Genome-Based Discovery of an Unprecedented Cyclization Mode in Fungal Sesterterpenoid Biosynthesis

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.

Two Sesterterpene Synthases from Lentzea atacamensis Demonstrate the Role of Conformational Variability in Terpene Biosynthesis

Mining of two multiproduct sesterterpene synthases from Lentzea atacamensis resulted in the identification of the synthases for lentzeadiene (LaLDS) and atacamatriene (LaATS). The main product of LaLDS (lentzeadiene) is a new compound, while one of the side products (lentzeatetraene) is the enantiomer of brassitetraene B and the other side product (sestermobaraene F) is known from a surprisingly distantly related sesterterpene synthase. LaATS produces six new compounds, one of which is the enantiomer of the known sesterterpene Bm1. Notably, for both enzymes the products cannot all be explained from one and the same starting conformation of geranylfarnesyl diphosphate, demonstrating the requirement of conformational flexibility of the substrate in the enzymes' active sites. For lentzeadiene an intriguing thermal [1,5]-sigmatropic rearrangement was discovered, reminiscent of the biosynthesis of vitamin D3. All enzyme reactions and the [1,5]-sigmatropic rearrangement were investigated through isotopic labeling experiments and DFT calculations. The results also emphasize the importance of conformational changes during terpene cyclizations.

Characterization and Engineering of Two Highly Paralogous Sesquiterpene Synthases Reveal a Regioselective Reprotonation Switch

Sesquiterpene synthases (STPSs) catalyze carbocation-driven cyclization reactions that can generate structurally diverse hydrocarbons. The deprotonation-reprotonation process is widely used in STPSs to promote structural diversity, largely attributable to the distinct regio/stereoselective reprotonations. However, the molecular basis for reprotonation regioselectivity remains largely understudied. Herein, we analyzed two highly paralogous STPSs, Artabotrys hexapetalus (-)-cyperene synthase (AhCS) and ishwarane synthase (AhIS), which catalyze reactions that are distinct from the regioselective protonation of germacrene A (GA), resulting in distinct skeletons of 5/5/6 tricyclic (-)-cyperene and 6/6/5/3 tetracyclic ishwarane, respectively. Isotopic labeling experiments demonstrated that these protonations occur at C3 and C6 of GA in AhCS and AhIS, respectively. The cryo-electron microscopy-derived AhCS complex structure provided the structural basis for identifying different key active site residues that may govern their functional disparity. The structure-guided mutagenesis of these residues resulted in successful functional interconversion between AhCS and AhIS, thus targeting the three active site residues [L311-S419-C458]/[M311-V419-A458] that may act as a C3/C6 reprotonation switch for GA. These findings facilitate the rational design or directed evolution of STPSs with structurally diverse skeletons.

Elucidating the interaction between equisetin and human serum albumin: A comprehensive study using spectroscopy, microcalorimetry and molecular docking approaches

Equisetin, a bioactive compound of marine origin, offers compelling inhibitory properties against HIV-1 transcriptase. To gain comprehensive insights into the interaction of Equisetin with human serum albumin (HSA), we utilized a multipronged approach involving spectroscopy, isothermal titration calorimetry (ITC) and molecular docking. Our fluorescence analyses confirmed that the interaction between Equisetin and HSA results in a significant quenching of HSA's fluorescence, primarily achieved through a dynamic mechanism aided by hydrogen bonding and van der Waals forces. Isothermal titration calorimetry (ITC) measurements revealed an impressive binding affinity of Equisetin for HSA, quantified to be 4.3 × 107 mol L-1. Molecular docking studies illustrated that Equisetin binds at site III of HSA, with specific amino acid residues, GLN-104 and LYS-106, playing a pivotal role. Further, our study discovered that the interaction induces slight unfolding of HSA's polypeptide chain and significant alterations in its secondary structure, thereby triggering the exposure of previously concealed hydrophobic regions. This comprehensive study enhances our understanding of Equisetin's interaction with serum proteins, potentially influencing its pharmacokinetics and pharmacodynamics, and opening avenues for future research and therapeutic applications.

