1
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Tang J, Matsuda Y. Discovery of fungal onoceroid triterpenoids through domainless enzyme-targeted global genome mining. Nat Commun 2024; 15:4312. [PMID: 38773118 PMCID: PMC11109268 DOI: 10.1038/s41467-024-48771-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 05/09/2024] [Indexed: 05/23/2024] Open
Abstract
Genomics-guided methodologies have revolutionized the discovery of natural products. However, a major challenge in the field of genome mining is determining how to selectively extract biosynthetic gene clusters (BGCs) for untapped natural products from numerous available genome sequences. In this study, we developed a fungal genome mining tool that extracts BGCs encoding enzymes that lack a detectable protein domain (i.e., domainless enzymes) and are not recognized as biosynthetic proteins by existing bioinformatic tools. We searched for BGCs encoding a homologue of Pyr4-family terpene cyclases, which are representative examples of apparently domainless enzymes, in approximately 2000 fungal genomes and discovered several BGCs with unique features. The subsequent characterization of selected BGCs led to the discovery of fungal onoceroid triterpenoids and unprecedented onoceroid synthases. Furthermore, in addition to the onoceroids, a previously unreported sesquiterpene hydroquinone, of which the biosynthesis involves a Pyr4-family terpene cyclase, was obtained. Our genome mining tool has broad applicability in fungal genome mining and can serve as a beneficial platform for accessing diverse, unexploited natural products.
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Affiliation(s)
- Jia Tang
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Yudai Matsuda
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China.
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2
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Yan D, Matsuda Y. Methyltransferase Domain-Focused Genome Mining for Fungal Polyketide Synthases. SMALL METHODS 2024:e2400107. [PMID: 38644685 DOI: 10.1002/smtd.202400107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/05/2024] [Indexed: 04/23/2024]
Abstract
A comparison of substrate-binding site amino acid residues in the C-methyltransferase (MT) domains of fungal nonreducing polyketide synthases (NR-PKSs) suggests that these residues are correlated with the methylation modes used by the PKSs. A PKS, designated as AsbPKS, with substrate-binding site residues distinct from those of other known PKSs is focused on. The characterization of AsbPKS revealed that it yields an isocoumarin derivative, anhydrosclerotinin B (1), the biosynthesis of which involves a previously unreported methylation pattern. This study demonstrates the utility of MT domain-focused genome mining for the discovery of PKSs with new functions.
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Affiliation(s)
- Dexiu Yan
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Yudai Matsuda
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
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3
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Rothchild KW, Hagar M, Berry D, Ryan KS. Two Iron(II), α-Ketoglutarate-Dependent Enzymes Encoded by the PPZ Gene Cluster of Metarhizium majus Enable Production of 8-Hydroxyperamine. J Am Chem Soc 2024; 146:10263-10267. [PMID: 38578094 DOI: 10.1021/jacs.4c01419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Entomopathogenic fungus Metarhizium majus contains the nine-gene PPZ cluster, with ppzA, encoding a peramine-producing nonribosomal peptide synthetase, as the central component. In this work, the roles of two α-ketoglutarate, iron-dependent oxygenases encoded by the PPZ genes ppzC and ppzD were elucidated. PpzD was found to produce both trans-4-hydroxy-l-proline and trans-3-hydroxy-l-proline in a 13.1:1 ratio, yielding a key precursor for peramine biosynthesis. PpzC was found to act directly on peramine, yielding the novel analogue 8-hydroxyperamine.
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Affiliation(s)
- Kristina W Rothchild
- Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Mostafa Hagar
- Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Daniel Berry
- Ferrier Research Institute, Victoria University of Wellington, Wellington, 6012, New Zealand
| | - Katherine S Ryan
- Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
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4
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Quan Z, Awakawa T. Recent developments in the engineered biosynthesis of fungal meroterpenoids. Beilstein J Org Chem 2024; 20:578-588. [PMID: 38505236 PMCID: PMC10949012 DOI: 10.3762/bjoc.20.50] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/21/2024] [Indexed: 03/21/2024] Open
Abstract
Meroterpenoids are hybrid compounds that are partially derived from terpenoids. This group of natural products displays large structural diversity, and many members exhibit beneficial biological activities. This mini-review highlights recent advances in the engineered biosynthesis of meroterpenoid compounds with C15 and C20 terpenoid moieties, with the reconstruction of fungal meroterpenoid biosynthetic pathways in heterologous expression hosts and the mutagenesis of key enzymes, including terpene cyclases and α-ketoglutarate (αKG)-dependent dioxygenases, that contribute to the structural diversity. Notable progress in genome sequencing has led to the discovery of many novel genes encoding these enzymes, while continued efforts in X-ray crystallographic analyses of these enzymes and the invention of AlphaFold2 have facilitated access to their structures. Structure-based mutagenesis combined with applications of unnatural substrates has further diversified the catalytic repertoire of these enzymes. The information in this review provides useful knowledge for the design of biosynthetic machineries to produce a variety of bioactive meroterpenoids.
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Affiliation(s)
- Zhiyang Quan
- RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Takayoshi Awakawa
- RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
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5
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Tang J, Matsuda Y. Functional analysis of transmembrane terpene cyclases involved in fungal meroterpenoid biosynthesis. Methods Enzymol 2024; 699:419-445. [PMID: 38942513 DOI: 10.1016/bs.mie.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Pyr4-family terpene cyclases are noncanonical transmembrane class II terpene cyclases that catalyze a variety of cyclization reactions in the biosynthesis of microbial terpenoids, such as meroterpenoids. However, although these cyclases are widely distributed in microorganisms, their three-dimensional structures have not been determined, possibly due to the transmembrane locations of these enzymes. In this chapter, we describe procedures for the functional analysis of transmembrane terpene cyclases based on their model structures generated using AlphaFold2. We used AdrI, the Pyr4-family terpene cyclase required for the biosynthesis of andrastin A and its homologs, as an example.
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Affiliation(s)
- Jia Tang
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, P.R. China
| | - Yudai Matsuda
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, P.R. China.
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6
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Yan D, Matsuda Y. Global genome mining-driven discovery of an unusual biosynthetic logic for fungal polyketide-terpenoid hybrids. Chem Sci 2024; 15:3011-3017. [PMID: 38404388 PMCID: PMC10882540 DOI: 10.1039/d3sc06001b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/16/2024] [Indexed: 02/27/2024] Open
Abstract
Genome mining has facilitated the efficient discovery of untapped natural products. We performed global genome mining in fungi and discovered a series of biosynthetic gene clusters (BGCs) that appeared to afford polyketide-terpenoid hybrids via a distinct biosynthetic mechanism from those adopted by known pathways. Characterization of one of the BGCs revealed that it yields the drimane-phthalide hybrid 1. During the biosynthesis of 1, the farnesyl group is unusually introduced by the dimethylallyltryptophan synthase-type prenyltransferase MfmD and is then cyclized by the Pyr4-family terpene cyclase MfmH. The replacement of MfmH with its homologue OcdTC gave another hybrid molecule with a monocyclic terpenoid moiety. Moreover, PsetPT, an MfmD homologue, was found to perform dimethylallylation and was then engineered to install a geranyl group. Our study unraveled an unusual biosynthetic mechanism for fungal phthalide-terpenoid hybrids and provided insights into how their structural diversification could be achieved.
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Affiliation(s)
- Dexiu Yan
- Department of Chemistry, City University of Hong Kong Tat Chee Avenue Kowloon Hong Kong SAR China
| | - Yudai Matsuda
- Department of Chemistry, City University of Hong Kong Tat Chee Avenue Kowloon Hong Kong SAR China
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7
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Monkcom EC, Gómez L, Lutz M, Ye S, Bill E, Costas M, Klein Gebbink RJM. Synthesis, Structure and Reactivity of a Mononuclear N,N,O-Bound Fe(II) α-Keto-Acid Complex. Chemistry 2024; 30:e202302710. [PMID: 37882223 DOI: 10.1002/chem.202302710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 10/27/2023]
Abstract
A bulky, tridentate phenolate ligand (ImPh2 NNOtBu ) was used to synthesise the first example of a mononuclear, facial, N,N,O-bound iron(II) benzoylformate complex, [Fe(ImPh2 NNOtBu )(BF)] (2). The X-ray crystal structure of 2 reveals that the iron centre is pentacoordinate (τ=0.5), with a vacant site located cis to the bidentate BF ligand. The Mössbauer parameters of 2 are consistent with high-spin iron(II), and are very close to those reported for α-ketoglutarate-bound non-heme iron enzyme active sites. According to NMR and UV-vis spectroscopies, the structural integrity of 2 is retained in both coordinating and non-coordinating solvents. Cyclic voltammetry studies show that the iron centre has a very low oxidation potential and is more prone to electrochemical oxidation than the redox-active phenolate ligand. Complex 2 reacts with NO to form a S=3 /2 {FeNO}7 adduct in which NO binds directly to the iron centre, according to EPR, UV-vis, IR spectroscopies and DFT analysis. Upon O2 exposure, 2 undergoes oxidative decarboxylation to form a diiron(III) benzoate complex, [Fe2 (ImPh2 NNOtBu )2 (μ2 -OBz)(μ2 -OH)2 ]+ (3). A small amount of hydroxylated ligand was also observed by ESI-MS, hinting at the formation of a high-valent iron(IV)-oxo intermediate. Initial reactivity studies show that 2 is capable of oxygen atom transfer reactivity with O2 , converting methyl(p-tolyl)sulfide to sulfoxide.
