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Srivastava P, Johns ST, Voice A, Morley K, Escorcia AM, Miller DJ, Allemann RK, van der Kamp MW. Simulation-Guided Engineering Enables a Functional Switch in Selinadiene Synthase toward Hydroxylation. ACS Catal 2024; 14:11034-11043. [PMID: 39050902 PMCID: PMC11264211 DOI: 10.1021/acscatal.4c02032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 07/01/2024] [Accepted: 07/01/2024] [Indexed: 07/27/2024]
Abstract
Engineering sesquiterpene synthases to form predefined alternative products is a major challenge due to their diversity in cyclization mechanisms and our limited understanding of how amino acid changes affect the steering of these mechanisms. Here, we use a combination of atomistic simulation and site-directed mutagenesis to engineer a selina-4(15),7(11)-diene synthase (SdS) such that its final reactive carbocation is quenched by trapped active site water, resulting in the formation of a complex hydroxylated sesquiterpene (selin-7(11)-en-4-ol). Initially, the SdS G305E variant produced 20% selin-7(11)-en-4-ol. As suggested by modeling of the enzyme-carbocation complex, selin-7(11)-en-4-ol production could be further improved by varying the pH, resulting in selin-7(11)-en-4-ol becoming the major product (48%) at pH 6.0. We incorporated the SdS G305E variant along with genes from the mevalonate pathway into bacterial BL21(DE3) cells and demonstrated the production of selin-7(11)-en-4-ol at a scale of 10 mg/L in batch fermentation. These results highlight opportunities for the simulation-guided engineering of terpene synthases to produce predefined complex hydroxylated sesquiterpenes.
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Affiliation(s)
| | - Sam T. Johns
- School
of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K.
| | - Angus Voice
- School
of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K.
| | - Katharine Morley
- School
of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K.
| | - Andrés M. Escorcia
- School
of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K.
| | - David J. Miller
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, U.K.
| | - Rudolf K. Allemann
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, U.K.
| | - Marc W. van der Kamp
- School
of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K.
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2
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Klucznik T, Syntrivanis LD, Baś S, Mikulak-Klucznik B, Moskal M, Szymkuć S, Mlynarski J, Gadina L, Beker W, Burke MD, Tiefenbacher K, Grzybowski BA. Computational prediction of complex cationic rearrangement outcomes. Nature 2024; 625:508-515. [PMID: 37967579 PMCID: PMC10864989 DOI: 10.1038/s41586-023-06854-3] [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] [Received: 07/05/2022] [Accepted: 11/08/2023] [Indexed: 11/17/2023]
Abstract
Recent years have seen revived interest in computer-assisted organic synthesis1,2. The use of reaction- and neural-network algorithms that can plan multistep synthetic pathways have revolutionized this field1,3-7, including examples leading to advanced natural products6,7. Such methods typically operate on full, literature-derived 'substrate(s)-to-product' reaction rules and cannot be easily extended to the analysis of reaction mechanisms. Here we show that computers equipped with a comprehensive knowledge-base of mechanistic steps augmented by physical-organic chemistry rules, as well as quantum mechanical and kinetic calculations, can use a reaction-network approach to analyse the mechanisms of some of the most complex organic transformations: namely, cationic rearrangements. Such rearrangements are a cornerstone of organic chemistry textbooks and entail notable changes in the molecule's carbon skeleton8-12. The algorithm we describe and deploy at https://HopCat.allchemy.net/ generates, within minutes, networks of possible mechanistic steps, traces plausible step sequences and calculates expected product distributions. We validate this algorithm by three sets of experiments whose analysis would probably prove challenging even to highly trained chemists: (1) predicting the outcomes of tail-to-head terpene (THT) cyclizations in which substantially different outcomes are encoded in modular precursors differing in minute structural details; (2) comparing the outcome of THT cyclizations in solution or in a supramolecular capsule; and (3) analysing complex reaction mixtures. Our results support a vision in which computers no longer just manipulate known reaction types1-7 but will help rationalize and discover new, mechanistically complex transformations.
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Affiliation(s)
- Tomasz Klucznik
- Allchemy, Highland, IN, USA
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Leonidas-Dimitrios Syntrivanis
- Roger Adams Laboratory, School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Chemistry, University of Basel, Basel, Switzerland.
| | - Sebastian Baś
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Barbara Mikulak-Klucznik
- Allchemy, Highland, IN, USA
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | | | | | - Jacek Mlynarski
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Louis Gadina
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Wiktor Beker
- Allchemy, Highland, IN, USA.
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland.
| | - Martin D Burke
- Roger Adams Laboratory, School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Molecule Maker Laboratory Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Molecule Maker Laboratory at the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Konrad Tiefenbacher
- Department of Chemistry, University of Basel, Basel, Switzerland.
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
| | - Bartosz A Grzybowski
- Allchemy, Highland, IN, USA.
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland.
- IBS Center for Algorithmic and Robotized Synthesis, CARS, Eonyang-eup, Ulju-gun, Ulsan, South Korea.
- Department of Chemistry, UNIST, Eonyang-eup, Ulju-gun, Ulsan, South Korea.
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3
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Li Z, Zhang L, Xu K, Jiang Y, Du J, Zhang X, Meng LH, Wu Q, Du L, Li X, Hu Y, Xie Z, Jiang X, Tang YJ, Wu R, Guo RT, Li S. Molecular insights into the catalytic promiscuity of a bacterial diterpene synthase. Nat Commun 2023; 14:4001. [PMID: 37414771 PMCID: PMC10325987 DOI: 10.1038/s41467-023-39706-9] [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: 02/24/2023] [Accepted: 06/19/2023] [Indexed: 07/08/2023] Open
Abstract
Diterpene synthase VenA is responsible for assembling venezuelaene A with a unique 5-5-6-7 tetracyclic skeleton from geranylgeranyl pyrophosphate. VenA also demonstrates substrate promiscuity by accepting geranyl pyrophosphate and farnesyl pyrophosphate as alternative substrates. Herein, we report the crystal structures of VenA in both apo form and holo form in complex with a trinuclear magnesium cluster and pyrophosphate group. Functional and structural investigations on the atypical 115DSFVSD120 motif of VenA, versus the canonical Asp-rich motif of DDXX(X)D/E, reveal that the absent second Asp of canonical motif is functionally replaced by Ser116 and Gln83, together with bioinformatics analysis identifying a hidden subclass of type I microbial terpene synthases. Further structural analysis, multiscale computational simulations, and structure-directed mutagenesis provide significant mechanistic insights into the substrate selectivity and catalytic promiscuity of VenA. Finally, VenA is semi-rationally engineered into a sesterterpene synthase to recognize the larger substrate geranylfarnesyl pyrophosphate.
