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Xu H, Dickschat JS. Isotopic labelings for mechanistic studies. Methods Enzymol 2024; 699:163-186. [PMID: 38942502 DOI: 10.1016/bs.mie.2024.01.011] [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
The intricate mechanisms in the biosynthesis of terpenes belong to the most challenging problems in natural product chemistry. Methods to address these problems include the structure-based site-directed mutagenesis of terpene synthases, computational approaches, and isotopic labeling experiments. The latter approach has a long tradition in biosynthesis studies and has recently experienced a revival, after genome sequencing enabled rapid access to biosynthetic genes and enzymes. Today, this allows for a combined approach in which isotopically labeled substrates can be incubated with recombinant terpene synthases. These clearly defined reaction setups can give detailed mechanistic insights into the reactions catalyzed by terpene synthases, and recent developments have substantially deepened our understanding of terpene biosynthesis. This chapter will discuss the state of the art and introduce some of the most important methods that make use of isotopic labelings in mechanistic studies on terpene synthases.
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Affiliation(s)
- Houchao Xu
- Kekulé-Institute for Organic Chemistry and Biochemistry, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany.
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2
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De Grazia G, Cucinotta L, Sciarrone D, Donato P, Trovato E, Riad N, Hattab ME, Mondello L, Rotondo A. Preparative three-dimensional GC and nuclear magnetic resonance for the isolation and identification of two sesquiterpene ethers from Dictyota Dichotoma. J Sep Sci 2023; 46:e2300261. [PMID: 37386802 DOI: 10.1002/jssc.202300261] [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] [Received: 04/17/2023] [Revised: 05/23/2023] [Accepted: 06/15/2023] [Indexed: 07/01/2023]
Abstract
Separation science plays a crucial role in the isolation of novel compounds contained in complex matrices. Yet their rationale employment needs preliminary structure elucidation, which usually requires sufficient aliquots of grade substances to characterize the molecule by nuclear magnetic resonance experiments. In this study, two peculiar oxa-tricycloundecane ethers were isolated by means of preparative multidimensional gas chromatography from the brown alga species Dictyota dichotoma (Huds.) Lam., aiming to assign their 3D structures. Density functional theory simulations were carried out to select the correct configurational species matching the experimental NMR data (in terms of enantiomeric couples). In this case, the theoretical approach was crucial as the protonic signal overlap and spectral overcrowding were preventing any other unambiguous structural information. Just after the identification through the density functional theory data matching of the correct relative configuration it was possible to verify an enhanced self-consistency with the experimental data, confirming the stereochemistry. The results obtained further pave the way toward structure elucidation of highly asymmetric molecules, whose configuration cannot be inferred by other means or strategies.
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Affiliation(s)
- Gemma De Grazia
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Lorenzo Cucinotta
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
- Traceability Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Danilo Sciarrone
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Paola Donato
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences, University of Messina, Messina, Italy
| | - Emanuela Trovato
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Nacera Riad
- Laboratory of Natural Products Chemistry and Biomolecules, Faculty of Sciences, University Blida 1, Blida, Algeria
| | - Mohamed El Hattab
- Laboratory of Natural Products Chemistry and Biomolecules, Faculty of Sciences, University Blida 1, Blida, Algeria
| | - Luigi Mondello
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Chromaleont S.R.L., University of Messina, Messina, Italy
| | - Archimede Rotondo
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences, University of Messina, Messina, Italy
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3
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Li C, Wang S, Yin X, Guo A, Xie K, Chen D, Sui S, Han Y, Liu J, Chen R, Dai J. Functional Characterization and Cyclization Mechanism of a Diterpene Synthase Catalyzing the Skeleton Formation of Cephalotane-Type Diterpenoids. Angew Chem Int Ed Engl 2023; 62:e202306020. [PMID: 37326357 DOI: 10.1002/anie.202306020] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 06/17/2023]
Abstract
CsCTS, a new diterpene synthase from Cephalotaxus sinensis responsible for forming cephalotene, the core skeleton of cephalotane-type diterpenoids with a highly rigid 6/6/5/7 tetracyclic ring system, was functionally characterized. The stepwise cyclization mechanism is proposed mainly based on structural investigation of its derailment products, and further demonstrated through isotopic labeling experiments and density functional theory calculations. Homology modeling and molecular dynamics simulation combined with site-directed mutagenesis revealed the critical amino acid residues for the unique carbocation-driven cascade cyclization mechanism of CsCTS. Altogether, this study reports the discovery of the diterpene synthase that catalyzes the first committed step of cephalotane-type diterpenoid biosynthesis and delineates its cyclization mechanism, laying the foundation to decipher and artificially construct the complete biosynthetic pathway of this type diterpenoids.
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Affiliation(s)
- Changkang Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, NHC Key Laboratory of Biosynthesis of Natural Products, and Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Shuai Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, NHC Key Laboratory of Biosynthesis of Natural Products, and Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, 252000, Shandong, China
| | - Xinxin Yin
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, NHC Key Laboratory of Biosynthesis of Natural Products, and Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Aobo Guo
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, NHC Key Laboratory of Biosynthesis of Natural Products, and Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Kebo Xie
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, NHC Key Laboratory of Biosynthesis of Natural Products, and Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Dawei Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, NHC Key Laboratory of Biosynthesis of Natural Products, and Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Songyang Sui
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, NHC Key Laboratory of Biosynthesis of Natural Products, and Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Yaotian Han
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, NHC Key Laboratory of Biosynthesis of Natural Products, and Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Jimei Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, NHC Key Laboratory of Biosynthesis of Natural Products, and Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Ridao Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, NHC Key Laboratory of Biosynthesis of Natural Products, and Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Jungui Dai
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, NHC Key Laboratory of Biosynthesis of Natural Products, and Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
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4
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Tarasova EV, Luchnikova NA, Grishko VV, Ivshina IB. Actinomycetes as Producers of Biologically Active Terpenoids: Current Trends and Patents. Pharmaceuticals (Basel) 2023; 16:872. [PMID: 37375819 DOI: 10.3390/ph16060872] [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: 03/15/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Terpenes and their derivatives (terpenoids and meroterpenoids, in particular) constitute the largest class of natural compounds, which have valuable biological activities and are promising therapeutic agents. The present review assesses the biosynthetic capabilities of actinomycetes to produce various terpene derivatives; reports the main methodological approaches to searching for new terpenes and their derivatives; identifies the most active terpene producers among actinomycetes; and describes the chemical diversity and biological properties of the obtained compounds. Among terpene derivatives isolated from actinomycetes, compounds with pronounced antifungal, antiviral, antitumor, anti-inflammatory, and other effects were determined. Actinomycete-produced terpenoids and meroterpenoids with high antimicrobial activity are of interest as a source of novel antibiotics effective against drug-resistant pathogenic bacteria. Most of the discovered terpene derivatives are produced by the genus Streptomyces; however, recent publications have reported terpene biosynthesis by members of the genera Actinomadura, Allokutzneria, Amycolatopsis, Kitasatosporia, Micromonospora, Nocardiopsis, Salinispora, Verrucosispora, etc. It should be noted that the use of genetically modified actinomycetes is an effective tool for studying and regulating terpenes, as well as increasing productivity of terpene biosynthesis in comparison with native producers. The review includes research articles on terpene biosynthesis by Actinomycetes between 2000 and 2022, and a patent analysis in this area shows current trends and actual research directions in this field.