Genomics-driven derivatization of the bioactive fungal sesterterpenoid variecolin: Creation of an unnatural analogue with improved anticancer properties

A biosynthetic gene cluster for the bioactive fungal sesterterpenoids variecolin (1) and variecolactone (2) was identified in Aspergillus aculeatus ATCC 16872. Heterologous production of 1 and 2 was achieved in Aspergillus oryzae by expressing the sesterterpene synthase VrcA and the cytochrome P450 VrcB. Intriguingly, the replacement of VrcB with homologous P450s from other fungal terpenoid pathways yielded three new variecolin analogues (5-7). Analysis of the compounds' anticancer activity in vitro and in vivo revealed that although 5 and 1 had comparable activities, 5 was associated with significantly reduced toxic side effects in cancer-bearing mice, indicating its potentially broader therapeutic window. Our study describes the first tests of variecolin and its analogues in animals and demonstrates the utility of synthetic biology for creating molecules with improved biological activities.

Biosynthesis and the Transcriptional Regulation of Terpenoids in Tea Plants (Camellia sinensis)

Terpenes, especially volatile terpenes, are important components of tea aroma due to their unique scents. They are also widely used in the cosmetic and medical industries. In addition, terpene emission can be induced by herbivory, wounding, light, low temperature, and other stress conditions, leading to plant defense responses and plant-plant interactions. The transcriptional levels of important core genes (including HMGR, DXS, and TPS) involved in terpenoid biosynthesis are up- or downregulated by the MYB, MYC, NAC, ERF, WRKY, and bHLH transcription factors. These regulators can bind to corresponding cis-elements in the promoter regions of the corresponding genes, and some of them interact with other transcription factors to form a complex. Recently, several key terpene synthesis genes and important transcription factors involved in terpene biosynthesis have been isolated and functionally identified from tea plants. In this work, we focus on the research progress on the transcriptional regulation of terpenes in tea plants (Camellia sinensis) and thoroughly detail the biosynthesis of terpene compounds, the terpene biosynthesis-related genes, the transcription factors involved in terpene biosynthesis, and their importance. Furthermore, we review the potential strategies used in studying the specific transcriptional regulation functions of candidate transcription factors that have been discriminated to date.

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.

Antiplasmodial Asperterpenoids from Two Aspergillus oryzae Transformants with Heterologous Expression of Sesterterpene Genes

The synthetic biology approach enables efficient and directional mining of target compounds during drug discovery. Ten new asperterpenoids (6-15) and five known analogues (1-5), possessing a rare 5/7/3/6/5 skeleton, were obtained from two Aspergillus oryzae transformants with heterologous expression of a terpene cyclase gene AstC with one or two P450 genes AstB/A under the guidance of molecular networking. Their planar structures were determined by 1D and 2D NMR and HR-ESI-MS. The absolute configurations of compounds 6 and 9-13 were determined by single crystal X-ray diffraction, and those of compounds 7-8 and 14-15 were compared with the ECD of known compounds. Seven of all the compounds are the first asperterpenoid oxidation products at C-17 or at C-25. In bioassay, compounds 1-2, 4-5, and 6-8 displayed moderate to strong eliminating activities against chloroquine-sensitive strain (P.f.3D7) with EC₅₀ values ranging from 2.1 to 19.3 μM. The structure-activity relationship (SAR) was discussed, which showed that substituents at C-3, C-11, C-17, C-18, and C-23 of asperterpenoids significantly affected anti-plasma parasite activity.

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.

Undescribed specialised metabolites from the endophytic fungus Emericella sp. XL029 and their antimicrobial activities

The fungus Emericella sp. XL029 isolated from leaves of Panax notoginseng was investigated for agents with potential antibacterial and antifungal activities using a one strain-many compounds (OSMAC) strategy. Fifteen compounds, including seven undescribed structures, were obtained from this species. Their structures were confirmed by extensive spectroscopic data, single-crystal X-ray crystallography and quantum chemistry calculations. Emerlactam A exhibited better antibacterial activity against multidrug-resistant Enterococcus faecium and antifungal activity against Helminthosporium maydis, with an MIC value of 12.5 μg/mL. Quiannulatic acid displayed significant antibacterial activity against multidrug-resistant Enterococcus faecium and multidrug-resistant Enterococcus faecalis with MIC values of 1.56 μg/mL and 3.13 μg/mL, respectively. 5-alkenylresorcinol exhibited significant antifungal activity against all tested phytopathogenic fungi with MIC values ranging from 6.25 to 12.5 μg/mL.

