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Harris LA, Saad H, Shelton K, Zhu L, Guo X, Mitchell DA. Tryptophan-Centric Bioinformatics Identifies New Lasso Peptide Modifications. Biochemistry 2024; 63:865-879. [PMID: 38498885 PMCID: PMC11197979 DOI: 10.1021/acs.biochem.4c00035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Lasso peptides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) defined by a macrolactam linkage between the N-terminus and the side chain of an internal aspartic acid or glutamic acid residue. Instead of adopting a branched-cyclic conformation, lasso peptides are "threaded", with the C-terminal tail passing through the macrocycle to present a kinetically trapped rotaxane conformation. The availability of enhanced bioinformatics methods has led to a significant increase in the number of secondary modifications found on lasso peptides. To uncover new ancillary modifications in a targeted manner, a bioinformatic strategy was developed to discover lasso peptides with modifications to tryptophan. This effort identified numerous putative lasso peptide biosynthetic gene clusters with core regions of the precursor peptides enriched in tryptophan. Parsing of these tryptophan (Trp)-rich biosynthetic gene clusters uncovered several putative ancillary modifying enzymes, including halogenases and dimethylallyltransferases expected to act upon Trp. Characterization of two gene products yielded a lasso peptide with two 5-Cl-Trp modifications (chlorolassin) and another bearing 5-dimethylallyl-Trp and 2,3-didehydro-Tyr modifications (wygwalassin). Bioinformatic analysis of the requisite halogenase and dimethylallyltransferase revealed numerous other putative Trp-modified lasso peptides that remain uncharacterized. We anticipate that the Trp-centric strategy reported herein may be useful in discovering ancillary modifications for other RiPP classes and, more generally, guide the functional prediction of enzymes that act on specific amino acids.
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Affiliation(s)
- Lonnie A. Harris
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Hamada Saad
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Kyle Shelton
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Lingyang Zhu
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Xiaorui Guo
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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2
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Han H, Peng S, Wang Q, Wang H, Wang P, Li C, Qi J, Liu C. Biochemical characterization of a multiple prenyltransferase from Tolypocladium inflatum. Appl Microbiol Biotechnol 2024; 108:275. [PMID: 38530470 DOI: 10.1007/s00253-024-13113-6] [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: 12/19/2023] [Revised: 03/08/2024] [Accepted: 03/19/2024] [Indexed: 03/28/2024]
Abstract
Prenylation plays a pivotal role in the diversification and biological activities of natural products. This study presents the functional characterization of TolF, a multiple prenyltransferase from Tolypocladium inflatum. The heterologous expression of tolF in Aspergillus oryzae, coupled with feeding the transformed strain with paxilline, resulted in the production of 20- and 22-prenylpaxilline. Additionally, TolF demonstrated the ability to prenylated the reduced form of paxilline, β-paxitriol. A related prenyltransferase TerF from Chaunopycnis alba, exhibited similar substrate tolerance and regioselectivity. In vitro enzyme assays using purified recombinant enzymes TolF and TerF confirmed their capacity to catalyze prenylation of paxilline, β-paxitriol, and terpendole I. Based on previous reports, terpendole I should be considered a native substrate. This work not only enhances our understanding of the molecular basis and product diversity of prenylation reactions in indole diterpene biosynthesis, but also provides insights into the potential of fungal indole diterpene prenyltransferase to alter their position specificities for prenylation. This could be applicable for the synthesis of industrially useful compounds, including bioactive compounds, thereby opening up new avenues for the development of novel biosynthetic strategies and pharmaceuticals. KEY POINTS: • The study characterizes TolF as a multiple prenyltransferase from Tolypocladium inflatum. • TerF from Chaunopycnis alba shows similar substrate tolerance and regioselectivity compared to TolF. • The research offers insights into the potential applications of fungal indole diterpene prenyltransferases.
