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Schwartz R, Zev S, Major DT. Mechanistic docking in terpene synthases using EnzyDock. Methods Enzymol 2024; 699:265-292. [PMID: 38942507 DOI: 10.1016/bs.mie.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Terpene Synthases (TPS) catalyze the formation of multicyclic, complex terpenes and terpenoids from linear substrates. Molecular docking is an important research tool that can further our understanding of TPS multistep mechanisms and guide enzyme design. Standard docking programs are not well suited to tackle the unique challenges of TPS, like the many chemical steps which form multiple stereo-centers, the weak dispersion interactions between the isoprenoid chain and the hydrophobic region of the active site, description of carbocation intermediates, and finding mechanistically meaningful sets of docked poses. To address these and other unique challenges, we developed the multistate, multiscale docking program EnzyDock and used it to study many TPS and other enzymes. In this review we discuss the unique challenges of TPS, the special features of EnzyDock developed to address these challenges and demonstrate its successful use in ongoing research on the bacterial TPS CotB2.
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Affiliation(s)
- Renana Schwartz
- Department of Chemistry and Institute for Nanotechnology Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Shani Zev
- Department of Chemistry and Institute for Nanotechnology Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Dan T Major
- Department of Chemistry and Institute for Nanotechnology Advanced Materials, Bar Ilan University, Ramat Gan, Israel.
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2
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Torrence IS, O'Brien TE, Siegel JB, Tantillo DJ. Docking carbocations into terpene synthase active sites using chemically meaningful constraints-The TerDockin approach. Methods Enzymol 2024; 699:231-263. [PMID: 38942505 DOI: 10.1016/bs.mie.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Terpenes are a diverse class of natural products which have long been sought after for their chemical properties as medicine, perfumes, and for food flavoring. Computational docking studies of terpene mechanisms have been a challenge due to the lack of strong directing groups which many docking programs rely on. In this chapter, we dive into our computational method Terdockin (Terpene-Docking) as a successful methodology in modeling terpene synthase mechanisms. This method could also be used as inspiration for any multi-ligand docking project.
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Affiliation(s)
- Ian S Torrence
- Department of Chemistry, University of California Davis, Davis, CA, United States
| | - Terrence E O'Brien
- Discovery Chemistry, Genentech, Inc., South San Francisco, CA, United States
| | - Justin B Siegel
- Department of Chemistry, University of California Davis, Davis, CA, United States; Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, CA, United States; Genome Center, University of California Davis, Davis, CA, Untied States.
| | - Dean J Tantillo
- Department of Chemistry, University of California Davis, Davis, CA, United States
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3
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Ludwig J, Curado-Carballada C, Hammer SC, Schneider A, Diether S, Kress N, Ruiz-Barragán S, Osuna S, Hauer B. Controlling Monoterpene Isomerization by Guiding Challenging Carbocation Rearrangement Reactions in Engineered Squalene-Hopene Cyclases. Angew Chem Int Ed Engl 2024; 63:e202318913. [PMID: 38270537 DOI: 10.1002/anie.202318913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/20/2024] [Accepted: 01/23/2024] [Indexed: 01/26/2024]
Abstract
The interconversion of monoterpenes is facilitated by a complex network of carbocation rearrangement pathways. Controlling these isomerization pathways is challenging when using common Brønsted and Lewis acid catalysts, which often produce product mixtures that are difficult to separate. In contrast, natural monoterpene cyclases exhibit high control over the carbocation rearrangement reactions but are reliant on phosphorylated substrates. In this study, we present engineered squalene-hopene cyclases from Alicyclobacillus acidocaldarius (AacSHC) that catalyze the challenging isomerization of monoterpenes with unprecedented precision. Starting from a promiscuous isomerization of (+)-β-pinene, we first demonstrate noticeable shifts in the product distribution solely by introducing single point mutations. Furthermore, we showcase the tuneable cation steering by enhancing (+)-borneol selectivity from 1 % to >90 % (>99 % de) aided by iterative saturation mutagenesis. Our combined experimental and computational data suggest that the reorganization of key aromatic residues leads to the restructuring of the water network that facilitates the selective termination of the secondary isobornyl cation. This work expands our mechanistic understanding of carbocation rearrangements and sets the stage for target-oriented skeletal reorganization of broadly abundant terpenes.
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Affiliation(s)
- Julian Ludwig
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Christian Curado-Carballada
- Institut de Química Computacional i Catàlisi (IQCC) and, Departament de Química, Universitat de Girona, Maria Aurèlia Capmany 69, 17003, Girona, Spain
| | - Stephan C Hammer
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
- Faculty of Chemistry, Organic Chemistry and Biocatalysis, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Andreas Schneider
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Svenja Diether
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Nico Kress
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Sergi Ruiz-Barragán
- Institut de Química Computacional i Catàlisi (IQCC) and, Departament de Química, Universitat de Girona, Maria Aurèlia Capmany 69, 17003, Girona, Spain
- Departament de Fisica, Universitat Politecnica de Catalunya, Rambla Sant Nebridi 22, 08222, Terrassa, Barcelona, Spain
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi (IQCC) and, Departament de Química, Universitat de Girona, Maria Aurèlia Capmany 69, 17003, Girona, Spain
- ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Spain
| | - Bernhard Hauer
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
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4
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Zhao Y, Liang Y, Luo G, Li Y, Han X, Wen M. Sequence-Structure Analysis Unlocking the Potential Functional Application of the Local 3D Motifs of Plant-Derived Diterpene Synthases. Biomolecules 2024; 14:120. [PMID: 38254720 PMCID: PMC10813164 DOI: 10.3390/biom14010120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 12/31/2023] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Plant-derived diterpene synthases (PdiTPSs) play a critical role in the formation of structurally and functionally diverse diterpenoids. However, the specificity or functional-related features of PdiTPSs are not well understood. For a more profound insight, we collected, constructed, and curated 199 functionally characterized PdiTPSs and their corresponding 3D structures. The complex correlations among their sequences, domains, structures, and corresponding products were comprehensively analyzed. Ultimately, our focus narrowed to the geometric arrangement of local structures. We found that local structural alignment can rapidly localize product-specific residues that have been validated by mutagenesis experiments. Based on the 3D motifs derived from the residues around the substrate, we successfully searched diterpene synthases (diTPSs) from the predicted terpene synthases and newly characterized PdiTPSs, suggesting that the identified 3D motifs can serve as distinctive signatures in diTPSs (I and II class). Local structural analysis revealed the PdiTPSs with more conserved amino acid residues show features unique to class I and class II, whereas those with fewer conserved amino acid residues typically exhibit product diversity and specificity. These results provide an attractive method for discovering novel or functionally equivalent enzymes and probing the product specificity in cases where enzyme characterization is limited.
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Affiliation(s)
- Yalan Zhao
- National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; (Y.Z.); (Y.L.); (G.L.); (X.H.)
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Yupeng Liang
- National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; (Y.Z.); (Y.L.); (G.L.); (X.H.)
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Gan Luo
- National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; (Y.Z.); (Y.L.); (G.L.); (X.H.)
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Yi Li
- College of Mathematics and Computer Science, Dali University, Dali 671003, China
| | - Xiulin Han
- National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; (Y.Z.); (Y.L.); (G.L.); (X.H.)
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Mengliang Wen
- National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; (Y.Z.); (Y.L.); (G.L.); (X.H.)
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China
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Ma X, Xu H, Tong Y, Luo Y, Dong Q, Jiang T. Structural and functional investigations of syn-copalyl diphosphate synthase from Oryza sativa. Commun Chem 2023; 6:240. [PMID: 37932442 PMCID: PMC10628199 DOI: 10.1038/s42004-023-01042-w] [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: 06/08/2023] [Accepted: 10/25/2023] [Indexed: 11/08/2023] Open
Abstract
The large superfamily of labdane-related diterpenoids is defined by the cyclization of linear geranylgeranyl pyrophosphate (GGPP), catalyzed by copalyl diphosphate synthases (CPSs) to form the basic decalin core, the copalyl diphosphates (CPPs). Three stereochemically distinct CPPs have been found in plants, namely (+)-CPP, ent-CPP and syn-CPP. Here, we used X-ray crystallography and cryo-EM methods to describe different oligomeric structures of a syn-copalyl diphosphate synthase from Oryza sativa (OsCyc1), and provided a cryo-EM structure of OsCyc1D367A mutant in complex with the substrate GGPP. Further analysis showed that tetramers are the dominant form of OsCyc1 in solution and are not necessary for enzyme activity in vitro. Through rational design, we identified an OsCyc1 mutant that can generate ent-CPP in addition to syn-CPP. Our work provides a structural and mechanistic basis for comparing different CPSs and paves the way for further enzyme design to obtain diterpene derivatives with specific chirality.
