Zhenhua
Guan
a,
Nanyu
Yao
a,
Wenling
Yuan
a,
Fengli
Li
a,
Yang
Xiao
a,
Mewlude
Rehmutulla
a,
Yuhan
Xie
a,
Chunmei
Chen
a,
Hucheng
Zhu
a,
Yuan
Zhou
a,
Qingyi
Tong
a,
Zheng
Xiang
*bc,
Ying
Ye
*a and
Yonghui
Zhang
*a
aHubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, People's Republic of China. E-mail: zhangyh@mails.tjmu.edu.cn; ying_ye@hust.edu.cn
bState Key Laboratory of Chemical Oncogenomics, Shenzhen Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, P. R. China
cInstitute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518132, China. E-mail: zxiang@pku.edu.cn
First published on 28th November 2024
Cotylenins (CNs) are bioactive fungal diterpene glycosides that exhibit stabilizing activity on 14-3-3 protein–protein interactions (PPIs), which has significant therapeutic potential. Although CNs were isolated as early as 1970, their biosynthetic pathway has remained unclear, and their limited supply has hindered further research. Here, we report the identification of the biosynthetic gene cluster cty and elucidation of the biosynthetic pathway of CNs. Our investigation reveals the roles of glycosyltransferase, methyltransferase, and prenyltransferase enzymes in the assembly and modification of the saccharide moiety, as well as the multifunctional oxidation activity of the P450 enzyme CtyA. We leveraged this knowledge to achieve the total biosynthesis of not only key intermediates such as CN-C, E, F, and I, but also a novel, unnatural CN derivative using heterologous expression. This showcases the potential of pathway enzymes as catalytic tools to expand the structural diversity of diterpene glycosides. Furthermore, the stabilization effects of pathway intermediates on 14-3-3 PPIs underscore the importance of saccharide modifications in bioactivity. These findings provide a foundation for future rational synthesis of cotylenin A and other structurally diverse derivatives, broadening the scope of diterpene glycoside production.
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Fig. 1 Chemical structures of representative CN natural products and biosynthetically related FC-A and BC-I. |
Compound 1 exerts its biological effects by stabilizing protein–protein interactions (PPIs) involving the 14-3-3 protein, a family of regulatory proteins that bind phosphorylated targets to modulate their function. This action impacts cancer-relevant pathways such as C-RAF signaling.8 Given the integral role of PPIs in cellular processes and disease pathogenesis,9 compound 1's ability to target 14-3-3 PPIs offers a novel approach for therapeutic intervention of cancer and other diseases. Furthermore, structurally related FC glycosides also demonstrate varying activity and selectivity towards 14-3-3 PPIs.10,11 However, studies on the activity of other natural CN products on 14-3-3 PPIs have not been reported, likely due to the difficulty in isolating these molecules.
Despite its biological significance, the preparation of 1 remains challenging due to several factors. The original producing organism, Cladosporium sp. 501-7W, has lost its ability to proliferate in culture,12 rendering microbial fermentation unfeasible. Additionally, the complexity of 1's molecular structure poses a significant hurdle, with the first total synthesis reported by Masahisa Nakada's research group in 2020 requiring a 25-step process starting from geraniol.13 Many studies have attempted to shorten the total synthesis steps by employing concise synthesis or enzymatic synthesis of its aglycone 7.14,15 However, even with these efforts, the intricate saccharide modifications continue to present difficulties in chemical synthesis.
These challenges underscore the need for alternative approaches, such as identifying the biosynthetic gene cluster (BGC) from other strains or employing synthetic biology strategies to develop more efficient and scalable methods to produce 1 and other CN derivatives. One such attempt involved knocking out genes in the FC-A BGC, thereby generating analogous glucosylated precursors for semisynthetic production.12 FC-A, which is structurally similar to CN-A, benefits from an available producing strain, and its BGC and biosynthetic pathway have been extensively studied by the Dairi group.7,12,16,17
In this study, we identified a BGC and achieved the production of crucial intermediates such as CN-C (2) and F (3) through heterologous expression in Aspergills oryzae NSAR1 (AO).18,19 Additionally, we characterized the glycosyltransferase and the modifying enzymes for the saccharide moiety, enabling enzymatic synthesis of previously unidentified intermediates and unnatural CN derivatives. Our research will make significant contributions to the ultimate biosynthesis of 1 and the preparation of its derivatives.