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Affiliation(s)
- Haiyan Han
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, No. 26 Hexing Road, Harbin, 150040, Heilongjiang, China
| | - Shuang Peng
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, No. 26 Hexing Road, Harbin, 150040, Heilongjiang, China
| | - Qian Wang
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, No. 26 Hexing Road, Harbin, 150040, Heilongjiang, China
| | - Hongwei Wang
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, No. 26 Hexing Road, Harbin, 150040, Heilongjiang, China
| | - Pengchao Wang
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, No. 26 Hexing Road, Harbin, 150040, Heilongjiang, China
| | - Chang Li
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin, 150040, China
| | - Jianzhao Qi
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, No. 26 Hexing Road, Harbin, 150040, Heilongjiang, China.
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, No.3 Taicheng Road, Yangling, 712100, China.
| | - Chengwei Liu
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, No. 26 Hexing Road, Harbin, 150040, Heilongjiang, China.
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3
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Schäfer T, Haun F, Gressler M, Spiteller P, Hoffmeister D. Parallel Evolution of Asco- and Basidiomycete O-Prenyltransferases. JOURNAL OF NATURAL PRODUCTS 2024; 87:576-582. [PMID: 38231181 DOI: 10.1021/acs.jnatprod.3c01120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Prenyltransferases (PTs) are involved in the biosynthesis of a multitude of pharmaceutically and agriculturally important plant, bacterial, and fungal compounds. Although numerous prenylated compounds have been isolated from Basidiomycota (mushroom-forming fungi), knowledge of the PTs catalyzing the transfer reactions in this group of fungi is scarce. Here, we report the biochemical characterization of an O- and C-prenylating dimethylallyltryptophan synthase (DMATS)-like enzyme LpTyrPT from the scurfy deceiver Laccaria proxima. This PT transfers dimethylallyl moieties to l-tyrosine at the para-O position and to l-tryptophan at atom C-7 and represents the first basidiomycete l-tyrosine PT described so far. Phylogenetic analysis of PTs in fungi revealed that basidiomycete l-tyrosine PTs have evolved independently from their ascomycete counterparts and might represent the evolutionary origin of PTs acting on phenolic compounds in secondary metabolism.
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Affiliation(s)
- Tim Schäfer
- Institute of Pharmacy, Friedrich Schiller University, Winzerlaer Strasse 2, 07745 Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Fabian Haun
- Institute of Pharmacy, Friedrich Schiller University, Winzerlaer Strasse 2, 07745 Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Markus Gressler
- Institute of Pharmacy, Friedrich Schiller University, Winzerlaer Strasse 2, 07745 Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Peter Spiteller
- Institute of Organic and Analytical Chemistry, University of Bremen, Leobener Straße 7, 28359 Bremen, Germany
| | - Dirk Hoffmeister
- Institute of Pharmacy, Friedrich Schiller University, Winzerlaer Strasse 2, 07745 Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Beutenbergstrasse 11a, 07745 Jena, Germany
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4
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Aoun AR, Mupparapu N, Nguyen DN, Kim TH, Nguyen CM, Pan Z, Elshahawi SI. Structure-guided Mutagenesis Reveals the Catalytic Residue that Controls the Regiospecificity of C6-Indole Prenyltransferases. ChemCatChem 2023; 15:e202300423. [PMID: 37366495 PMCID: PMC10292028 DOI: 10.1002/cctc.202300423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Indexed: 06/28/2023]
Abstract
Indole is a significant structural moiety and functionalization of the C-H bond in indole-containing molecules expands their chemical space, and modifies their properties and/or activities. Indole prenyltransferases (IPTs) catalyze the direct regiospecific installation of prenyl, C5 carbon units, on indole-derived compounds. IPTs have shown relaxed substrate flexibility enabling them to be used as tools for indole functionalization. However, the mechanism by which certain IPTs target a specific carbon position is not fully understood. Herein, we use structure-guided site-directed mutagenesis, in vitro enzymatic reactions, kinetics and structural-elucidation of analogs to verify the key catalytic residues that control the regiospecificity of all characterized regiospecific C6 IPTs. Our results also demonstrate that substitution of PriB_His312 to Tyr leads to the synthesis of analogs prenylated at different positions than C6. This work contributes to understanding of how certain IPTs can access a challenging position in indole-derived compounds.