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Affiliation(s)
- Xiaoli Ma
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Haifeng Xu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuru Tong
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, China
| | - Yunfeng Luo
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Qinghua Dong
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Tao Jiang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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6
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Whitehead J, Leferink NGH, Johannissen LO, Hay S, Scrutton NS. Decoding Catalysis by Terpene Synthases. ACS Catal 2023; 13:12774-12802. [PMID: 37822860 PMCID: PMC10563020 DOI: 10.1021/acscatal.3c03047] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/31/2023] [Indexed: 10/13/2023]
Abstract
The review by Christianson, published in 2017 on the twentieth anniversary of the emergence of the field, summarizes the foundational discoveries and key advances in terpene synthase/cyclase (TS) biocatalysis (Christianson, D. W. Chem Rev2017, 117 (17), 11570-11648. DOI: 10.1021/acs.chemrev.7b00287). Here, we review the TS literature published since then, bringing the field up to date and looking forward to what could be the near future of TS rational design. Many revealing discoveries have been made in recent years, building on the knowledge and fundamental principles uncovered during those initial two decades of study. We use these to explore TS reaction chemistry and see how a combined experimental and computational approach helps to decipher the complexities of TS catalysis. Revealed are a suite of catalytic motifs which control product outcome in TSs, some obvious, some more subtle. We examine each in detail, using the most recent papers and insights to illustrate how exactly this fascinating class of enzymes takes a single acyclic substrate and turns it into the many thousands of complex terpenoids found in Nature. We then explore some of the recent strategies for TS engineering, including machine learning and other data-driven approaches. From this, rational and predictive engineering of TSs, "designer terpene synthases", will begin to emerge as a realistic goal.
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Affiliation(s)
- Joshua
N. Whitehead
- Manchester
Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Nicole G. H. Leferink
- Future
Biomanufacturing Research Hub (FBRH), Manchester Institute of Biotechnology,
Department of Chemistry, The University
of Manchester, Manchester, M1 7DN, United
Kingdom
| | - Linus O. Johannissen
- Manchester
Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Sam Hay
- Manchester
Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Nigel S. Scrutton
- Manchester
Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
- Future
Biomanufacturing Research Hub (FBRH), Manchester Institute of Biotechnology,
Department of Chemistry, The University
of Manchester, Manchester, M1 7DN, United
Kingdom
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7
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Lanier ER, Andersen TB, Hamberger B. Plant terpene specialized metabolism: complex networks or simple linear pathways? THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:1178-1201. [PMID: 36891828 PMCID: PMC11166267 DOI: 10.1111/tpj.16177] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/28/2023] [Accepted: 03/06/2023] [Indexed: 05/31/2023]
Abstract
From the perspectives of pathway evolution, discovery and engineering of plant specialized metabolism, the nature of the biosynthetic routes represents a critical aspect. Classical models depict biosynthesis typically from an end-point angle and as linear, for example, connecting central and specialized metabolism. As the number of functionally elucidated routes increased, the enzymatic foundation of complex plant chemistries became increasingly well understood. The perception of linear pathway models has been severely challenged. With a focus on plant terpenoid specialized metabolism, we review here illustrative examples supporting that plants have evolved complex networks driving chemical diversification. The completion of several diterpene, sesquiterpene and monoterpene routes shows complex formation of scaffolds and their subsequent functionalization. These networks show that branch points, including multiple sub-routes, mean that metabolic grids are the rule rather than the exception. This concept presents significant implications for biotechnological production.
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Affiliation(s)
| | | | - Björn Hamberger
- Department of Biochemistry and Molecular Biology, Michigan State University, Molecular Plant Sciences Building, 1066 Bogue Street, East Lansing, Michigan, 48824, USA
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8
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Wang Z, Nelson DR, Zhang J, Wan X, Peters RJ. Plant (di)terpenoid evolution: from pigments to hormones and beyond. Nat Prod Rep 2023; 40:452-469. [PMID: 36472136 PMCID: PMC9945934 DOI: 10.1039/d2np00054g] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: up to 2014-2022.Diterpenoid biosynthesis in plants builds on the necessary production of (E,E,E)-geranylgeranyl diphosphate (GGPP) for photosynthetic pigment production, with diterpenoid biosynthesis arising very early in land plant evolution, enabling stockpiling of the extensive arsenal of (di)terpenoid natural products currently observed in this kingdom. This review will build upon that previously published in the Annual Review of Plant Biology, with a stronger focus on enzyme structure-function relationships, as well as additional insights into the evolution of (di)terpenoid metabolism since generated.
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Affiliation(s)
- Zhibiao Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China.,Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50014, USA.
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Juan Zhang
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, Research Center of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100024, China.
| | - Xiangyuan Wan
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, Research Center of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100024, China.
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50014, USA.
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9
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Tong Y, Ma X, Hu T, Chen K, Cui G, Su P, Xu H, Gao W, Jiang T, Huang L. Structural and mechanistic insights into the precise product synthesis by a bifunctional miltiradiene synthase. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:165-175. [PMID: 36161753 PMCID: PMC9829396 DOI: 10.1111/pbi.13933] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 07/22/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
Selaginella moellendorffii miltiradiene synthase (SmMDS) is a unique bifunctional diterpene synthase (diTPS) that catalyses the successive cyclization of (E,E,E)-geranylgeranyl diphosphate (GGPP) via (+)-copalyl diphosphate (CPP) to miltiradiene, which is a crucial precursor of important medicinal compounds, such as triptolide, ecabet sodium and carnosol. Miltiradiene synthetic processes have been studied in monofunctional diTPSs, while the precise mechanism by which active site amino acids determine product simplicity and the experimental evidence for reaction intermediates remain elusive. In addition, how bifunctional diTPSs work compared to monofunctional enzymes is attractive for detailed research. Here, by mutagenesis studies of SmMDS, we confirmed that pimar-15-en-8-yl+ is an intermediate in miltiradiene synthesis. Moreover, we determined the apo-state and the GGPP-bound state crystal structures of SmMDS. By structure analysis and mutagenesis experiments, possible contributions of key residues both in class I and II active sites were suggested. Based on the structural and functional analyses, we confirmed the copal-15-yl+ intermediate and unveiled more details of the catalysis process in the SmMDS class I active site. Moreover, the structural and experimental results suggest an internal channel for (+)-CPP produced in the class II active site moving towards the class I active site. Our research is a good example for intermediate identification of diTPSs and provides new insights into the product specificity determinants and intermediate transport, which should greatly facilitate the precise controlled synthesis of various diterpenes.
