterpenoids.

Discovery of non-squalene triterpenes

All known triterpenes are generated by triterpene synthases (TrTSs) from squalene or oxidosqualene¹. This approach is fundamentally different from the biosynthesis of short-chain (C₁₀–C₂₅) terpenes that are formed from polyisoprenyl diphosphates^2–4. In this study, two fungal chimeric class I TrTSs, Talaromyces verruculosus talaropentaene synthase (TvTS) and Macrophomina phaseolina macrophomene synthase (MpMS), were characterized. Both enzymes use dimethylallyl diphosphate and isopentenyl diphosphate or hexaprenyl diphosphate as substrates, representing the first examples, to our knowledge, of non-squalene-dependent triterpene biosynthesis. The cyclization mechanisms of TvTS and MpMS and the absolute configurations of their products were investigated in isotopic labelling experiments. Structural analyses of the terpene cyclase domain of TvTS and full-length MpMS provide detailed insights into their catalytic mechanisms. An AlphaFold2-based screening platform was developed to mine a third TrTS, Colletotrichum gloeosporioides colleterpenol synthase (CgCS). Our findings identify a new enzymatic mechanism for the biosynthesis of triterpenes and enhance understanding of terpene biosynthesis in nature.

Chimeric triterpene synthases are identified that catalyse non-squalene-dependent triterpene biosynthesis.

Hedycaryol – Central Intermediates in Sesquiterpene Biosynthesis, Part II

The known sesquiterpenes that arise biosynthetically from hedycaryol are summarised. Reasonings for the assignments of their absolute configurations are discussed. The analysis provided here suggests that reprotonations at the C1=C10 double bond of hedycaryol are directed toward C1 and generally lead to 6–6 bicyclic compounds, while reprotonations at the C4=C5 double bond occur at C4 and result in 5–7 bicyclic compounds. Read more in the Review by H. Xu and J. S. Dickschat (DOI: 10.1002/chem.202200405).

Genome Mining Reveals a New Cyclopentane-forming Sesterterpene Synthase with Unprecedented Stereo-control

Fungal bifunctional terpene synthases (BFTSs) catalyze formation of diverse ring systems in diterpene/sesterterpene structures. Through genome mining of fungal BFTSs, we discovered a novel sesterterpenoids gene cluster pst, consisting of...

Discovery and characterization of a novel sub-group of UbiA-type terpene cyclases with a distinct motif I

A novel sub-group of UbiA-type TCs with a distinct motif I were identified from fungi to generate structurally diverse sesquiterpenes.