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Affiliation(s)
- Ahmed R Aoun
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Rinker Health Science Campus, Irvine, CA 92618
| | - Nagaraju Mupparapu
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Rinker Health Science Campus, Irvine, CA 92618
| | - Diem N Nguyen
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Rinker Health Science Campus, Irvine, CA 92618
| | - Tae Ho Kim
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Rinker Health Science Campus, Irvine, CA 92618
| | - Christopher M Nguyen
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Rinker Health Science Campus, Irvine, CA 92618
| | - Zhengfeiyue Pan
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Rinker Health Science Campus, Irvine, CA 92618
| | - Sherif I Elshahawi
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Rinker Health Science Campus, Irvine, CA 92618
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5
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Liu Y, Ozaki T, Minami A, Oikawa H. Oxidative bicyclic ring system formation involving indole diterpene biosynthesis: Remarkable substrate tolerance of a prenyltransferase and flavoprotein oxidase. Tetrahedron Lett 2023. [DOI: 10.1016/j.tetlet.2023.154374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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6
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Qiu C, Liu Y, Wu Y, Zhao L, Pei J. Functional Characterization and Screening of Promiscuous Kinases and Isopentenyl Phosphate Kinases for the Synthesis of DMAPP via a One-Pot Enzymatic Cascade. Int J Mol Sci 2022; 23:12904. [PMID: 36361694 PMCID: PMC9654404 DOI: 10.3390/ijms232112904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 06/29/2024] Open
Abstract
Dimethylallyl diphosphate (DMAPP) is a key intermediate metabolite in the synthesis of isoprenoids and is also the prenyl donor for biosynthesizing prenylated flavonoids. However, it is difficult to prepare DMAPP via chemical and enzymatic methods. In this study, three promiscuous kinases from Shigella flexneri (SfPK), Escherichia coli (EcPK), and Saccharomyces cerevisiae (ScPK) and three isopentenyl phosphate kinases from Methanolobus tindarius (MtIPK), Methanothermobacter thermautotrophicus str. Delta H (MthIPK), and Arabidopsis thaliana (AtIPK) were cloned and expressed in Escherichia coli. The enzymatic properties of recombinant enzymes were determined. The Kcat/Km value of SfPK for DMA was 6875 s-1 M-1, which was significantly higher than those of EcPK and ScPK. The Kcat/Km value of MtIPK for DMAP was 402.9 s-1 M-1, which was ~400% of that of MthIPK. SfPK was stable at pH 7.0-9.5 and had a 1 h half-life at 65 °C. MtIPK was stable at pH 6.0-8.5 and had a 1 h half-life at 50 °C. The stability of SfPK and MtIPK was better than that of the other enzymes. Thus, SfPK and MtIPK were chosen to develop a one-pot enzymatic cascade for producing DMAPP from DMA because of their catalytic efficiency and stability. The optimal ratio between SfPK and MtIPK was 1:8. The optimal pH and temperature for the one-pot enzymatic cascade were 7.0 and 35 °C, respectively. The optimal concentrations of ATP and DMA were 10 and 80 mM, respectively. Finally, maximum DMAPP production reached 1.23 mM at 1 h under optimal conditions. Therefore, the enzymatic method described herein for the biosynthesis of DMAPP from DMA can be widely used for the synthesis of isoprenoids and prenylated flavonoids.
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Affiliation(s)
- Cong Qiu
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing 210037, China
| | - Yang Liu
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing 210037, China
| | - Yangbao Wu
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing 210037, China
| | - Linguo Zhao
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing 210037, China
| | - Jianjun Pei
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing 210037, China
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7
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Hou Y, Chen M, Sun Z, Ma G, Chen D, Wu H, Yang J, Li Y, Xu X. The Biosynthesis Related Enzyme, Structure Diversity and Bioactivity Abundance of Indole-Diterpenes: A Review. Molecules 2022; 27:6870. [PMID: 36296463 PMCID: PMC9611320 DOI: 10.3390/molecules27206870] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/20/2022] [Accepted: 10/10/2022] [Indexed: 11/18/2022] Open
Abstract
Indole diterpenes are a large class of secondary metabolites produced by fungi, possessing a cyclic diterpenoid backbone and an indole moiety. Novel structures and important biological activity have made indole diterpenes one of the focuses of synthetic chemists. Although the discovery, identification, structural diversity, biological activity and especially structure-activity relationship of indole diterpenes have been reported in some papers in recent years, they are absent of a systematic and comprehensive analysis, and there is no elucidation of enzymes related to this kind of natural product. Therefore, it is necessary to summarize the relevant reports to provide new perspectives for the following research. In this review, for the first time, the function of related synthases and the structure-activity relationship of indole diterpenes are expounded, and the recent research advances of them are emphasized.