Based on these characteristics, we identified an Pa-like cluster from the genomic library of our own fungus Talaromyces adpressus (TA), which encodes the FS and glycosyltransferase. However, it lacks the prenyltransferase. Since this cluster is located at the end of the scaffold, it is suspected to be incomplete. Using cblaster,20 we found a highly similar but longer BGC in the Talaromyces verruculosus TS63-9 strain (Fig. S1†), which encodes both a prenyltransferase and a MTase. Subsequently, we performed a local BLAST search for these two enzymes in our TA strain and found two homologous enzymes located next to each other at the end of another scaffold. By connecting the ends of these two scaffolds, we obtained a more complete BGC, which we named the cty cluster (Fig. 2). We then conducted a comparative analysis of this cluster with the Pa cluster and the brassicicenes BGC abn (Fig. 2).21
BC-I (8) is a common intermediate for both CN and BC compounds, formed by the five genes abnABCDE21,22 in abn cluster (Fig. S2 and S16†), which have highly similar counterparts ctyCFGHI in the cty cluster (Fig. 2 and Table S3†). After the formation of BC-I, the subsequent steps of 9-hydroxylation, glucosylation, and prenylation are similar for FCs and CNs. Not surprisingly, we found that the three modifying enzymes in the FC pathway, Pa-orf6 (glycosyltransferase), Pa-orf7 (C-9 hydroxylase), and Pa-orf11 (prenyltransferase), have highly similar homologous genes in the cty cluster: ctyD, ctyB, and ctyJ, respectively (Fig. 2 and Table S3†). Additionally, we identified two genes unique to the cty cluster, including ctyE, which encodes a MTase annotated as a ribosomal RNA small subunit methyltransferase, and ctyA, a P450 enzyme with low homology to the P450 enzymes in the other two clusters, possibly catalyzing a novel oxidation reaction (Table S3†). Based on this information, we propose that the cty cluster is likely responsible for the biosynthesis of CNs.
We first heterologously expressed the gene encoding terpene synthase CtyF and confirmed it produced fusicoccadiene (Fig. S15†). Given the high homology between CtyCFGHI and the BC-I (8)-producing enzymes AbnABCDE, we hypothesized that AO-ctyCFGHI also produces 8. Therefore, instead of constructing AO-ctyCFGHI, we assumed 8 as its product and used it to feed the transformants of other cty genes to quickly verify their functions. Taking the modification sequence for biosynthesizing FCs as a reference, we constructed the following transformants: AO-ctyB, AO-ctyBD, AO-ctyBDE, AO-ctyBDEJ, and AO-ctyABDEJ, and analyzed the feeding products using LC-MS. In AO-ctyB fed with 8, we detected a new peak with a molecular weight (mw) increase of 16 Da (Fig. 3A(ii)), which was isolated and identified as compound 7 through NMR spectroscopy (Fig. S17, S18 and Table S4†). Recent years have seen progress in achieving C9 beta-hydroxylation of CN glycosides through organic catalysis due to the research by Nakada, Shenvi, and Renata, who have continuously improved the stereoselectivity of the reaction.13–15 We recently reported that Orf7 in the Pa cluster can efficiently catalyze this reaction enzymatically.23 Here, we discovered that CtyB has the same function. In AO-ctyBD adding 8, we detected a new peak with a mw equals to 7 + 162 Da (Fig. 3A(iii)), which was isolated and identified as the glucosylated product 6 (Fig. S19–S21 and Table S5†). We then introduced the MTase ctyE, and after feeding 8, LC-MS detected a new peak with a mw equals to 6 + 14 Da (Fig. 3A(iv)). Scale up fermentation and isolation identified this compound as the methylated product 5 (Fig. S22–S25 and Table S6†). To verify the function of the prenyltransferase, we further introduced ctyJ into the previous transformant, and after feeding 8, LC-MS detected a new peak with a mw equals to 5 + 68 Da (Fig. 3A(v)). Scale up fermentation and isolation identified this compound as the prenylated product 4 (Fig. S26–S28 and Table S7†). Next, we introduced the last uncharacterized P450 oxidase CtyA, and expected to obtain products with oxidative modifications on the glucosyl moiety. After feeding 8, LC-MS detected two new peaks with mw equals to 4 + 32 Da and + 30 Da (Fig. 3A(vii)). Scale up fermentation and isolation identified these compounds as 3 (Fig. S29–S32 and Table S8†) and 2 (Fig. S33–S36 and Table S9†), respectively. Additionally, in the AO-ctyABDJ transformant lacking the MTase ctyE, feeding 8 resulted in small amounts of compounds 12 (mw 619 Da) and 13 (mw 635 Da) (Fig. 3A(vi)). Compound 12 was isolated, but due to its small amount, it was difficult to purify completely. However, 1D and 2D NMR allowed structural assignment (Fig. S37–S42 and Table S10†), revealing a C3′′-4′′ epoxy structure, with no oxidation at the C1′′. This indicates that CtyJ and CtyA can accept substrates without methylation at the C6′ position, forming a monooxygenated epoxy product by CtyA. Due to the low yield, 13 could not be isolated for NMR analysis., but based on its molecular formula and elution time, we infer that its structure is a further hydroxylation product of compound 12 at C1′′ position (Fig. 4).