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Affiliation(s)
- Zhong Li
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, China
| | - Lilan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Kangwei Xu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510006, China
| | - Yuanyuan Jiang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, China
| | - Jieke Du
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, China
| | - Xingwang Zhang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, China
| | - Ling-Hong Meng
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao, Shandong, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, China
| | - Qile Wu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, China
| | - Lei Du
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, China
| | - Xiaoju Li
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, China
| | - Yuechan Hu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Zhenzhen Xie
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Xukai Jiang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, China
| | - Ya-Jie Tang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, China
| | - Ruibo Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510006, China.
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China.
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, 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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Kim HY, Kim JH. Sesquiterpenoids Isolated from the Rhizomes of Genus Atractylodes. Chem Biodivers 2022; 19:e202200703. [PMID: 36323637 DOI: 10.1002/cbdv.202200703] [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: 07/26/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022]
Abstract
Atractylodes plants have been used in traditional herbal medicine to treat gastrointestinal diseases and contain various chemical compounds. Sesquiterpenoids are the most important therapeutic compounds in Atractylodes rhizomes. Based on studies reported from 2000 to 2022, we classified sesquiterpenoids by their chemical skeletons and original resources. Moreover, we discussed their biosynthesis and physicochemical and pharmacological features. We reported sesquiterpenoids with skeletal moieties, such as monocyclic sesquiterpenes (bisabolene- and elemene-type), bicyclic sesquiterpenes (eudesmane-, isopterocarpolone-, hydroxycarissone-, eremophilane-, bisesquiterpenoid-, guaiane- and spirovetivane-type and eudesmane lactones) and tricyclic sesquiterpenes (cyperene- and patchoulene-type), with their biosynthetic pathways, chemical modifications and in vivo metabolites. The pharmacological activities of sesquiterpenoids as anti-inflammatory, anti-tumor, anti-diabetic and anti-microbial and for treating gastrointestinal disorders have been reported for this genus.
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Affiliation(s)
- Han-Young Kim
- Department of Korean Medical Science, School of Korean Medicine, Pusan National University, Yangsan, 50612, Korea
| | - Jung-Hoon Kim
- Division of Pharmacology, School of Korean Medicine, Pusan National University, Yangsan, 50612, Korea
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6
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Ezediokpu MN, Krause K, Kunert M, Hoffmeister D, Boland W, Kothe E. Ectomycorrhizal Influence on the Dynamics of Sesquiterpene Release by Tricholoma vaccinum. J Fungi (Basel) 2022; 8:jof8060555. [PMID: 35736037 PMCID: PMC9224709 DOI: 10.3390/jof8060555] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/15/2022] [Accepted: 05/23/2022] [Indexed: 02/04/2023] Open
Abstract
Tricholoma vaccinum is an ectomycorrhizal basidiomycete with high host specificity. The slow-growing fungus is able to produce twenty sesquiterpenes, including α-barbatene, sativene, isocaryophyllene, α-cuprenene, β-cedrene, ß-copaene, 4-epi-α-acoradiene, and chamigrene in axenic culture. For the three major compounds, Δ6-protoilludene, β-barbatene, and an unidentified oxygenated sesquiterpene (m/z 218.18), changed production during co-cultivation with the ectomycorrhizal partner tree, Picea abies, could be shown with distinct dynamics. During the mycorrhizal growth of T. vaccinum–P. abies, Δ6-protoilludene and the oxygenated sesquiterpene appeared at similar times, which warranted further studies of potential biosynthesis genes. In silico analyses identified a putative protoilludene synthesis gene, pie1, as being up-regulated in the mycorrhizal stage, in addition to the previously identified, co-regulated geosmin synthase, ges1. We therefore hypothesize that the sesquiterpene synthase pie1 has an important role during mycorrhization, through Δ6-protoilludene and/or its accompanied oxygenated sesquiterpene production.
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Affiliation(s)
- Marycolette Ndidi Ezediokpu
- Institute of Microbiology, Microbial Communication, Friedrich Schiller University Jena, Neugasse 25, 07743 Jena, Germany; (M.N.E.); (K.K.)
- Max Planck Institute for Chemical Ecology, Bioorganic Chemistry, Hans-Knöll-Straße 8, 07745 Jena, Germany; (M.K.); (W.B.)
| | - Katrin Krause
- Institute of Microbiology, Microbial Communication, Friedrich Schiller University Jena, Neugasse 25, 07743 Jena, Germany; (M.N.E.); (K.K.)
| | - Maritta Kunert
- Max Planck Institute for Chemical Ecology, Bioorganic Chemistry, Hans-Knöll-Straße 8, 07745 Jena, Germany; (M.K.); (W.B.)
| | - Dirk Hoffmeister
- Department of Pharmaceutical Microbiology, Hans Knöll Institute, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany;
| | - Wilhelm Boland
- Max Planck Institute for Chemical Ecology, Bioorganic Chemistry, Hans-Knöll-Straße 8, 07745 Jena, Germany; (M.K.); (W.B.)
| | - Erika Kothe
- Institute of Microbiology, Microbial Communication, Friedrich Schiller University Jena, Neugasse 25, 07743 Jena, Germany; (M.N.E.); (K.K.)
- Correspondence: ; Tel.: +49-3641-949291
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7
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Leferink NGH, Scrutton NS. Predictive Engineering of Class I Terpene Synthases Using Experimental and Computational Approaches. Chembiochem 2021; 23:e202100484. [PMID: 34669250 PMCID: PMC9298401 DOI: 10.1002/cbic.202100484] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/15/2021] [Indexed: 12/18/2022]
Abstract
Terpenoids are a highly diverse group of natural products with considerable industrial interest. Increasingly, engineered microbes are used for the production of terpenoids to replace natural extracts and chemical synthesis. Terpene synthases (TSs) show a high level of functional plasticity and are responsible for the vast structural diversity observed in natural terpenoids. Their relatively inert active sites guide intrinsically reactive linear carbocation intermediates along one of many cyclisation paths via exertion of subtle steric and electrostatic control. Due to the absence of a strong protein interaction with these intermediates, there is a remarkable lack of sequence‐function relationship within the TS family, making product‐outcome predictions from sequences alone challenging. This, in combination with the fact that many TSs produce multiple products from a single substrate hampers the design and use of TSs in the biomanufacturing of terpenoids. This review highlights recent advances in genome mining, computational modelling, high‐throughput screening, and machine‐learning that will allow more predictive engineering of these fascinating enzymes in the near future.