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Affiliation(s)
- Yuru Tong
- National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
- School of Pharmaceutical SciencesCapital Medical UniversityBeijingChina
| | - Xiaoli Ma
- National Laboratory of BiomacromoleculesInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
| | - Tianyuan Hu
- School of Pharmaceutical SciencesCapital Medical UniversityBeijingChina
| | - Kang Chen
- National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
| | - Guanghong Cui
- National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
| | - Ping Su
- National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
| | - Haifeng Xu
- National Laboratory of BiomacromoleculesInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Wei Gao
- Beijing Shijitan HospitalCapital Medical UniversityBeijingChina
| | - Tao Jiang
- National Laboratory of BiomacromoleculesInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Luqi Huang
- National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
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10
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Wang J, Mao Y, Ma Y, Yang J, Jin B, Lin H, Tang J, Zeng W, Zhao Y, Gao W, Peters RJ, Guo J, Cui G, Huang L. Diterpene synthases from Leonurus japonicus elucidate epoxy-bridge formation of spiro-labdane diterpenoids. PLANT PHYSIOLOGY 2022; 189:99-111. [PMID: 35157086 PMCID: PMC9070827 DOI: 10.1093/plphys/kiac056] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Spiro-9,13-epoxy-labdane diterpenoids are commonly found in Leonurus species, particularly in Leonurus japonicus Houtt., which is a medicinal herb of long-standing use in Asia and in which such spiro-heterocycles are present in at least 38 diterpenoids. Here, through generation of a transcriptome and functional characterization of six diterpene synthases (diTPSs) from L. japonicus, including three class II diTPSs (LjTPS1, LjTPS3, and LjTPS4) and three class I diTPSs (LjTPS5, LjTPS6, and LjTPS7), formation of the spiro-9,13-epoxy-labdane backbone was elucidated, along with identification of the relevant diTPSs for production of other labdane-related diterpenes. Similar to what has been found with diTPSs from other plant species, while LjTPS3 specifically produces the carbon-9 (C9) hydroxylated bicycle peregrinol diphosphate (PPP), the subsequently acting LjTPS6 yields a mixture of four products, largely labda-13(16),14-dien-9-ol, but with substantial amounts of viteagnusin D and the C13-S/R epimers of 9,13-epoxy-labda-14-ene. Notably, structure-function analysis identified a critical residue in LjTPS6 (I420) in which single site mutations enable specific production of the 13S epimer. Indeed, extensive mutagenesis demonstrated that LjTPS6:I420G reacts with PPP to both specifically and efficiently produce 9,13S-epoxy-labda-14-ene, providing a specialized synthase for further investigation of derived diterpenoid biosynthesis. The results reported here provide a strong foundation for future studies of the intriguing spiro-9,13-epoxy-labdane diterpenoid metabolism found in L. japonicus.
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Affiliation(s)
- Jian Wang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yaping Mao
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ying Ma
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jian Yang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Baolong Jin
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Huixin Lin
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jinfu Tang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Wen Zeng
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yujun Zhao
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Wei Gao
- Beijing Shijitan Hospital, Capital Medical University, Beijing 10038, China
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Juan Guo
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Guanghong Cui
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Luqi Huang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
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11
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Abstract
As a midsized gene family conserved more by lineage than function, the typical plant terpene synthases (TPSs) could be a valuable tool to examine plant evolution. TPSs are pivotal in biosynthesis of gibberellins and related phytohormones as well as in formation of the extensive arsenal of specialized plant metabolites mediating ecological interactions whose production is often lineage specific. Yet the origin and early evolution of the TPS family is not well understood. Systematic analysis of an array of transcriptomes and sequenced genomes indicated that the TPS family originated after the divergence of land plants from charophytic algae. Phylogenetic and biochemical analyses support the hypothesis that the ancestral TPS gene encoded a bifunctional class I and II diterpene synthase producing the ent-kaurene required for phytohormone production in all extant lineages of land plants. Moreover, the ancestral TPS gene likely underwent duplication at least twice early in land plant evolution. Together these two gave rise to three TPS lineages leading to the extant TPS-c, TPS-e/f, and the remaining TPS (h/d/a/b/g) subfamilies, with the latter dedicated to secondary rather than primary metabolism while the former two contain those genes involved in ent-kaurene production. Nevertheless, parallel evolution from the ent-kaurene–producing class I and class II diterpene synthases has led to roles for TPS-e/f and -c subfamily members in secondary metabolism as well. These results clarify TPS evolutionary history and provide context for the role of these genes in producing the vast diversity of terpenoid natural products observed today in various land plant lineages.
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12
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Xu H, Lackus ND, Köllner TG, Dickschat JS. Isotopic Labeling Experiments Solve the Hedycaryol Problem. Org Lett 2022; 24:587-591. [PMID: 34985289 DOI: 10.1021/acs.orglett.1c04021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Hedycaryol is a widespread sesquiterpene alcohol and important biosynthetic intermediate toward eudesmols and guaiols. A full NMR assignment for this compound has been hampered because of the unique molecular mechanics of its conformers in complex mixtures. This problem was solved through the enzymatic synthesis of isotopically labeled materials using a mutated plant and a bacterial enzyme for access to both enantiomers of hedycaryol, which also allowed us to follow the stereochemical course of its Cope rearrangement.
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Affiliation(s)
- Houchao Xu
- Kekulé Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Nathalie D Lackus
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745 Jena, Germany
| | - Tobias G Köllner
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745 Jena, Germany
| | - Jeroen S Dickschat
- Kekulé Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
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13
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Wang X, Wang Z, Zhu G, Jiang L, Zhang W, Huang Y, Cong Z, Zhao YL, Xu JH, Hsiang T, Zhang L, Chen Q, Liu X. Chemical control over the conversion between bicyclic and polycyclic terpenes by fungal bifunctional terpene synthases. Chem Commun (Camb) 2022; 58:9476-9479. [DOI: 10.1039/d2cc03644d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The mutation on site 89 in the BFTSs alters the carbocation transportation pathway, which changes the sesterterpene structure.
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Affiliation(s)
- Xinye Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Zhixin Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Guoliang Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Lan Jiang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Weiyan Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yiyi Huang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Zhanren Cong
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, MOE-LSB & MOE-LSC, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Qi Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xueting Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
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14
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Yang R, Du Z, Qiu T, Sun J, Shen Y, Huang L. Discovery and Functional Characterization of a Diverse Diterpene Synthase Family in the Medicinal Herb Isodon lophanthoides Var. gerardiana. PLANT & CELL PHYSIOLOGY 2021; 62:1423-1435. [PMID: 34133748 DOI: 10.1093/pcp/pcab089] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 06/09/2021] [Accepted: 06/16/2021] [Indexed: 06/12/2023]
Abstract
Isodon lophanthoides var. gerardiana (Lamiaceae), also named xihuangcao, is a traditional Chinese medicinal herb that exhibits a broad range of pharmacological activities. Abietane-type diterpenoids are the characteristic constituents of I. lophanthoides, yet their biosynthesis has not been elucidated. Although the aerial parts are the most commonly used organs of I. lophanthoides, metabolite profiling by gas chromatography-mass spectrometry showed the underground parts also contain large amounts of labdane diterpenoids including abietatriene, miltiradiene and ferruginol, which are distinct from the 13-hydroxy-8(14)-abietene detected in the aerial parts. Comparative transcriptome analysis of root and leaf samples identified a diverse diterpene synthase family including 6 copalyl diphosphate synthase (IlCPS1-6) and 5 kaurene synthase-like (IlKSL1-5). Here we report the functional characterization of six of these enzymes using yeast heterologous expression system. Both IlCPS1 and IlCPS3 synthesized (+)-copalyl diphosphate (CPP), in combination with IlKSL1 resulted in miltiradiene, precursor of abietane-type diterpenoids, while coupling with IlKSL5 led to the formation of hydroxylated diterpene scaffold nezukol. Expression profiling and phylogenetic analysis further support the distinct evolutionary relationship and spatial distribution of IlCPS1 and IlCPS3. IlCPS2 converted GGPP into labda-7,13E-dien-15-ol diphosphate. IlCPS6 was identified as ent-CPS, indicating a role in gibberellin metabolism. We further identified a single residue that determined the water addition of nezukol synthase IlKSL5. Substitution of alanine 513 with isoleucine completely altered the product outcome from hydroxylated nezukol to isopimara-7,15-diene. Together, these findings elucidated the early steps of bioactive abietane-type diterpenoid biosynthesis in I. lophanthoides and the catalytic mechanism of nezukol synthase.