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Affiliation(s)
- Emily C Monkcom
- Organic Chemistry and Catalysis, Institute for Sustainable and Circular Chemistry, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Laura Gómez
- Serveis Tècnics de Recerca, Universitat de Girona, Pic de Peguera 15, Parc Cientific, 17003, Girona, Spain
| | - Martin Lutz
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Shengfa Ye
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion, 45470, Mülheim an der Ruhr, Germany
| | - Miquel Costas
- Institut de Química Computacional i Catàlisi, Universitat de Girona, Pic de Peguera 15, Parc Cientific, 17003, Girona, Spain
| | - Robertus J M Klein Gebbink
- Organic Chemistry and Catalysis, Institute for Sustainable and Circular Chemistry, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
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8
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Yan D, Arakelyan J, Wan T, Raina R, Chan TK, Ahn D, Kushnarev V, Cheung TK, Chan HC, Choi I, Ho PY, Hu F, Kim Y, Lau HL, Law YL, Leung CS, Tong CY, Wong KK, Yim WL, Karnaukhov NS, Kong RY, Babak MV, Matsuda Y. Genomics-driven derivatization of the bioactive fungal sesterterpenoid variecolin: Creation of an unnatural analogue with improved anticancer properties. Acta Pharm Sin B 2024; 14:421-432. [PMID: 38261827 PMCID: PMC10793096 DOI: 10.1016/j.apsb.2023.08.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/25/2023] [Accepted: 08/24/2023] [Indexed: 01/25/2024] Open
Abstract
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.
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Affiliation(s)
- Dexiu Yan
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- iGEM Team “VarieCure”, City University of Hong Kong, Hong Kong SAR, China
| | - Jemma Arakelyan
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- iGEM Team “VarieCure”, City University of Hong Kong, Hong Kong SAR, China
| | - Teng Wan
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- iGEM Team “VarieCure”, City University of Hong Kong, Hong Kong SAR, China
| | - Ritvik Raina
- iGEM Team “VarieCure”, City University of Hong Kong, Hong Kong SAR, China
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong SAR, China
| | - Tsz Ki Chan
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- iGEM Team “VarieCure”, City University of Hong Kong, Hong Kong SAR, China
| | - Dohyun Ahn
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- iGEM Team “VarieCure”, City University of Hong Kong, Hong Kong SAR, China
| | - Vladimir Kushnarev
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - Tsz Kiu Cheung
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- iGEM Team “VarieCure”, City University of Hong Kong, Hong Kong SAR, China
| | - Ho Ching Chan
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- iGEM Team “VarieCure”, City University of Hong Kong, Hong Kong SAR, China
| | - Inseo Choi
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- iGEM Team “VarieCure”, City University of Hong Kong, Hong Kong SAR, China
| | - Pui Yi Ho
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- iGEM Team “VarieCure”, City University of Hong Kong, Hong Kong SAR, China
| | - Feijun Hu
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- iGEM Team “VarieCure”, City University of Hong Kong, Hong Kong SAR, China
| | - Yujeong Kim
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- iGEM Team “VarieCure”, City University of Hong Kong, Hong Kong SAR, China
| | - Hill Lam Lau
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- iGEM Team “VarieCure”, City University of Hong Kong, Hong Kong SAR, China
| | - Ying Lo Law
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- iGEM Team “VarieCure”, City University of Hong Kong, Hong Kong SAR, China
| | - Chi Seng Leung
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- iGEM Team “VarieCure”, City University of Hong Kong, Hong Kong SAR, China
| | - Chun Yin Tong
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- iGEM Team “VarieCure”, City University of Hong Kong, Hong Kong SAR, China
| | - Kai Kap Wong
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- iGEM Team “VarieCure”, City University of Hong Kong, Hong Kong SAR, China
| | - Wing Lam Yim
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- iGEM Team “VarieCure”, City University of Hong Kong, Hong Kong SAR, China
| | - Nikolay S. Karnaukhov
- Moscow Clinical Research Center Named After A.S. Loginov, Moscow 111123, Russian Federation
| | - Richard Y.C. Kong
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- iGEM Team “VarieCure”, City University of Hong Kong, Hong Kong SAR, China
| | - Maria V. Babak
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- iGEM Team “VarieCure”, City University of Hong Kong, Hong Kong SAR, China
| | - Yudai Matsuda
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- iGEM Team “VarieCure”, City University of Hong Kong, Hong Kong SAR, China
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9
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Zhang Z, Sun Z, Song J, Guo H, Wang Y, Hu X. Construction of the A-B-C Ring of Simplicissin through an Oxidative Dearomatization/Iodination/[3+2] Annulation Cascade. Org Lett 2023. [PMID: 38018904 DOI: 10.1021/acs.orglett.3c03464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
As an attractive DMOA-derived spiromeroterpenoid, simplicissin shares a common A-B-C ring skeleton with other natural analogues. On the basis of the development of an oxidative dearomatization/iodination/[3+2] annulation cascade, a concise synthetic pathway to the A-B-C ring of simplicissin has been successfully established, and the substrate generality of the novel oxidative dearomatization/iodination/[3+2] annulation cascade has been checked.
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Affiliation(s)
- Ziwei Zhang
- Department of Chemistry & Material Science, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education of China, Northwest University, Xi'an 710127, China
| | - Zezhong Sun
- Department of Chemistry & Material Science, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education of China, Northwest University, Xi'an 710127, China
| | - Jianing Song
- Department of Chemistry & Material Science, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education of China, Northwest University, Xi'an 710127, China
| | - Hao Guo
- Department of Chemistry & Material Science, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education of China, Northwest University, Xi'an 710127, China
| | - Yunxia Wang
- Department of Chemistry & Material Science, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education of China, Northwest University, Xi'an 710127, China
| | - Xiangdong Hu
- Department of Chemistry & Material Science, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education of China, Northwest University, Xi'an 710127, China
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10
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Zhang L, Liu X, Wang X, Zhu G, Song H, Cheng R, Naowarojna N, Costello CE, Liu P. Correspondence on "Structural Insight into the Catalytic Mechanism of the Endoperoxide Synthase FtmOx1". Angew Chem Int Ed Engl 2023; 62:e202218643. [PMID: 37541669 PMCID: PMC10528348 DOI: 10.1002/anie.202218643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Indexed: 08/06/2023]
Abstract
In their recent Angewandte Chemie publication (doi: 10.1002/anie.202112063), Cen, Wang, Zhou et al. reported the crystal structure of a ternary complex of the non-heme iron endoperoxidase FtmOx1 (PDB entry 7ETK). The biochemical data assessed in this study were from a retracted study (doi: 10.1038/nature15519) by Zhang, Liu, Zhang et al.; no additional biochemical data were included, yet there was no discussion on the source of the biochemical data in the report by Cen, Wang, Zhou et al. Based on this new crystal structure and subsequent QM/MM-MD calculations, Cen, Wang, Zhou et al. concluded that their work provided evidence supporting the CarC-like mechanistic model for FtmOx1 catalysis. However, the authors did not accurately describe either the CarC-like model or the COX-like model, and they did not address the differences between them. Further, and contrary to their interpretations in the manuscript, the authors' data are consistent with the COX-like model once the details of the CarC-like and COX-like models have been carefully analyzed.