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Affiliation(s)
- Nicole G H Leferink
- Future Biomanufacturing Research Hub, Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Nigel S Scrutton
- Future Biomanufacturing Research Hub, Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
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Abstract
The Streptomyces clavuligerus genome consists in a linear chromosome of about 6.7 Mb and four plasmids (pSCL1 to pSCL4), the latter one of 1.8 Mb. Deletion of pSCL4, results in viable mutants with high instability in the chromosome arms, which may lead to chromosome circularisation. Transcriptomic and proteomic studies comparing different mutants with the wild-type strain improved our knowledge on the biosynthesis and regulation of clavulanic acid, cephamycin C and holomycin. Additional knowledge has been obtained on the SARP-type CcaR activator and the network of connections with other regulators (Brp, AreB, AdpA, BldG, RelA) controlling ccaR expression. The transcriptional pattern of the cephamycin and clavulanic acid clusters is supported by the binding of CcaR to different promoters and confirmed that ClaR is a CcaR-dependent activator that controls the late steps of clavulanic biosynthesis. Metabolomic studies allowed the detection of new metabolites produced by S. clavuligerus such as naringenin, desferroxamines, several N-acyl tunicamycins, the terpenes carveol and cuminyl alcohol or bafilomycin J. Heterologous expression of S. clavuligerus terpene synthases resulted in the formation of no less than 15 different terpenes, although none of them was detected in S. clavuligerus culture broth. In summary, application of the Omic tools results in a better understanding of the molecular biology of S. clavuligerus, that allows the use of this strain as an industrial actinobacterial platform and helps to improve CA production.
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Affiliation(s)
- Paloma Liras
- Microbiology Section. Department of Molecular Biology University of León, León 24071. Spain
| | - Juan F Martín
- Microbiology Section. Department of Molecular Biology University of León, León 24071. Spain
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9
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Hou A, Goldfuss B, Dickschat JS. Functional Switch and Ethyl Group Formation in the Bacterial Polytrichastrene Synthase from Chryseobacterium polytrichastri. Angew Chem Int Ed Engl 2021; 60:20781-20785. [PMID: 34318977 PMCID: PMC8518897 DOI: 10.1002/anie.202109465] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 07/27/2021] [Indexed: 12/19/2022]
Abstract
A reinvestigation of the linalool synthase from Chryseobacterium polytrichastri uncovered its diterpene synthase activity, yielding polytrichastrene A and polytrichastrol A with new skeletons, besides known wanju-2,5-diene and thunbergol. The enzyme mechanism was investigated by isotopic labeling experiments and DFT calculations to explain an unusual ethyl group formation. Rationally designed exchanges of active site residues showed major functional switches, resulting for I66F in the production of five more new compounds, including polytrichastrene B and polytrichastrol B, while A87T, A192V and the double exchange A87T, A192V gave a product shift towards wanju-2,5-diene.
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Affiliation(s)
- Anwei Hou
- Kekulé-Institute for Organic Chemistry and BiochemistryUniversity of BonnGerhard-Domagk-Straße 153121BonnGermany
| | - Bernd Goldfuss
- Department of ChemistryUniversity of CologneGreinstraße 450939CologneGermany
| | - Jeroen S. Dickschat
- Kekulé-Institute for Organic Chemistry and BiochemistryUniversity of BonnGerhard-Domagk-Straße 153121BonnGermany
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10
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Hu T, Feng H, Zhao Y, Yang W, Liu R, Li G. Biochemical and functional characterization of two microbial type terpene synthases from moss Stereodon subimponens. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:750-760. [PMID: 34217131 DOI: 10.1016/j.plaphy.2021.06.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Terpenes constitute a large class of plant secondary metabolites. Usually, there is only one type of terpene synthase in seed plants, which is called typical plant terpene synthase. Currently, as a new family of plant terpene synthases, microbial terpene synthase-like (MTPSL) is identificated in nonseed plants. However, our knowledge about the biological function of most MTPSLs in nonseed plants is very limited. Here, we investigated the biochemical and functional characterization of the enzymes encoded by two MTPSLs from moss Stereodon subimponens, SsMTPSL1 and SsMTPSL2. A phylogenetic tree analysis showed that SsMTPSL1 and SsMTPSL2 are homologous to AaMTPSL1, AaMTPSL3, ApMTPSL1, and ApMTPSL3 from hornworts. The enzyme activity experiment demonstrated that SsMTPSL1 has monoterpene synthase and sesquiterpene synthase activity, and SsMTPSL2 has monoterpene synthase activity. Next, we selected SsMTPSL1 to study its biochemical functions. Anti-bacterial activity test in vitro showed that the products of SsMTPSL1 have an anti-bacterial effect on Escherichia coli, Pseudomonas syringae pv. Tomato DC3000 (Pst DC3000), and Staphylococcus aureus. To further understand the function of SsMTPSL1, the transgenic Arabidopsis thaliana plant of SsMTPSL1 is inoculated by Pst DC3000, and the result showed that SsMTPSL1 enhances the resistance of A. thaliana to Pst DC3000. All in all, this study provides new information about the functions of moss MTPSLs.
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Affiliation(s)
- Tian Hu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, The People's Republic of China
| | - Hao Feng
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, The People's Republic of China
| | - Yapei Zhao
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, The People's Republic of China
| | - Wei Yang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, The People's Republic of China
| | - Ruiqi Liu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, The People's Republic of China
| | - Guanglin Li
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, The People's Republic of China.