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Affiliation(s)
- Yong Hou
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Jinghong 666100, China
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Meiying Chen
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Jinghong 666100, China
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Zhaocui Sun
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Jinghong 666100, China
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Guoxu Ma
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Jinghong 666100, China
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Deli Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Haifeng Wu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Junshan Yang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Yihang Li
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Jinghong 666100, China
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Xudong Xu
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Jinghong 666100, China
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, China
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8
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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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9
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Isogai S, Okahashi N, Asama R, Nakamura T, Hasunuma T, Matsuda F, Ishii J, Kondo A. Synthetic production of prenylated naringenins in yeast using promiscuous microbial prenyltransferases. Metab Eng Commun 2021; 12:e00169. [PMID: 33868922 PMCID: PMC8040282 DOI: 10.1016/j.mec.2021.e00169] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 01/19/2021] [Accepted: 03/01/2021] [Indexed: 11/29/2022] Open
Abstract
Reconstitution of prenylflavonoids using the flavonoid biosynthetic pathway and prenyltransferases (PTs) in microbes can be a promising attractive alternative to plant-based production or chemical synthesis. Here, we demonstrate that promiscuous microbial PTs can be a substitute for regiospecific but mostly unidentified botanical PTs. To test the prenylations of naringenin, we constructed a yeast strain capable of producing naringenin from l-phenylalanine by genomic integration of six exogenous genes encoding components of the naringenin biosynthetic pathway. Using this platform strain, various microbial PTs were tested for prenylnaringenin production. In vitro screening demonstrated that the fungal AnaPT (a member of the tryptophan dimethylallyltransferase family) specifically catalyzed C-3′ prenylation of naringenin, whereas SfN8DT-1, a botanical PT, specifically catalyzed C-8 prenylation. In vivo, the naringenin-producing strain expressing the microbial AnaPT exhibited heterologous microbial production of 3′-prenylnaringenin (3′-PN), in contrast to the previously reported in vivo production of 8-prenylnaringenin (8-PN) using the botanical SfN8DT-1. These findings provide strategies towards expanding the production of a variety of prenylated compounds, including well-known prenylnaringenins and novel prenylflavonoids. These results also suggest the opportunity for substituting botanical PTs, both known and unidentified, that display relatively strict regiospecificity of the prenyl group transfer. Promiscuous microbial prenyltransferases replaced regiospecific botanical enzymes. A stable yeast strain that produced naringenin from l-phenylalanine was constructed. A fungal prenyltransferase (AnaPT) catalyzed C-3′ prenylation of naringenin. AnaPT catalyzed the first microbial production of 3′-prenylnaringenin. Microbial prenyltransferases permit the production of various prenylated compounds.