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Affiliation(s)
- Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China,
University of Science and Technology, Shanghai 200237 (China)
| | - Xueting Liu
- State Key Laboratory of Bioreactor Engineering, East China,
University of Science and Technology, Shanghai 200237 (China)
| | - Xinye Wang
- State Key Laboratory of Bioreactor Engineering, East China,
University of Science and Technology, Shanghai 200237 (China)
| | - Guoliang Zhu
- State Key Laboratory of Bioreactor Engineering, East China,
University of Science and Technology, Shanghai 200237 (China)
| | - Heng Song
- College of Chemistry and Molecular Sciences, Wuhan University,
Wuhan 430072 (China)
| | - Ronghai Cheng
- Department of Chemistry, Boston University, Boston, 02215 MA
(USA)
| | | | | | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, 02215 MA
(USA)
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11
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Awakawa T, Liu W, Bai T, Taniguchi T, Abe I. Orthoester formation in fungal meroterpenoid austalide F biosynthesis. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220037. [PMID: 36633279 PMCID: PMC9835590 DOI: 10.1098/rstb.2022.0037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/03/2022] [Indexed: 01/13/2023] Open
Abstract
Fungal meroterpenoids are important bioactive natural products. Their biosynthetic machineries are highly diverse, and reconstitutions lead to the production of unnatural meroterpenoids. In this study, heterologous gene expression in Aspergillus oryzae and in vitro assays elucidated the biosynthetic pathway of the orthoester-containing fungal meroterpenoid austalide F. Remarkably, the α-ketoglutarate-dependent oxygenase AstB produces the hemiacetal intermediate, and the methyltransferase AstL transfers a methyl group on it to construct the orthoester functionality. This study presents the extraordinary orthoester biosynthetic machinery and provides valuable insights into the creation of unnatural novel bioactive meroterpenoids through engineered biosynthesis. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
- RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Wei Liu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tongxuan Bai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tomo Taniguchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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12
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Awakawa T, Mori T, Ushimaru R, Abe I. Structure-based engineering of α-ketoglutarate dependent oxygenases in fungal meroterpenoid biosynthesis. Nat Prod Rep 2023; 40:46-61. [PMID: 35642933 DOI: 10.1039/d2np00014h] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Non-heme iron- and α-ketoglutarate-dependent oxygenases (αKG OXs) are key enzymes that play a major role in diversifying the structure of fungal meroterpenoids. They activate a specific C-H bond of the substrate to first generate radical species, which is usually followed by oxygen rebound to produce cannonical hydroxylated products. However, in some cases remarkable chemistry induces dramatic structural changes in the molecular scaffolds, depending on the stereoelectronic characters of the substrate/intermediates and the resulting conformational changes/movements of the active site of the enzyme. Their molecular bases have been extensively investigated by crystallographic structural analyses and structure-based mutagenesis, which revealed intimate structural details of the enzyme reactions. This information facilitates the manipulation of the enzyme reactions to create unnatural, novel molecules for drug discovery. This review summarizes recent progress in the structure-based engineering of αKG OX enzymes, involved in the biosynthesis of polyketide-derived fungal meroterpenoids. The literature published from 2016 through February 2022 is reviewed.
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Affiliation(s)
- Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, the University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan. .,Collaborative Research Institute for Innovative Microbiology, the University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences, the University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan. .,Collaborative Research Institute for Innovative Microbiology, the University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, the University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan. .,Collaborative Research Institute for Innovative Microbiology, the University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.,ACT-X, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, the University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan. .,Collaborative Research Institute for Innovative Microbiology, the University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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13
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Zhang T, Gu G, Liu G, Su J, Zhan Z, Zhao J, Qian J, Cai G, Cen S, Zhang D, Yu L. Late-stage cascade of oxidation reactions during the biosynthesis of oxalicine B in Penicillium oxalicum. Acta Pharm Sin B 2023; 13:256-270. [PMID: 36815048 PMCID: PMC9939320 DOI: 10.1016/j.apsb.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/01/2022] [Accepted: 09/01/2022] [Indexed: 11/01/2022] Open
Abstract
Oxalicine B (1) is an α-pyrone meroterpenoid with a unique bispirocyclic ring system derived from Penicillium oxalicum. The biosynthetic pathway of 15-deoxyoxalicine B (4) was preliminarily reported in Penicillium canescens, however, the genetic base and biochemical characterization of tailoring reactions for oxalicine B (1) has remained enigmatic. In this study, we characterized three oxygenases from the metabolic pathway of oxalicine B (1), including a cytochrome P450 hydroxylase OxaL, a hydroxylating Fe(II)/α-KG-dependent dioxygenase OxaK, and a multifunctional cytochrome P450 OxaB. Intriguingly, OxaK can catalyze various multicyclic intermediates or shunt products of oxalicines with impressive substrate promiscuity. OxaB was further proven via biochemical assays to have the ability to convert 15-hydroxdecaturin A (3) to 1 with a spiro-lactone core skeleton through oxidative rearrangement. We also solved the mystery of OxaL that controls C-15 hydroxylation. Chemical investigation of the wild-type strain and deletants enabled us to identify 10 metabolites including three new compounds, and the isolated compounds displayed potent anti-influenza A virus bioactivities exhibiting IC50 values in the range of 4.0-19.9 μmol/L. Our studies have allowed us to propose a late-stage biosynthetic pathway for oxalicine B (1) and create downstream derivatizations of oxalicines by employing enzymatic strategies.
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Affiliation(s)
- Tao Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Guowei Gu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Guodong Liu
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
| | - Jinhua Su
- The Third Medical Center, The General Hospital of People's Liberation Army, Beijing 100039, China
| | - Zhilai Zhan
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jianyuan Zhao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jinxiu Qian
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Guowei Cai
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Dewu Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China,Corresponding authors. Tel./fax: +86 10 63187118.
| | - Liyan Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China,Corresponding authors. Tel./fax: +86 10 63187118.
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14
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Ushimaru R, Abe I. Unusual Dioxygen-Dependent Reactions Catalyzed by Nonheme Iron Enzymes in Natural Product Biosynthesis. ACS Catal 2022. [DOI: 10.1021/acscatal.2c05247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- ACT-X, Japan Science and Technology Agency (JST), Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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15
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Yan D, Matsuda Y. Biosynthetic Elucidation and Structural Revision of Brevione E: Characterization of the Key Dioxygenase for Pathway Branching from Setosusin Biosynthesis. Angew Chem Int Ed Engl 2022; 61:e202210938. [DOI: 10.1002/anie.202210938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Dexiu Yan
- Department of Chemistry City University of Hong Kong Tat Chee Avenue Kowloon, Hong Kong SAR China
| | - Yudai Matsuda
- Department of Chemistry City University of Hong Kong Tat Chee Avenue Kowloon, Hong Kong SAR China
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16
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Zhu G, Yan W, Wang X, Cheng R, Naowarojna N, Wang K, Wang J, Song H, Wang Y, Liu H, Xia X, Costello CE, Liu X, Zhang L, Liu P. Dissecting the Mechanism of the Nonheme Iron Endoperoxidase FtmOx1 Using Substrate Analogues. JACS AU 2022; 2:1686-1698. [PMID: 35911443 PMCID: PMC9326825 DOI: 10.1021/jacsau.2c00248] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
FtmOx1 is a nonheme iron (NHFe) endoperoxidase, catalyzing three disparate reactions, endoperoxidation, alcohol dehydrogenation, and dealkylation, under in vitro conditions; the diversity complicates its mechanistic studies. In this study, we use two substrate analogues to simplify the FtmOx1-catalyzed reaction to either a dealkylation or an alcohol dehydrogenation reaction for structure-function relationship analysis to address two key FtmOx1 mechanistic questions: (1) Y224 flipping in the proposed COX-like model vs α-ketoglutarate (αKG) rotation proposed in the CarC-like mechanistic model and (2) the involvement of a Y224 radical (COX-like model) or a Y68 radical (CarC-like model) in FtmOx1-catalysis. When 13-oxo-fumitremorgin B (7) is used as the substrate, FtmOx1-catalysis changes from the endoperoxidation to a hydroxylation reaction and leads to dealkylation. In addition, consistent with the dealkylation side-reaction in the COX-like model prediction, the X-ray structure of the FtmOx1•CoII•αKG•7 ternary complex reveals a flip of Y224 to an alternative conformation relative to the FtmOx1•FeII•αKG binary complex. Verruculogen (2) was used as a second substrate analogue to study the alcohol dehydrogenation reaction to examine the involvement of the Y224 radical or Y68 radical in FtmOx1-catalysis, and again, the results from the verruculogen reaction are more consistent with the COX-like model.