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.

Anti-inflammatory aromadendrane- and cadinane-type sesquiterpenoids from the South China Sea sponge Acanthella cavernosa

One new aromadendrane-type sesquiterpenoid, namely ximaocavernosin P [(+)-1], and three new cadinane-type sesquiterpenoids, namely (+)-maninsigin D [(+)-4], (+)- and (−)-ximaocavernosin Q [(+)- and (−)-5], together with five related known ones [2, 3, (−)-4, 6, and 7], were isolated from the Hainan sponge Acanthella cavernosa. Compounds 4 and 5 were isolated as racemic forms, which were further separated to the corresponding enantiomers [(+)-4/(−)-4 and (+)-5/(−)-5], respectively, by using chiral-phase HPLC. The structures of new compounds were elucidated by extensive spectroscopic analysis and comparison with the reported data. In addition, the absolute configuration of optically pure (+)-1 and 2 were determined by time-dependent density functional theory/electronic circular dichroism (TDDFT-ECD) calculations or X-ray diffraction analysis. A plausible biosynthetic pathway of these sesquiterpenoids and their internal correlation were proposed and discussed. In an in vitro bioassay, (+)-aristolone (3) exhibited promising anti-inflammatory activity by the inhibition of LPS-induced TNF-α and CCL2 release in RAW 264.7 macrophages.

Mechanism of the Bifunctional Multiple Product Sesterterpene Synthase AcAS from Aspergillus calidoustus

The multiproduct chimeric sesterterpene synthase AcAS from Aspergillus calidoustus yielded spirocyclic calidoustene, which exhibits a novel skeleton, besides five known sesterterpenes. The complex cyclisation mechanism to all six compounds was investigated by isotopic labelling experiments in combination with DFT calculations. Chemically synthesised 8-hydroxyfarnesyl diphosphate was converted with isopentenyl diphosphate and AcAS into four oxygenated sesterterpenoids that structurally resemble cytochrome P450 oxidation products of the sesterterpene hydrocarbons. Protein engineering of AcAS broadened the substrate scope and gave significantly improved enzyme yields.

Enzymatic Synthesis of Variediene Analogs

Five analogs of dimethylallyl diphosphate (DMAPP) with additional or shifted Me groups were converted with isopentenyl diphosphate (IPP) and the fungal variediene synthase from Aspergillus brasiliensis (AbVS). These enzymatic reactions resulted in the formation of several new terpene analogs that were isolated and structurally characterised by NMR spectroscopy. Several DMAPP analogs showed a changed reactivity giving access to compounds with unusual skeletons. Their formation is mechanistically rationalised and the absolute configurations of all obtained compounds were determined through a stereoselective deuteration strategy, revealing absolute configurations that are analogous to that of the natural enzyme product variediene.

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...

A Modular Approach to Angularly Fused Polyquinanes via Ring-Rearrangement Metathesis: Synthetic Access to Cameroonanol Analogues and the Basic Core of Subergorgic Acid and Crinipellin

We describe a modular approach to angularly fused polyquinanes that are core units of many natural products such as cameroonanol, subergorgic acid, and crinepellin, etc. in excellent yields by employing atom-economic ring-rearrangement metathesis as a key step. Our work highlights, the synthesis of cameroonanol analogues 1-6 and their ester derivatives by using the stereoselective reduction of the carbonyl group by using DIBAL-H- and DCC-mediated coupling as the key reactions. The subergorgic acid core 7 was produced by LDA-mediated kinetically controlled regio- and stereoselective ring-junction allylation as a critical step. Moreover, it is worth mentioning that the present strategy relies on a less explored exo-dicyclopentadiene-1-one (8) and produces highly congested polycyclic frameworks containing up to seven contiguous stereogenic centers including quaternary carbons up to two. All of the new molecules were characterized by NMR data. The structure and relative stereochemistry of some compounds were confirmed by chemical methods and further supported by single-crystal X-ray diffraction studies. The newly reported tri- and tetraquinane skeletons are present in many naturally occurring bioactive polyquinanes. Hence, this strategy is useful for designing various "druglike molecules" and expands the chemical space of cyclopentanoids that are useful in medicinal chemistry.