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Fig. 4 Reconstitution of the biosynthetic pathway of CNs in this work and the semi-synthesis of ISIR-050. |
The feeding results indicate that CtyA is multifunctional, capable of introducing an epoxide on the prenyl C3′′-4′′ double bond and oxidizing the prenyl C1′′ to a hydroxyl and aldehyde group. To further investigate the order of its modifications, we constructed AO-ctyA and examined the biotransformation products over a time gradient. The results showed that feeding 4 to AO-NSAR1 did not result in any detectable oxygenated products, and the substrate remained unconsumed (Fig. 3B(iv)). In AO-ctyA, small amounts of a monooxygenated compound 11 were observed at 1.5 and 2.5 days (Fig. 3B(i and ii)), but 2 and 3 were more predominant. After 3.5 days, 11 almost disappeared, with only 2 and 3 remaining (Fig. 3B(iii)). To investigate if CtyA can also transform the C1′′ hydroxyl group to an aldehyde group, 3 was fed into AO-ctyA for 3.5 days, resulting in the production of 2 (Fig. 3B(v)), while feeding 3 to AO-NSAR1 did not observe the formation of 2 (Fig. 3B(vi)). The mw of 11 corresponds to the molecular formula C33H54O10, but it could not be isolated due to its low yield. Based on the structure of 12, we speculate that 11 is the epoxidized product of 4 at the C3′′-4′′ double bond (Fig. 3B(i and ii)). These in vivo experiments demonstrate that CtyA is a multifunctional oxidase, capable of both epoxidizing the terminal double bond on the glucosylated prenyl group and performing 4-electron oxidation on the methyl group.
Converting 2 to 1 requires only one more oxidation step to form an oxygen bridge between C4′ and C1′′. We proceeded by introducing genes from the extended region of the cty cluster (Fig. S4(i, ii, iii, iv) and Table S3†), particularly focusing on the FAD enzyme hp5 with potential oxidase functions. Unfortunately, none of the transformants produced CN-A (Fig. S4(v)†). This suggests two possibilities: either the final catalytic enzyme is outside the cty cluster, or the enzyme required for the formation of 1 is absent in the TA strain. To verify these possibilities, we fed the previously obtained pathway intermediates 8, 6, 4, and 2 to TA in multiple medium, but 1 was still not detected (Fig. S3†). This result suggests that while the TA strain harbors the BGC for CNs, the exact capability of the strain to produce CN-A remains unclear. Further efforts will be needed to identify new strains or novel oxidases to achieve the complete biosynthesis of CN-A.
In vivo experiments showed that the prenyltransferase CtyJ catalyzes the prenylation of the C4′-hydroxyl group on the saccharide of 5, whereas the Pa-orf11 (H7CE84.1) from the Pa cluster is reported to prenylate the C6′-position on the FC's saccharide moiety. To investigate the substrate specificity of these PTs and try to prepare artificial combinatorial molecules, we reacted CtyJ and Pa-orf11 with 6 separately. Both enzymes exhibited regioselectivity by recognizing the substrate and catalyzing prenylation reactions at specific sites, producing 9 (Fig. S43–S48 and Table S11†) and an unnatural molecule 10 (Fig. S49–S54 and Table S12†), respectively (Fig. 5B). Prenylation on saccharides is rare; a recent example is the work by Zou's group, which reported that the prenyltransferase CosD can introduce a prenyl group onto linear saccharide.25 Phylogenetic analysis revealed that CtyJ, Pa-orf11, and CosD belong to typical fungal prenyltransferases and share high homology (Fig. S6†).
In vivo experiments showed that the MTase CtyE converts 6 into 5. Purified CtyE exhibited the same activity, but it cannot recognize the prenylated product 9 (Fig. 5C). This result clarifies that methylation occurs before prenylation in the pathway (Fig. 4). According to the protein structure predicted by Alphafold2, CtyE belongs to the Type I MTase family (Fig. S7†).26 MTases acting on saccharides are rare in fungi but are more common in bacteria, appearing in pathways such as the polyketide glycoside elloramycin27 and the macrolide mycinamicin.28 Phylogenetic analysis of representative MTases from fungal and bacterial secondary metabolites showed that CtyE has higher homology with bacterial MTases (Fig. S8†). This interesting phenomenon suggests that bacteria might have first evolved MTases for metabolizing 6, and this capability was later acquired by fungi through gene transfer.