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Affiliation(s)
- Ekaterina V Tarasova
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia
| | - Natalia A Luchnikova
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia
- Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia
| | - Victoria V Grishko
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia
| | - Irina B Ivshina
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia
- Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia
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Xu H, Goldfuss B, Schnakenburg G, Dickschat JS. The enzyme mechanism of patchoulol synthase. Beilstein J Org Chem 2022; 18:13-24. [PMID: 35047079 PMCID: PMC8744462 DOI: 10.3762/bjoc.18.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/17/2021] [Indexed: 12/21/2022] Open
Abstract
Different mechanisms for the cyclisation of farnesyl pyrophosphate to patchoulol by the patchoulol synthase are discussed in the literature. They are based on isotopic labelling experiments, but the results from these experiments are contradictory. The present work reports on a reinvestigation of patchoulol biosynthesis by isotopic labelling experiments and computational chemistry. The results are in favour of a pathway through the neutral intermediates germacrene A and α-bulnesene that are both reactivated by protonation for further cyclisation steps, while previously discussed intra- and intermolecular hydrogen transfers are not supported. Furthermore, the isolation of the new natural product (2S,3S,7S,10R)-guaia-1,11-dien-10-ol from patchouli oil is reported.
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Affiliation(s)
- Houchao Xu
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Bernd Goldfuss
- Department of Chemistry, University of Cologne, Greinstraße 4, 50939 Cologne, Germany
| | - Gregor Schnakenburg
- Institute of Inorganic Chemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
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7
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Hou A, Dickschat JS. Targeting active site residues and structural anchoring positions in terpene synthases. Beilstein J Org Chem 2021; 17:2441-2449. [PMID: 34621406 PMCID: PMC8450962 DOI: 10.3762/bjoc.17.161] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/10/2021] [Indexed: 12/22/2022] Open
Abstract
The sesterterpene synthase SmTS1 from Streptomyces mobaraensis contains several unusual residues in positions that are otherwise highly conserved. Site-directed mutagenesis experiments for these residues are reported that showed different effects, resulting in some cases in an improved catalytic activity, but in other cases in a loss of enzyme function. For other enzyme variants a functional switch was observed, turning SmTS1 from a sesterterpene into a diterpene synthase. This article gives rational explanations for these findings that may generally allow for protein engineering of other terpene synthases to improve their catalytic efficiency or to change their functions.
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Affiliation(s)
- Anwei Hou
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
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Abstract
Covering: up to mid-2020 Terpenoids, also called isoprenoids, are the largest and most structurally diverse family of natural products. Found in all domains of life, there are over 80 000 known compounds. The majority of characterized terpenoids, which include some of the most well known, pharmaceutically relevant, and commercially valuable natural products, are produced by plants and fungi. Comparatively, terpenoids of bacterial origin are rare. This is counter-intuitive to the fact that recent microbial genomics revealed that almost all bacteria have the biosynthetic potential to create the C5 building blocks necessary for terpenoid biosynthesis. In this review, we catalogue terpenoids produced by bacteria. We collected 1062 natural products, consisting of both primary and secondary metabolites, and classified them into two major families and 55 distinct subfamilies. To highlight the structural and chemical space of bacterial terpenoids, we discuss their structures, biosynthesis, and biological activities. Although the bacterial terpenome is relatively small, it presents a fascinating dichotomy for future research. Similarities between bacterial and non-bacterial terpenoids and their biosynthetic pathways provides alternative model systems for detailed characterization while the abundance of novel skeletons, biosynthetic pathways, and bioactivies presents new opportunities for drug discovery, genome mining, and enzymology.
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Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Tyler A Alsup
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Baofu Xu
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Zining Li
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
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9
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Ruiz-Ferrer C, Román-Marín LU, Hernández-Hernández JD, Cerda-García-Rojas CM, Joseph-Nathan P. Novel Sesquiterpenoid Skeletons by Wagner-Meerwein Rearrangements of Longipinane-9,13-diol-1-one Derivatives. JOURNAL OF NATURAL PRODUCTS 2021; 84:1087-1095. [PMID: 33733766 DOI: 10.1021/acs.jnatprod.0c01160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The partial or total hydrolysis of (3R,4S,5S,6S,9R,10R,11R)-9,13-diangeloyloxylongipinan-1-one (1), isolated from the roots of Stevia viscida, gave alcohols 2 or 3, respectively, which were subjected to molecular rearrangements with boron trifluoride etherate. Compound 2 afforded (3R,4R,5R,6S,9R,10S,11S)-11,13-oxyneomorelian-1-one (10) and (4S,5R,6S,8S,10R)-10,13-oxyneojiquilp-2-en-1-one (11), both possessing novel sesquiterpenoid skeletons. In turn, 3 provided (3R,4R,5S,6S,9R,11R)-13-hydroxymoreli-10(14)-en-1-one (7) and 10. Acetylation of 3 gave 4, thus allowing reduction of the C-1 carbonyl group to yield 5, which was rearranged to (1S,3R,4S,5S,6S,9R,10R,11R)-13-acetoxy-9,11-epoxyjiquilpane (6), while an attempt to mesylate 3 directly gave rearranged (3R,4R,5S,6S,9R,11R)-13-mesyloxymoreli-10(14)-en-1-one (8) through expulsion of the C-9 mesylate group by the antiperiplanar C-4-C-10 bond migration to C-4-C-9. In addition, treatment of 1 with boron trifluoride etherate generated (3R,4R,5S,6S,9R,11R)-13-angeloyloxymoreli-10(14)-en-1-one (9). The structures of 2-11 were elucidated by 1D and 2D NMR experiments and those of 2, 3, 8, 10, and 11 were confirmed by single-crystal X-ray diffraction analysis.
