Reconstitution of biosynthetic machinery of fungal polyketides: unexpected oxidations of biosynthetic intermediates by expression host

Neuroprotective α-pyrones from Nigrospora oryzae, an endophytic fungus residing in Taxus chinensis var. mairei

Endophytes coevolve with plant hosts and thus are more probable to acquire the character (in favor) of producing undescribed bioactive metabolites. Consequently, the topic has been intensely investigated for over two decades, but endophytic metabolites with neuroprotective effect remain scarce. The study presents the discovery of eight undescribed (named solanapyrones U-Z and prosolanapyrones A and B) and six known pyrones (solanapyrones A-C and E-G) from the culture of Nigrospora oryzae, an endophytic fungus associated with Taxus chinensis var. mairei. The structures and absolute configurations of undescribed pyrones were elucidated by extensive spectroscopic analysis, modified Mosher's method, and induced circular dichroism (ICD) spectrum. Solanapyrones A and B and an undescribed pyrone (solanapyrone U) were demonstrated to be more neuroprotective than clenbuterol in inducing bone marrow mesenchymal stem cells (bMSCs) to secret nerve growth factor (NGF). The work updates the pyrone chemodiversity in nature and extends the biofunction repertoire of solanapyrone-related polyketides.

Absolute configuration of cyclopropanes and the structural revision of pyrones from Marine-derived fungus Stagonospora sp. SYSU-MS7888

Two new cyclopropane derivatives (1-2) and seven undescribed α-pyrone derivatives (3-9), along with one known congener (10) were obtained from the marine fungus Stagonospora sp. SYSU-MS7888, which was isolated from the South China Sea. Their planar structures were established through extensive spectroscopic analyses including 1D and 2D NMR and HR-ESIMS. The absolute configurations were identified on basis of the quantum chemical calculations of ECD and NMR, as well as the modified Mosher's method. It's particularly noteworthy that the tetrasubstituted furopyrans, chenopodolans A-F, possessing phytotoxicity and zootoxicity, were structural misassignments. The structures of chenopodolans featuring with furopyran skeleton were revised as common trisubstituted α-pyrones by computational chemistry, NMR spectroscopic method, and empirical rule. Compounds 1, 2, 7, and 9 showed significant anti-inflammatory activity with IC₅₀ values ranging from 3.6 to 22.8 μM, which is better than the positive control indomethacin (IC₅₀ = 26.5 ± 1.13 μM). This discovery holds potential for the development of new anti-inflammatory agents.

Norditerpenoids biosynthesized by variediene synthase-associated P450 machinery along with modifications by the host cell Aspergillus oryzae

The chemical diversity of terpenoids is typically established by terpene synthase-catalyzed cyclization and diversified by post-tailoring modifications. Fungal bifunctional terpene synthase (BFTS) associated P450 enzymes have shown significant catalytic potentials through the development of various new terpenoids with different biological activities. This study discovered the BFTS and its related gene cluster from the plant endophytic fungus Didymosphaeria variabile 17020. Heterologous expression of the BFTS in Saccharomyces cerevisiae resulted in the characterization of a major product diterpene variediene (1), along with two new minor products neovariediene and neoflexibilene. Further heterologous expression of the BFTS and one cytochrome P450 enzyme VndE (CYP6138B1) in Aspergillus oryzae NSAR1 led to the identification of seven norditerpenoids (19 carbons) with a structurally unique 5/5 bicyclic ring system. Interestingly, in vivo experiments suggested that the cyclized terpene variediene (1) was modified by VndE along with the endogenous enzymes from the host cell A. oryzae through serial chemical conversions, followed by multi-site hydroxylation via A. oryzae endogenous enzymes. Our work revealed that the two-enzymes biosynthetic system and host cell machinery could produce structurally unique terpenoids.

Heterologous expression of a polyketide synthase ACRTS2 in Aspregillus oryzae produces host selective ACR-toxins: Co-production of minor metabolites

Previously, we succeeded to produce the core structure of the host-selective ACR-toxin (1) on brown leaf spot on rough lemon when the polyketide synthase ACRTS2 gene was heterologously expressed in Aspergillus oryzae (AO). To confirm the production of 1 in AO, the detection limit and suppressing decarboxylation were improved, and these efforts led us to conclude the direct production of 1 instead of its decarboxylation product. During this examination, minor ACR-toxin-related metabolites were found. Their structure determination enabled us to propose a decarboxylation mechanism and novel branching route forming byproducts from the coupling of the dihydropyrone moiety of 1 with the acetaldehyde and kojic acid abundant in AO. The involvement of putative cyclase ACRTS3 in the chain release of linear polyketide was excluded by the co-expression analysis of ACRTS2 and ACRTS3. Taken together, we concluded the production of 1 in AO is solely responsible for ACRTS2.