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Affiliation(s)
- Shota Isogai
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.,Technology Research Association of Highly Efficient Gene Design (TRAHED), Kobe, Japan
| | - Nobuyuki Okahashi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ririka Asama
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Tomomi Nakamura
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.,Technology Research Association of Highly Efficient Gene Design (TRAHED), Kobe, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.,Technology Research Association of Highly Efficient Gene Design (TRAHED), Kobe, Japan.,Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Jun Ishii
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.,Technology Research Association of Highly Efficient Gene Design (TRAHED), Kobe, Japan.,Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.,Technology Research Association of Highly Efficient Gene Design (TRAHED), Kobe, Japan.,Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.,Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.,Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, 230-0045, Japan
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10
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Functional characterization of the idtF and idtP genes in the Claviceps paspali indole diterpene biosynthetic gene cluster. Folia Microbiol (Praha) 2020; 65:605-613. [PMID: 32077051 PMCID: PMC7244603 DOI: 10.1007/s12223-020-00777-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 01/29/2020] [Indexed: 11/09/2022]
Abstract
Claviceps paspali is used in the pharmaceutical industry for the production of ergot alkaloids. This fungus also biosynthesizes paspalitrems, indole diterpene (IDT) mycotoxins that cause significant economic losses in agriculture and represent safety concerns for ergot alkaloid manufacture. Here, we use Agrobacterium-mediated transformation to replace the idtP and the idtF genes in the IDT biosynthetic gene cluster of C. paspali with a selectable marker gene. We show that the ΔidtP knockout mutant produces paspaline, the first IDT intermediate of the pathway. The ΔidtF strain produces unprenylated IDTs such as paspalinine and paspaline. These experiments validate the function of idtP as the gene encoding the cytochrome P450 monooxygenase that oxidizes and demethylates paspaline to produce 13-desoxypaxilline, and that of idtF as the gene that encodes the α-prenyltransferase that prenylates paspalinine at the C20 or the C21 positions to yield paspalitrems A and C, respectively. In addition, we also show that axenic cultures of the wild type, the ΔidtP and the ΔidtF mutant C. paspali strains fail to produce an assembly of IDTs that are present in C. paspali–Paspalum spp. associations.
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11
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Van de Bittner KC, Cameron RC, Bustamante LY, Bundela R, Kessans SA, Vorster J, Nicholson MJ, Parker EJ. Nodulisporic acid E biosynthesis: in vivo characterisation of NodD1, an indole-diterpene prenyltransferase that acts on an emindole SB derived indole-diterpene scaffold. MEDCHEMCOMM 2019; 10:1160-1164. [PMID: 31391888 PMCID: PMC6640557 DOI: 10.1039/c9md00143c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/22/2019] [Indexed: 11/21/2022]
Abstract
Prenylation of aromatic compounds is a key tailoring reaction in biosynthesis of bioactive indole-diterpenes. Here, we identify NodD1 as the enzyme responsible for the bisprenylation of nodulisporic acid F. This prenyltransferase showed a preference for its natural indole-diterpene substrate whereas other related enzymes were not able to catalyse this conversion.
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Affiliation(s)
- Kyle C Van de Bittner
- Ferrier Research Institute , Victoria University of Wellington , Kelburn , Wellington 6012 , New Zealand . ;
| | - Rosannah C Cameron
- Ferrier Research Institute , Victoria University of Wellington , Kelburn , Wellington 6012 , New Zealand . ;
| | - Leyla Y Bustamante
- Ferrier Research Institute , Victoria University of Wellington , Kelburn , Wellington 6012 , New Zealand . ;
| | - Rudranuj Bundela
- Ferrier Research Institute , Victoria University of Wellington , Kelburn , Wellington 6012 , New Zealand . ;
| | - Sarah A Kessans
- Biomolecular Interaction Centre and School of Biological Sciences , University of Canterbury , PO Box 4800 , Christchurch 8140 , New Zealand
| | - Jan Vorster
- School of Chemical and Physical Sciences , Victoria University of Wellington , PO Box 6012 , Wellington , New Zealand
| | - Matthew J Nicholson
- Ferrier Research Institute , Victoria University of Wellington , Kelburn , Wellington 6012 , New Zealand . ;
| | - Emily J Parker
- Ferrier Research Institute , Victoria University of Wellington , Kelburn , Wellington 6012 , New Zealand . ;
- Maurice Wilkins Centre for Molecular Biodiscovery , New Zealand
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12