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Affiliation(s)
- Cecilia Ruiz-Ferrer
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, Morelia, Michoacán 58030, Mexico
| | - Luisa U Román-Marín
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, Morelia, Michoacán 58030, Mexico
| | - Juan D Hernández-Hernández
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, Morelia, Michoacán 58030, Mexico
| | - Carlos M Cerda-García-Rojas
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado 14-740, Mexico City 07000, Mexico
| | - Pedro Joseph-Nathan
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado 14-740, Mexico City 07000, Mexico
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10
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Xu H, Dickschat JS. Revision of the Cyclisation Mechanism for the Diterpene Spiroviolene and Investigations of Its Mass Spectrometric Fragmentation. Chembiochem 2021; 22:850-854. [PMID: 33084237 PMCID: PMC7983979 DOI: 10.1002/cbic.202000682] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/21/2020] [Indexed: 01/15/2023]
Abstract
The diterpene spiroviolene, its diterpene synthase from Streptomyces violens and the experimentally determined terpene cyclisation mechanism were reported in 2017. Recently, the structure of spiroviolene was revised based on a total synthesis, with consequences for the cyclisation mechanism. Herein, a reinvestigation of the terpene cyclisation to spiroviolene and the mass spectrometric fragmentation mechanism investigated by 13 C-labelling experiments are presented.
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Affiliation(s)
- Houchao Xu
- Kekulé Institute for Organic Chemistry and BiochemistryUniversity of BonnGerhard-Domagk-Straße 153121BonnGermany
| | - Jeroen S. Dickschat
- Kekulé Institute for Organic Chemistry and BiochemistryUniversity of BonnGerhard-Domagk-Straße 153121BonnGermany
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Lauterbach L, Goldfuss B, Dickschat JS. Two Diterpene Synthases from Chryseobacterium: Chryseodiene Synthase and Wanjudiene Synthase. Angew Chem Int Ed Engl 2020; 59:11943-11947. [PMID: 32342621 PMCID: PMC7383580 DOI: 10.1002/anie.202004691] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Indexed: 01/11/2023]
Abstract
Two bacterial diterpene synthases (DTSs) from Chryseobacterium were characterised. The first enzyme yielded the new compound chryseodiene that closely resembles the known fusicoccane diterpenes from fungi, but its experimentally and computationally studied cyclisation mechanism is fundamentally different to the mechanism of fusicoccadiene synthase. The second enzyme produced wanjudiene, a diterpene hydrocarbon with a new skeleton, besides traces of the enantiomer of bonnadiene that was recently discovered from Allokutzneria albata.
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Affiliation(s)
- Lukas Lauterbach
- Kekulé-Institute for Organic Chemistry and BiochemistryUniversity of BonnGerhard-Domagk-Straße 153121BonnGermany
| | - Bernd Goldfuss
- Institute for Organic ChemistryUniversity of CologneGreinstraße 450939CologneGermany
| | - Jeroen S. Dickschat
- Kekulé-Institute for Organic Chemistry and BiochemistryUniversity of BonnGerhard-Domagk-Straße 153121BonnGermany
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Lauterbach L, Goldfuss B, Dickschat JS. Zwei Diterpensynthasen aus
Chryseobacterium
: Chryseodien‐Synthase und Wanjudien‐Synthase. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004691] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Lukas Lauterbach
- Kekulé-Institut für Organische Chemie und Biochemie Universität Bonn Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| | - Bernd Goldfuss
- Institut für Organische Chemie, Universität zu Köln Greinstraße 4 50939 Köln Deutschland
| | - Jeroen S. Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie Universität Bonn Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
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Reddy GK, Leferink NGH, Umemura M, Ahmed ST, Breitling R, Scrutton NS, Takano E. Exploring novel bacterial terpene synthases. PLoS One 2020; 15:e0232220. [PMID: 32353014 PMCID: PMC7192455 DOI: 10.1371/journal.pone.0232220] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 04/09/2020] [Indexed: 01/15/2023] Open
Abstract
Terpenes are the largest class of natural products with extensive structural diversity and are widely used as pharmaceuticals, herbicides, flavourings, fragrances, and biofuels. While they have mostly been isolated from plants and fungi, the availability and analysis of bacterial genome sequence data indicates that bacteria also possess many putative terpene synthase genes. In this study, we further explore this potential for terpene synthase activity in bacteria. Twenty two potential class I terpene synthase genes (TSs) were selected to represent the full sequence diversity of bacterial synthase candidates and recombinantly expressed in E. coli. Terpene synthase activity was detected for 15 of these enzymes, and included mono-, sesqui- and diterpene synthase activities. A number of confirmed sesquiterpene synthases also exhibited promiscuous monoterpene synthase activity, suggesting that bacteria are potentially a richer source of monoterpene synthase activity then previously assumed. Several terpenoid products not previously detected in bacteria were identified, including aromandendrene, acora-3,7(14)-diene and longiborneol. Overall, we have identified promiscuous terpene synthases in bacteria and demonstrated that terpene synthases with substrate promiscuity are widely distributed in nature, forming a rich resource for engineering terpene biosynthetic pathways for biotechnology.
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Affiliation(s)
- Gajendar Komati Reddy
- Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, England, United Kingdom
| | - Nicole G. H. Leferink
- Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, England, United Kingdom
- Future Biomanfacturing Research Hub (FBRH), Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, England, United Kingdom
| | - Maiko Umemura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST, Tsukuba, Ibaraki, Japan
| | - Syed T. Ahmed
- Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, England, United Kingdom
| | - Rainer Breitling
- Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, England, United Kingdom
| | - Nigel S. Scrutton
- Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, England, United Kingdom
- Future Biomanfacturing Research Hub (FBRH), Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, England, United Kingdom
| | - Eriko Takano
- Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, England, United Kingdom
- Future Biomanfacturing Research Hub (FBRH), Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, England, United Kingdom
- * E-mail:
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Rinkel J, Dickschat JS. Mechanistic Studies on Trichoacorenol Synthase from Amycolatopsis benzoatilytica. Chembiochem 2020; 21:807-810. [PMID: 31553510 PMCID: PMC7155024 DOI: 10.1002/cbic.201900584] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Indexed: 01/17/2023]
Abstract
Isotopic labeling experiments performed with a newly identified bacterial trichoacorenol synthase established a 1,5-hydride shift occurring in the cyclization mechanism. During EI-MS analysis, major fragments of the sesquiterpenoid were shown to arise via cryptic hydrogen movements. Therefore, the interpretation of earlier results regarding the cyclization mechanism obtained by feeding experiments in Trichoderma is revised.