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Affiliation(s)
- Ruikang Yang
- Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, 12 Jichang Rd, Guangzhou 510405, China
| | - Zuying Du
- Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, 12 Jichang Rd, Guangzhou 510405, China
- The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Ting Qiu
- Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, 12 Jichang Rd, Guangzhou 510405, China
- The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Jie Sun
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of biotechnology and bioengineering, Zhejiang University of Technology, 18 Chaowang Rd Hangzhou 310014, Zhejiang, China
| | - Yanting Shen
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, 232 Waihuan Rd, Guangzhou 510006, China
| | - Lili Huang
- Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, 12 Jichang Rd, Guangzhou 510405, China
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, 232 Waihuan Rd, Guangzhou 510006, China
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15
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Xing B, Yu J, Chi C, Ma X, Xu Q, Li A, Ge Y, Wang Z, Liu T, Jia H, Yin F, Guo J, Huang L, Yang D, Ma M. Functional characterization and structural bases of two class I diterpene synthases in pimarane-type diterpene biosynthesis. Commun Chem 2021; 4:140. [PMID: 36697656 PMCID: PMC9814573 DOI: 10.1038/s42004-021-00578-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/08/2021] [Indexed: 01/28/2023] Open
Abstract
Pimarane-type diterpenoids are widely distributed in all domains of life, but no structures or catalytic mechanisms of pimarane-type diterpene synthases (DTSs) have been characterized. Here, we report that two class I DTSs, Sat1646 and Stt4548, each accept copalyl diphosphate (CPP) as the substrate to produce isopimara-8,15-diene (1). Sat1646 can also accept syn-CPP and produce syn-isopimaradiene/pimaradiene analogues (2-7), among which 2 possesses a previously unreported "6/6/7" ring skeleton. We solve the crystal structures of Sat1646, Sat1646 complexed with magnesium ions, and Stt4548, thereby revealing the active sites of these pimarane-type DTSs. Substrate modeling and subsequent site-directed mutagenesis experiments demonstrate different structural bases of Sat1646 and Stt4548 for 1 production. Comparisons with previously reported DTSs reveal their distinct carbocation intermediate stabilization mechanisms, which control the conversion of a single substrate CPP into structurally diverse diterpene products. These results illustrate the structural bases for enzymatic catalyses of pimarane-type DTSs, potentially facilitating future DTS engineering and combinatorial biosynthesis.
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Affiliation(s)
- Baiying Xing
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Jiahui Yu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Changbiao Chi
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Xueyang Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Qingxia Xu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Annan Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Yuanjie Ge
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Zhengdong Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Tan Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Hongli Jia
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Fuling Yin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Juan Guo
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Luqi Huang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Donghui Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China.
| | - Ming Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China.
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16
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Huang ZY, Ye RY, Yu HL, Li AT, Xu JH. Mining methods and typical structural mechanisms of terpene cyclases. BIORESOUR BIOPROCESS 2021; 8:66. [PMID: 38650244 PMCID: PMC10992375 DOI: 10.1186/s40643-021-00421-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/24/2021] [Indexed: 12/13/2022] Open
Abstract
Terpenoids, formed by cyclization and/or permutation of isoprenes, are the most diverse and abundant class of natural products with a broad range of significant functions. One family of the critical enzymes involved in terpenoid biosynthesis is terpene cyclases (TCs), also known as terpene synthases (TSs), which are responsible for forming the ring structure as a backbone of functionally diverse terpenoids. With the recent advances in biotechnology, the researches on terpene cyclases have gradually shifted from the genomic mining of novel enzyme resources to the analysis of their structures and mechanisms. In this review, we summarize both the new methods for genomic mining and the structural mechanisms of some typical terpene cyclases, which are helpful for the discovery, engineering and application of more and new TCs.
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Affiliation(s)
- Zheng-Yu Huang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, Frontiers Science Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai, 200237, China
| | - Ru-Yi Ye
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, Frontiers Science Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai, 200237, China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, Frontiers Science Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai, 200237, China
| | - Ai-Tao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, Frontiers Science Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai, 200237, China.
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17
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Schneider A, Jegl P, Hauer B. Stereoselective Directed Cationic Cascades Enabled by Molecular Anchoring in Terpene Cyclases. Angew Chem Int Ed Engl 2021; 60:13251-13256. [PMID: 33769659 PMCID: PMC8251838 DOI: 10.1002/anie.202101228] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/15/2021] [Indexed: 01/27/2023]
Abstract
Cascade reactions appeared as a cutting‐edge strategy to streamline the assembly of complex structural scaffolds from naturally available precursors in an atom‐, as well as time, labor‐ and cost‐efficient way. We herein report a strategy to control cationic cyclization cascades by exploiting the ability of anchoring dynamic substrates in the active site of terpene cyclases via designed hydrogen bonding. Thereby, it is possible to induce “directed” cyclizations in contrast to established “non‐stop” cyclizations (99:1) and predestinate cascade termination at otherwise catalytically barely accessible intermediates. As a result, we are able to provide efficient access to naturally widely occurring apocarotenoids, value‐added flavors and fragrances in gram‐scale by replacing multi‐stage synthetic routes to a single step with unprecedented selectivity (>99.5 % ee) and high yields (up to 89 %).
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Affiliation(s)
- Andreas Schneider
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart-Vaihingen, Germany
| | - Philipp Jegl
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart-Vaihingen, Germany
| | - Bernhard Hauer
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart-Vaihingen, Germany
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18
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Schneider A, Jegl P, Hauer B. Stereoselektive gerichtete kationische Kaskaden ermöglicht durch molekulare Verankerung in Terpencyclasen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Andreas Schneider
- Institut der Biochemie und technischen Biochemie Universität Stuttgart Allmandring 31 70569 Stuttgart-Vaihingen Deutschland
| | - Philipp Jegl
- Institut der Biochemie und technischen Biochemie Universität Stuttgart Allmandring 31 70569 Stuttgart-Vaihingen Deutschland
| | - Bernhard Hauer
- Institut der Biochemie und technischen Biochemie Universität Stuttgart Allmandring 31 70569 Stuttgart-Vaihingen Deutschland
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19
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Computer-Aid Directed Evolution of GPPS and PS Enzymes. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6653500. [PMID: 33791370 PMCID: PMC7994089 DOI: 10.1155/2021/6653500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/20/2021] [Accepted: 03/03/2021] [Indexed: 11/18/2022]
Abstract
Pinene, a natural active monoterpene, is widely used as a flavoring agent, perfume, medicine, and biofuel. Although genetically engineered microorganisms have successfully produced pinene, to date, the biological yield of pinene is much lower than that of semiterpenes (isoprene) and sesquiterpenes (farnesene). In addition to the low heterologous expression of geranyl pyrophosphate synthase (GPPS) and pinene synthase (PS), cytotoxicity due to accumulation of the monoterpene also limits the production of pinene in microorganisms. In this study, we attempted to use two strategies to increase the biological yield of pinene. By deleting the random coils of GPPS and PS alone or in combination, a strain with a 335% yield increase was obtained. Additionally, upon computer-guided molecular modeling and docking of GPPS with isopentenyl pyrophosphate (IPP), its substrate, the key sites located within the catalytic pocket for substrate binding, was predicted. After screening, a strain harboring the T273R mutation of GPPS was selected among a batch of mutations of the key sites with a 154% increase in pinene yield.
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20
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Xu J, Peng G, Xu J, Li Y, Tong L, Yang D. Probing of the plasticity of the active site in pinene synthase elucidates its potential evolutionary mechanism. PHYTOCHEMISTRY 2021; 181:112573. [PMID: 33142148 DOI: 10.1016/j.phytochem.2020.112573] [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: 06/27/2019] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 06/11/2023]
Abstract
Terpenes form a class of highly diverse natural products. The diversity of terpenes is created by terpene synthases. During the reaction, carbocation intermediates form and their rearrangement could lead to the formation of various products. Terpene synthases determine the final product profile by controlling the conformation of the intermediate or stabilizing the carbocation. Pinene synthase is a monoterpene synthase catalyzing the cyclization of geranyl pyrophosphate (GPP) to form pinene. Our study suggests that by mutating the aromatic residue F482 to Ala, Val, Ile and Thr, the enzyme can be converted to sabinene synthase, with more than 90% of its total terpene products becoming sabinene, which indicates the aromaticity of this residue is essential for stabilizing the pinyl carbocation. We also identified a mutation S491A that could cause an about 29% increase in the overall activity of the enzyme without altering its produce selectivity. Molecular dynamic simulation indicates this mutation could decrease the flexibility of the enzyme when it forms a complex with the pinyl carbocation. Our study suggests the active pocket of pinene synthase has a certain level of plasticity, making it relatively easy to change the product selectivity or overall activity. This property could have an important implication in the evolution of terpene synthases and thereby terpene diversity, as by changing a few residues an enzyme could synthesize a completely different terpene product in a significant amount, which allows selection to take place.