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11
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Hou A, Goldfuss B, Dickschat JS. Funktionaler Schalter und Ethylgruppenbildung der Bakteriellen Polytrichastrensynthase aus
Chryseobacterium polytrichastri. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109465] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Anwei Hou
- Kekulé-Institut für Organische Chemie und Biochemie Universität Bonn Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| | - Bernd Goldfuss
- Department 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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12
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Chen X, Zhang C, Lindley ND. Metabolic Engineering Strategies for Sustainable Terpenoid Flavor and Fragrance Synthesis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:10252-10264. [PMID: 31865696 DOI: 10.1021/acs.jafc.9b06203] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Terpenoids derived from plant material are widely applied in the flavor and fragrance industry. Traditional extraction methods are unsustainable, but microbial synthesis offers a promising solution to attain efficient production of natural-identical terpenoids. Overproduction of terpenoids in microbes requires careful balancing of the synthesis pathway constituents within the constraints of host cell metabolism. Advances in metabolic engineering have greatly facilitated overcoming the challenges of achieving high titers, rates, and yields (TRYs). The review summarizes recent development in the molecular biology toolbox to achieve high TRYs for terpenoid biosynthesis, mainly in the two industrial platform microorganisms: Escherichia coli and Saccharomyces cerevisiae. The biosynthetic pathways, including alternative pathway designs, are briefly introduced, followed by recently developed methodologies used for pathway, genome, and strain optimization. Integrated applications of these tools are important to achieve high "TRYs" of terpenoid production and pave the way for translating laboratory research into successful commercial manufacturing.
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Affiliation(s)
- Xixian Chen
- Biotransformation Innovation Platform, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore 138673
| | - Congqiang Zhang
- Biotransformation Innovation Platform, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore 138673
| | - Nicholas D Lindley
- Biotransformation Innovation Platform, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore 138673
- TBI, Université de Toulouse, CNRS, INRA, INSA,31077 Toulouse, France
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13
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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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14
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Kalkreuter E, Pan G, Cepeda AJ, Shen B. Targeting Bacterial Genomes for Natural Product Discovery. Trends Pharmacol Sci 2019; 41:13-26. [PMID: 31822352 DOI: 10.1016/j.tips.2019.11.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/05/2019] [Accepted: 11/07/2019] [Indexed: 11/19/2022]
Abstract
Bacterial natural products (NPs) and their analogs constitute more than half of the new small molecule drugs developed over the past few decades. Despite this success, interest in natural products from major pharmaceutical companies has decreased even as genomics has uncovered the large number of biosynthetic gene clusters (BGCs) that encode for novel natural products. To date, there is still a lack of universal strategies and enabling technologies to discover natural products at scale and speed. This review highlights several of the opportunities provided by genome sequencing and bioinformatics, challenges associated with translating genomes into natural products, and examples of successful strain prioritization and BGC activation strategies that have been used in the genomic era for natural product discovery from cultivatable bacteria.
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Affiliation(s)
- Edward Kalkreuter
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Guohui Pan
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Alexis J Cepeda
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA; Natural Products Library Initiative at The Scripps Research Institute, The Scripps Research Institute, Jupiter, FL 33458, USA.
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15
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Muangphrom P, Misaki M, Suzuki M, Shimomura M, Suzuki H, Seki H, Muranaka T. Identification and characterization of (+)-α-bisabolol and 7-epi-silphiperfol-5-ene synthases from Artemisia abrotanum. PHYTOCHEMISTRY 2019; 164:144-153. [PMID: 31151061 DOI: 10.1016/j.phytochem.2019.05.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 04/30/2019] [Accepted: 05/10/2019] [Indexed: 06/09/2023]
Abstract
Triquinane is a type of sesquiterpenoid with a unique structure that contains a fused tricyclopentane ring and exhibits a wide range of bioactivities. Like other sesquiterpenoids, the first committed step in triquinane-type sesquiterpenoid biosynthesis is the cyclization of farnesyl pyrophosphate (FPP), a common precursor of all sesquiterpenoids, catalyzed by sesquiterpene synthase. Artemisia abrotanum L. (Asteraceae), a common plant used in the culinary and cosmetics industries, has been reported to accumulate high levels of triquinane silphiperfol-5-en-3-one A. This compound is potentially biosynthesized from the cyclization of FPP into 7-epi-silphiperfol-5-ene followed by a multi-step oxidation to silphiperfol-5-en-3-one A. In this study, we aimed to identify the sesquiterpene synthase responsible for the synthesis of 7-epi-silphiperfol-5-ene. We performed RNA sequencing of A. abrotanum leaves and gene candidates were mined by homology searches using the triquinane α-isocomene synthase of chamomile (MrTPS2) as query. After gene cloning, we obtained five variants of putative sesquiterpene synthase showing greater than 85% amino acid identity to MrTPS2 and greater than 95% amino acid identity to each other. Heterologous expression of these variants in a FPP-high-producing yeast strain revealed the first four variants to be (+)-α-bisabolol synthases (AabrBOS1-4). However, the fifth candidate cyclized FPP into 7-epi-silphiperfol-5-ene and can therefore be defined as a 7-epi-silphiperfol-5-ene synthase (AabrSPS). These findings revealed the first committed enzyme involved in silphiperfol-5-en-3-one A and (+)-α-bisabolol biosyntheses in A. abrotanum. Furthermore, the results of this study will be useful for enhancing the production of these compounds for further applications.
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Affiliation(s)
- Paskorn Muangphrom
- Department of Biotechnology, Graduate School of Engineering, Osaka University 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Momoka Misaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Munenori Suzuki
- Department of Biotechnology, Graduate School of Engineering, Osaka University 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan; KNC Laboratories Co., Ltd., 3-2-34 Takatsukadai, Nishi-ku, Kobe, Hyogo, 651-2271, Japan; Kihara Institute for Biological Research, Yokohama City University 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813, Japan
| | - Masaya Shimomura
- Kihara Institute for Biological Research, Yokohama City University 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813, Japan
| | - Hideyuki Suzuki
- Department of Applied Genomics, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Hikaru Seki
- Department of Biotechnology, Graduate School of Engineering, Osaka University 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan; Kihara Institute for Biological Research, Yokohama City University 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813, Japan.