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Affiliation(s)
- Jan Rinkel
- Kekulé Institute of Organic Chemistry and BiochemistryUniversity of BonnGerhard-Domagk-Strasse 153121BonnGermany
| | - Jeroen S. Dickschat
- Kekulé Institute of Organic Chemistry and BiochemistryUniversity of BonnGerhard-Domagk-Strasse 153121BonnGermany
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15
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Armenta-Salinas C, Guzmán-Mejía R, García-Gutiérrez HA, Román-Marín LU, Hernández-Hernández JD, Cerda-García-Rojas CM, Joseph-Nathan P. Novel Sesquiterpene Skeletons by Multiple Wagner-Meerwein Rearrangements of a Longipinane-1,9-diol Derivative. JOURNAL OF NATURAL PRODUCTS 2019; 82:3410-3420. [PMID: 31773961 DOI: 10.1021/acs.jnatprod.9b00784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The tricyclic sesquiterpene (1R,3R,4S,5S,7S,8S,9S,10R,11R)-7,8-diangeloyloxylongipinan-1,9-diol, or rasteviol (7), underwent multiple Wagner-Meerwein molecular rearrangements and several hydride shifts when treated with Et2O-BF3 to generate the six new compounds (1R,3R,4S,5R,7S,8S,9S,10R,11S)-7,8-diangeloyloxy-1,9-epoxyjiquilpane (8), (1R,3R,4S,5R,7R,8S,9S,11S)-8-angeloyloxy-1,7-epoxyzamor-10(14)-ene (11), (2S,3R,4R,5R,6R,7R,8S,9S,10S)-7,8-diangeloyloxy-6,9-epoxyjanitziane (14), (4R,5R,7S,8S,9S,10S,11S)-7,8-diangeloyloxy-9-hydroxyjiquilp-3(15)-ene (16), (2S,3S,5R,7S,8R,10S,11R)-7,8-diangeloyloxyiratzian-9-one (18), and (2S,3S,5R,10S,11R)-8-angeloyloxyiratzi-7-en-9-one (22), of which 8, 11, 14, and 18 possess new hydrocarbon skeletons. Their structures were determined by 1D and 2D NMR in combination with single-crystal X-ray diffraction analyses of derivatives 10, 15, 20, and 21, which allowed confirmation of their absolute configurations by means of the Flack and Hooft parameters. In addition, some reaction mechanism information was gained from deuterium labeling experiments.
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Affiliation(s)
- Concepción Armenta-Salinas
- Instituto de Investigaciones Químico Biológicas , Universidad Michoacana de San Nicolás de Hidalgo , Ciudad Universitaria, Morelia , Michoacán , 58030 Mexico
| | - Ramón Guzmán-Mejía
- Instituto de Investigaciones Químico Biológicas , Universidad Michoacana de San Nicolás de Hidalgo , Ciudad Universitaria, Morelia , Michoacán , 58030 Mexico
| | - Hugo A García-Gutiérrez
- Instituto de Investigaciones Químico Biológicas , Universidad Michoacana de San Nicolás de Hidalgo , Ciudad Universitaria, Morelia , Michoacán , 58030 Mexico
| | - Luisa U Román-Marín
- Instituto de Investigaciones Químico Biológicas , Universidad Michoacana de San Nicolás de Hidalgo , Ciudad Universitaria, Morelia , Michoacán , 58030 Mexico
| | - Juan D Hernández-Hernández
- Instituto de Investigaciones Químico Biológicas , Universidad Michoacana de San Nicolás de Hidalgo , Ciudad Universitaria, Morelia , Michoacán , 58030 Mexico
| | - Carlos M Cerda-García-Rojas
- Departamento de Química , Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional , Apartado 14-740 , Mexico City , 07000 Mexico
| | - Pedro Joseph-Nathan
- Departamento de Química , Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional , Apartado 14-740 , Mexico City , 07000 Mexico
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16
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Helfrich EJN, Lin GM, Voigt CA, Clardy J. Bacterial terpene biosynthesis: challenges and opportunities for pathway engineering. Beilstein J Org Chem 2019; 15:2889-2906. [PMID: 31839835 PMCID: PMC6902898 DOI: 10.3762/bjoc.15.283] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/01/2019] [Indexed: 12/27/2022] Open
Abstract
Terpenoids are the largest and structurally most diverse class of natural products. They possess potent and specific biological activity in multiple assays and against diseases, including cancer and malaria as notable examples. Although the number of characterized terpenoid molecules is huge, our knowledge of how they are biosynthesized is limited, particularly when compared to the well-studied thiotemplate assembly lines. Bacteria have only recently been recognized as having the genetic potential to biosynthesize a large number of complex terpenoids, but our current ability to associate genetic potential with molecular structure is severely restricted. The canonical terpene biosynthetic pathway uses a single enzyme to form a cyclized hydrocarbon backbone followed by modifications with a suite of tailoring enzymes that can generate dozens of different products from a single backbone. This functional promiscuity of terpene biosynthetic pathways renders terpene biosynthesis susceptible to rational pathway engineering using the latest developments in the field of synthetic biology. These engineered pathways will not only facilitate the rational creation of both known and novel terpenoids, their development will deepen our understanding of a significant branch of biosynthesis. The biosynthetic insights gained will likely empower a greater degree of engineering proficiency for non-natural terpene biosynthetic pathways and pave the way towards the biotechnological production of high value terpenoids.