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Affiliation(s)
- Guoliang Zhu
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wupeng Yan
- School
of Life Sciences and Biotechnology, Shanghai
Jiao Tong University, Shanghai 200237, China
| | - Xinye Wang
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ronghai Cheng
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Nathchar Naowarojna
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Kun Wang
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jun Wang
- School
of Life Sciences and Biotechnology, Shanghai
Jiao Tong University, Shanghai 200237, China
| | - Heng Song
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan, Hubei Province 430072, China
| | - Yuyang Wang
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Hairong Liu
- Key
Biosensor Laboratory of Shandong Province, Biology Institute, Qilu University of Technology (Shandong Academy
of Sciences), Jinan, Shandong Province 250013, China
| | - Xuekui Xia
- Key
Biosensor Laboratory of Shandong Province, Biology Institute, Qilu University of Technology (Shandong Academy
of Sciences), Jinan, Shandong Province 250013, China
| | - Catherine E. Costello
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Xueting Liu
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Lixin Zhang
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Pinghua Liu
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
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17
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Tao H, Abe I. Harnessing Fe(II)/α-ketoglutarate-dependent oxygenases for structural diversification of fungal meroterpenoids. Curr Opin Biotechnol 2022; 77:102763. [PMID: 35878474 DOI: 10.1016/j.copbio.2022.102763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/14/2022] [Accepted: 06/30/2022] [Indexed: 11/17/2022]
Abstract
Fungal meroterpenoids are structurally diverse natural products with important biological activities. During their biosynthesis, α-ketoglutarate-dependent oxygenases (αKG-DOs) catalyze a wide range of chemically challenging transformation reactions, including desaturation, epoxidation, oxidative rearrangement, and endoperoxide formation, by selective C-H bond activation, to produce molecules with more complex and divergent structures. Investigations on the structure-function relationships of αKG-DO enzymes have revealed the intimate molecular bases of their catalytic versatility and reaction mechanisms. Notably, the catalytic repertoire of αKG-DOs is further expanded by only subtle changes in their active site and lid-like loop-region architectures. Owing to their remarkable biocatalytic potential, αKG-DOs are ideal candidates for future chemoenzymatic synthesis and enzyme engineering for the generation of terpenoids with diverse structures and biological activities.
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Affiliation(s)
- Hui Tao
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan.
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18
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Mining new meroterpenoids from the marine red alga-derived endophytic Penicillium chermesinum EN-480 by comparative transcriptome analysis. Bioorg Chem 2022; 128:106021. [PMID: 35882090 DOI: 10.1016/j.bioorg.2022.106021] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/06/2022] [Accepted: 07/09/2022] [Indexed: 11/24/2022]
Abstract
As the development of genetic and bioinformatic, the strategy of "bottom-up", combined with genome and transcriptome techniques, was considered as an efficient and practical method to break through the limitation of traditional discovery of natural products. Generally, comparative transcriptome analysis could be useful to guide the optimization of fungal cultivation conditions in which the transcriptional level of interesting compounds is higher. The transcriptome analysis of the algal endophytic fungus Penicillium chermesinum EN-480 indicated that fermentation of this fungus in modified rice solid medium could produce some metabolites different from those cultivated in other media. Four new meroterpenoids (compounds 1-4, namely, chermesins E-H) were characterized and their structures were determined by HRESIMS and NMR spectra. The absolute configurations were confirmed by NOESY experiments, X-ray diffraction analysis, and comparison of ECD cotton effects. Antimicrobial activities against human- and aqua-bacteria as well as against plant-pathogenic fungi were assayed. The plausible biosynthesis pathway of these compounds was discussed.
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19
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Yang F, Porco JA. Unified, Asymmetric Total Synthesis of the Asnovolins and Related Spiromeroterpenoids: A Fragment Coupling Approach. J Am Chem Soc 2022; 144:12970-12978. [DOI: 10.1021/jacs.2c05366] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Feng Yang
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - John A. Porco
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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20
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Mori T, Abe I. Structural basis for endoperoxide-forming oxygenases. Beilstein J Org Chem 2022; 18:707-721. [PMID: 35821691 PMCID: PMC9235837 DOI: 10.3762/bjoc.18.71] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/10/2022] [Indexed: 12/04/2022] Open
Abstract
Endoperoxide natural products are widely distributed in nature and exhibit various biological activities. Due to their chemical features, endoperoxide and endoperoxide-derived secondary metabolites have attracted keen attention in the field of natural products and organic synthesis. In this review, we summarize the structural analyses, mechanistic investigations, and proposed reaction mechanisms of endoperoxide-forming oxygenases, including cyclooxygenase, fumitremorgin B endoperoxidase (FtmOx1), and the asnovolin A endoperoxygenase NvfI.
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Affiliation(s)
- Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
- PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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21
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Lin CY, Muñoz AL, Laremore TN, Silakov A, Krebs C, Boal AK, Bollinger JM. Use of Noncanonical Tyrosine Analogues to Probe Control of Radical Intermediates during Endoperoxide Installation by Verruculogen Synthase (FtmOx1). ACS Catal 2022; 12:6968-6979. [PMID: 37744570 PMCID: PMC10516331 DOI: 10.1021/acscatal.2c01037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Important bioactive natural products, including prostaglandin H2 and artemisinin, contain reactive endoperoxides. Known enzymatic pathways for endoperoxide installation require multiple hydrogen-atom transfers (HATs). For example, iron(II)- and 2-oxoglutarate-dependent verruculogen synthase (FtmOx1; EC 1.14.11.38) mediates HAT from aliphatic C21 of fumitremorgin B, capture of O2 by the C21 radical (C21•), addition of the peroxyl radical (C21-O-O•) to olefinic C27, and HAT to the resultant C26•. Recent studies proposed conflicting roles for FtmOx1 tyrosine residues, Tyr224 and Tyr68, in the HATs from C21 and to C26•. Here, analysis of variant proteins bearing a ring-halogenated tyrosine or (amino)phenylalanine in place of either residue establishes that Tyr68 is the hydrogen donor to C26•, while Tyr224 has no essential role. The radicals that accumulate rapidly in FtmOx1 variants bearing a HAT-competent tyrosine analog at position 68 exhibit hypsochromically shifted absorption and, in cases of fluorine substitution, 19F-coupled electron-paramagnetic-resonance (EPR) spectra. By contrast, functional Tyr224-substituted variants generate radicals with unaltered light-absorption and EPR signatures as they produce verruculogen. The alternative major product of the Tyr68Phe variant, which forms competitively with verruculogen also in wild-type FtmOx1 in 2H2O and in the variant with the less readily oxidized 2,3-F2Tyr at position 68, is identified by mass spectrometry and isotopic labeling as the 26-hydroxy-21,27-endoperoxide compound formed after capture of another equivalent of O2 by the longer lived C26•. The results highlight the considerable chemical challenges the enzyme must navigate in averting both oxygen rebound and a second O2 coupling to obtain verruculogen selectively over other possible products.
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Affiliation(s)
- Chi-Yun Lin
- Department of Chemistry, The Pennsylvania State University; University Park, PA 16802, USA
| | - Angel L. Muñoz
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University; University Park, PA 16802, USA
| | - Tatiana N. Laremore
- Huck Institutes of the Life Sciences, The Pennsylvania State University; University Park, PA 16802, USA
| | - Alexey Silakov
- Department of Chemistry, The Pennsylvania State University; University Park, PA 16802, USA
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University; University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University; University Park, PA 16802, USA
| | - Amie K. Boal
- Department of Chemistry, The Pennsylvania State University; University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University; University Park, PA 16802, USA
| | - J. Martin Bollinger
- Department of Chemistry, The Pennsylvania State University; University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University; University Park, PA 16802, USA
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22
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CRISPR/Cas9-Based Genome Editing and Its Application in Aspergillus Species. J Fungi (Basel) 2022; 8:jof8050467. [PMID: 35628723 PMCID: PMC9143064 DOI: 10.3390/jof8050467] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 02/04/2023] Open
Abstract
Aspergillus, a genus of filamentous fungi, is extensively distributed in nature and plays crucial roles in the decomposition of organic materials as an important environmental microorganism as well as in the traditional fermentation and food processing industries. Furthermore, due to their strong potential to secrete a large variety of hydrolytic enzymes and other natural products by manipulating gene expression and/or introducing new biosynthetic pathways, several Aspergillus species have been widely exploited as microbial cell factories. In recent years, with the development of next-generation genome sequencing technology and genetic engineering methods, the production and utilization of various homo-/heterologous-proteins and natural products in Aspergillus species have been well studied. As a newly developed genome editing technology, the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system has been used to edit and modify genes in Aspergilli. So far, the CRISPR/Cas9-based approach has been widely employed to improve the efficiency of gene modification in the strain type Aspergillus nidulans and other industrially important and pathogenic Aspergillus species, including Aspergillus oryzae, Aspergillus niger, and Aspergillus fumigatus. This review highlights the current development of CRISPR/Cas9-based genome editing technology and its application in basic research and the production of recombination proteins and natural products in the Aspergillus species.