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Affiliation(s)
- Jingwei Xu
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Guanzu Peng
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Jinkun Xu
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yi Li
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Li Tong
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Dong Yang
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
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21
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Kariya K, Ube N, Ueno M, Teraishi M, Okumoto Y, Mori N, Ueno K, Ishihara A. Natural variation of diterpenoid phytoalexins in cultivated and wild rice species. PHYTOCHEMISTRY 2020; 180:112518. [PMID: 32950772 DOI: 10.1016/j.phytochem.2020.112518] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/02/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
Rice (Oryza sativa) leaves accumulate phytoalexins in response to pathogen attack. The major phytoalexins in rice are diterpenoids such as momilactones, phytocassanes, and oryzalexins. We analyzed the abundance of momilactones A and B and phytocassanes A and D in UV-light-irradiated leaves of cultivars from the World Rice Core Collection (WRC). Both types of phytoalexins were detected in most cultivars; however, their accumulated amounts varied greatly from cultivar to cultivar. The amounts of momilactones A and B tended to be higher in japonica cultivars than those in indica cultivars. However, the accumulated amounts of phytocassanes were not related to differences in subspecies. In addition, variation in phytoalexin content was observed for seven wild rice species. During the analysis of momilactone A in cultivars from the WRC, two unknown compounds were detected in'Jaguary' and 'Basilanon'. We isolated these compounds from UV-light-irradiated leaves and determined their structures. The compound isolated from 'Jaguary' was an isomer of momilactone A that had an abietane skeleton, while that from 'Basilanon' was di-dehydrogenated phytocassane A; these compounds were denoted as oryzalactone and phytocassane G. Oryzalactone accumulated in only three cultivars, whereas phytocassane G accumulated in almost all of the cultivars from the WRC. These findings indicate the existence of large natural variation in the phytoalexin composition in rice.
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Affiliation(s)
- Keisuke Kariya
- Graduate School of Sustainability Science, Tottori University, Tottori, 680-8553, Japan
| | - Naoki Ube
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan
| | - Makoto Ueno
- Faculty of Life and Environmental Science, Shimane University, Nishikawatsu 1060, Matsue, 690-8504, Japan
| | - Masayoshi Teraishi
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-Cho, Kyoto, 606-8502, Japan
| | - Yutaka Okumoto
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-Cho, Kyoto, 606-8502, Japan
| | - Naoki Mori
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-Cho, Kyoto, 606-8502, Japan
| | - Kotomi Ueno
- Faculty of Agriculture, Tottori University, Tottori, 680-8553, Japan
| | - Atsushi Ishihara
- Faculty of Agriculture, Tottori University, Tottori, 680-8553, Japan.
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22
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Tasnim S, Gries R, Mattsson J. Identification of Three Monofunctional Diterpene Synthases with Specific Enzyme Activities Expressed during Heartwood Formation in Western Redcedar ( Thuja plicata) Trees. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1018. [PMID: 32806789 PMCID: PMC7464036 DOI: 10.3390/plants9081018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/08/2020] [Accepted: 08/09/2020] [Indexed: 11/28/2022]
Abstract
Upon harvest, Western redcedar (WRC; Thuja plicata) trees have a high incidence and extent of heartwood rot. While monoterpenoids and lignans have been linked to rot resistance in this species, other specialized metabolites, such as diterpenes, are likely to contribute to rot resistance. Here we report the cloning and functional assessment of three putative diterpene synthase (TpdiTPS) genes expressed during heartwood formation in WRC. The predicted proteins of the three genes lack either of the two catalytically independent active sites typical of most diTPS, indicating monofunctional rather than bifunctional activity. To identify potential catalytic activities of these proteins, we expressed them in genetically engineered Escherichia coli strains that produce four potential substrates, geranylgeranyl diphosphate (GGDP), ent, syn, and normal stereoisomers of copalyl diphosphate (CDP). We found that TpdiTPS3 used GGDP to produce CDP. TpdiTPS2 used normal CDP to produce levopimaradiene. TpdiTPS1 showed stereoselectivity as it used normal CDP to produce sandaracopimaradiene and syn-CDP to produce syn-stemod-13(17)-ene. These genes and protein enzymatic activities have not been previously reported in WRC and provide an opportunity to assess their potential roles in heartwood rot resistance in this economically important species.
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Affiliation(s)
| | | | - Jim Mattsson
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada; (S.T.); (R.G.)
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23
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Raz K, Levi S, Gupta PK, Major DT. Enzymatic control of product distribution in terpene synthases: insights from multiscale simulations. Curr Opin Biotechnol 2020; 65:248-258. [PMID: 32679412 DOI: 10.1016/j.copbio.2020.06.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/03/2020] [Accepted: 06/07/2020] [Indexed: 11/25/2022]
Abstract
In this opinion, we review some recent work on terpene biosynthesis using multiscale simulation approaches, with special focus on contributions from our group. Terpene synthases generate terpenes employing rich carbocation chemistry, including highly specific ring formations, proton, hydride, methyl, and methylene migrations, followed by reaction quenching. In these enzymes, the main catalytic challenge is not rate enhancement, but rather control of intrinsically reactive carbocations and the resulting product distribution. Herein, we review multiscale simulations of selected mono-, sesqui-, and diterpene synthases. We point to the many tools adopted by terpene synthases to achieve correct substrate fold, carbocation formation, carbocation reaction environment, and reaction quenching. A better understanding of the toolbox employed by terpene synthases is expected to aid in the search for new enzymatic and biomimetic synthetic routes to natural and unnatural terpenes.
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Affiliation(s)
- Keren Raz
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Shani Levi
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Prashant Kumar Gupta
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel.
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Liang J, Wang L, Liu J, Shen Q, Fu J, Peters RJ, Wang Q. Probing Enzymatic Structure and Function in the Dihydroxylating Sesquiterpene Synthase ZmEDS. Biochemistry 2020; 59:2660-2666. [PMID: 32558549 DOI: 10.1021/acs.biochem.0c00395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Terpene synthases (TPSs) play a vital role in forming the complex hydrocarbon backbones that underlie terpenoid diversity. Notably, some TPSs can add water prior to terminating the catalyzed reaction, leading to hydroxyl groups, which are critical for biological activity. A particularly intriguing example of this is the maize (Zea mays) sesquiterpene TPS whose major product is eudesmanediol, ZmEDS. This production of dual hydroxyl groups is presumably enabled by protonation of the singly hydroxylated transient stable intermediate hedycaryol. To probe the enzymatic structure-function relationships underlying this unusual reaction, protein modeling and docking were used to direct mutagenesis of ZmEDS. Previously, an F303A mutant was shown to produce only hedycaryol, suggesting a role in protonation. Here this is shown to be dependent on the steric bulk positioning of hedycaryol, including a supporting role played by the nearby F299, rather than π-cation interaction. Among the additional residues investigated here, G411 at the conserved kink in helix G is of particular interest, as substitution of this leads to predominant production of the distinct (-)-valerianol, while substitution for the aliphatic I279 and V306 can lead to significant production of the alternative eudesmane-type diols 2,3-epi-cryptomeridiol and 3-epi-cryptomeridol, respectively. Altogether, nine residues that are important for this unusual reaction were investigated here, with the results not only emphasizing the importance of reactant positioning suggested by the stereospecificity observed among the various product types but also highlighting the potential role of the Mg2+-diphosphate complex as the general acid for the protonation-initiated (bi)cyclization of hedycaryol.