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Affiliation(s)
- Eric J N Helfrich
- Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, Boston, United States
| | - Geng-Min Lin
- Massachusetts Institute of Technology, Department of Biological Engineering, Cambridge, United States
| | - Christopher A Voigt
- Massachusetts Institute of Technology, Department of Biological Engineering, Cambridge, United States
| | - Jon Clardy
- Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, Boston, United States
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17
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Jia Q, Chen X, Köllner TG, Rinkel J, Fu J, Labbé J, Xiong W, Dickschat JS, Gershenzon J, Chen F. Terpene Synthase Genes Originated from Bacteria through Horizontal Gene Transfer Contribute to Terpenoid Diversity in Fungi. Sci Rep 2019; 9:9223. [PMID: 31239482 PMCID: PMC6592883 DOI: 10.1038/s41598-019-45532-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 06/07/2019] [Indexed: 12/18/2022] Open
Abstract
Fungi are successful eukaryotes of wide distribution. They are known as rich producers of secondary metabolites, especially terpenoids, which are important for fungi-environment interactions. Horizontal gene transfer (HGT) is an important mechanism contributing to genetic innovation of fungi. However, it remains unclear whether HGT has played a role in creating the enormous chemical diversity of fungal terpenoids. Here we report that fungi have acquired terpene synthase genes (TPSs), which encode pivotal enzymes for terpenoid biosynthesis, from bacteria through HGT. Phylogenetic analysis placed the majority of fungal and bacterial TPS genes from diverse taxa into two clades, indicating ancient divergence. Nested in the bacterial TPS clade is a number of fungal TPS genes that are inferred as the outcome of HGT. These include a monophyletic clade of nine fungal TPS genes, designated as BTPSL for bacterial TPS-like genes, from eight species of related entomopathogenic fungi, including seven TPSs from six species in the genus Metarhizium. In vitro enzyme assays demonstrate that all seven BTPSL genes from the genus Metarhizium encode active enzymes with sesquiterpene synthase activities of two general product profiles. By analyzing the catalytic activity of two resurrected ancestral BTPSLs and one closely related bacterial TPS, the trajectory of functional evolution of BTPSLs after HGT from bacteria to fungi and functional divergence within Metarhizium could be traced. Using M. brunneum as a model species, both BTPSLs and typical fungal TPSs were demonstrated to be involved in the in vivo production of terpenoids, illustrating the general importance of HGT of TPS genes from bacteria as a mechanism contributing to terpenoid diversity in fungi.
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Affiliation(s)
- Qidong Jia
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA. .,Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
| | - Xinlu Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Tobias G Köllner
- Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, D-07745, Jena, Germany
| | - Jan Rinkel
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Jianyu Fu
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Jessy Labbé
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Wangdan Xiong
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Jonathan Gershenzon
- Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, D-07745, Jena, Germany
| | - Feng Chen
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA. .,Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA.
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18
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Li W, Xu R, Yan X, Liang D, Zhang L, Qin X, Caiyin Q, Zhao G, Xiao W, Hu Z, Qiao J. De novo leaf and root transcriptome analysis to explore biosynthetic pathway of Celangulin V in Celastrus angulatus maxim. BMC Genomics 2019; 20:7. [PMID: 30611193 PMCID: PMC6321707 DOI: 10.1186/s12864-018-5397-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 12/19/2018] [Indexed: 02/06/2023] Open
Abstract
Background Celastrus angulatus Maxim is a kind of crucial and traditional insecticidal plant widely distributed in the mountains of southwest China. Celangulin V is the efficient insecticidal sesquiterpenoid of C. angulatus and widely used in pest control in China, but the low yield and discontinuous supply impeded its further popularization and application. Fortunately, the development of synthetic biology provided an opportunity for sustainable supply of Celangulin V, for which understanding its biosynthetic pathway is indispensable. Results In this study, six cDNA libraries were prepared from leaf and root of C. angulatus before global transcriptome analyses using the BGISEQ-500 platform. A total of 104,950 unigenes were finally obtained with an average length of 1200 bp in six transcriptome databases of C. angulatus, in which 51,817 unigenes classified into 25 KOG classifications, 39,866 unigenes categorized into 55 GO functional groups, and 48,810 unigenes assigned to 135 KEGG pathways, 145 of which were putative biosynthetic genes of sesquiterpenoid and triterpenoid. 16 unigenes were speculated to be related to Celangulin V biosynthesis. De novo assembled sequences were verified by Quantitative Real-Time PCR (qRT-PCR) analysis. Conclusions This study is the first report on transcriptome analysis of C. angulatus, and 16 unigenes probably involved in the biosynthesis of Celangulin V were finally collected. The transcriptome data will make great contributions to research for this specific insecticidal plant and the further gene mining for biosynthesis of Celangulin V and other sesquiterpene polyol esters. Electronic supplementary material The online version of this article (10.1186/s12864-018-5397-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Weiguo Li
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Ranran Xu
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Xiaoguang Yan
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Dongmei Liang
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Lei Zhang
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Xiaoyu Qin
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Qinggele Caiyin
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Guangrong Zhao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Wenhai Xiao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Zhaonong Hu
- College of Plant Protection, Institute of Pesticide Science, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.,Key Laboratory of Botanical Pesticide R&D in Shaanxi Province, Yangling, Shaanxi, 712100, People's Republic of China
| | - Jianjun Qiao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China. .,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China. .,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China.
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19
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Tantillo DJ. Bedeutung der inhärenten Substratreaktivität bei enzymvermittelten Cyclisierungen/Umlagerungen von Carbokationen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702363] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Dean J. Tantillo
- Department of Chemistry University of California—Davis 1 Shields Avenue Davis CA 95616 USA
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20
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Tantillo DJ. Importance of Inherent Substrate Reactivity in Enzyme-Promoted Carbocation Cyclization/Rearrangements. Angew Chem Int Ed Engl 2017; 56:10040-10045. [PMID: 28349600 DOI: 10.1002/anie.201702363] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Indexed: 11/08/2022]
Abstract
The importance of inherent substrate reactivity for terpene synthase enzymes is discussed, with a focus on recent experimental tests of predictions derived from computations on gas-phase reactivity of carbocations.
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Affiliation(s)
- Dean J Tantillo
- Department of Chemistry, University of California-Davis, 1 Shields Avenue, Davis, CA, 95616, USA
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21
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Hussain A, Rather MA, Dar MS, Aga MA, Ahmad N, Manzoor A, Qayum A, Shah A, Mushtaq S, Ahmad Z, Hassan QP. Novel bioactive molecules from Lentzea violacea strain AS 08 using one strain-many compounds (OSMAC) approach. Bioorg Med Chem Lett 2017; 27:2579-2582. [DOI: 10.1016/j.bmcl.2017.03.075] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/01/2017] [Accepted: 03/24/2017] [Indexed: 10/19/2022]
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22
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Affiliation(s)
- Jeroen S. Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry; Rheinische Friedrich Wilhelms University of Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Germany
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23
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Rabe P, Rinkel J, Dolja E, Schmitz T, Nubbemeyer B, Luu TH, Dickschat JS. Mechanistische Studien an zwei bakteriellen Diterpencyclasen: Spiroviolen-Synthase und Tsukubadien-Synthase. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201612439] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Patrick Rabe
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| | - Jan Rinkel
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| | - Etilia Dolja
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| | - Thomas Schmitz
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| | - Britta Nubbemeyer
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| | - T. Hoang Luu
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| | - Jeroen S. Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
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24
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Rabe P, Rinkel J, Dolja E, Schmitz T, Nubbemeyer B, Luu TH, Dickschat JS. Mechanistic Investigations of Two Bacterial Diterpene Cyclases: Spiroviolene Synthase and Tsukubadiene Synthase. Angew Chem Int Ed Engl 2017; 56:2776-2779. [PMID: 28146322 DOI: 10.1002/anie.201612439] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Indexed: 01/14/2023]
Abstract
The mechanisms of two diterpene cyclases from streptomycetes-one with an unknown product that was identified as the spirocyclic hydrocarbon spiroviolene and one with the known product tsukubadiene-were investigated in detail by isotope labeling experiments. Although the structures of the products were very different, the cyclization mechanisms of both enzymes proceed through the same initial cyclization reactions, before they diverge towards the individual products, which is reflected in the close phylogenetic relationship of the enzymes.