Synthaser: a CD-Search enabled Python toolkit for analysing domain architecture of fungal secondary metabolite megasynth(et)ases

BACKGROUND

Fungi are prolific producers of secondary metabolites (SMs), which are bioactive small molecules with important applications in medicine, agriculture and other industries. The backbones of a large proportion of fungal SMs are generated through the action of large, multi-domain megasynth(et)ases such as polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs). The structure of these backbones is determined by the domain architecture of the corresponding megasynth(et)ase, and thus accurate annotation and classification of these architectures is an important step in linking SMs to their biosynthetic origins in the genome.

RESULTS

Here we report synthaser, a Python package leveraging the NCBI's conserved domain search tool for remote prediction and classification of fungal megasynth(et)ase domain architectures. Synthaser is capable of batch sequence analysis, and produces rich textual output and interactive visualisations which allow for quick assessment of the megasynth(et)ase diversity of a fungal genome. Synthaser uses a hierarchical rule-based classification system, which can be extensively customised by the user through a web application ( http://gamcil.github.io/synthaser ). We show that synthaser provides more accurate domain architecture predictions than comparable tools which rely on curated profile hidden Markov model (pHMM)-based approaches; the utilisation of the NCBI conserved domain database also allows for significantly greater flexibility compared to pHMM approaches. In addition, we demonstrate how synthaser can be applied to large scale genome mining pipelines through the construction of an Aspergillus PKS similarity network.

CONCLUSIONS

Synthaser is an easy to use tool that represents a significant upgrade to previous domain architecture analysis tools. It is freely available under a MIT license from PyPI ( https://pypi.org/project/synthaser ) and GitHub ( https://github.com/gamcil/synthaser ).

DFT Study on the Biosynthesis of Verrucosane Diterpenoids and Mangicol Sesterterpenoids: Involvement of Secondary-Carbocation-Free Reaction Cascades

Some experimental observations indicate that a sequential formation of secondary (2°) carbocations might be involved in some biosynthetic pathways, including those of verrucosane-type diterpenoids and mangicol-type sesterterpenoids, but it remains controversial whether or not such 2° cations are viable intermediates. Here, we performed comprehensive density functional theory calculations of these biosynthetic pathways. The results do not support previously proposed pathways/mechanisms: in particular, we find that none of the putative 2° carbocation intermediates is involved in either of the biosynthetic pathways. In verrucosane biosynthesis, the proposed 2° carbocations (II and IV) in the early stage are bypassed by the formation of the adjacent 3° carbocations and by unusual skeletal rearrangement reactions, and in the later stage, the putative 2° carbocation intermediates (VI, VII, and VIII) are not present as the proposed forms but as nonclassical structures between homoallyl and cyclopropylcarbinyl cations. In the mangicol biosynthesis, one of the two proposed 2° carbocations (X) is bypassed by a C-C bond-breaking reaction to generate a 3° carbocation with a C=C bond, while the other (XI) is bypassed by a strong hyperconjugative interaction leading to a nonclassical carbocation. We propose new biosynthetic pathways/mechanisms for the verrucosane-type diterpenoids and mangicol-type sesterterpenoids. These pathways are in good agreement with the findings of previous biosynthetic studies, including isotope-labeling experiments and byproducts analysis, and moreover can account for the biosynthesis of related terpenes.

Mining methods and typical structural mechanisms of terpene cyclases

Terpenoids, formed by cyclization and/or permutation of isoprenes, are the most diverse and abundant class of natural products with a broad range of significant functions. One family of the critical enzymes involved in terpenoid biosynthesis is terpene cyclases (TCs), also known as terpene synthases (TSs), which are responsible for forming the ring structure as a backbone of functionally diverse terpenoids. With the recent advances in biotechnology, the researches on terpene cyclases have gradually shifted from the genomic mining of novel enzyme resources to the analysis of their structures and mechanisms. In this review, we summarize both the new methods for genomic mining and the structural mechanisms of some typical terpene cyclases, which are helpful for the discovery, engineering and application of more and new TCs.