| | - Toshiya Muranaka
- Department of Biotechnology, Graduate School of Engineering, Osaka University 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan; Kihara Institute for Biological Research, Yokohama City University 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813, Japan
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16
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Karunanithi PS, Zerbe P. Terpene Synthases as Metabolic Gatekeepers in the Evolution of Plant Terpenoid Chemical Diversity. FRONTIERS IN PLANT SCIENCE 2019; 10:1166. [PMID: 31632418 PMCID: PMC6779861 DOI: 10.3389/fpls.2019.01166] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/26/2019] [Indexed: 05/18/2023]
Abstract
Terpenoids comprise tens of thousands of small molecule natural products that are widely distributed across all domains of life. Plants produce by far the largest array of terpenoids with various roles in development and chemical ecology. Driven by selective pressure to adapt to their specific ecological niche, individual species form only a fraction of the myriad plant terpenoids, typically representing unique metabolite blends. Terpene synthase (TPS) enzymes are the gatekeepers in generating terpenoid diversity by catalyzing complex carbocation-driven cyclization, rearrangement, and elimination reactions that enable the transformation of a few acyclic prenyl diphosphate substrates into a vast chemical library of hydrocarbon and, for a few enzymes, oxygenated terpene scaffolds. The seven currently defined clades (a-h) forming the plant TPS family evolved from ancestral triterpene synthase- and prenyl transferase-type enzymes through repeated events of gene duplication and subsequent loss, gain, or fusion of protein domains and further functional diversification. Lineage-specific expansion of these TPS clades led to variable family sizes that may range from a single TPS gene to families of more than 100 members that may further function as part of modular metabolic networks to maximize the number of possible products. Accompanying gene family expansion, the TPS family shows a profound functional plasticity, where minor active site alterations can dramatically impact product outcome, thus enabling the emergence of new functions with minimal investment in evolving new enzymes. This article reviews current knowledge on the functional diversity and molecular evolution of the plant TPS family that underlies the chemical diversity of bioactive terpenoids across the plant kingdom.
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Affiliation(s)
- Prema S Karunanithi
- Department of Plant Biology, University of California Davis, Davis, CA, United States
| | - Philipp Zerbe
- Department of Plant Biology, University of California Davis, Davis, CA, United States
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17
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Blank PN, Pemberton TA, Chow JY, Poulter CD, Christianson DW. Crystal Structure of Cucumene Synthase, a Terpenoid Cyclase That Generates a Linear Triquinane Sesquiterpene. Biochemistry 2018; 57:6326-6335. [PMID: 30346736 DOI: 10.1021/acs.biochem.8b00899] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Linear triquinanes are sesquiterpene natural products with hydrocarbon skeletons consisting of three fused five-membered rings. Importantly, several of these compounds exhibit useful anticancer, anti-inflammatory, and antibiotic properties. However, linear triquinanes pose significant challenges to organic synthesis because of the structural and stereochemical complexity of their hydrocarbon skeletons. To illuminate nature's solution to the generation of linear triquinanes, we now describe the crystal structure of Streptomyces clavuligerus cucumene synthase. This sesquiterpene cyclase catalyzes the stereospecific cyclization of farnesyl diphosphate to form a linear triquinane product, (5 S,7 S,10 R,11 S)-cucumene. Specifically, we report the structure of the wild-type enzyme at 3.05 Å resolution and the structure of the T181N variant at 1.96 Å resolution, both in the open active site conformations without any bound ligands. The high-resolution structure of T181N cucumene synthase enables inspection of the active site contour, which adopts a three-dimensional shape complementary to a linear triquinane. Several aromatic residues outline the active site contour and are believed to facilitate cation-π interactions that would stabilize carbocation intermediates in catalysis. Thus, aromatic residues in the active site not only define the template for catalysis but also play a role in reducing activation barriers in the multistep cyclization cascade.
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Affiliation(s)
- Patrick N Blank
- Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States
| | - Travis A Pemberton
- Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States
| | - Jeng-Yeong Chow
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - C Dale Poulter
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States
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18
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Rinkel J, Litzenburger M, Bernhardt R, Dickschat JS. An Isotopic Labelling Strategy to Study Cytochrome P450 Oxidations of Terpenes. Chembiochem 2018; 19:1498-1501. [DOI: 10.1002/cbic.201800215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Jan Rinkel
- Kekulé-Institute of Organic Chemistry and BiochemistryUniversity of Bonn Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| | - Martin Litzenburger
- Institute of BiochemistrySaarland University Campus Building B2.2 66123 Saarbrücken Germany
| | - Rita Bernhardt
- Institute of BiochemistrySaarland University Campus Building B2.2 66123 Saarbrücken Germany
| | - Jeroen S. Dickschat
- Kekulé-Institute of Organic Chemistry and BiochemistryUniversity of Bonn Gerhard-Domagk-Strasse 1 53121 Bonn Germany
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19
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Sesquiterpene Synthase-3-Hydroxy-3-Methylglutaryl Coenzyme A Synthase Fusion Protein Responsible for Hirsutene Biosynthesis in Stereum hirsutum. Appl Environ Microbiol 2018; 84:AEM.00036-18. [PMID: 29625976 DOI: 10.1128/aem.00036-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/25/2018] [Indexed: 01/09/2023] Open
Abstract
The wood-rotting mushroom Stereum hirsutum is a known producer of a large number of namesake hirsutenoids, many with important bioactivities. Hirsutenoids form a structurally diverse and distinct class of sesquiterpenoids. No genes involved in hirsutenoid biosynthesis have yet been identified or their enzymes characterized. Here, we describe the cloning and functional characterization of a hirsutene synthase as an unexpected fusion protein of a sesquiterpene synthase (STS) with a C-terminal 3-hydroxy-3-methylglutaryl-coenzyme A (3-hydroxy-3-methylglutaryl-CoA) synthase (HMGS) domain. Both the full-length fusion protein and truncated STS domain are highly product-specific 1,11-cyclizing STS enzymes with kinetic properties typical of STSs. Complementation studies in Saccharomyces cerevisiae confirmed that the HMGS domain is also functional in vivo Phylogenetic analysis shows that the hirsutene synthase domain does not form a clade with other previously characterized sesquiterpene synthases from Basidiomycota. Comparative gene structure analysis of this hirsutene synthase with characterized fungal enzymes reveals a significantly higher intron density, suggesting that this enzyme may be acquired by horizontal gene transfer. In contrast, the HMGS domain is clearly related to other fungal homologs. This STS-HMGS fusion protein is part of a biosynthetic gene cluster that includes P450s and oxidases that are expressed and could be cloned from cDNA. Finally, this unusual fusion of a terpene synthase to an HMGS domain, which is not generally recognized as a key regulatory enzyme of the mevalonate isoprenoid precursor pathway, led to the identification of additional HMGS duplications in many fungal genomes, including the localization of HMGSs in other predicted sesquiterpenoid biosynthetic gene clusters.IMPORTANCE Hirsutenoids represent a structurally diverse class of bioactive sesquiterpenoids isolated from fungi. Identification of their biosynthetic pathways will provide access to this chemodiversity for the discovery and synthesis of molecules with new bioactivities. The identification and successful cloning of the previously elusive hirsutene synthase from the S. hirsutum provide important insights and strategies for biosynthetic gene discovery in Basidiomycota. The finding of a terpene synthase-HMGS fusion, the discovery of other sesquiterpenoid biosynthetic gene clusters with dedicated HMGS genes, and HMGS gene duplications in fungal genomes give new importance to the role of HMGS as a key regulatory enzyme in isoprenoid and sterol biosynthesis that should be exploited for metabolic engineering.