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Affiliation(s)
- Jin Liang
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.,Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Liping Wang
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Jiang Liu
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Qinqin Shen
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Jingye Fu
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Qiang Wang
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
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Bagnaresi P, Cattivelli L. Ab initio GO-based mining for non-tandem-duplicated functional clusters in three model plant diploid genomes. PLoS One 2020; 15:e0234782. [PMID: 32559249 PMCID: PMC7304597 DOI: 10.1371/journal.pone.0234782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/02/2020] [Indexed: 11/20/2022] Open
Abstract
A functional Non-Tandem Duplicated Cluster (FNTDC) is a group of non-tandem-duplicated genes that are located closer than expected by mere chance and have a role in the same biological function. The identification of secondary-compounds–related FNTDC has gained increased interest in recent years, but little ab-initio attempts aiming to the identification of FNTDCs covering all biological functions, including primary metabolism compounds, have been carried out. We report an extensive FNTDC dataset accompanied by a detailed assessment on parameters used for genome scanning and their impact on FNTDC detection. We propose 70% identity and 70% alignment coverage as intermediate settings to exclude tandem duplicated genes and a dynamic scanning window of 24 genes. These settings were applied to rice, arabidopsis and grapevine genomes to call for FNTDCs. Besides the best-known secondary metabolism clusters, we identified many FNTDCs associated to primary metabolism ranging from macromolecules synthesis/editing, TOR signalling, ubiquitination, proton and electron transfer complexes. Using the intermediate FNTDC setting parameters (at P-value 1e-6), 130, 70 and 140 candidate FNTDCs were called in rice, arabidopsis and grapevine, respectively, and 20 to 30% of GO tags associated to called FNTDC were common among the 3 genomes. The datasets developed along with this work provide a rich framework for pinpointing candidate FNTDCs reflecting all GO-BP tags covering both primary and secondary metabolism with large macromolecular complexes/metabolons as the most represented FNTDCs. Noteworthy, several FNTDCs are tagged with GOs referring to organelle-targeted multi-enzyme complex, a finding that suggest the migration of endosymbiont gene chunks towards nuclei could be at the basis of these class of candidate FNTDCs. Most FNTDC appear to have evolved prior of genome duplication events. More than one-third of genes interspersed/adjacent to called FNTDCs lacked any functional annotation; however, their co-localization may provide hints towards a candidate biological role.
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Affiliation(s)
- Paolo Bagnaresi
- CREA Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
- * E-mail:
| | - Luigi Cattivelli
- CREA Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
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26
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Ma LT, Lee YR, Tsao NW, Wang SY, Zerbe P, Chu FH. Biochemical characterization of diterpene synthases of Taiwania cryptomerioides expands the known functional space of specialized diterpene metabolism in gymnosperms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1254-1272. [PMID: 31448467 DOI: 10.1111/tpj.14513] [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: 06/14/2019] [Revised: 08/13/2019] [Accepted: 08/19/2019] [Indexed: 05/20/2023]
Abstract
Taiwania cryptomerioides is a monotypic gymnosperm species, valued for the high decay resistance of its wood. This durability has been attributed to the abundance of terpenoids, especially the major diterpenoid metabolite ferruginol, with antifungal and antitermite activity. Specialized diterpenoid metabolism in gymnosperms primarily recruits bifunctional class-I/II diterpene synthases (diTPSs), whereas monofunctional class-II and class-I enzymes operate in angiosperms. In this study, we identified a previously unrecognized group of monofunctional diTPSs in T. cryptomerioides, which suggests a distinct evolutionary divergence of the diTPS family in this species. Specifically, five monofunctional diTPS functions not previously observed in gymnosperms were characterized, including monofunctional class-II enzymes forming labda-13-en-8-ol diphosphate (LPP, TcCPS2) and (+)-copalyl diphosphate (CPP, TcCPS4), and three class-I diTPSs producing biformene (TcKSL1), levopimaradiene (TcKSL3) and phyllocladanol (TcKSL5), respectively. Methyl jasmonate (MeJA) elicited the accumulation of levopimaradiene and the corresponding biosynthetic diTPS genes, TcCPS4 and TcKSL3, is consistent with a possible role in plant defense. Furthermore, TcCPS4 and TcKSL3 are likely to contribute to abietatriene biosynthesis via levopimaradiene as an intermediate in ferruginol biosynthesis in Taiwania. In conclusion, this study provides deeper insight into the functional landscape and molecular evolution of specialized diterpenoid metabolism in gymnosperms as a basis to better understand the role of these metabolites in tree chemical defense.
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Affiliation(s)
- Li-Ting Ma
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, 10617, Taiwan
| | - Yi-Ru Lee
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, 10617, Taiwan
| | - Nai-Wen Tsao
- Department of Forestry, National Chung-Hsing University, Taichung, 402, Taiwan
| | - Sheng-Yang Wang
- Department of Forestry, National Chung-Hsing University, Taichung, 402, Taiwan
| | - Philipp Zerbe
- Department of Plant Biology, University of California at Davis, Davis, CA, 95616, USA
| | - Fang-Hua Chu
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, 10617, Taiwan
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27
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Jia M, Zhang Y, Siegel JB, Tantillo DJ, Peters RJ. Switching on a Nontraditional Enzymatic Base - Deprotonation by Serine in the ent-Kaurene Synthase from Bradyrhizobium japonicum. ACS Catal 2019; 9:8867-8871. [PMID: 32489716 DOI: 10.1021/acscatal.9b02783] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Terpene synthases often catalyze complex carbocation cascade reactions. It has been previously shown that single residue switches involving replacement of a key aliphatic residue with serine or threonine can "short-circuit" such reactions, presumed to act indirectly via dipole stabilization of intermediate carbocations. Here a similar switch was found in the structurally characterized ent-kaurene synthase from Bradyrhizobium japonicum. Application of a recently developed computational approach to terpene synthases, TerDockin, surprisingly indicates direct action of the introduced serine hydroxyl as a catalytic base. Notably, this model suggests alternative interpretation of previous results, and potential routes towards reengineering terpene synthase activity more generally.
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Affiliation(s)
- Meirong Jia
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Yue Zhang
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Justin B. Siegel
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
- Department of Biochemistry and Molecular Medicine, University of California-Davis, Davis, California 95616, United States
- Genome Center, University of California-Davis, Davis, California 95616, United States
| | - Dean J. Tantillo
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Reuben J. Peters
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
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28
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Jin B, Guo J, Tang J, Tong Y, Ma Y, Chen T, Wang Y, Shen Y, Zhao Y, Lai C, Cui G, Huang L. An alternative splicing alters the product outcome of a class I terpene synthase in Isodon rubescens. Biochem Biophys Res Commun 2019; 512:310-313. [PMID: 30890335 DOI: 10.1016/j.bbrc.2019.03.057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 03/10/2019] [Indexed: 10/27/2022]
Abstract
The labdane-related diterpenoids are an important superfamily of natural products. Their structural diversity mainly depends on diterpene synthases, which generate the hydrocarbon skeletal structures. Isodon rubescens contains an expanded family of class I terpene synthases with different functions. Here we report a novel class I terpene synthase cDNA (IrKSL3a) with loss of 18 nucleotides compared with the reported cDNA sequence (IrKSL3). Inspection of IrKSL3 genomic sequence indicated that IrKSL3a and IrKSL3 transcripts may be generated by an alternative splicing event that utilizes different 3' splice site. In vitro assays showed that IrKSL3a produced isopimaradiene and miltiradiene, while IrKSL3 only produced miltiradiene. Protein sequence alignment found the six residues encoded by the alternative exon was unique to IrKSL3, which are 17 residues away from the conserved DDXXD motif. A deletion mutant of IrKSL3 showed that maintaining two residues within the six-amino acid is sufficient for miltiradiene production, while the other mutants lost nearly all enzymatic function. Our results illustrated how product outcomes can be changed by alternative splicing, and further gave an interesting example for studying the loop conformation in tuning product outcome in class I terpene synthase.