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

Chimeric terpene synthases, termed PTTSs, are a unique family of enzymes occurring only in fungi. Characterizing PTTSs is challenging due to the complex reactions they catalyze and the structural complexity of their products. Here, by devising an efficient precursor-providing yeast chassis and incorporating a high-throughput automated platform, we identified 34 active PTTSs, which was considerably more than the number of known functional PTTSs. This effective and rapid pipeline can be employed for the characterization of other PTTSs or related terpenoid biosynthetic enzymes. By systematically analyzing the presence/absence of PTTS genes together with phylogenetic analysis, the ancestral PTTS gene was inferred to have undergone duplication and functional divergence, which led to the development of two distinct cyclization mechanisms.

Chimeric terpene synthases, which consist of C-terminal prenyltransferase (PT) and N-terminal class I terpene synthase (TS) domains (termed PTTSs here), is unique to fungi and produces structurally diverse di- and sesterterpenes. Prior to this study, 20 PTTSs had been functionally characterized. Our understanding of the origin and functional evolution of PTTS genes is limited. Our systematic search of sequenced fungal genomes among diverse taxa revealed that PTTS genes were restricted to Dikarya. Phylogenetic findings indicated different potential models of the origin and evolution of PTTS genes. One was that PTTS genes originated in the common Dikarya ancestor and then underwent frequent gene loss among various subsequent lineages. To understand their functional evolution, we selected 74 PTTS genes for biochemical characterization in an efficient precursor-providing yeast system employing chassis-based, robot-assisted, high-throughput automatic assembly. We found 34 PTTS genes that encoded active enzymes and collectively produced 24 di- and sesterterpenes. About half of these di- and sesterterpenes were also the products of the 20 known PTTSs, indicating functional conservation, whereas the PTTS products included the previously unknown sesterterpenes, sesterevisene (1), and sesterorbiculene (2), suggesting that a diversity of PTTS products awaits discovery. Separating functional PTTSs into two monophyletic groups implied that an early gene duplication event occurred during the evolution of the PTTS family followed by functional divergence with the characteristics of distinct cyclization mechanisms.

The untapped potential of plant sesterterpenoids: chemistry, biological activities and biosynthesis

Covering: 1969 up to 2021Sesterterpenoids, biosynthetically derived from the precursor, namely geranylfarnesyl diphosphate (GFDP) are amongst the rarest of all isoprenoids with approximately 1300 compounds known. Most sesterterpenoids originate from marine organisms (especially sponges), while only about 15% of these compounds are isolated from several families of plants such as Lamiaceae, Gentianaceae, and Nartheciaceae. Many plant sesterterpenoids possess highly oxygenated and complex cyclic skeletons and exhibit remarkable biological activities involving cytotoxic, anti-inflammatory, antimicrobial, and antifeedant properties. Thus, due to their intrinsic chemical complexity and intriguing biological profiles, plant sesterterpenoids have attracted continuing interest from both chemists and biologists. However, the biosynthesis and distribution of sesterterpenoids in the plant kingdom still remain elusive, although substantial progress has been achieved in recent years. This review provides an overall coverage of sesterterpenoids originating from plant sources, followed by a classification of their chemical skeletons, which summarizes the distribution, chemistry, biological activities, biosynthesis and evolution of plant sesterterpenoids, aiming at strengthening the research efforts toward the untapped great potential of these unique natural product resources.

One Polyketide Synthase, Two Distinct Products: Trans-Acting Enzyme-Controlled Product Divergence in Calbistrin Biosynthesis

Calbistrins are fungal polyketides consisting of the characteristic decalin and polyene moieties. Although the biosynthetic gene cluster of calbistrin A was recently identified, the pathway of calbistrin A biosynthesis has largely remained uninvestigated. Herein, we investigated the mechanism by which the backbone structures of calbistrins are formed, by heterologous and in vitro reconstitution of the biosynthesis and a structural biological study. Intriguingly, our analyses revealed that the decalin and polyene portions of calbistrins are synthesized by the single polyketide synthase (PKS) CalA, with the aid of the trans-acting enoylreductase CalK and the trans-acting C-methyltransferase CalH, respectively. We also determined that the esterification of the two polyketide parts is catalyzed by the acyltransferase CalD. Our study has uncovered a novel dual-functional PKS and thus broadened our understanding of how fungi synthesize diverse polyketide natural products.

