Abstract

Indole terpenoids make up a large group of secondary metabolites that display an enticing array of bioactivities. While indole diterpene (IDT) and rarely indole sesquiterpene (IST) pathways have been found individually in filamentous fungi, here we show that both cluster types are encoded within the genome of Tolypocladium album. Through heterologous reconstruction, we demonstrate the SES cluster encodes for IST biosynthesis and can tailor IDT substrates produced by the TER cluster.
Complex secondary metabolites (SM) are synthesized via a collaboration between multiple enzymes, which are often encoded by genes that are physically colocated in biosynthetic gene clusters (BGCs).1,2 Typically these clusters encode all of the genes required to produce a specific group of SMs and many also encode their own regulatory elements. This clustering is commonly observed in both eukaryotes and prokaryotes, and various hypotheses have been put forward to explain this phenomenon.3−6 BGCs have been classically discovered by identifying metabolites of interest and then examining the genomes of the producing organisms.7,8 The application of modern omics approaches to SM biosynthesis has revealed many gene clusters that are not expressed (silent BGCs) as well as clusters that are seemingly not associated with any known SM (cryptic BGCs).9 Additionally, examples of biosynthetic reliance on unclustered genes and collaboration between independent BGCs suggest greater complexity than the paradigm of the independent and self-contained BGC delivering a single specific set of SMs.10−13
Indole diterpenes (IDTs) are a class of alkaloid SMs that exhibit a wide range of potent biological activities, including anticancer, antiviral, and insecticidal activities.14 These SMs are primarily produced by filamentous fungi and possess remarkable structural diversity. The indole core and cyclized terpene backbone can be elaborated by a plethora of decorative modifications to afford numerous compounds. This combination of therapeutic potential and complex chemistry has led to extensive investigation into IDT synthesis and biosynthesis.15−17 Conversely, the closely related indole sesquiterpenes (ISTs) are seemingly rare in nature, with only two reported occurrences in filamentous fungi (Figure 1B).18−20
Figure 1.
Selected fungal-derived IDTs and ISTs. (A) Terpendole E (9) and derivatives. (B) Prelecanindole (1) and derivatives.
These indole terpenoid SMs largely adhere to the “one BGC, one SM group” model;21,22 however, several cases of out-of-cluster activity do exist in IDT biosynthesis. For example, an unclustered terpene-cyclase in Aspergillus flavus shown to work in conjunction with a known BGC to deliver various IDTs.10
Tolypocladium album (Chaunopycnis alba, Albophoma yamanashiensis)23−25 is a filamentous fungus best known for producing the terpendoles, a large and complex group of IDTs first described nearly three decades ago (Figure 1A).26−28 The biosynthesis of the terpendoles has received significant attention due to their presence in various fungal species29−32 and promising bioactivities such as Eg5-kinesin inhibition.33,34 It has been shown previously that the TER biosynthetic gene cluster (BGC) in T. album encodes the machinery required to produce a range of IDTs known as the terpendoles,35 yet the specific biosynthetic routes and the associated machinery for the full array of related congeners still lack characterization. Here we describe the identification and characterization of a previously undescribed BGC in T. album that encodes the enzymes necessary for IST production, and we show that elements of this IST cluster are also able to deliver IDT decorations, expanding the array of biosynthetically accessible terpendoles.
We first examined the whole genome sequence (WGS) of T. album strain FO-254 (GenBank: BCKH00000000) using antiSMASH36 and BLAST37 with the intention of uncovering novel IDT tailoring genes. In addition to the previously described TER cluster coding for IDT biosynthesis,35 we identified a gene cluster spanning 13 kb and encoding five putative indole-terpenoid biosynthetic enzymes (herein named the SES cluster) (Figure 2; Table S8). This cluster shared significant similarity with the IST-producing SPD cluster from Cordana terrestris strain FKA-25, which is responsible for the generation of prelecanindole (1), lecanindole B (4), 16,17-diprenyllecanindole B (6), and sespendole (7).38 All five SES genes had orthologs in the SPD cluster with a minimum of 67% predicted amino acid identity (Table S9). A major point of difference between the SES and SPD clusters was the lack of an ortholog to spdH, a predicted oxidoreductase previously reported to play a role in the oxidation of prelecanindole (1) to lecanindole B (4).38 Neither was an unclustered orthologue of spdH found elsewhere in the T. album genome.