The P450 enzyme CtyA exhibited consecutive oxidation activity on the prenyl group in vivo. We introduced its cDNA into S. cerevisiae RC01 which contains an integrated copy of cytochrome P450 reductase (AtCPR) from Aspergillus terreus,29 extracted the microsomes, and tested the in vitro activity (Fig. 5D). The results showed that CtyA can oxidize 4 to 11 and 3, but the efficiency is much lower than that in AO, and 2 was not detected. The in vitro results confirmed CtyA's ability to oxidize two distinct positions on the prenyl group, suggesting that after the formation of the epoxide, a change in the relative position of the intermediate brings the C1′′ position closer to the Heme iron center (Fig. S9†). We also examined CtyA's activity on 10, which has a shifted prenyl position, but no conversion was observed (Fig. S10†).
Based on the results from the in vivo and in vitro experiments, we have elucidated for the first time the biosynthetic pathways of several reported CN diterpene glycosides, including cotylenin E (5), I (4), F (3), and C (2) (Fig. 4), remaining only one oxidation step away from forming the oxygen bridge in CN-A (1). Additionally, by recombining the relevant genes in AO, we have isolated and identified previously unreported intermediates 6, 9, and 12 in the CNs pathway, as well as an artificial molecule 10 by borrowing the prenyltransferase from Pa cluster.
We have identified the CN BGC for the first time, enabling comparison with the known brassicicene and fusicoccin BGCs to understand the genetic basis of their structural differences. In comparing the abn and cty clusters, both share homologous genes involved in the production of BC-I (8). The abn cluster lacks glycosylation genes but contains a unique P450 enzyme for oxidative rearrangement,22 leading to the formation of the 5-9-5 scaffold as revised by our group;33 On the other hand, in the comparison between the Pa and cty clusters, both contain C9-hydroxylase and glycosyltransferase genes, facilitating similar glucosylation, but distinct modifying enzymes specific to the aglycone and sugar units drive structural variations between them. It is noteworthy that FCs primarily affect stomatal opening by stabilizing the interaction between plant 14-3-3 protein and H+-ATPase, whereas CNs promote cell elongation and division.34 The difference between FC and CN derivatives is reported to be due to the 12-hydroxyl group in FCs, which prevents complex formation with mode-1 ligands.35 Additionally, the unique enzymes CtyA (P450) and CtyE (methyltransferase) in the cty cluster for sugar moiety modifications have shown important activity-enhancing functions in our preliminary structure–activity relationship studies. These comparisons reveal critical insights into how genetic variations within BGCs influence the structure and bioactivity of these diterpenoids. Furthermore, our cblaster analysis indicates that the cty cluster is not widely distributed (Fig. S1†), which may help explain why CN-producing strains are relatively rare.
The discovery of the cty cluster provides a rich set of catalytic elements, facilitating the biosynthesis and chemoenzymatic synthesis of CNs. Additionally, combinatorial biosynthesis with the Pa cluster can generate more derivative molecules (such as compound 10 in this study). These derivatives can be employed to investigate whether their structural differences enhance the selectivity of 14-3-3 proteins for various target proteins, which is crucial for developing highly selective, druggable PPI stabilizers.
Unfortunately, the final step leading to CN-A remains unresolved in this study. Despite our attempts using various fermentation conditions and intermediate feeding in our TA strain, CN-A was not observed. This raises the possibility that the entire BGC may be silent. The cluster lacks obvious regulatory elements such as BGC-specific transcription factors, suggesting the need to explore various stimuli to activate it. Understanding the regulatory mechanisms of CN biosynthesis will provide further insight into their physiological and ecological functions.
Beyond simply elucidating the biosynthesis, our work revealed the potential of pathway enzymes as tools for rational design and the total biosynthesis of new compounds. This is exemplified by our successful creation of the unnatural cotylenin derivative 10, achieved through leveraging enzyme substrate promiscuity and regioselectivity across homologous BGCs. Furthermore, we revealed for the first time the stabilizing activity of CN biosynthetic intermediates on 14-3-3 PPIs. Future efforts will focus on identifying new strains or novel oxidases to achieve the complete biosynthesis of CN-A.
Footnote |
† Electronic supplementary information (ESI) available: Strains and methods, additional tables and figures, and NMR data. See DOI: https://doi.org/10.1039/d4sc05963h |
This journal is © The Royal Society of Chemistry 2025 |