Total Synthesis of Panaginsene

The total synthesis of panaginsene has been accomplished in 11 linear steps starting from methyl 3,3-dimethyl-5-oxocyclopent-1-ene-1-carboxylate. The key steps are a Sharpless asymmetric epoxidation and Ti(III)-mediated reductive epoxide opening-radical cyclization to construct the chiral quaternary carbon stereocenter followed by a very challenging HWE olefination reaction on an 1,3-keto aldehyde and a late stage McMurry olefination using low valent titanium to construct the highly constrained angular tetrasubstituted olefin in a five-membered ring.

Large-scale culture as a complementary and practical method for discovering natural products with novel skeletons

Covering: up to July 2020Fungal metabolites with diverse and novel scaffolds can be assembled from well-known biosynthetic precursors through various mechanisms. Recent examples of novel alkaloids (e.g., cytochalasans and diketopiperazine derivatives), terpenes (e.g., sesterterpenes and diterpenes) and polyketides produced by fungi are presented through case studies. We show that large-scale culture is a complementary and practical method for genome mining and OSMAC approaches to discover natural products of unprecedented skeletal classes from fungi. We also summarize the discovery strategies and challenges for characterizing these compounds.

Genome Mining Reveals a Multiproduct Sesterterpenoid Biosynthetic Gene Cluster in Aspergillus ustus

Genome mining of Aspergillus ustus 094102 enabled the discovery of a multiproduct bifunctional terpene synthase (BTS), AuAS. Heterologous expression of AuAS led to the discovery of five new sesterterpenes, and coexpression of the upstream CYP450 monooxygenase (AuAP450) generated four new sesterterpene alcohols. Additionally, aspergilol A showed cytotoxic activities against MCF-7, MDA-MB231, and HepG2 cancer cells (IC₅₀ 21.20-48.76 μM), and aspergilol B exhibited a cytotoxic effect on MCF-7 cells (IC₅₀ 27.41 μM).

Cytochrome P450 enzymes in fungal natural product biosynthesis

Covering: 2015 to the end of 2020 Fungal-derived polyketides, non-ribosomal peptides, terpenoids and their hybrids contribute significantly to the chemical space of total natural products. Cytochrome P450 enzymes play essential roles in fungal natural product biosynthesis with their broad substrate scope, great catalytic versatility and high frequency of involvement. Due to the membrane-bound nature, the functional and mechanistic understandings for fungal P450s have been limited for quite a long time. However, recent technical advances, such as the efficient and precise genome editing techniques and the development of several filamentous fungal strains as heterologous P450 expression hosts, have led to remarkable achievements in fungal P450 studies. Here, we provide a comprehensive review to cover the most recent progresses from 2015 to 2020 on catalytic functions and mechanisms, research methodologies and remaining challenges in the fast-growing field of fungal natural product biosynthetic P450s.

Sesterterpenoids: chemistry, biology, and biosynthesis

Covering: July 2012 to December 2019Over the last seven years, expanding research efforts focused on sesterterpenoids has led to the isolation, identification, and characterization of numerous structurally novel and biologically active sesterterpenoids. These newly reported sesterterpenoids provide diverse structures that often incorporate unprecedented ring systems and new carbon skeletons, as well as unusual functional group arrays. Biological activities of potential biomedical importance including suppression of cancer cell growth, inhibition of enzymatic activity, and modulation of receptor signaling, as well as ecologically important functions such as antimicrobial effects and deterrence of herbivorous insects have been associated with a variety of sesterterpenoids. There has also been a rapid growth in our knowledge of the genomics, enzymology, and specific pathways associated with sesterterpene biosynthesis. This has opened up new opportunities for future sesterterpene discovery and diversification through the expression of new cryptic metabolites and the engineered manipulation of associated biosynthetic machinery and processes. In this paper we reviewed 498 new sesterterpenoids, including their structures, source organisms, country of origin, relevant bioactivities, and biosynthesis.

The Biosynthetic Gene Cluster for Sestermobaraenes-Discovery of a Geranylfarnesyl Diphosphate Synthase and a Multiproduct Sesterterpene Synthase from Streptomyces mobaraensis

A biosynthetic gene cluster from Streptomyces mobaraensis encoding the first cases of a bacterial geranylfarnesyl diphosphate synthase and a type I sesterterpene synthase was identified. The structures of seven sesterterpenes produced by these enzymes were elucidated, including their absolute configurations. The enzyme mechanism of the sesterterpene synthase was investigated by extensive isotope labeling experiments.