Figure 2.
IDT and IST BGC from Cordana terrestris (GenBank: LC380446), Tolypocladium album, and Epichloë festucae (GenBank: CP031387). PT1 and PT2 represent distinct prenyltransferase domains within the ORF. ORFs were colored according to predicted or verified function and homology.
From these analyses of the SES genes, we predicted that IST biosynthesis may also occur in T. album analogous to the previously established sespendole biosynthetic pathway (Scheme 1). However, although IDTs had been reported from this organism, no ISTs had been reported, and none could be detected from samples grown under various laboratory conditions (Supporting Information). This result prompted us to investigate gene expression using RNA sequencing, which confirmed a lack of expression of SES genes under standard shaking culture conditions and a low level of expression in static culture conditions coinciding with the beginning of conidiation (Table S10). Hence, we chose to characterize the SES cluster and its predicted role in IST biosynthesis using heterologous expression in the filamentous fungi Penicillium paxilli.
Scheme 1. Proposed Biosynthetic Pathways of (A) Indole-sesquiterpenes by the SPD and SES clusters (B) Indole-diterpenes by the TER cluster.
The stereochemistry for 8 is tentatively assigned based on literature comparison, and the absolute stereochemistry of 7 could not be unambiguously determined from spectral data (see Tables S11 and S12).
Formation of the core IST moiety requires indole terpene condensation, terpene epoxidation, and terpene cyclization. Based on sequence homology to the previously characterized SPD genes, three SES genes were predicted to encode for each of these steps, namely, sesE (indole-prenyltransferase), sesM (FAD-dependent monooxygenase), and sesB (terpene cyclase). These three genes were expressed in an IDT cluster-deficient strain of P. paxilli (CY2), and production of the IST prelecanindole (1) was detected (Figure 3, II; Figure S1), confirming that the SES cluster does encode for IST biosynthesis. For comparison, the previously characterized genes spdEMB were also expressed in the P. paxilli CY2 strain and 1 was similarly produced (Figure 3, VI; Figure S2).
Figure 3.
HR-ESI-LC-MS2 chromatograms of indole-terpenoids produced by SPD and SES genes involved in biosynthesis of ISTs. Traces show selected extracted ion chromatograms (EICs) of key fragments associated with each compound (Table S12). Peaks labeled with an asterisk are putative isomers of 1.