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23
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Patel JR, Oh J, Wang S, Crawford JM, Isaacs FJ. Cross-kingdom expression of synthetic genetic elements promotes discovery of metabolites in the human microbiome. Cell 2022; 185:1487-1505.e14. [PMID: 35366417 PMCID: PMC10619838 DOI: 10.1016/j.cell.2022.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 02/04/2022] [Accepted: 03/07/2022] [Indexed: 12/12/2022]
Abstract
Small molecules encoded by biosynthetic pathways mediate cross-species interactions and harbor untapped potential, which has provided valuable compounds for medicine and biotechnology. Since studying biosynthetic gene clusters in their native context is often difficult, alternative efforts rely on heterologous expression, which is limited by host-specific metabolic capacity and regulation. Here, we describe a computational-experimental technology to redesign genes and their regulatory regions with hybrid elements for cross-species expression in Gram-negative and -positive bacteria and eukaryotes, decoupling biosynthetic capacity from host-range constraints to activate silenced pathways. These synthetic genetic elements enabled the discovery of a class of microbiome-derived nucleotide metabolites-tyrocitabines-from Lactobacillus iners. Tyrocitabines feature a remarkable orthoester-phosphate, inhibit translational activity, and invoke unexpected biosynthetic machinery, including a class of "Amadori synthases" and "abortive" tRNA synthetases. Our approach establishes a general strategy for the redesign, expression, mobilization, and characterization of genetic elements in diverse organisms and communities.
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Affiliation(s)
- Jaymin R Patel
- Department of Molecular, Cellular, & Developmental Biology, Yale University, New Haven, CT, USA; Systems Biology Institute, Yale University, West Haven, CT, USA; Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Joonseok Oh
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA; Department of Chemistry, Yale University, New Haven, CT, USA
| | - Shenqi Wang
- Department of Molecular, Cellular, & Developmental Biology, Yale University, New Haven, CT, USA; Systems Biology Institute, Yale University, West Haven, CT, USA
| | - Jason M Crawford
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA; Department of Chemistry, Yale University, New Haven, CT, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA.
| | - Farren J Isaacs
- Department of Molecular, Cellular, & Developmental Biology, Yale University, New Haven, CT, USA; Systems Biology Institute, Yale University, West Haven, CT, USA; Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
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24
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Mechanistic investigations of hirsutene biosynthesis catalyzed by a chimeric sesquiterpene synthase from Steccherinum ochraceum. Fungal Genet Biol 2022; 161:103700. [DOI: 10.1016/j.fgb.2022.103700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/22/2022] [Accepted: 04/24/2022] [Indexed: 11/21/2022]
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25
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Wojdyla Z, Borowski T. Properties of the Reactants and Their Interactions within and with the Enzyme Binding Cavity Determine Reaction Selectivities. The Case of Fe(II)/2-Oxoglutarate Dependent Enzymes. Chemistry 2022; 28:e202104106. [PMID: 34986268 DOI: 10.1002/chem.202104106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Indexed: 12/12/2022]
Abstract
Fe(II)/2-oxoglutarate dependent dioxygenases (ODDs) share a double stranded beta helix (DSBH) fold and utilise a common reactive intermediate, ferryl species, to catalyse oxidative transformations of substrates. Despite the structural similarities, ODDs accept a variety of substrates and facilitate a wide range of reactions, that is hydroxylations, desaturations, (oxa)cyclisations and ring rearrangements. In this review we present and discuss the factors contributing to the observed (regio)selectivities of ODDs. They span from inherent properties of the reactants, that is, substrate molecule and iron cofactor, to the interactions between the substrate and the enzyme's binding cavity; the latter can counterbalance the effect of the former. Based on results of both experimental and computational studies dedicated to ODDs, we also line out the properties of the reactants which promote reaction outcomes other than the "default" hydroxylation. It turns out that the reaction selectivity depends on a delicate balance of interactions between the components of the investigated system.
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Affiliation(s)
- Zuzanna Wojdyla
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Niezapominajek 8, 30239 Krakow, Poland
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Niezapominajek 8, 30239 Krakow, Poland
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26
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Wu L, Wang Z, Cen Y, Wang B, Zhou J. Structural Insight into the Catalytic Mechanism of the Endoperoxide Synthase FtmOx1. Angew Chem Int Ed Engl 2022; 61:e202112063. [PMID: 34796596 DOI: 10.1002/anie.202112063] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Indexed: 11/11/2022]
Abstract
The 2-oxoglutarate (2OG)-dependent non-heme enzyme FtmOx1 catalyzes the endoperoxide biosynthesis of verruculogen. Although several mechanistic studies have been carried out, the catalytic mechanism of FtmOx1 is not well determined owing to the lack of a reliable complex structure of FtmOx1 with fumitremorgin B. Herein we provide the X-ray crystal structure of the ternary complex FtmOx1⋅2OG⋅fumitremorgin B at a resolution of 1.22 Å. Our structures show that the binding of fumitremorgin B induces significant compression of the active pocket and that Y68 is in close proximity to C26 of the substrate. Further MD simulation and QM/MM calculations support a CarC-like mechanism, in which Y68 acts as the H atom donor for quenching the C26-centered substrate radical. Our results are consistent with all available experimental data and highlight the importance of accurate complex structures in the mechanistic study of enzymatic catalysis.
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Affiliation(s)
- Lian Wu
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine (IRI), Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zhanfeng Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Yixin Cen
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine (IRI), Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Jiahai Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
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27
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Wei X, Wang WG, Matsuda Y. Branching and converging pathways in fungal natural product biosynthesis. Fungal Biol Biotechnol 2022; 9:6. [PMID: 35255990 PMCID: PMC8902786 DOI: 10.1186/s40694-022-00135-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/19/2022] [Indexed: 12/15/2022] Open
Abstract
AbstractIn nature, organic molecules with great structural diversity and complexity are synthesized by utilizing a relatively small number of starting materials. A synthetic strategy adopted by nature is pathway branching, in which a common biosynthetic intermediate is transformed into different end products. A natural product can also be synthesized by the fusion of two or more precursors generated from separate metabolic pathways. This review article summarizes several representative branching and converging pathways in fungal natural product biosynthesis to illuminate how fungi are capable of synthesizing a diverse array of natural products.
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28
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Wu M, Shao J, Zhu J, Zi J. Chamaejasnoids A-E, a 2,3-seco-guaiane sesquiterpenoid with a 5/6/7 bridged ring system and related metabolites from Stellera chamaejasme L. Fitoterapia 2022; 158:105171. [DOI: 10.1016/j.fitote.2022.105171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/04/2022] [Accepted: 03/08/2022] [Indexed: 12/01/2022]
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29
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Mori T, Yu Z, Tao H, Abe I. Rational Engineering of the Nonheme Iron- and 2-Oxoglutarate-Dependent Oxygenase SptF. Org Lett 2022; 24:1737-1741. [PMID: 35194997 DOI: 10.1021/acs.orglett.2c00409] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The Fe- and 2-oxoglutarate-dependent oxygenase SptF is a promising powerful biocatalys with unusual catalytic versatility and promiscuity. The site-specific random substitution of N150, I63, and N65, which are involved in substrate interactions, generated three compounds that were not produced by the SptF wild type. The substrate binding mode was dramatically altered by the introduction of only one or two substitutions. These results provide insights into the engineering of Fe- and 2-oxoglutarate-dependent oxygenases for chemoenzymatic syntheses of bioactive compounds.
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Affiliation(s)
- Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.,PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Ziheng Yu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hui Tao
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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30
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Williams K, de Mattos-Shipley KMJ, Willis CL, Bailey AM. In silico analyses of maleidride biosynthetic gene clusters. Fungal Biol Biotechnol 2022; 9:2. [PMID: 35177129 PMCID: PMC8851701 DOI: 10.1186/s40694-022-00132-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/23/2022] [Indexed: 01/09/2023] Open
Abstract
Maleidrides are a family of structurally related fungal natural products, many of which possess diverse, potent bioactivities. Previous identification of several maleidride biosynthetic gene clusters, and subsequent experimental work, has determined the 'core' set of genes required to construct the characteristic medium-sized alicyclic ring with maleic anhydride moieties. Through genome mining, this work has used these core genes to discover ten entirely novel putative maleidride biosynthetic gene clusters, amongst both publicly available genomes, and encoded within the genome of the previously un-sequenced epiheveadride producer Wicklowia aquatica CBS 125634. We have undertaken phylogenetic analyses and comparative bioinformatics on all known and putative maleidride biosynthetic gene clusters to gain further insights regarding these unique biosynthetic pathways.