Combined Comparative Genomics and Gene Expression Analyses Provide Insights into the Terpene Synthases Inventory in Trichoderma

Trichoderma is a fungal genus comprising species used as biocontrol agents in crop plant protection and with high value for industry. The beneficial effects of these species are supported by the secondary metabolites they produce. Terpenoid compounds are key players in the interaction of Trichoderma spp. with the environment and with their fungal and plant hosts; however, most of the terpene synthase (TS) genes involved in their biosynthesis have yet not been characterized. Here, we combined comparative genomics of TSs of 21 strains belonging to 17 Trichoderma spp., and gene expression studies on TSs using T. gamsii T6085 as a model. An overview of the diversity within the TS-gene family and the regulation of TS genes is provided. We identified 15 groups of TSs, and the presence of clade-specific enzymes revealed a variety of terpenoid chemotypes evolved to cover different ecological demands. We propose that functional differentiation of gene family members is the driver for the high number of TS genes found in the genomes of Trichoderma. Expression studies provide a picture in which different TS genes are regulated in many ways, which is a strong indication of different biological functions.

Enzymatic Plasticity Inspired by the Diterpene Cyclase CotB2

Enzymatic plasticity, as a modern term referring to the functional conversion of an enzyme, is significant for enzymatic activity redesign. The bacterial diterpene cyclase CotB2 is a typical plastic enzyme by which its native form precisely conducts a chemical reaction while its mutants diversify the catalytic functions drastically. Many efforts have been made to disclose the mysteries of CotB2 enzyme catalysis. However, the catalytic details and regulatory mechanism toward the precise chemo- and stereoselectivity are still elusive. In this work, multiscale simulations are employed to illuminate the biocyclization mechanisms of the linear substrate into the final product cyclooctat-9-en-7-ol with a 5-8-5 fused ring scaffold, and the derailment products arising from the premature quenching of reactive carbocation intermediates are also discussed. The two major regulatory factors, local electrostatic stabilization effects from aromatic residues or polar residue in pocket and global features of active site including pocket-contour and pocket-hydrophobicity, are responsible for the enzymatic plasticity of CotB2. Further comparative studies of representative Euphorbiaceae and fungal diterpene cyclase (RcCS and PaFS) show a correlation between pocket plasticity and product diversity, which inspires a tentative enzyme product prediction and the rational diterpene cyclases' reengineering in the future.

On the mechanism of ophiobolin F synthase and the absolute configuration of its product by isotopic labelling experiments

An ophiobolin F synthase homolog was discovered from Aspergillus calidoustus CBS121601. The cyclisation mechanism of this terpene synthase was investigated by extensive isotopic labelling experiments and the absolute configuration of its product ophiobolin F was elucidated by enantioselective deuteration.

Reconstitution of biosynthetic machinery of fungal natural products in heterologous hosts

Ascomycota and basidiomycota fungi are prolific sources of biologically active natural products. Recent genomic data and bioinformatic analysis indicate that fungi possess a large number of biosynthetic gene clusters for bioactive natural products but more than 90% are silent. Heterologous expression in the filamentous fungi as hosts is one of the powerful tools to expression of the silent gene clusters. This review introduces recent studies on the total biosynthesis of representative family members via common platform intermediates, genome mining of novel di- and sesterterpenoids including detailed cyclization pathway, and development of expression host for basidiomycota genes with efficient genome editing method. In addition, this review will discuss the several strategies, for the generation of structural diversity, which are found through these studies.

A Family of Related Fungal and Bacterial Di- and Sesterterpenes: Studies on Fusaterpenol and Variediene

The absolute configuration of fusaterpenol (GJ1012E) has been revised by an enantioselective deuteration strategy. A bifunctional enzyme with a terpene synthase and a prenyltransferase domain from Aspergillus brasiliensis was characterised as variediene synthase, and the absolute configuration of its product was elucidated. The uniform absolute configurations of these and structurally related di- and sesterterpenes together with a common stereochemical course for the geminal methyl groups of GGPP unravel a similar conformational fold of the substrate in the active sites of the terpene synthases. For variediene, a thermal reaction observed during GC/MS analysis was studied in detail for which a surprising mechanism was uncovered.