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Kozák L, Szilágyi Z, Tóth L, Pócsi I, Molnár I. Tremorgenic and neurotoxic paspaline-derived indole-diterpenes: biosynthetic diversity, threats and applications. Appl Microbiol Biotechnol 2019; 103:1599-1616. [PMID: 30613899 DOI: 10.1007/s00253-018-09594-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/15/2018] [Accepted: 12/20/2018] [Indexed: 12/18/2022]
Abstract
Indole-diterpenes (IDTs) such as the aflatrems, janthitrems, lolitrems, paspalitrems, penitrems, shearinines, sulpinines, and terpendoles are biogenetically related but structurally varied tremorgenic and neurotoxic mycotoxins produced by fungi. All these metabolites derive from the biosynthetic intermediate paspaline, a frequently occurring IDT on its own right. In this comprehensive review, we highlight the similarities and differences of the IDT biosynthetic pathways that lead to the generation of the main paspaline-derived IDT subgroups. We survey the taxonomic distribution and the regulation of IDT production in various fungi and compare the organization of the known IDT biosynthetic gene clusters. A detailed assessment of the highly diverse biological activities of these mycotoxins leads us to emphasize the significant losses that paspaline-derived IDTs cause in agriculture, and compels us to warn about the various hazards they represent towards human and livestock health. Conversely, we also describe the potential utility of these versatile molecules as lead compounds for pharmaceutical drug discovery, and examine the prospects for their industrial scale manufacture in genetically manipulated IDT producers or domesticated host microorganisms in synthetic biological production systems.
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Affiliation(s)
- László Kozák
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
- Teva Pharmaceutical Works Ltd., Debrecen, Hungary
| | | | - László Tóth
- Teva Pharmaceutical Works Ltd., Debrecen, Hungary
| | - István Pócsi
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary.
| | - István Molnár
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary.
- Southwest Center for Natural Products Research, School of Natural Resources and the Environment, University of Arizona, Tucson, USA.
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13
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Kudo K, Liu C, Matsumoto T, Minami A, Ozaki T, Toshima H, Gomi K, Oikawa H. Heterologous Biosynthesis of Fungal Indole Sesquiterpene Sespendole. Chembiochem 2018; 19:1492-1497. [DOI: 10.1002/cbic.201800187] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Kosei Kudo
- Division of ChemistryGraduate School of ScienceHokkaido University Sapporo 060-0810 Japan
| | - Chengwei Liu
- Division of ChemistryGraduate School of ScienceHokkaido University Sapporo 060-0810 Japan
| | - Tomoyuki Matsumoto
- Division of ChemistryGraduate School of ScienceHokkaido University Sapporo 060-0810 Japan
| | - Atsushi Minami
- Division of ChemistryGraduate School of ScienceHokkaido University Sapporo 060-0810 Japan
| | - Taro Ozaki
- Division of ChemistryGraduate School of ScienceHokkaido University Sapporo 060-0810 Japan
| | - Hiroaki Toshima
- Department of Bioresource ScienceCollege of AgricultureIbaraki University Inashiki Ibaraki 300-0393 Japan
| | - Katsuya Gomi
- Graduate School of Agricultural ScienceTohoku University Sendai 981-8555 Japan
| | - Hideaki Oikawa
- Division of ChemistryGraduate School of ScienceHokkaido University Sapporo 060-0810 Japan
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14
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Pan LL, Song LF, Miao Y, Yang Y, Merz KM. Mechanism of Formation of the Nonstandard Product in the Prenyltransferase Reaction of the G115T Mutant of FtmPT1: A Case of Reaction Dynamics Calling the Shots? Biochemistry 2017; 56:2995-3007. [PMID: 28570807 DOI: 10.1021/acs.biochem.7b00248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
FtmPT1 is a fungal indole prenyltransferase that affords Tryprostatin B from Brevianamide F and dimethylallyl pyrophosphate; however, when a single residue in the active site is mutated (Gly115Thr), a novel five-membered ring compound is obtained as the major product with Tryprostatin B as the minor product. Herein, we describe detailed studies of the catalysis of the Gly115Thr mutant of FtmPT1 with a focus on the observed regioselectivity of the reaction. We employ one- and two-dimensional potential of mean force simulations to explore the catalytic mechanism, along with molecular dynamics simulations exploring the reaction dynamics of the prenyl transfer reaction. Single-point electronic structure calculations were also used to explore the performance of the self-consistent charge density functional tight-binding method to model specific reaction steps. Importantly, we observe that the two reaction pathways have comparable activation parameters and propose that the origin of the novel product is predicated, at least in part, on the topology of the potential energy surface as revealed by reaction dynamics studies.