Trichoderma reesei Contains a Biosynthetic Gene Cluster That Encodes the Antifungal Agent Ilicicolin H

The trili biosynthetic gene cluster (BGC) from the well-studied organism Trichoderma reesei was studied by heterologous expression in the fungal host Aspergillus oryzae. Coexpression of triliA and triliB produces two new acyl tetramic acids. Addition of the ring-expanding cytochrome P450 encoded by triliC then yields a known pyridone intermediate to ilicicolin H and a new chain-truncated shunt metabolite. Finally, addition of the intramolecular Diels-Alderase encoded by triliD affords a mixture of 8-epi ilicicolin H and ilicicolin H itself, showing that the T. reesei trili BGC encodes biosynthesis of this potent antifungal agent. Unexpected A. oryzae shunt pathways are responsible for the production of the new compounds, emphasising the role of fungal hosts in catalysing diversification reactions.

Early Oxidative Transformations During the Biosynthesis of Terrein and Related Natural Products

The mycotoxin terrein is derived from the C₁₀‐precursor 6‐hydroxymellein (6‐HM) via an oxidative ring contraction. Although the corresponding biosynthetic gene cluster (BGC) has been identified, details of the enzymatic oxidative transformations are lacking. Combining heterologous expression and in vitro studies we show that the flavin‐dependent monooxygenase (FMO) TerC catalyzes the initial oxidative decarboxylation of 6‐HM. The reactive intermediate is further hydroxylated by the second FMO TerD to yield a highly oxygenated aromatic species, but further reconstitution of the pathway was hampered. A related BGC was identified in the marine‐derived Roussoella sp. DLM33 and confirmed by heterologous expression. These studies demonstrate that the biosynthetic pathways of terrein and related (polychlorinated) congeners diverge after oxidative decarboxylation of the lactone precursor that is catalyzed by a conserved FMO and further indicate that early dehydration of the side chain is an essential step.

Total Mycosynthesis: Rational Bioconstruction and Bioengineering of Fungal Natural Products

Total biosynthesis in fungi is beginning to compete with traditional chemical total synthesis campaigns. Herein, the advantages, disadvantages and future opportunities are discussed within the scope of several recent examples.

1 Introduction

2 Synthetic Examples

2.1 2-Pyridones

2.2 Cytochalasans

2.3 Sorbicillinoids

2.4 Decalins: Solanapyrone

2.5 α-Pyrone Polyenes: Citreoviridin and Aurovertin

2.6 Anditomin and Related Meroterpenoids

2.7 Tropolone Sesquiterpenoids

3 Conclusion

Chemical and Genetic Studies on the Formation of Pyrrolones During the Biosynthesis of Cytochalasans

A key step during the biosynthesis of cytochalasans is a proposed Knoevenagel condensation to form the pyrrolone core, enabling the subsequent 4+2 cycloaddition reaction that results in the characteristic octahydroisoindolone motif of all cytochalasans. In this work, we investigate the role of the highly conserved α,β-hydrolase enzymes PyiE and ORFZ during the biosynthesis of pyrichalasin H and the ACE1 metabolite, respectively, using gene knockout and complementation techniques. Using synthetic aldehyde models we demonstrate that the Knoevenagel condensation proceeds spontaneously but results in the 1,3-dihydro-2H-pyrrol-2-one tautomer, rather than the required 1,5-dihydro-2H-pyrrol-2-one tautomer. Taken together our results suggest that the α,β-hydrolase enzymes are essential for first ring cyclisation, but the precise nature of the intermediates remains to be determined.

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.