Sequence comparisons show that sesE and spdE each encode two distinct prenyltransferase domains (denoted PT1 and PT2, Figure 2) within a single open reading frame (ORF).38 Consistent with this observation, both SesE and SpdE were able to catalyze the transfer of farnesyl pyrophosphate (FPP) to the indole moiety to make farnesyl indole and were also observed to modify 1 through aromatic prenylation. Whereas SesE yielded only 16-prenylprelecanindole (2), SpdE yielded both 2 and 16,17-diprenylprelecanindole (3). To pinpoint this dual functionality of SesE and SpdE, the first indole prenyltransferase domains (PT1) encoded by the sesE and spdE genes were excised and expressed independently of the second indole prenyltransferase domains (PT2). Accordingly, when sesE[PT1] was expressed with sesMB in P. paxilli, 1 was produced but not 2 (Figure 3, I; Figure S3). Similarly, spdE[PT1] expressed with spdMB (Figure 3, V; Figure S4) produced 1 but not 2 or 3, demonstrating that the PT1 domain is responsible for the farnesyl transfer onto the indole donor and suggesting that the PT2 domain is responsible for the aromatic prenylation observed with the full-length sesE or spdE genes. A similar dual domain encoding ORF, ltmE, also plays a role in aromatic prenylation in lolitrem biosynthesis in E. festucae; however, no additional catalytic role has been ascribed to the protein, and E. festcuae appears to lack other enzymes with a role in IST biosynthesis.39
To assess the next step in the pathway, sesQ (encoding a cytochrome P450 monooxygenase) was expressed together with sesEMB in P. paxilli, and production of 16-prenyllecanindole B (5) and 16, 17-diprenyllecanindole B (6) was detected (Figure 3, III; Figure S5), demonstrating that this monooxygenase oxidizes both C7 and C9 positions. Both 5 and 6 were also detected when spdQ and spdH were expressed with spdEMB in P. paxilli (Figure 3, VII; Figure S6). When the truncated sesE[PT1] was expressed with sesMBQ in P. paxilli, we observed the formation of 4 and the partially oxidized product 9-desoxylecanindole B (S1) (Figure S7). Similarly, we observed the production of 4 in the spdE[PT1]MBQH transformants (Figure S8). Additionally, we found that SpdQ was sufficient to perform oxidation of 1 to 4 in our experiments, and we were unable to attribute any function to SpdH. (Figures S9 and S10). When the full-length SesE was included, we observed diprenylation of 4 but only monoprenylation of 1, whereas we found that SpdE catalyzed the diprenylation of both 4 and 1. This observation implies that SpdE has a substrate tolerance broader than that of the newly characterized SesE. We next examined whether 4 was the required intermediate in the biosynthetic pathway or if 2 and 3 might instead be oxidized to 5 and 6, respectively, bypassing 4. An extract containing a mixture of 1, 2, and 3 (isolated from P. paxilli expressing spdEMB) was fed to P. paxilli transformants expressing sesQ or spdQH. Both transformants showed a depletion of 1 and an accumulation of 4 but neither a change in the abundance of 2 and 3 nor accumulation of 5 and 6, suggesting that 2 and 3 are shunt products rather than pathway intermediates (Figure S11).
To elucidate the ultimate step in the pathway, the last remaining IST cluster gene sesJ (encoding a further cytochrome P450 monooxygenase) was expressed alongside sesEMBQ in P. paxilli. SesJ catalyzed the formation of a compound with identical mass and similar spectral properties to sespendole (7) and a cyclized product cyclosespendole (8) forming the A/B ring structure on the indole moiety (Figure 3, IV; Figure S12). While this multistep reaction involving epoxidation, hydroxylation, and oxidative cyclization had not been observed within an IST biosynthetic pathway, this same A/B ring structure is observed in lolitrem biosynthesis through the action of P450 monooxygenase LtmJ.39,40 Our spectroscopic analysis of 8 was consistent with the trans ring junction configuration previously described for the lolitrems.41 In addition to 8, we isolated a minor (approximately 20% by peak area) diasteroisomeric compound (8′) from P. paxilli expressing sesEMBQJ with spectroscopic data consistent with the cis ring junction configuration (Table S11, Figure S13).42 This observation of minor cis diastereomers has also been noted in lolitrem biosynthesis. In contrast, expressing spdJ alongside spdEMBQH in P. paxilli produced 7 as expected, but surprisingly we also observed the formation of another compound (labeled here as 7′; Figure 3, VIII; Figure S14) in a higher apparent yield (the ratio of 7 to 7′ was approximately 1:3.5 based on peak area). This compound has identical mass and remarkably similar NMR spectra to 7 and we infer a diastereomeric relationship between 7 and 7′ by analogy to a previously proposed relationship between two paxilline-derived compounds produced by Aspergillus oryzae expressing spdJ or ltmJ (Table S11).38
Given this unexpected finding, we examined the substrate specificity of SesJ, SpdJ, and LtmJ through chemical feeding experiments. An extract containing 6 (isolated from P. paxilli strain expressing spdEMBQH) was fed to P. paxilli transformants expressing either sesJ, spdJ, or ltmJ. As expected, spdJ produced 7 and 7′ whereas sesJ and ltmJ each produced 7, 8, and 8′ (Figure S15). When 7 or 7′ were separately fed to P. paxilli transformants expressing sesJ or ltmJ, 7 was cyclized to 8 and 8′ by both gene products but 7′ was not cyclized by either (Figure 4A and B; Figures S16 and S17). Transformants expressing spdJ did not cyclize 7 or 7′ (Figure 4A and B; Figures S16 and S17). These observations imply that 7 is indeed the intermediate to 8 and that 7′ is a shunt product that cannot be cyclized and is only formed in the absence of efficient further processing.