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Affiliation(s)
- Baolong Jin
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China; State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Juan Guo
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Jinfu Tang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Yuru Tong
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Ying Ma
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Tong Chen
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Yanan Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Ye Shen
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Yujun Zhao
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Changjiangsheng Lai
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Guanghong Cui
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Luqi Huang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China; State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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29
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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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30
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Jia M, O’Brien TE, Zhang Y, Siegel JB, Tantillo DJ, Peters RJ. Changing Face: A Key Residue for the Addition of Water by Sclareol Synthase. ACS Catal 2018; 8:3133-3137. [PMID: 29713562 DOI: 10.1021/acscatal.8b00121] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Sclareol synthase from Salvia sclarea (SsSS) naturally acts on 8α-hydroxy-copalyl diphosphate (1), stereoselectively adding water to produce (13R)-sclareol (2a), and similarly yields hydroxylated products with manifold other such bicyclic diterpene precursors. Here a key residue for this addition of water was identified. Strikingly, substitution with glutamine switches stereochemical outcome with 1, leading to selective production of (13S)-sclareol (2b). Moreover, changes to the stereospecificity of water addition with the structurally closely-related substrate copalyl diphosphate (4) could be accomplished with alternative substitutions. Thus, this approach is expected to provide biosynthetic access to both epimers of 13-hydroxylated derivatives of manifold labdane-related diterpenes.
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Affiliation(s)
- Meirong Jia
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Terrence E. O’Brien
- Department of Chemistry, University of California−Davis, Davis, California 95616, United States
| | - Yue Zhang
- Department of Chemistry, University of California−Davis, Davis, California 95616, United States
| | - Justin B. Siegel
- Department of Chemistry, University of California−Davis, Davis, California 95616, United States
- Department of Biochemistry and Molecular Medicine, University of California−Davis, Davis, California 95616, United States
- Genome Center, University of California−Davis, Davis, California 95616, United States
| | - Dean J. Tantillo
- Department of Chemistry, University of California−Davis, Davis, California 95616, United States
| | - Reuben J. Peters
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
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31
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Roncero AM, Tobal IE, Moro RF, Díez D, Marcos IS. Halimane diterpenoids: sources, structures, nomenclature and biological activities. Nat Prod Rep 2018; 35:955-991. [DOI: 10.1039/c8np00016f] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Diterpenes with a halimane skeleton constitute a small group of natural products that can be biogenetically considered as being between labdane and clerodane diterpenoids.
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Affiliation(s)
- Alejandro M. Roncero
- Departamento de Química Orgánica
- Facultad de Ciencias Químicas
- Universidad de Salamanca
- 37008 Salamanca
- Spain
| | - Ignacio E. Tobal
- Departamento de Química Orgánica
- Facultad de Ciencias Químicas
- Universidad de Salamanca
- 37008 Salamanca
- Spain
| | - Rosalina F. Moro
- Departamento de Química Orgánica
- Facultad de Ciencias Químicas
- Universidad de Salamanca
- 37008 Salamanca
- Spain
| | - David Díez
- Departamento de Química Orgánica
- Facultad de Ciencias Químicas
- Universidad de Salamanca
- 37008 Salamanca
- Spain
| | - Isidro S. Marcos
- Departamento de Química Orgánica
- Facultad de Ciencias Químicas
- Universidad de Salamanca
- 37008 Salamanca
- Spain
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32
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Bozkurt E, Soares TA, Rothlisberger U. Can Biomimetic Zinc Compounds Assist a (3 + 2) Cycloaddition Reaction? A Theoretical Perspective. J Chem Theory Comput 2017; 13:6382-6390. [DOI: 10.1021/acs.jctc.7b00819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Esra Bozkurt
- Laboratory
of Computational Chemistry and Biochemistry LCBC, ISIC, FSB BSP, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Thereza A. Soares
- Laboratory
of Computational Chemistry and Biochemistry LCBC, ISIC, FSB BSP, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Department
of Fundamental Chemistry, Federal University of Pernambuco, Recife 50740-560, Brazil
| | - Ursula Rothlisberger
- Laboratory
of Computational Chemistry and Biochemistry LCBC, ISIC, FSB BSP, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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33
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Abstract
![]()
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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34
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Hansen NL, Nissen JN, Hamberger B. Two residues determine the product profile of the class II diterpene synthases TPS14 and TPS21 of Tripterygium wilfordii. PHYTOCHEMISTRY 2017; 138:52-56. [PMID: 28279524 DOI: 10.1016/j.phytochem.2017.02.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/16/2017] [Accepted: 02/22/2017] [Indexed: 05/22/2023]
Abstract
The medicinal plant Tripterygium wilfordii (Celastraceae) contains a pair of class II diterpene synthases (diTPS) of specialized labdane-type metabolism that, despite remarkably close homology, form strikingly different products. TwTPS21 catalyzes bicyclization of the linear C20 precursor geranylgeranyl diphosphate to ent-copal-8-ol diphosphate, while TwTPS14 forms kolavenyl diphosphate. To determine the amino acid signature controlling the functional divergence of the homologues, we modeled their structures based on an existing crystal structure of the Arabidopsis ent-copalyl diphosphate synthase, archetypal of diTPSs in general metabolism of gibberellin phytohormones. Of the residues differing between TwTPS21 and TwTPS14 two located to the predicted active site, and we hypothesized that these are responsible for the functional differentiation of the enzymes. Using site-directed mutagenesis, we generated a panel of six variants, where one, or both positions were exchanged between the enzymes. In coupled heterologous assays with a corresponding class I diTPS, TwTPS2, complete product interchange was observed in variants with both reciprocal mutations, while substitutions of either residue gave mixed product profiles. Two mutants, TwTPS14:Y265H and TwTPS21:A325V, also produced ent-copalyl diphosphate, highlighting the evolutionary potential of enzymes of this family to drive rapid diversification of plant diterpene biosynthesis through neo-functionalization. Our study contributes to the understanding of structure-function relation in plant class II diTPSs and complements previous mutational studies of Arabidopsis ent-copalyl diphosphate synthase with additional examples from the specialized metabolism of T. wilfordii.
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Affiliation(s)
- Nikolaj L Hansen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Denmark; Center for Synthetic Biology "bioSYNergy" and Copenhagen Plant Sciences Centre, Denmark
| | - Jakob N Nissen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Denmark; Center for Synthetic Biology "bioSYNergy" and Copenhagen Plant Sciences Centre, Denmark
| | - Björn Hamberger
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Denmark; Center for Synthetic Biology "bioSYNergy" and Copenhagen Plant Sciences Centre, Denmark.
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35
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Xu J, Ai Y, Wang J, Xu J, Zhang Y, Yang D. Converting S-limonene synthase to pinene or phellandrene synthases reveals the plasticity of the active site. PHYTOCHEMISTRY 2017; 137:34-41. [PMID: 28215610 DOI: 10.1016/j.phytochem.2017.02.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 01/25/2017] [Accepted: 02/11/2017] [Indexed: 05/27/2023]
Abstract
S-limonene synthase is a model monoterpene synthase that cyclizes geranyl pyrophosphate (GPP) to form S-limonene. It is a relatively specific enzyme as the majority of its products are composed of limonene. In this study, we converted it to pinene or phellandrene synthases after introducing N345A/L423A/S454A or N345I mutations. Further studies on N345 suggest the polarity of this residue plays a critical role in limonene production by stabilizing the terpinyl cation intermediate. If it is mutated to a non-polar residue, further cyclization or hydride shifts occurs so the carbocation migrates towards the pyrophosphate, leading to the production of pinene or phellandrene. On the other hand, mutant enzymes that still possess a polar residue at this position produce limonene as the major product. N345 is not the only polar residue that may stabilize the terpinyl cation because it is not strictly conserved among limonene synthases across species and there are also several other polar residues in this area. These residues could form a "polar pocket" that may collectively play this stabilizing role. Our study provides important insights into the catalytic mechanism of limonene synthases. Furthermore, it also has wider implications on the evolution of terpene synthases.
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Affiliation(s)
- Jinkun Xu
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875 China
| | - Ying Ai
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875 China
| | - Jianhui Wang
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875 China
| | - Jingwei Xu
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875 China
| | - Yongkang Zhang
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875 China
| | - Dong Yang
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875 China.