Alternative transcription start sites of the enolase-encoding gene enoA are stringently used in glycolytic/gluconeogenic conditions in Aspergillus oryzae

Gene expression using alternative transcription start sites (TSSs) is an important transcriptional regulatory mechanism for environmental responses in eukaryotes. Here, we identify two alternative TSSs in the enolase-encoding gene (enoA) in Aspergillus oryzae, an industrially important filamentous fungus. TSS use in enoA is strictly dependent on the difference in glycolytic and gluconeogenic carbon sources. Transcription from the upstream TSS (uTSS) or downstream TSS (dTSS) predominantly occurs under gluconeogenic or glycolytic conditions, respectively. In addition to enoA, most glycolytic genes involved in reversible reactions possess alternative TSSs. The fbaA gene, which encodes fructose-bisphosphate aldolase, also shows stringent alternative TSS selection, similar to enoA. Alignment of promoter sequences of enolase-encoding genes in Aspergillus predicted two conserved regions that contain a putative cis-element required for enoA transcription from each TSS. However, uTSS-mediated transcription of the acuN gene, an enoA ortholog in Aspergillus nidulans, is not strictly dependent on carbon source, unlike enoA. Furthermore, enoA transcript levels in glycolytic conditions are higher than in gluconeogenic conditions. Conversely, acuN is more highly transcribed in gluconeogenic conditions. This suggests that the stringent usage of alternative TSSs and higher transcription in glycolytic conditions in enoA may reflect that the A. oryzae evolutionary genetic background was domesticated by exclusive growth in starch-rich environments. These findings provide novel insights into the complexity and diversity of transcriptional regulation of glycolytic/gluconeogenic genes among Aspergilli.

Investigating the biosynthesis of Sch-642305 in the fungus Phomopsis sp. CMU-LMA

The biosynthetic pathway of the fungal metabolite Sch-642305 was determined by a series of knockout and heterologous expression experiments.

Heterologous production of fungal natural products: Reconstitution of biosynthetic gene clusters in model host Aspergillus oryzae

While exploring phytotoxic metabolites from phytopathogenic fungi in the 1970s, we became interested in biosynthetic enzymes that catalyze Diels-Alder reactions involving biosynthesis of several phytotoxins that we isolated. Target enzymes were successfully characterized, and this triggered the identification of various Diels-Alderases in a recent decade. Through our Diels-Alderase project in 1990s, we recognized a highly efficient expression system of various biosynthetic genes with Aspergillus oryzae as a host. With the development of tools such as genomic data and bioinformatics analysis to identify biosynthetic gene clusters for natural products, we developed a highly reliable methodology such as hot spot knock-in to elucidate the biosynthetic pathways of representative fungal metabolites including phytotoxic substances. This methodology allows total biosynthesis of natural products and genome mining using silent biosynthetic gene clusters to obtain novel bioactive metabolites. Further applications of this technology are discussed.

Elucidation of biosynthetic pathway of a plant hormone abscisic acid in phytopathogenic fungi

Abscisic acid (ABA) is one of the plant hormones that regulates physiological functions in various organisms, including plants, sponges, and humans. The biosynthetic machinery in plants is firmly established, while that in fungi is still unclear. Here, we elucidated the functions of the four biosynthetic genes, bcABA1-bcABA4, found in Botrytis cinerea by performing biotransformation experiments and in vitro enzymatic reactions with putative biosynthetic intermediates. The first-committed step is the cyclization of farnesyl diphosphate to give α-ionylideneethane catalyzed by a novel sesquiterpene synthase, BcABA3, which exhibits low amino acid sequence identities with sesquiterpene synthases. Subsequently, two cytochrome P450s, BcABA1 and BcABA2, mediate oxidative modifications of the cyclized product to afford 1ʹ,4ʹ-trans-dihydroxy-α-ionylideneacetic acid, which undergoes alcohol oxidation to furnish ABA. Our results demonstrated that production of ABA does not depend on the nucleotide sequence of bcABA genes. The present study set the stage to investigate the role of ABA in infections.