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Mitsuhashi T, Abe I. Chimeric Terpene Synthases Possessing both Terpene Cyclization and Prenyltransfer Activities. Chembiochem 2018; 19:1106-1114. [PMID: 29675947 DOI: 10.1002/cbic.201800120] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Indexed: 12/12/2022]
Abstract
Prenyltransferase (PT) and terpene synthase (TPS) are key enzymes in the formation of the basic carbon skeletons of terpenoids. The PTs determine the prenyl carbon chain length, whereas TPSs generate the structural complexity of the molecular scaffolds, forming various ring structures. Normally, PTs and TPSs are separate, independent enzymes. However, in 2007, a chimeric enzyme, in which the PT was fused with the TPS, was found in a fungus. Recent studies have revealed that such chimeric TPSs are widely distributed in fungi and function in the biosyntheses of various terpene natural products, including sesterterpenes, which are a relatively rare group of terpenoids. This review summarizes the accumulated knowledge of these recently discovered, unique, chimeric TPSs.
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Affiliation(s)
- Takaaki Mitsuhashi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - 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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21
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Affiliation(s)
- Jacquelyn S. Fetrow
- Office of the President, Albright College, Reading, Pennsylvania, United States of America
- * E-mail:
| | - Patricia C. Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
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22
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Burkhardt I, Dickschat JS. The absolute configuration of isochamigrene: new insights into the cyclisation mechanism of trichodiene synthase. Chem Commun (Camb) 2018; 54:3540-3542. [DOI: 10.1039/c8cc01744a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The enantioselective synthesis of isochamigrene clarified its absolute configuration and biosynthetic relation to trichodiene.
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Affiliation(s)
- Immo Burkhardt
- 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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23
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Ellens KW, Christian N, Singh C, Satagopam VP, May P, Linster CL. Confronting the catalytic dark matter encoded by sequenced genomes. Nucleic Acids Res 2017; 45:11495-11514. [PMID: 29059321 PMCID: PMC5714238 DOI: 10.1093/nar/gkx937] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 10/03/2017] [Indexed: 01/02/2023] Open
Abstract
The post-genomic era has provided researchers with a deluge of protein sequences. However, a significant fraction of the proteins encoded by sequenced genomes remains without an identified function. Here, we aim at determining how many enzymes of uncertain or unknown function are still present in the Saccharomyces cerevisiae and human proteomes. Using information available in the Swiss-Prot, BRENDA and KEGG databases in combination with a Hidden Markov Model-based method, we estimate that >600 yeast and 2000 human proteins (>30% of their proteins of unknown function) are enzymes whose precise function(s) remain(s) to be determined. This illustrates the impressive scale of the ‘unknown enzyme problem’. We extensively review classical biochemical as well as more recent systematic experimental and computational approaches that can be used to support enzyme function discovery research. Finally, we discuss the possible roles of the elusive catalysts in light of recent developments in the fields of enzymology and metabolism as well as the significance of the unknown enzyme problem in the context of metabolic modeling, metabolic engineering and rare disease research.
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Affiliation(s)
- Kenneth W Ellens
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Nils Christian
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Charandeep Singh
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Venkata P Satagopam
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Carole L Linster
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
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24
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Kersten RD, Lee S, Fujita D, Pluskal T, Kram S, Smith JE, Iwai T, Noel JP, Fujita M, Weng JK. A Red Algal Bourbonane Sesquiterpene Synthase Defined by Microgram-Scale NMR-Coupled Crystalline Sponge X-ray Diffraction Analysis. J Am Chem Soc 2017; 139:16838-16844. [PMID: 29083151 DOI: 10.1021/jacs.7b09452] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Sesquiterpene scaffolds are the core backbones of many medicinally and industrially important natural products. A plethora of sesquiterpene synthases, widely present in bacteria, fungi, and plants, catalyze the formation of these intricate structures often with multiple stereocenters starting from linear farnesyl diphosphate substrates. Recent advances in next-generation sequencing and metabolomics technologies have greatly facilitated gene discovery for sesquiterpene synthases. However, a major bottleneck limits biochemical characterization of recombinant sesquiterpene synthases: the absolute structural elucidation of the derived sesquiterpene products. Here, we report the identification and biochemical characterization of LphTPS-A, a sesquiterpene synthase from the red macroalga Laurencia pacifica. Using the combination of transcriptomics, sesquiterpene synthase expression in yeast, and microgram-scale nuclear magnetic resonance-coupled crystalline sponge X-ray diffraction analysis, we resolved the absolute stereochemistry of prespatane, the major sesquiterpene product of LphTPS-A, and thereby functionally define LphTPS-A as the first bourbonane-producing sesquiterpene synthase and the first biochemically characterized sesquiterpene synthase from red algae. Our study showcases a workflow integrating multiomics approaches, synthetic biology, and the crystalline sponge method, which is generally applicable for uncovering new terpene chemistry and biochemistry from source-limited living organisms.