Fungi: outstanding source of novel chemical scaffolds

A large number of remarkable studies on the secondary metabolites of fungi have been conducted in recent years. This review gives an overview of one hundred and sixty-seven molecules with novel skeletons and their bioactivities that have been reported in seventy-nine articles published from 2013 to 2017. Our statistical data showed that endophytic fungi and marine-derived fungi are the major sources of novel bioactive secondary metabolites.

Roquefornine A, a sesterterpenoid with a 5/6/5/5/6-fused ring system from the fungus Penicillium roqueforti YJ-14

Roquefornine A, a sesterterpenoid with an unprecedented 5/6/5/5/6-membered pentacyclic system, was characterized from Penicillium roqueforti YJ-14.

Prenylated quinolinone alkaloids and prenylated isoindolinone alkaloids from the fungus Aspergillus nidulans

Two undescribed prenylated quinolinone alkaloids, aspoquinolones E and F, and three undescribed prenylated isoindolinone alkaloids aspernidines F-H, were isolated from the fungus Aspergillus nidulans. Their structures and configurations were elucidated based on spectroscopic analyses and ECD spectra. Aspoquinolones E and F possess a C₁₀ moiety with an unusual 2,2,4-trimethyl-3oxa-bicyclo[3.1.0]hexane unit, and aspernidines F-H own a C₁₅ side chain. These compounds were evaluated for cytotoxic activities against five human cancer cell lines, compounds 1 and 5 exhibited strong inhibitory activities against A-549 and SW-480 cells with IC₅₀ values of 3.50 and 4.77 μM, respectively.

Sesterterpenoids

Sesterterpenoids are known as a relatively small group of natural products. However, they represent a variety of simple to more complex structural types. This contribution focuses on the chemical structures of sesterterpenoids and how their structures are constructed in Nature.

Use of the kojA promoter, involved in kojic acid biosynthesis, for polyketide production in Aspergillus oryzae: implications for long-term production

BACKGROUND

Aspergillus oryzae, a useful industrial filamentous fungus, produces limited varieties of secondary metabolites, such as kojic acid. Thus, for the production of valuable secondary metabolites by genetic engineering, the species is considered a clean host, enabling easy purification from cultured cells. A. oryzae has been evaluated for secondary metabolite production utilizing strong constitutive promoters of genes responsible for primary metabolism. However, secondary metabolites are typically produced by residual nutrition after microbial cells grow to the stationary phase and primary metabolism slows. We focused on a promoter of the secondary metabolism gene kojA, a component of the kojic acid biosynthetic gene cluster, for the production of other secondary metabolites by A. oryzae.

RESULTS

A kojA disruptant that does not produce kojic acid was utilized as a host strain for production. Using this host strain, a mutant that expressed a polyketide synthase gene involved in polyketide secondary metabolite production under the kojA gene promoter was constructed. Then, polyketide production and polyketide synthase gene expression were observed every 24 h in liquid culture. From days 0 to 10 of culture, the polyketide was continuously produced, and the synthase gene expression was maintained. Therefore, the kojA promoter was activated, and it enabled the continuous production of polyketide for 10 days.

CONCLUSIONS

The combined use of the kojA gene promoter and a kojA disruptant proved useful for the continuous production of a polyketide secondary metabolite in A. oryzae. These findings suggest that this combination can be applied to other secondary metabolites for long-term production.

Inherent atomic mobility changes in carbocation intermediates during the sesterterpene cyclization cascade

We previously showed that the regio- and stereoselectivity in terpene-forming reactions are determined by the conformations of the carbocation intermediates, which reflect the initial conformation of the substrate, geranylfarnesyl diphosphate (GFPP). However, it remains unclear how the initial conformation of GFPP is controlled, and which part(s) of the GFPP molecule are important for its fixation inside the substrate-binding pocket. Here, we present the first detailed analysis of the inherent atomic mobility in carbocation intermediates during sesterterpene biosynthesis. We identified two methyl groups as the least mobile of all the carbons of the carbocation intermediates in the first half of the cyclization cascade. Our analysis suggests that these two methyl groups are critical for the preorganization of GFPP in the biosynthetic pathways leading to sesterfisherol and quiannulatene.