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Affiliation(s)
- Patrick Rabe
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Jan Rinkel
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Etilia Dolja
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Thomas Schmitz
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Britta Nubbemeyer
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - T Hoang Luu
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
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25
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Rinkel J, Rabe P, Zur Horst L, Dickschat JS. A detailed view on 1,8-cineol biosynthesis by Streptomyces clavuligerus. Beilstein J Org Chem 2016; 12:2317-2324. [PMID: 28144299 PMCID: PMC5238540 DOI: 10.3762/bjoc.12.225] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 10/28/2016] [Indexed: 12/29/2022] Open
Abstract
The stereochemical course of the cyclisation reaction catalysed by the bacterial 1,8-cineol synthase from Streptomyces clavuligerus was investigated using stereospecifically deuterated substrates. In contrast to the well investigated plant enzyme from Salvia officinalis, the reaction proceeds via (S)-linalyl diphosphate and the (S)-terpinyl cation, while the final cyclisation reaction is in both cases a syn addition, as could be shown by incubation of (2-13C)geranyl diphosphate in deuterium oxide.
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Affiliation(s)
- Jan Rinkel
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Patrick Rabe
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Laura Zur Horst
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
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26
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Rinkel J, Rabe P, Garbeva P, Dickschat JS. Über 1,3-Hydridverschiebungen in Sesquiterpen-Cyclisierungen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608042] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jan Rinkel
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| | - Patrick Rabe
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| | - Paolina Garbeva
- Nederlands Instituut voor Ecologie; Koninklijke Nederlandse Akademie van Wetenschappen; Droevendaalsesteeg 10 6708 PB Wageningen Niederlande
| | - Jeroen S. Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
- Nederlands Instituut voor Ecologie; Koninklijke Nederlandse Akademie van Wetenschappen; Droevendaalsesteeg 10 6708 PB Wageningen Niederlande
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27
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Rinkel J, Rabe P, Garbeva P, Dickschat JS. Lessons from 1,3-Hydride Shifts in Sesquiterpene Cyclizations. Angew Chem Int Ed Engl 2016; 55:13593-13596. [PMID: 27666571 DOI: 10.1002/anie.201608042] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Indexed: 11/09/2022]
Abstract
Stereospecifically labelled precursors were subjected to conversion by seven bacterial sesquiterpene cyclases to investigate the stereochemistry of their initial 1,10-cyclisation-1,3-hydride shift cascades. Enzymes with products of known absolute configuration showed a coherent stereochemical course, except for (-)-α-amorphene synthase, for which the obtained results are better explained by an initial 1,6-cyclisation. The link between the absolute configuration of the product and the stereochemical course of the 1,3-hydride shifts enabled assignment of the absolute configurations of three enzyme products, which were confirmed independently through the absolute configuration of the common byproduct germacrene D-4-ol.
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Affiliation(s)
- Jan Rinkel
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Patrick Rabe
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Paolina Garbeva
- Nederlands Instituut voor Ecologie, Koninklijke Nederlandse Akademie van Wetenschappen, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Jeroen S Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany. .,Nederlands Instituut voor Ecologie, Koninklijke Nederlandse Akademie van Wetenschappen, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.
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28
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Rabe P, Schmitz T, Dickschat JS. Mechanistic investigations on six bacterial terpene cyclases. Beilstein J Org Chem 2016; 12:1839-1850. [PMID: 27829890 PMCID: PMC5082573 DOI: 10.3762/bjoc.12.173] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 08/01/2016] [Indexed: 11/26/2022] Open
Abstract
The products obtained by incubation of farnesyl diphosphate (FPP) with six purified bacterial terpene cyclases were characterised by one- and two-dimensional NMR spectroscopic methods, allowing for a full structure elucidation. The absolute configurations of four terpenes were determined based on their optical rotary powers. Incubation experiments with 13C-labelled isotopomers of FPP in buffers containing water or deuterium oxide allowed for detailed insights into the cyclisation mechanisms of the bacterial terpene cyclases.
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Affiliation(s)
- Patrick Rabe
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Thomas Schmitz
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
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29
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Okada M, Matsuda Y, Mitsuhashi T, Hoshino S, Mori T, Nakagawa K, Quan Z, Qin B, Zhang H, Hayashi F, Kawaide H, Abe I. Genome-Based Discovery of an Unprecedented Cyclization Mode in Fungal Sesterterpenoid Biosynthesis. J Am Chem Soc 2016; 138:10011-8. [DOI: 10.1021/jacs.6b05799] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Masahiro Okada
- Graduate
School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yudai Matsuda
- Graduate
School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takaaki Mitsuhashi
- Graduate
School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shotaro Hoshino
- 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
| | - Kazuya Nakagawa
- Institute
of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8
Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Zhiyang Quan
- Graduate
School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Bin Qin
- Graduate
School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Huiping Zhang
- RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Fumiaki Hayashi
- RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroshi Kawaide
- Institute
of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8
Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Ikuro Abe
- Graduate
School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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30
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Klapschinski TA, Rabe P, Dickschat JS. Pristinol, a Sesquiterpene Alcohol with an Unusual Skeleton from Streptomyces pristinaespiralis. Angew Chem Int Ed Engl 2016; 55:10141-4. [PMID: 27403888 DOI: 10.1002/anie.201605425] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Indexed: 11/11/2022]
Abstract
A terpene cyclase from Streptomyces pristinaespiralis was characterized as the synthase for (+)-(2S,3S,9R)-pristinol. The structure of this sesquiterpene alcohol, which has a new carbon skeleton, was established by NMR spectroscopy and single-wavelength anomalous-dispersion X-ray crystallography. Extensive isotopic labelling experiments were performed to distinguish between various possible cyclization mechanisms of the terpene cyclase and to decipher the EI-MS fragmentation mechanism for pristinol.
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Affiliation(s)
- Tim A Klapschinski
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Patrick Rabe
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany.