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Affiliation(s)
- Katherine Williams
- grid.5337.20000 0004 1936 7603School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Ave, Bristol, BS8 1TQ UK
| | - Kate M. J. de Mattos-Shipley
- grid.5337.20000 0004 1936 7603School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Ave, Bristol, BS8 1TQ UK
| | - Christine L. Willis
- grid.5337.20000 0004 1936 7603School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS UK
| | - Andrew M. Bailey
- grid.5337.20000 0004 1936 7603School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Ave, Bristol, BS8 1TQ UK
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31
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Wu L, Wang Z, Cen Y, Wang B, Zhou J. Structural Insight into the Catalytic Mechanism of the Endoperoxide Synthase FtmOx1. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Lian Wu
- The Research Center of Chiral Drugs Innovation Research Institute of Traditional Chinese Medicine (IRI) Shanghai University of Traditional Chinese Medicine Shanghai 201203 China
- Key Laboratory of Synthetic Biology CAS Center for Excellence in Molecular Plant Sciences University of Chinese Academy of Sciences Shanghai 200032 China
| | - Zhanfeng Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Yixin Cen
- The Research Center of Chiral Drugs Innovation Research Institute of Traditional Chinese Medicine (IRI) Shanghai University of Traditional Chinese Medicine Shanghai 201203 China
- Key Laboratory of Synthetic Biology CAS Center for Excellence in Molecular Plant Sciences University of Chinese Academy of Sciences Shanghai 200032 China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Jiahai Zhou
- CAS Key Laboratory of Quantitative Engineering Biology Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
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32
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Chen MH, Li YS, Hsu NS, Lin KH, Wang YL, Wang ZC, Chang CF, Lin JP, Chang CY, Li TL. Structural and Mechanistic Bases for StnK3 and Its Mutant-Mediated Lewis-Acid-Dependent Epimerization and Retro-Aldol Reactions. ACS Catal 2022. [DOI: 10.1021/acscatal.1c04790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mei-Hua Chen
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Yi-Shan Li
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ning-Shian Hsu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Kuan-Hung Lin
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yung-Lin Wang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Zhe-Chong Wang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Jin-Ping Lin
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chin-Yuan Chang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Tsung-Lin Li
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei 115, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung City 402, Taiwan
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33
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Tao H, Mori T, Chen H, Lyu S, Nonoyama A, Lee S, Abe I. Molecular insights into the unusually promiscuous and catalytically versatile Fe(II)/α-ketoglutarate-dependent oxygenase SptF. Nat Commun 2022; 13:95. [PMID: 35013177 PMCID: PMC8748661 DOI: 10.1038/s41467-021-27636-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/01/2021] [Indexed: 11/23/2022] Open
Abstract
Non-heme iron and α-ketoglutarate-dependent (Fe/αKG) oxygenases catalyze various oxidative biotransformations. Due to their catalytic flexibility and high efficiency, Fe/αKG oxygenases have attracted keen attention for their application as biocatalysts. Here, we report the biochemical and structural characterizations of the unusually promiscuous and catalytically versatile Fe/αKG oxygenase SptF, involved in the biosynthesis of fungal meroterpenoid emervaridones. The in vitro analysis revealed that SptF catalyzes several continuous oxidation reactions, including hydroxylation, desaturation, epoxidation, and skeletal rearrangement. SptF exhibits extremely broad substrate specificity toward various meroterpenoids, and efficiently produced unique cyclopropane-ring-fused 5/3/5/5/6/6 and 5/3/6/6/6 scaffolds from terretonins. Moreover, SptF also hydroxylates steroids, including androsterone, testosterone, and progesterone, with different regiospecificities. Crystallographic and structure-based mutagenesis studies of SptF revealed the molecular basis of the enzyme reactions, and suggested that the malleability of the loop region contributes to the remarkable substrate promiscuity. SptF exhibits great potential as a promising biocatalyst for oxidation reactions.
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Affiliation(s)
- Hui Tao
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan.
- PRESTO, Japan Science and Technology Agency, Saitama, Japan.
| | - Heping Chen
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Shuang Lyu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Shoukou Lee
- Sumitomo Dainippon Pharma Co., Ltd, Osaka, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan.
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34
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Tang J, Matsuda Y. Discovery of branching meroterpenoid biosynthetic pathways in Aspergillus insuetus: involvement of two terpene cyclases with distinct cyclization modes. Chem Sci 2022; 13:10361-10369. [PMID: 36277653 PMCID: PMC9473517 DOI: 10.1039/d2sc02994d] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/17/2022] [Indexed: 12/14/2022] Open
Abstract
Branching meroterpenoid biosynthetic pathways were discovered in the fungus Aspergillus insuetus CBS 107.25, in which two terpene cyclases, InsA7 and InsB2, accept the same substrate but generate distinctly cyclized products.
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Affiliation(s)
- Jia Tang
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Yudai Matsuda
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
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35
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Xiao ZH, Dong J, Li A, Dai JM, Li YP, Hu QF, Shao LD, Matsuda Y, Wang WG. Biocatalytic and chemical derivatization of fungal meroditerpenoid chevalone E. Org Chem Front 2022. [DOI: 10.1039/d2qo00055e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fungal meroditerpenoids include diverse molecules with structural complexity and a broad range of biological activities. We have previously obtained meroditerpenoid chevalone E (1) and its oxidized analogues by heterologously expressing...
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36
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Sangster JJ, Marshall JR, Turner NJ, Mangas-Sanchez J. New Trends and Future Opportunities in the Enzymatic Formation of C-C, C-N, and C-O bonds. Chembiochem 2021; 23:e202100464. [PMID: 34726813 PMCID: PMC9401909 DOI: 10.1002/cbic.202100464] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/29/2021] [Indexed: 01/04/2023]
Abstract
Organic chemistry provides society with fundamental products we use daily. Concerns about the impact that the chemical industry has over the environment is propelling major changes in the way we manufacture chemicals. Biocatalysis offers an alternative to other synthetic approaches as it employs enzymes, Nature's catalysts, to carry out chemical transformations. Enzymes are biodegradable, come from renewable sources, operate under mild reaction conditions, and display high selectivities in the processes they catalyse. As a highly multidisciplinary field, biocatalysis benefits from advances in different areas, and developments in the fields of molecular biology, bioinformatics, and chemical engineering have accelerated the extension of the range of available transformations (E. L. Bell et al., Nat. Rev. Meth. Prim. 2021, 1, 1-21). Recently, we surveyed advances in the expansion of the scope of biocatalysis via enzyme discovery and protein engineering (J. R. Marshall et al., Tetrahedron 2021, 82, 131926). Herein, we focus on novel enzymes currently available to the broad synthetic community for the construction of new C-C, C-N and C-O bonds, with the purpose of providing the non-specialist with new and alternative tools for chiral and sustainable chemical synthesis.
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Affiliation(s)
- Jack J Sangster
- Department of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - James R Marshall
- Department of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Nicholas J Turner
- Department of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Juan Mangas-Sanchez
- Institute of Chemical Synthesis and Homogeneous Catalysis, Spanish National Research Council (CSIC), Pedro Cerbuna 12, 50009, Zaragoza, Spain.,ARAID Foundation, Zaragoza, Spain
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37
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Jiang J, Li X, Mori T, Awakawa T, Abe I. Novel Cyclohexyl Meroterpenes Produced by Combinatorial Biosynthesis. Chem Pharm Bull (Tokyo) 2021; 69:444-446. [PMID: 33952854 DOI: 10.1248/cpb.c21-00123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Structurally diverse fungal meroterpenoids are promising drug seed compounds. To obtain unnatural, novel meroterpene scaffolds, we tested combinatorial biosynthesis by co-expressing functionally distinct terpene cyclase (TPC) genes, pyr4, ascF, andB, or cdmG, with the biosynthetic genes for the production of a TPC substrate, (10'R)-epoxyfarnesyl-dimethylorsellinic acid-3,5-methyl ester, in Aspergillus oryzae NSAR1 as a heterologous host. As a result, all of the tested TPCs afforded the same two novel mono-cyclization products. This study provides important information on the substrate scope of the TPCs, and will contribute to the production of unnatural, novel molecules for future drug discovery.
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Affiliation(s)
- Jinyan Jiang
- Graduate School of Pharmaceutical Sciences, The University of Tokyo
| | - Xinyang Li
- Graduate School of Pharmaceutical Sciences, The University of Tokyo
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo.,PRESTO, Japan Science and Technology Agency
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
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38
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Mori T, Zhai R, Ushimaru R, Matsuda Y, Abe I. Molecular insights into the endoperoxide formation by Fe(II)/α-KG-dependent oxygenase NvfI. Nat Commun 2021; 12:4417. [PMID: 34285212 PMCID: PMC8292354 DOI: 10.1038/s41467-021-24685-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 06/30/2021] [Indexed: 11/08/2022] Open
Abstract
Endoperoxide-containing natural products are a group of compounds with structurally unique cyclized peroxide moieties. Although numerous endoperoxide-containing compounds have been isolated, the biosynthesis of the endoperoxides remains unclear. NvfI from Aspergillus novofumigatus IBT 16806 is an endoperoxidase that catalyzes the formation of fumigatonoid A in the biosynthesis of novofumigatonin. Here, we describe our structural and functional analyses of NvfI. The structural elucidation and mutagenesis studies indicate that NvfI does not utilize a tyrosyl radical in the reaction, in contrast to other characterized endoperoxidases. Further, the crystallographic analysis reveals significant conformational changes of two loops upon substrate binding, which suggests a dynamic movement of active site during the catalytic cycle. As a result, NvfI installs three oxygen atoms onto a substrate in a single enzyme turnover. Based on these results, we propose a mechanism for the NvfI-catalyzed, unique endoperoxide formation reaction to produce fumigatonoid A.