Safety of the fungal workhorses of industrial biotechnology: update on the mycotoxin and secondary metabolite potential of Aspergillus niger, Aspergillus oryzae, and Trichoderma reesei

This review presents an update on the current knowledge of the secondary metabolite potential of the major fungal species used in industrial biotechnology, i.e., Aspergillus niger, Aspergillus oryzae, and Trichoderma reesei. These species have a long history of safe use for enzyme production. Like most microorganisms that exist in a challenging environment in nature, these fungi can produce a large variety and number of secondary metabolites. Many of these compounds present several properties that make them attractive for different industrial and medical applications. A description of all known secondary metabolites produced by these species is presented here. Mycotoxins are a very limited group of secondary metabolites that can be produced by fungi and that pose health hazards in humans and other vertebrates when ingested in small amounts. Some mycotoxins are species-specific. Here, we present scientific basis for (1) the definition of mycotoxins including an update on their toxicity and (2) the clarity on misclassification of species and their mycotoxin potential reported in literature, e.g., A. oryzae has been wrongly reported as an aflatoxin producer, due to misclassification of Aspergillus flavus strains. It is therefore of paramount importance to accurately describe the mycotoxins that can potentially be produced by a fungal species that is to be used as a production organism and to ensure that production strains are not capable of producing mycotoxins during enzyme production. This review is intended as a reference paper for authorities, companies, and researchers dealing with secondary metabolite assessment, risk evaluation for food or feed enzyme production, or considerations on the use of these species as production hosts.

Total Biosynthesis of Brassicicenes: Identification of a Key Enzyme for Skeletal Diversification

The biosynthetic pathway of brassicicenes, derived from the phytopathogen Pseudocercospora fijiensis, was fully reconstituted. Heterologous expression of the eight genes highly expressed in infected leaf tissues generated a new brassicicene derivative as a final product. Together with the characterization of P450 from Alternaria brassicicola, a late stage of the biosynthetic pathway, which generates remarkable structural diversity, has been proposed. Notably, a unique P450 that converts 3 to the structurally distinct 4 and 6 was identified.

Total Biosynthesis of Antiangiogenic Agent (-)-Terpestacin by Artificial Reconstitution of the Biosynthetic Machinery in Aspergillus oryzae

The total biosynthesis of (-)-terpestacin was achieved by heterologous expression of four biosynthetic enzyme genes ( tpcA- D) in Aspergillus oryzae. After construction of preterpestacin I by the action of bifunctional terpene synthase (TpcA), two cytochrome P450s (TpcBC) activate inert C-H bond to install three hydroxyl groups on the A-ring in stereo- and regioselective manners. Subsequently, a flavin-dependent oxidase (TpcD) catalyzes oxidation of the vicinal diol moiety to give a α-diketone, which undergoes an enolization to furnish terpestacin. The successful synthesis of structurally elaborated terpestacin showed that a reconstitution approach that harnesses several biosynthetic enzyme genes in A. oryzae could be a promising alternative to the current chemical synthesis of natural terpenoids.

The biosynthesis of cytochalasans

This highlight summarises the recent advances in elucidating and engineering the biosynthesis of cytochalasan natural products.

Linker Flexibility Facilitates Module Exchange in Fungal Hybrid PKS-NRPS Engineering

Polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) each give rise to a vast array of complex bioactive molecules with further complexity added by the existence of natural PKS-NRPS fusions. Rational genetic engineering for the production of natural product derivatives is desirable for the purpose of incorporating new functionalities into pre-existing molecules, or for optimization of known bioactivities. We sought to expand the range of natural product diversity by combining modules of PKS-NRPS hybrids from different hosts, hereby producing novel synthetic natural products. We succeeded in the construction of a functional cross-species chimeric PKS-NRPS expressed in Aspergillus nidulans. Module swapping of the two PKS-NRPS natural hybrids CcsA from Aspergillus clavatus involved in the biosynthesis of cytochalasin E and related Syn2 from rice plant pathogen Magnaporthe oryzae lead to production of novel hybrid products, demonstrating that the rational re-design of these fungal natural product enzymes is feasible. We also report the structure of four novel pseudo pre-cytochalasin intermediates, niduclavin and niduporthin along with the chimeric compounds niduchimaeralin A and B, all indicating that PKS-NRPS activity alone is insufficient for proper assembly of the cytochalasin core structure. Future success in the field of biocombinatorial synthesis of hybrid polyketide-nonribosomal peptides relies on the understanding of the fundamental mechanisms of inter-modular polyketide chain transfer. Therefore, we expressed several PKS-NRPS linker-modified variants. Intriguingly, the linker anatomy is less complex than expected, as these variants displayed great tolerance with regards to content and length, showing a hitherto unreported flexibility in PKS-NRPS hybrids, with great potential for synthetic biology-driven biocombinatorial chemistry.