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31
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Klapschinski TA, Rabe P, Dickschat JS. Pristinol, ein Sesquiterpen-Alkohol mit ungewöhnlichem Gerüst ausStreptomyces pristinaespiralis. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605425] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Tim A. Klapschinski
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| | - Patrick Rabe
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| | - Jeroen S. Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
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32
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Rabe P, Dickschat JS. The EIMS fragmentation mechanisms of the sesquiterpenes corvol ethers A and B, epi-cubebol and isodauc-8-en-11-ol. Beilstein J Org Chem 2016; 12:1380-94. [PMID: 27559388 PMCID: PMC4979868 DOI: 10.3762/bjoc.12.132] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 06/24/2016] [Indexed: 11/23/2022] Open
Abstract
Farnesyl diphosphate (FPP) and all fifteen positional isomers of ((13)C1)FPP were enzymatically converted by the bacterial terpene cyclases corvol ether synthase from Kitasatospora setae, the epi-cubebol synthase from Streptosporangium roseum, and the isodauc-8-en-11-ol synthase from Streptomyces venezuelae. The enzyme products were analysed by GC-MS and GC-QTOF MS(2) and the obtained data were used to delineate the EIMS fragmentation mechanisms of the two sesquiterpene ethers corvol ethers A and B, and the sesquiterpene alcohols epi-cubebol and isodauc-8-en-11-ol.
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Affiliation(s)
- Patrick Rabe
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
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33
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Burkhardt I, Siemon T, Henrot M, Studt L, Rösler S, Tudzynski B, Christmann M, Dickschat JS. Mechanistic Characterisation of Two Sesquiterpene Cyclases from the Plant Pathogenic FungusFusarium fujikuroi. Angew Chem Int Ed Engl 2016; 55:8748-51. [DOI: 10.1002/anie.201603782] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Indexed: 11/05/2022]
Affiliation(s)
- Immo Burkhardt
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Germany
| | - Thomas Siemon
- Institut für Chemie und Biochemie - Organische Chemie; Freie Universität Berlin; Takustraße 3 14195 Berlin Germany
| | - Matthias Henrot
- Institut für Chemie und Biochemie - Organische Chemie; Freie Universität Berlin; Takustraße 3 14195 Berlin Germany
| | - Lena Studt
- Institut für Biologie und Biotechnologie der Pflanzen; Westfälische Wilhelms-Universität Münster; Schlossplatz 8 48143 Münster Germany
- Institut für Angewandte Genetik und Zellbiologie; Universität für Bodenkultur Wien; Konrad-Lorenz-Straße 24/I 3430 Tulln an der Donau Austria
| | - Sarah Rösler
- Institut für Biologie und Biotechnologie der Pflanzen; Westfälische Wilhelms-Universität Münster; Schlossplatz 8 48143 Münster Germany
| | - Bettina Tudzynski
- Institut für Biologie und Biotechnologie der Pflanzen; Westfälische Wilhelms-Universität Münster; Schlossplatz 8 48143 Münster Germany
| | - Mathias Christmann
- Institut für Chemie und Biochemie - Organische Chemie; Freie Universität Berlin; Takustraße 3 14195 Berlin Germany
| | - Jeroen S. Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Germany
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34
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Burkhardt I, Siemon T, Henrot M, Studt L, Rösler S, Tudzynski B, Christmann M, Dickschat JS. Mechanistische Charakterisierung von zwei Sesquiterpen-Cyclasen aus dem phytopathogenen PilzFusarium fujikuroi. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603782] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Immo Burkhardt
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| | - Thomas Siemon
- Institut für Chemie und Biochemie - Organische Chemie; Freie Universität Berlin; Takustraße 3 14195 Berlin Deutschland
| | - Matthias Henrot
- Institut für Chemie und Biochemie - Organische Chemie; Freie Universität Berlin; Takustraße 3 14195 Berlin Deutschland
| | - Lena Studt
- Institut für Biologie und Biotechnologie der Pflanzen; Westfälische Wilhelms-Universität Münster; Schlossplatz 8 48143 Münster Deutschland
- Institut für Angewandte Genetik und Zellbiologie; Universität für Bodenkultur Wien; Konrad-Lorenz-Straße 24/I 3430 Tulln an der Donau Österreich
| | - Sarah Rösler
- Institut für Biologie und Biotechnologie der Pflanzen; Westfälische Wilhelms-Universität Münster; Schlossplatz 8 48143 Münster Deutschland
| | - Bettina Tudzynski
- Institut für Biologie und Biotechnologie der Pflanzen; Westfälische Wilhelms-Universität Münster; Schlossplatz 8 48143 Münster Deutschland
| | - Mathias Christmann
- Institut für Chemie und Biochemie - Organische Chemie; Freie Universität Berlin; Takustraße 3 14195 Berlin Deutschland
| | - Jeroen S. Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
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35
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Jeroen S. Dickschat. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/anie.201511670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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36
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Rabe P, Klapschinski TA, Dickschat JS. Position-Specific Mass Shift Analysis: A Systematic Method for Investigating the EI-MS Fragmentation Mechanism of epi-Isozizaene. Chembiochem 2016; 17:1333-7. [PMID: 27123899 DOI: 10.1002/cbic.201600237] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Indexed: 11/10/2022]
Abstract
The EI-MS fragmentation mechanism of the bacterial sesquiterpene epi-isozizaene was investigated through enzymatic conversion of all 15 synthetic ((13) C1 )FPP isotopomers with the epi-isozizaene synthase from Streptomyces albus and GC-MS and GC-QTOF analysis including MS-MS. A systematic method, which we wish to call position-specific mass shift analysis, for the identification of the full set of fragmentation reactions was developed.
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Affiliation(s)
- Patrick Rabe
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Tim A Klapschinski
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany.
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37
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Jeroen S. Dickschat. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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38
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Abstract
This review summarises the characterised bacterial terpene cyclases and their products and discusses the enzyme mechanisms.
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Affiliation(s)
- Jeroen S. Dickschat
- University of Bonn
- Kekulé-Institute of Organic Chemistry and Biochemistry
- 53121 Bonn
- Germany
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39
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Rabe P, Rinkel J, Klapschinski TA, Barra L, Dickschat JS. A method for investigating the stereochemical course of terpene cyclisations. Org Biomol Chem 2016; 14:158-64. [DOI: 10.1039/c5ob01998b] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The products of three bacterial terpene cyclases were characterised and the mechanisms of their formations were investigated using isotopic labellings.