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Affiliation(s)
- Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
| | - Rui Zhai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- ACT-X, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Yudai Matsuda
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
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39
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Awakawa T, Abe I. Reconstitution of Polyketide-Derived Meroterpenoid Biosynthetic Pathway in Aspergillus oryzae. J Fungi (Basel) 2021; 7:jof7060486. [PMID: 34208768 PMCID: PMC8235479 DOI: 10.3390/jof7060486] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/12/2021] [Accepted: 06/14/2021] [Indexed: 02/03/2023] Open
Abstract
The heterologous gene expression system with Aspergillus oryzae as the host is an effective method to investigate fungal secondary metabolite biosynthetic pathways for reconstruction to produce un-natural molecules due to its high productivity and genetic tractability. In this review, we focus on biosynthetic studies of fungal polyketide-derived meroterpenoids, a group of bioactive natural products, by means of the A. oryzae heterologous expression system. The heterologous expression methods and the biosynthetic reactions are described in detail for future prospects to create un-natural molecules via biosynthetic re-design.
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Affiliation(s)
- Takayoshi Awakawa
- Laboratory of Natural Products Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
- Correspondence: (T.A.); (I.A.)
| | - Ikuro Abe
- Laboratory of Natural Products Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
- Correspondence: (T.A.); (I.A.)
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40
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Wei X, Chen X, Chen L, Yan D, Wang WG, Matsuda Y. Heterologous Biosynthesis of Tetrahydroxanthone Dimers: Determination of Key Factors for Selective or Divergent Synthesis. JOURNAL OF NATURAL PRODUCTS 2021; 84:1544-1549. [PMID: 33891392 DOI: 10.1021/acs.jnatprod.1c00022] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Tetrahydroxanthone dimers are fungal products, among which secalonic acid D (1) is one of the most studied compounds because of its potent biological activity. Because the biosynthetic gene cluster of 1 has been previously identified, we sought to heterologously produce 1 in Aspergillus oryzae by expressing the relevant biosynthetic genes. However, our initial attempt of the total biosynthesis of 1 failed; instead, it produced four isomers of 1 due to the activity of an endogenous enzyme of A. oryzae. Subsequent overexpression of the Baeyer-Villiger monooxygenase, AacuH, which competes with the endogenous enzyme, altered the product profile and successfully generated 1. Characterization of the key biosynthetic enzymes revealed the surprising substrate promiscuity of the dimerizing enzyme, AacuE, and indicated that efficient synthesis of 1 requires highly selective preparation of the tetrahydroxanthone monomer, which is apparently controlled by AacuH. This study facilitates engineered biosynthesis of tetrahydroxanthone dimers both in a selective and divergent manner.
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Affiliation(s)
- Xingxing Wei
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR 999077, People's Republic of China
| | - Xiaoxuan Chen
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR 999077, People's Republic of China
| | - Lin Chen
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR 999077, People's Republic of China
| | - Dexiu Yan
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR 999077, People's Republic of China
| | - Wei-Guang Wang
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, Kunming 650031, People's Republic of China
| | - Yudai Matsuda
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR 999077, People's Republic of China
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41
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Ali HS, Henchman RH, Visser SP. Mechanism of Oxidative Ring‐Closure as Part of the Hygromycin Biosynthesis Step by a Nonheme Iron Dioxygenase. ChemCatChem 2021. [DOI: 10.1002/cctc.202100393] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Hafiz Saqib Ali
- Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
- Department of Chemistry The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Richard H. Henchman
- Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
- Department of Chemistry The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Sam P. Visser
- Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
- Department of Chemical Engineering and Analytical Science The University of Manchester Oxford Road Manchester M13 9PL UK
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42
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Meyer F, Frey R, Ligibel M, Sager E, Schroer K, Snajdrova R, Buller R. Modulating Chemoselectivity in a Fe(II)/α-Ketoglutarate-Dependent Dioxygenase for the Oxidative Modification of a Nonproteinogenic Amino Acid. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00678] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Fabian Meyer
- Competence Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Raphael Frey
- Competence Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Mathieu Ligibel
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry, 4056 Basel, Switzerland
| | - Emine Sager
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry, 4056 Basel, Switzerland
| | - Kirsten Schroer
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry, 4056 Basel, Switzerland
| | - Radka Snajdrova
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry, 4056 Basel, Switzerland
| | - Rebecca Buller
- Competence Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
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43
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Han J, Jiang L, Zhang L, Quinn RJ, Liu X, Feng Y. Peculiarities of meroterpenoids and their bioproduction. Appl Microbiol Biotechnol 2021; 105:3987-4003. [PMID: 33937926 DOI: 10.1007/s00253-021-11312-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/14/2021] [Accepted: 04/20/2021] [Indexed: 02/05/2023]
Abstract
Meroterpenoids are a class of terpenoid-containing hybrid natural products with impressive structural architectures and remarkable pharmacological activities. Remarkable advances in enzymology and synthetic biology have greatly contributed to the elucidation of the molecular basis for their biosynthesis. Here, we review structurally unique meroterpenoids catalyzed by novel enzymes and unusual enzymatic reactions over the period of last 5 years. We also discuss recent progress on the biomimetic synthesis of chrome meroterpenoids and synthetic biology-driven biomanufacturing of tropolone sesquiterpenoids, merochlorins, and plant-derived meroterpenoid cannabinoids. In particular, we focus on the novel enzymes involved in the biosynthesis of polyketide-terpenoids, nonribosomal peptide-terpenoids, terpenoid alkaloids, and meroterpenoid with unique structures. The biological activities of these meroterpenoids are also discussed. The information reviewed here might provide useful clues and lay the foundation for developing new meroterpenoid-derived drugs. KEY POINTS: • Meroterpenoids possess intriguing structural features and relevant biological activities. • Novel enzymes are involved in the biosynthesis of meroterpenoids with unique structures. • Biomimetic synthesis and synthetic biology enable the construction and manufacturing of complex meroterpenoids.
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Affiliation(s)
- Jianying Han
- Griffith Institute for Drug Discovery, Griffith University, QLD, Brisbane, 4111, Australia
| | - Lan Jiang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, QLD, Brisbane, 4111, Australia
| | - Xueting Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Yunjiang Feng
- Griffith Institute for Drug Discovery, Griffith University, QLD, Brisbane, 4111, Australia.
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Yan D, Matsuda Y. Genome Mining-Driven Discovery of 5-Methylorsellinate-Derived Meroterpenoids from Aspergillus funiculosus. Org Lett 2021; 23:3211-3215. [PMID: 33821662 DOI: 10.1021/acs.orglett.1c00951] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Heterologous expression of a cryptic gene cluster in the fungus Aspergillus funiculosus CBS 116.56 led to the discovery of four new meroterpenoids, funiculolides A-D (1-4), derived from the aromatic polyketide 5-methylorsellinic acid (5-MOA). Intriguingly, funiculolide D (4), the apparent end product of the pathway, harbors an unusual spirocyclopentanone moiety, which is synthesized by the oxidative rearrangement catalyzed by the ferrous iron and α-ketoglutarate-dependent dioxygenase FncG.
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Affiliation(s)
- Dexiu Yan
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Yudai Matsuda
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
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Tao H, Mori T, Wei X, Matsuda Y, Abe I. One Polyketide Synthase, Two Distinct Products: Trans-Acting Enzyme-Controlled Product Divergence in Calbistrin Biosynthesis. Angew Chem Int Ed Engl 2021; 60:8851-8858. [PMID: 33480463 DOI: 10.1002/anie.202016525] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Indexed: 12/17/2022]
Abstract
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.