Figure 4.

HRES-LC-MS2 chromatograms of chemical feeding experiments. Transformants fed with (A) pure 7, (B) pure 7′, and (C) extract containing 9. (D) Biosynthetic pathway of 13/13′ from 9. Structural assignments of compounds are based on MS data and are therefore tentative (see Figures S20–S24, Table S15).
Given the co-occurrence of both IDT TER and IST SES BGCs within T. album, we evaluated the crossover between the biosynthetic componentry. In a small-scale chemical feeding experiment, an extract containing terpendole E (9) was fed to P. paxilli transformants expressing sesE or sesEJ. Both strains converted 9 to prenylterpendole E (10) and diprenylterpendole E (11) (Figure 4C; Figures S18 and S19) whereas SesJ further modified 11 to produce an epoxyalcohol (12) intermediate and the cyclized lolicine A (13) and isomer (13′) (Figure 4C; Figures S20–S24).43 In equivalent feeding experiments using spdE and spdEJ, 10, 11, and 12 were observed in addition to the isomeric 12′ (Figure 4C; Figures S18 and S19), mirroring the observation of diastereomeric 7 and 7′ in the IST pathway reconstruction. Importantly, the ability of SesE and SesJ to modify a terpendole skeleton indicates that the SES and TER clusters of T. album can collaborate to generate alternate metabolites.
Our characterization of the SES gene cluster in T. album is only the third example of IST biosynthesis reported in the fungal kingdom, and to the best of our knowledge T. album is the first fungus identified with functional IDT and IST clusters. The well-established role of T. album as a diverse IDT producer has obfuscated its capability for IST biosynthesis, providing a functionality that enables an expanded repertoire of IDTs to be biosynthesized. To understand how widespread this dual functionality is, we undertook further analysis of available genomic data. We uncovered orthologous TER BGCs in 13 Tolypocladium species (Table S13), four of which contained complete orthologous SES clusters and two of which contained partial clusters (Table S14, Figure S25).
Here, we fully characterize an IST cluster, a cluster that bears a strong functional relationship to the SPD IST cluster in C. terrestris and the LTM IDT cluster in E. festucae, demonstrating the ability to form the lolitrem A/B ring structure characteristic of these highly decorated IDTs. We have also determined the precise roles of dual function indole prenyltransferases. Broad substrate tolerances in the tailoring components also deliver functional crosstalk between the TER and SES clusters, representing a unique example of intercluster cooperation within a single organism.
Acknowledgments
This work was financially supported by the New Zealand Ministry of Business, Innovation, and Employment (Grant #RTVU1809).
Data Availability Statement
The data underlying this study are available in the published article and its Supporting Information.
Supporting Information Available
The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.orglett.3c02412.
Experimental procedures, gene cluster prediction and comparisons, primer and plasmid details, additional LC-MS traces, and NMR data and spectra (PDF)
The authors declare no competing financial interest.
Supplementary Material
References
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This section collects any data citations, data availability statements, or supplementary materials included in this article.
Supplementary Materials
Data Availability Statement
The data underlying this study are available in the published article and its Supporting Information.