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Affiliation(s)
- Roland D Kersten
- Whitehead Institute for Biomedical Research , 455 Main Street, Cambridge, Massachusetts 02142, United States
| | - Shoukou Lee
- Graduate School of Engineering, The University of Tokyo, JST-ACCEL , Tokyo 113-8654, Japan
| | - Daishi Fujita
- Whitehead Institute for Biomedical Research , 455 Main Street, Cambridge, Massachusetts 02142, United States.,Graduate School of Engineering, The University of Tokyo, JST-ACCEL , Tokyo 113-8654, Japan
| | - Tomáš Pluskal
- Whitehead Institute for Biomedical Research , 455 Main Street, Cambridge, Massachusetts 02142, United States
| | - Susan Kram
- Scripps Institution of Oceanography, University of California, San Diego , La Jolla, California 92093, United States
| | - Jennifer E Smith
- Scripps Institution of Oceanography, University of California, San Diego , La Jolla, California 92093, United States
| | - Takahiro Iwai
- Graduate School of Engineering, The University of Tokyo, JST-ACCEL , Tokyo 113-8654, Japan
| | - Joseph P Noel
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies , La Jolla, California 92037, United States
| | - Makoto Fujita
- Graduate School of Engineering, The University of Tokyo, JST-ACCEL , Tokyo 113-8654, Japan
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research , 455 Main Street, Cambridge, Massachusetts 02142, United States.,Department of Biology, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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25
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Abstract
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The
year 2017 marks the twentieth anniversary of terpenoid cyclase
structural biology: a trio of terpenoid cyclase structures reported
together in 1997 were the first to set the foundation for understanding
the enzymes largely responsible for the exquisite chemodiversity of
more than 80000 terpenoid natural products. Terpenoid cyclases catalyze
the most complex chemical reactions in biology, in that more than
half of the substrate carbon atoms undergo changes in bonding and
hybridization during a single enzyme-catalyzed cyclization reaction.
The past two decades have witnessed structural, functional, and computational
studies illuminating the modes of substrate activation that initiate
the cyclization cascade, the management and manipulation of high-energy
carbocation intermediates that propagate the cyclization cascade,
and the chemical strategies that terminate the cyclization cascade.
The role of the terpenoid cyclase as a template for catalysis is paramount
to its function, and protein engineering can be used to reprogram
the cyclization cascade to generate alternative and commercially important
products. Here, I review key advances in terpenoid cyclase structural
and chemical biology, focusing mainly on terpenoid cyclases and related
prenyltransferases for which X-ray crystal structures have informed
and advanced our understanding of enzyme structure and function.
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Affiliation(s)
- David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
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26
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Rinkel J, Rabe P, Chen X, Köllner TG, Chen F, Dickschat JS. Mechanisms of the Diterpene Cyclases β-Pinacene Synthase fromDictyostelium discoideumand Hydropyrene Synthase fromStreptomyces clavuligerus. Chemistry 2017; 23:10501-10505. [DOI: 10.1002/chem.201702704] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Indexed: 11/08/2022]
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
| | - Xinlu Chen
- Department of Plant Sciences; University of Tennessee; 2431 Joe Johnson Drive Knoxville TN 37996-4561 USA
| | - Tobias G. Köllner
- Max Planck Institute for Chemical Ecology; Hans-Knöll-Straße 8 07745 Jena Germany
| | - Feng Chen
- Department of Plant Sciences; University of Tennessee; 2431 Joe Johnson Drive Knoxville TN 37996-4561 USA
| | - Jeroen S. Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry; University of Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Germany
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27
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Systematic identification of functional residues of Artemisia annua amorpha-4,11-diene synthase. Biochem J 2017; 474:2191-2202. [DOI: 10.1042/bcj20170060] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 05/17/2017] [Accepted: 05/19/2017] [Indexed: 11/17/2022]
Abstract
Terpene synthases (TPSs) are responsible for the extremely diversified and complex structure of terpenoids. Amorpha-4,11-diene synthase (ADS) has a high (90%) fidelity in generating the sesquiterpene precursor for the biosynthesis of artemisinin, an antimalarial drug, however, little is known about how active site residues of ADS are involved in carbocation rearrangement and cyclization reactions. Here, we identify seven residues that are key to most of the catalytic steps in ADS. By structural modeling and amino acid sequence alignments of ADS with two functionally relevant sesquiterpene synthases from Artemisia annua, we performed site-directed mutagenesis and found that a single substitution, T296V, impaired the ring closure activity almost completely, and tetra-substitutions (L374Y/L404V/L405I/G439S) led to an enzyme generating 80% monocyclic bisabolyl-type sesquiterpenes, whereas a double mutant (T399L/T447G) showed compromised activity in regioselective deprotonation to yield 34.7 and 37.7% normal and aberrant deprotonation products, respectively. Notably, Thr296, Leu374, Gly439, Thr399, and Thr447, which play a major role in directing catalytic cascades, are located around conserved metal-binding motifs and function through impacting the folding of the substrate/intermediate, implying that residues surrounding the two motifs could be valuable targets for engineering TPS activity. Using this knowledge, we substantially increased amorpha-4,11-diene production in a near-additive manner by engineering Thr399 and Thr447 for product release. Our results provide new insight for the rational design of enzyme activity using synthetic biology.
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28
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Cheema J, Faraldos JA, O'Maille PE. REVIEW: Epistasis and dominance in the emergence of catalytic function as exemplified by the evolution of plant terpene synthases. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 255:29-38. [PMID: 28131339 DOI: 10.1016/j.plantsci.2016.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 10/17/2016] [Accepted: 11/12/2016] [Indexed: 06/06/2023]
Abstract
Epistasis, the interaction between mutations and the genetic background, is a pervasive force in evolution that is difficult to predict yet derives from a simple principle - biological systems are interconnected. Therefore, one effect may be intimately linked to another, hence interdependent. Untangling epistatic interactions between and within genes is a vibrant area of research. Deriving a mechanistic understanding of epistasis is a major challenge. Particularly, elucidating how epistasis can attenuate the effects of otherwise dominant mutations that control phenotypes. Using the emergence of terpene cyclization in specialized metabolism as an excellent example, this review describes the process of discovery and interpretation of dominance and epistasis in relation to current efforts. Specifically, we outline experimental approaches to isolating epistatic networks of mutations in protein structure, formally quantifying epistatic interactions, then building biochemical models with chemical mechanisms in efforts to achieve an understanding of the physical basis for epistasis. From these models we describe informed conjectures about past evolutionary events that underlie the emergence, divergence and specialization of terpene synthases to illustrate key principles of the constraining forces of epistasis in enzyme function.
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Affiliation(s)
- Jitender Cheema
- John Innes Centre, Computational and Systems Biology, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Juan A Faraldos
- John Innes Centre, Department of Metabolic Biology, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Paul E O'Maille
- John Innes Centre, Department of Metabolic Biology, Norwich Research Park, Norwich NR4 7UH, UK; Institute of Food Research, Food & Health Programme, Norwich Research Park, Norwich NR4 7UA, UK.