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Affiliation(s)
- Hui Tao
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.,PRESTO (Japan) Science and Technology Agency, Kawaguchi, Saitama, 332-0012, Japan
| | - Xingxing Wei
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Yudai Matsuda
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
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Tao H, Mori T, Wei X, Matsuda Y, Abe I. One Polyketide Synthase, Two Distinct Products:
Trans
‐Acting Enzyme‐Controlled Product Divergence in Calbistrin Biosynthesis. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hui Tao
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Yayoi 1-1-1, Bunkyo-ku Tokyo 113-8657 Japan
- PRESTO (Japan) Science and Technology Agency Kawaguchi Saitama 332-0012 Japan
| | - Xingxing Wei
- Department of Chemistry City University of Hong Kong Tat Chee Avenue Kowloon Hong Kong SAR China
| | - Yudai Matsuda
- Department of Chemistry City University of Hong Kong Tat Chee Avenue Kowloon Hong Kong SAR China
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Yayoi 1-1-1, Bunkyo-ku Tokyo 113-8657 Japan
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47
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Jiang C, Lv G, Tu Y, Cheng X, Duan Y, Zeng B, He B. Applications of CRISPR/Cas9 in the Synthesis of Secondary Metabolites in Filamentous Fungi. Front Microbiol 2021; 12:638096. [PMID: 33643273 PMCID: PMC7905030 DOI: 10.3389/fmicb.2021.638096] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/18/2021] [Indexed: 12/19/2022] Open
Abstract
Filamentous fungi possess the capacity to produce a wide array of secondary metabolites with diverse biological activities and structures, such as lovastatin and swainsonine. With the advent of the post-genomic era, increasing amounts of cryptic or uncharacterized secondary metabolite biosynthetic gene clusters are continually being discovered. However, owing to the longstanding lack of versatile, comparatively simple, and highly efficient genetic manipulation techniques, the broader exploration of industrially important secondary metabolites has been hampered thus far. With the emergence of CRISPR/Cas9-based genome editing technology, this dilemma may be alleviated, as this advanced technique has revolutionized genetic research and enabled the exploitation and discovery of new bioactive compounds from filamentous fungi. In this review, we introduce the CRISPR/Cas9 system in detail and summarize the latest applications of CRISPR/Cas9-mediated genome editing in filamentous fungi. We also briefly introduce the specific applications of the CRISPR/Cas9 system and CRISPRa in the improvement of secondary metabolite contents and discovery of novel biologically active compounds in filamentous fungi, with specific examples noted. Additionally, we highlight and discuss some of the challenges and deficiencies of using the CRISPR/Cas9-based genome editing technology in research on the biosynthesis of secondary metabolites as well as future application of CRISPR/Cas9 strategy in filamentous fungi are highlighted and discussed.
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Affiliation(s)
- Chunmiao Jiang
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Gongbo Lv
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Yayi Tu
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Xiaojie Cheng
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Yitian Duan
- School of Information, Renmin University of China, Beijing, China
| | - Bin Zeng
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China.,College of Pharmacy, Shenzhen Technology University, Shenzhen, China
| | - Bin He
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
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48
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Enzymology and biosynthesis of the orsellinic acid derived medicinal meroterpenoids. Curr Opin Biotechnol 2020; 69:52-59. [PMID: 33383296 DOI: 10.1016/j.copbio.2020.11.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 11/02/2020] [Accepted: 11/30/2020] [Indexed: 01/07/2023]
Abstract
The advent of synthetic biology has yielded fruitful studies on orsellinic acid-derived meroterpenoids, which reportedly possess important biological activities. Genomics and transcriptomics have significantly accelerated the discovery of the biosynthetic genes for orsellinic acid-derived fungal and plant meroterpenoids. Subsequently, a well-developed heterologous host provides a convenient platform to generate a supply of useful natural products. Furthermore, in vitro reconstitution and genome editing tools have been increasingly employed as efficient means to fully understand the enzyme reaction mechanisms. With the knowledge of the biosynthetic machinery, combinatorial and engineered biosyntheses have yielded novel molecules with improved bioactivities. These studies will lay the foundation for the production of meroterpenoids with novel medicinal properties.
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Mitsuhashi T, Barra L, Powers Z, Kojasoy V, Cheng A, Yang F, Taniguchi Y, Kikuchi T, Fujita M, Tantillo DJ, Porco JA, Abe I. Exploiting the Potential of Meroterpenoid Cyclases to Expand the Chemical Space of Fungal Meroterpenoids. Angew Chem Int Ed Engl 2020; 59:23772-23781. [PMID: 32931152 PMCID: PMC8957209 DOI: 10.1002/anie.202011171] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Indexed: 12/20/2022]
Abstract
Fungal meroterpenoids are a diverse group of hybrid natural products with impressive structural complexity and high potential as drug candidates. In this work, we evaluate the promiscuity of the early structure diversity-generating step in fungal meroterpenoid biosynthetic pathways: the multibond-forming polyene cyclizations catalyzed by the yet poorly understood family of fungal meroterpenoid cyclases. In total, 12 unnatural meroterpenoids were accessed chemoenzymatically using synthetic substrates. Their complex structures were determined by 2D NMR studies as well as crystalline-sponge-based X-ray diffraction analyses. The results obtained revealed a high degree of enzyme promiscuity and experimental results which together with quantum chemical calculations provided a deeper insight into the catalytic activity of this new family of non-canonical, terpene cyclases. The knowledge obtained paves the way to design and engineer artificial pathways towards second generation meroterpenoids with valuable bioactivities based on combinatorial biosynthetic strategies.
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Affiliation(s)
- Takaaki Mitsuhashi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan)
- Division of Advanced Molecular Science, Institute for Molecular Science, National Institutes of Natural Sciences 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787 (Japan)
| | - Lena Barra
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Zachary Powers
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, Boston, Massachusetts, 02215 (USA)
| | - Volga Kojasoy
- Department of Chemistry, University of California Davis 1 Shields Avenue, Davis, California 95616 (USA)
| | - Andrea Cheng
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, Boston, Massachusetts, 02215 (USA)
| | - Feng Yang
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, Boston, Massachusetts, 02215 (USA)
| | - Yoshimasa Taniguchi
- Central Laboratories for Key Technologies, Kirin Holdings Co. Ltd. 1-13-5, Fukuura Kana-zawa-ku, Yokohama-shi, Kanagawa, 236-0004 (Japan)
| | - Takashi Kikuchi
- Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima-shi, Tokyo 196-8666 (Japan)
| | - Makoto Fujita
- Division of Advanced Molecular Science, Institute for Molecular Science, National Institutes of Natural Sciences 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787 (Japan)
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 (Japan)
| | - Dean J. Tantillo
- Department of Chemistry, University of California Davis 1 Shields Avenue, Davis, California 95616 (USA)
| | - John A. Porco
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, Boston, Massachusetts, 02215 (USA)
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan)
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657 (Japan)
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50
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Yang B, Gao J, Pei Q, Xu H, Yu H. Engineering Prodrug Nanomedicine for Cancer Immunotherapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2002365. [PMID: 33304763 PMCID: PMC7709995 DOI: 10.1002/advs.202002365] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/16/2020] [Indexed: 12/11/2022]
Abstract
Immunotherapy has shifted the clinical paradigm of cancer management. However, despite promising initial progress, immunotherapeutic approaches to cancer still suffer from relatively low response rates and the possibility of severe side effects, likely due to the low inherent immunogenicity of tumor cells, the immunosuppressive tumor microenvironment, and significant inter- and intratumoral heterogeneity. Recently, nanoformulations of prodrugs have been explored as a means to enhance cancer immunotherapy by simultaneously eliciting antitumor immune responses and reversing local immunosuppression. Prodrug nanomedicines, which integrate engineering advances in chemistry, oncoimmunology, and material science, are rationally designed through chemically modifying small molecule drugs, peptides, or antibodies to yield increased bioavailability and spatiotemporal control of drug release and activation at the target sites. Such strategies can help reduce adverse effects and enable codelivery of multiple immune modulators to yield synergistic cancer immunotherapy. In this review article, recent advances and translational challenges facing prodrug nanomedicines for cancer immunotherapy are overviewed. Last, key considerations are outlined for future efforts to advance prodrug nanomedicines aimed to improve antitumor immune responses and combat immune tolerogenic microenvironments.
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Affiliation(s)
- Bin Yang
- State Key Laboratory of Drug Research & Center of PharmaceuticsShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China
- Department of Medical UltrasoundShanghai Tenth People's HospitalUltrasound Research and Education InstituteTongji University School of MedicineTongji University Cancer CenterShanghai200072China
| | - Jing Gao
- State Key Laboratory of Drug Research & Center of PharmaceuticsShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China
- Department of Medical UltrasoundShanghai Tenth People's HospitalUltrasound Research and Education InstituteTongji University School of MedicineTongji University Cancer CenterShanghai200072China
| | - Qing Pei
- State Key Laboratory of Drug Research & Center of PharmaceuticsShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China
| | - Huixiong Xu
- Department of Medical UltrasoundShanghai Tenth People's HospitalUltrasound Research and Education InstituteTongji University School of MedicineTongji University Cancer CenterShanghai200072China
| | - Haijun Yu
- State Key Laboratory of Drug Research & Center of PharmaceuticsShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China
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