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Affiliation(s)
- Patrick Rabe
- Kekulé-Institut für Organische Chemie und Biochemie
- Rheinische Friedrich-Wilhelms-Universität Bonn
- 53121 Bonn
- Germany
| | - Jan Rinkel
- Kekulé-Institut für Organische Chemie und Biochemie
- Rheinische Friedrich-Wilhelms-Universität Bonn
- 53121 Bonn
- Germany
| | - Tim A. Klapschinski
- Kekulé-Institut für Organische Chemie und Biochemie
- Rheinische Friedrich-Wilhelms-Universität Bonn
- 53121 Bonn
- Germany
| | - Lena Barra
- Kekulé-Institut für Organische Chemie und Biochemie
- Rheinische Friedrich-Wilhelms-Universität Bonn
- 53121 Bonn
- Germany
| | - Jeroen S. Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie
- Rheinische Friedrich-Wilhelms-Universität Bonn
- 53121 Bonn
- Germany
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40
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Rinkel J, Dickschat JS. Recent highlights in biosynthesis research using stable isotopes. Beilstein J Org Chem 2015; 11:2493-508. [PMID: 26734097 PMCID: PMC4685789 DOI: 10.3762/bjoc.11.271] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 11/23/2015] [Indexed: 02/03/2023] Open
Abstract
The long and successful history of isotopic labeling experiments within natural products research has both changed and deepened our understanding of biosynthesis. As demonstrated in this article, the usage of isotopes is not at all old-fashioned, but continues to give important insights into biosynthetic pathways of secondary metabolites. This review with 85 cited references is structured by separate discussions of compounds from different classes including polyketides, non-ribosomal peptides, their hybrids, terpenoids, and aromatic compounds formed via the shikimate pathway. The text does not aim at a comprehensive overview, but instead a selection of recent important examples of isotope usage within biosynthetic studies is presented, with a special emphasis on mechanistic surprises.
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Affiliation(s)
- Jan Rinkel
- Kekulé-Institute of Organic Chemistry and Biochemistry, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
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41
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Rabe P, Janusko A, Goldfuss B, Dickschat JS. Experimental and Theoretical Studies on Corvol Ether Biosynthesis. Chembiochem 2015; 17:146-9. [DOI: 10.1002/cbic.201500543] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Patrick Rabe
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| | - Aron Janusko
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| | - Bernd Goldfuss
- Department für Chemie; Universität zu Köln; Greinstrasse 4 50939 Köln Germany
| | - Jeroen S. Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Strasse 1 53121 Bonn Germany
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42
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Rabe P, Barra L, Rinkel J, Riclea R, Citron CA, Klapschinski TA, Janusko A, Dickschat JS. Konformationsanalyse, thermische Umlagerung und EI‐MS‐Fragmentierungsmechanismus von (1(10)
E
,4
E
,6
S
,7
R
)‐Germacradien‐6‐ol durch
13
C‐Markierungsexperimente. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507615] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Patrick Rabe
- Kekulé‐Institut für Organische Chemie und Biochemie, Rheinische Friedrich‐Wilhelms‐Universität Bonn, Gerhard‐Domagk‐Straße 1, 53121 Bonn (Deutschland)
| | - Lena Barra
- Kekulé‐Institut für Organische Chemie und Biochemie, Rheinische Friedrich‐Wilhelms‐Universität Bonn, Gerhard‐Domagk‐Straße 1, 53121 Bonn (Deutschland)
| | - Jan Rinkel
- Kekulé‐Institut für Organische Chemie und Biochemie, Rheinische Friedrich‐Wilhelms‐Universität Bonn, Gerhard‐Domagk‐Straße 1, 53121 Bonn (Deutschland)
| | - Ramona Riclea
- Kekulé‐Institut für Organische Chemie und Biochemie, Rheinische Friedrich‐Wilhelms‐Universität Bonn, Gerhard‐Domagk‐Straße 1, 53121 Bonn (Deutschland)
| | - Christian A. Citron
- Kekulé‐Institut für Organische Chemie und Biochemie, Rheinische Friedrich‐Wilhelms‐Universität Bonn, Gerhard‐Domagk‐Straße 1, 53121 Bonn (Deutschland)
| | - Tim A. Klapschinski
- Kekulé‐Institut für Organische Chemie und Biochemie, Rheinische Friedrich‐Wilhelms‐Universität Bonn, Gerhard‐Domagk‐Straße 1, 53121 Bonn (Deutschland)
| | - Aron Janusko
- Kekulé‐Institut für Organische Chemie und Biochemie, Rheinische Friedrich‐Wilhelms‐Universität Bonn, Gerhard‐Domagk‐Straße 1, 53121 Bonn (Deutschland)
| | - Jeroen S. Dickschat
- Kekulé‐Institut für Organische Chemie und Biochemie, Rheinische Friedrich‐Wilhelms‐Universität Bonn, Gerhard‐Domagk‐Straße 1, 53121 Bonn (Deutschland)
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43
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Rabe P, Barra L, Rinkel J, Riclea R, Citron CA, Klapschinski TA, Janusko A, Dickschat JS. Conformational Analysis, Thermal Rearrangement, and EI-MS Fragmentation Mechanism of (1(10)E,4E,6S,7R)-Germacradien-6-ol by (13)C-Labeling Experiments. Angew Chem Int Ed Engl 2015; 54:13448-51. [PMID: 26361082 DOI: 10.1002/anie.201507615] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Indexed: 11/07/2022]
Abstract
An uncharacterized terpene cyclase from Streptomyces pratensis was identified as (+)-(1(10)E,4E,6S,7R)-germacradien-6-ol synthase. The enzyme product exists as two interconvertible conformers, resulting in complex NMR spectra. For the complete assignment of NMR data, all fifteen ((13)C1)FPP isotopomers (FPP=farnesyl diphosphate) and ((13)C15)FPP were synthesized and enzymatically converted. The products were analyzed using various NMR techniques, including (13)C, (13)C COSY experiments. The ((13)C)FPP isotopomers were also used to investigate the thermal rearrangement and EI fragmentation of the enzyme product.
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Affiliation(s)
- Patrick Rabe
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn (Germany)
| | - Lena Barra
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn (Germany)
| | - Jan Rinkel
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn (Germany)
| | - Ramona Riclea
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn (Germany)
| | - Christian A Citron
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn (Germany)
| | - Tim A Klapschinski
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn (Germany)
| | - Aron Janusko
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn (Germany)
| | - Jeroen S Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn (Germany).
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44
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Abstract
A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as eudistidine A from a marine ascidian Eudistoma sp.
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