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29
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Rabe P, Samborskyy M, Leadlay PF, Dickschat JS. Isoafricanol synthase from Streptomyces malaysiensis. Org Biomol Chem 2017; 15:2353-2358. [DOI: 10.1039/c7ob00234c] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A terpene cyclases from Streptomyces malaysiensis was characterised as (+)-isoafricanol synthase and its mechanism was investigated using isotopically labelled substrates.
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Affiliation(s)
- Patrick Rabe
- 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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30
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Hammer SC, Syrén PO, Hauer B. Substrate Pre-Folding and Water Molecule Organization Matters for Terpene Cyclase Catalyzed Conversion of Unnatural Substrates. ChemistrySelect 2016. [DOI: 10.1002/slct.201600572] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Stephan C. Hammer
- Division of Chemistry; Chemical Engineering; California Institute of Technology; Pasadena, CA 91125 USA
| | - Per-Olof Syrén
- School of Chemical Science and Engineering; Division of Applied Physical Chemistry; KTH Royal Institute of Technology; 100 44 Stockholm Sweden
| | - Bernhard Hauer
- Institute of Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 D-70569 Stuttgart Germany
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31
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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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32
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Tian B, Poulter CD, Jacobson MP. Defining the Product Chemical Space of Monoterpenoid Synthases. PLoS Comput Biol 2016; 12:e1005053. [PMID: 27517297 PMCID: PMC4982680 DOI: 10.1371/journal.pcbi.1005053] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 07/09/2016] [Indexed: 11/18/2022] Open
Abstract
Terpenoid synthases create diverse carbon skeletons by catalyzing complex carbocation rearrangements, making them particularly challenging for enzyme function prediction. To begin to address this challenge, we have developed a computational approach for the systematic enumeration of terpenoid carbocations. Application of this approach allows us to systematically define a nearly complete chemical space for the potential carbon skeletons of products from monoterpenoid synthases. Specifically, 18758 carbocations were generated, which we cluster into 74 cyclic skeletons. Five of the 74 skeletons are found in known natural products; some of the others are plausible for new functions, either in nature or engineered. This work systematizes the description of function for this class of enzymes, and provides a basis for predicting functions of uncharacterized enzymes. To our knowledge, this is the first computational study to explore the complete product chemical space of this important class of enzymes. Terpenoids, as one of the largest classes of natural products, provide complex carbocycle structures for many drugs (e.g. taxol) and prodrugs. The diverse carbocycle structures arise from complex carbocation rearrangements catalyzed by terpenoid synthases. Many putative terpene synthase enzymes identified in genome sequencing efforts remain functionally uncharacterized, and some of these will undoubtedly have novel products, potentially including previously undiscovered carbocycles. In this work, we present a computational approach that systematically enumerates all plausible carbocations of monoterpenoid synthases in order to define and organize the potentially large product chemical space of this important class of enzymes.
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Affiliation(s)
- Boxue Tian
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, California, United States of America
| | - C. Dale Poulter
- Department of Chemistry, University of Utah, Salt Lake City, Utah, United States of America
| | - Matthew P. Jacobson
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail:
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33
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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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34
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O'Brien TE, Bertolani SJ, Tantillo DJ, Siegel JB. Mechanistically informed predictions of binding modes for carbocation intermediates of a sesquiterpene synthase reaction. Chem Sci 2016; 7:4009-4015. [PMID: 30155043 PMCID: PMC6013805 DOI: 10.1039/c6sc00635c] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 03/18/2016] [Indexed: 11/21/2022] Open
Abstract
Sesquiterpenoids comprise a class of terpenoid natural products with thousands of compounds that are highly diverse in structure, generally containing a polycyclic carbon backbone that is constructed by a sesquiterpene synthase. Decades of experimental and computational studies have demonstrated that these enzymes generate a carbocation in the active site, which undergoes a series of structural rearrangements until a product is formed via deprotonation or nucleophile attack. However, for the vast majority of these enzymes the productive binding orientation of the intermediate carbocations has remained unclear. In this work, a method that combines quantum mechanics and computational docking is used to generate an all-atom model of every putative intermediate formed in the context of the enzyme active site for tobacco epi-aristolochene synthase (TEAS). This method identifies a single pathway that links the first intermediate to the last, enabling us to propose the first high-resolution model for the reaction intermediates in the active site of TEAS, and providing testable predictions.
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Affiliation(s)
- T E O'Brien
- Department of Chemistry , University of California Davis , Davis , California , USA . ;
| | - S J Bertolani
- Department of Chemistry , University of California Davis , Davis , California , USA . ;
| | - D J Tantillo
- Department of Chemistry , University of California Davis , Davis , California , USA . ;
| | - J B Siegel
- Department of Chemistry , University of California Davis , Davis , California , USA . ; .,Department of Biochemistry and Molecular Medicine , University of California Davis , Davis , California , USA.,Genome Center , University of California Davis , Davis , California , USA
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35
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Rudolf JD, Yan X, Shen B. Genome neighborhood network reveals insights into enediyne biosynthesis and facilitates prediction and prioritization for discovery. J Ind Microbiol Biotechnol 2016; 43:261-76. [PMID: 26318027 PMCID: PMC4753101 DOI: 10.1007/s10295-015-1671-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/09/2015] [Indexed: 01/24/2023]
Abstract
The enediynes are one of the most fascinating families of bacterial natural products given their unprecedented molecular architecture and extraordinary cytotoxicity. Enediynes are rare with only 11 structurally characterized members and four additional members isolated in their cycloaromatized form. Recent advances in DNA sequencing have resulted in an explosion of microbial genomes. A virtual survey of the GenBank and JGI genome databases revealed 87 enediyne biosynthetic gene clusters from 78 bacteria strains, implying that enediynes are more common than previously thought. Here we report the construction and analysis of an enediyne genome neighborhood network (GNN) as a high-throughput approach to analyze secondary metabolite gene clusters. Analysis of the enediyne GNN facilitated rapid gene cluster annotation, revealed genetic trends in enediyne biosynthetic gene clusters resulting in a simple prediction scheme to determine 9- versus 10-membered enediyne gene clusters, and supported a genomic-based strain prioritization method for enediyne discovery.
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Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Xiaohui Yan
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA.
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL, 33458, USA.
- Natural Products Library Initiative, The Scripps Research Institute, Jupiter, FL, 33458, USA.
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36
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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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37
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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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38
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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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39
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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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40
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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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