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Affiliation(s)
- Li-Li Pan
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University , 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Lin Frank Song
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University , 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Yipu Miao
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University , 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Yue Yang
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory , 7000 East Avenue, Livermore, California 94550, United States
| | - Kenneth M Merz
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University , 578 South Shaw Lane, East Lansing, Michigan 48824, United States.,Institute for Cyber Enabled Research, Michigan State University , 567 Wilson Road, Room 1440, East Lansing, Michigan 48824, United States
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15
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Abstract
Covering: up to September 2015. Meroterpenoids are hybrid natural products that partially originate from the terpenoid pathway. The meroterpenoids derived from fungi display quite diverse structures, with a wide range of biological properties. This review summarizes the molecular bases for their biosyntheses, which were recently elucidated with modern techniques, and also discusses the plausible biosynthetic pathways of other related natural products lacking genetic information. (Complementary to the coverage of literature by Geris and Simpson in Nat. Prod. Rep., 2009, 26, 1063-1094.).
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Affiliation(s)
- Yudai Matsuda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan.
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan.
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16
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17
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18
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Abstract
This review provides a summary of recent research advances in elucidating the biosynthesis of fungal indole alkaloids. The different strategies used to incorporate and derivatize the indole/indoline moieties in various families of fungal indole alkaloids will be discussed, including tryptophan-containing nonribosomal peptides, polyketide-nonribosomal peptide hybrids, and alkaloids derived from other indole building blocks. This review also includes a discussion regarding the downstream modifications that generate chemical and structural diversity among indole alkaloids.
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Affiliation(s)
- Wei Xu
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90096, USA.
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19
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Tagami K, Minami A, Fujii R, Liu C, Tanaka M, Gomi K, Dairi T, Oikawa H. Rapid Reconstitution of Biosynthetic Machinery for Fungal Metabolites inAspergillus oryzae: Total Biosynthesis of Aflatrem. Chembiochem 2014; 15:2076-80. [DOI: 10.1002/cbic.201402195] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Indexed: 01/08/2023]
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20
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Liu C, Noike M, Minami A, Oikawa H, Dairi T. A fungal prenyltransferase catalyzes the regular di-prenylation at positions 20 and 21 of paxilline. Biosci Biotechnol Biochem 2014; 78:448-54. [DOI: 10.1080/09168451.2014.882759] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Abstract
A putative indole diterpene biosynthetic gene cluster composed of eight genes was identified in a genome database of Phomopsis amygdali, and from it, biosynthetic genes of fusicoccin A were cloned and characterized. The six genes showed significant similarities to pax genes, which are essential to paxilline biosynthesis in Penicillium paxilli. Recombinants of the three putative prenyltransferase genes in the cluster were overexpressed in Escherichia coli and characterized by means of in vitro experiments. AmyG is perhaps a GGDP synthase. AmyC and AmyD were confirmed to be prenyltransferases catalyzing the transfer of GGDP to IGP and a regular di-prenylation at positions 20 and 21 of paxilline, respectively. AmyD is the first know example of an enzyme with this function. The Km values for AmyD were calculated to be 7.6 ± 0.5 μM for paxilline and 17.9 ± 1.7 μM for DMAPP at a kcat of 0.12 ± 0.003/s.
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Affiliation(s)
- Chengwei Liu
- Graduate School of Engineering, Hokkaido University, Sapporo, Japan
| | - Motoyoshi Noike
- Graduate School of Engineering, Hokkaido University, Sapporo, Japan
| | - Atsushi Minami
- Graduate School of Science, Hokkaido University, Sapporo, Japan
| | - Hideaki Oikawa
- Graduate School of Science, Hokkaido University, Sapporo, Japan
| | - Tohru Dairi
- Graduate School of Engineering, Hokkaido University, Sapporo, Japan
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