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36
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Pemberton TA, Chen M, Harris GG, Chou WKW, Duan L, Köksal M, Genshaft AS, Cane DE, Christianson DW. Exploring the Influence of Domain Architecture on the Catalytic Function of Diterpene Synthases. Biochemistry 2017; 56:2010-2023. [PMID: 28362483 DOI: 10.1021/acs.biochem.7b00137] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Terpenoid synthases catalyze isoprenoid cyclization reactions underlying the generation of more than 80,000 natural products. Such dramatic chemodiversity belies the fact that these enzymes generally consist of only three domain folds designated as α, β, and γ. Catalysis by class I terpenoid synthases occurs exclusively in the α domain, which is found with α, αα, αβ, and αβγ domain architectures. Here, we explore the influence of domain architecture on catalysis by taxadiene synthase from Taxus brevifolia (TbTS, αβγ), fusicoccadiene synthase from Phomopsis amygdali (PaFS, (αα)6), and ophiobolin F synthase from Aspergillus clavatus (AcOS, αα). We show that the cyclization fidelity and catalytic efficiency of the α domain of TbTS are severely compromised by deletion of the βγ domains; however, retention of the β domain preserves significant cyclization fidelity. In PaFS, we previously demonstrated that one α domain similarly influences catalysis by the other α domain [ Chen , M. , Chou , W. K. W. , Toyomasu , T. , Cane , D. E. , and Christianson , D. W. ( 2016 ) ACS Chem. Biol. 11 , 889 - 899 ]. Here, we show that the hexameric quaternary structure of PaFS enables cluster channeling. We also show that the α domains of PaFS and AcOS can be swapped so as to make functional chimeric αα synthases. Notably, both cyclization fidelity and catalytic efficiency are altered in all chimeric synthases. Twelve newly formed and uncharacterized C20 diterpene products and three C25 sesterterpene products are generated by these chimeras. Thus, engineered αβγ and αα terpenoid cyclases promise to generate chemodiversity in the greater family of terpenoid natural products.
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Affiliation(s)
- Travis A Pemberton
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Mengbin Chen
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Golda G Harris
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Wayne K W Chou
- Department of Chemistry, Brown University , Box H, Providence, Rhode Island 02912, United States
| | - Lian Duan
- Department of Chemistry, Brown University , Box H, Providence, Rhode Island 02912, United States
| | - Mustafa Köksal
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Alex S Genshaft
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - David E Cane
- Department of Chemistry, Brown University , Box H, Providence, Rhode Island 02912, 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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Chen X, Berim A, Dayan FE, Gang DR. A (-)-kolavenyl diphosphate synthase catalyzes the first step of salvinorin A biosynthesis in Salvia divinorum. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1109-1122. [PMID: 28204567 PMCID: PMC5441855 DOI: 10.1093/jxb/erw493] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Salvia divinorum (Lamiaceae) is an annual herb used by indigenous cultures of Mexico for medicinal and ritual purposes. The biosynthesis of salvinorin A, its major bioactive neo-clerodane diterpenoid, remains virtually unknown. This investigation aimed to identify the enzyme that catalyzes the first reaction of salvinorin A biosynthesis, the formation of (-)-kolavenyl diphosphate [(-)-KPP], which is subsequently dephosphorylated to afford (-)-kolavenol. Peltate glandular trichomes were identified as the major and perhaps exclusive site of salvinorin accumulation in S. divinorum. The trichome-specific transcriptome was used to identify candidate diterpene synthases (diTPSs). In vitro and in planta characterization of a class II diTPS designated as SdKPS confirmed its activity as (-)-KPP synthase and its involvement in salvinorin A biosynthesis. Mutation of a phenylalanine into histidine in the active site of SdKPS completely converts the product from (-)-KPP into ent-copalyl diphosphate. Structural elements were identified that mediate the natural formation of the neo-clerodane backbone by this enzyme and suggest how SdKPS and other diTPSs may have evolved from ent-copalyl diphosphate synthase.
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Affiliation(s)
- Xiaoyue Chen
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164,USA
| | - Anna Berim
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164,USA
| | - Franck E Dayan
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177, USA
| | - David R Gang
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164,USA
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Hare SR, Tantillo DJ. Dynamic behavior of rearranging carbocations - implications for terpene biosynthesis. Beilstein J Org Chem 2016; 12:377-90. [PMID: 27340434 PMCID: PMC4902080 DOI: 10.3762/bjoc.12.41] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/15/2016] [Indexed: 11/23/2022] Open
Abstract
This review describes unexpected dynamical behaviors of rearranging carbocations and the modern computational methods used to elucidate these aspects of reaction mechanisms. Unique potential energy surface topologies associated with these rearrangements have been discovered in recent years that are not only of fundamental interest, but also provide insight into the way Nature manipulates chemical space to accomplish specific chemical transformations. Cautions for analyzing both experimental and theoretical data on carbocation rearrangements are included throughout.
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Affiliation(s)
- Stephanie R Hare
- Department of Chemistry, University of California–Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Dean J Tantillo
- Department of Chemistry, University of California–Davis, 1 Shields Avenue, Davis, CA 95616, USA
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Identification of amino acid networks governing catalysis in the closed complex of class I terpene synthases. Proc Natl Acad Sci U S A 2016; 113:E958-67. [PMID: 26842837 DOI: 10.1073/pnas.1519680113] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Class I terpene synthases generate the structural core of bioactive terpenoids. Deciphering structure-function relationships in the reactive closed complex and targeted engineering is hampered by highly dynamic carbocation rearrangements during catalysis. Available crystal structures, however, represent the open, catalytically inactive form or harbor nonproductive substrate analogs. Here, we present a catalytically relevant, closed conformation of taxadiene synthase (TXS), the model class I terpene synthase, which simulates the initial catalytic time point. In silico modeling of subsequent catalytic steps allowed unprecedented insights into the dynamic reaction cascades and promiscuity mechanisms of class I terpene synthases. This generally applicable methodology enables the active-site localization of carbocations and demonstrates the presence of an active-site base motif and its dominating role during catalysis. It additionally allowed in silico-designed targeted protein engineering that unlocked the path to alternate monocyclic and bicyclic synthons representing the basis of a myriad of bioactive terpenoids.
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Cui G, Duan L, Jin B, Qian J, Xue Z, Shen G, Snyder JH, Song J, Chen S, Huang L, Peters RJ, Qi X. Functional Divergence of Diterpene Syntheses in the Medicinal Plant Salvia miltiorrhiza. PLANT PHYSIOLOGY 2015; 169:1607-18. [PMID: 26077765 PMCID: PMC4634056 DOI: 10.1104/pp.15.00695] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 06/10/2015] [Indexed: 05/18/2023]
Abstract
The medicinal plant Salvia miltiorrhiza produces various tanshinone diterpenoids that have pharmacological activities such as vasorelaxation against ischemia reperfusion injury and antiarrhythmic effects. Their biosynthesis is initiated from the general diterpenoid precursor (E,E,E)-geranylgeranyl diphosphate by sequential reactions catalyzed by copalyl diphosphate synthase (CPS) and kaurene synthase-like cyclases. Here, we report characterization of these enzymatic families from S. miltiorrhiza, which has led to the identification of unique pathways, including roles for separate CPSs in tanshinone production in roots versus aerial tissues (SmCPS1 and SmCPS2, respectively) as well as the unique production of ent-13-epi-manoyl oxide by SmCPS4 and S. miltiorrhiza kaurene synthase-like2 in floral sepals. The conserved SmCPS5 is involved in gibberellin plant hormone biosynthesis. Down-regulation of SmCPS1 by RNA interference resulted in substantial reduction of tanshinones, and metabolomics analysis revealed 21 potential intermediates, indicating a complex network for tanshinone metabolism defined by certain key biosynthetic steps. Notably, the correlation between conservation pattern and stereochemical product outcome of the CPSs observed here suggests a degree of correlation that, especially when combined with the identity of certain key residues, may be predictive. Accordingly, this study provides molecular insights into the evolutionary diversification of functional diterpenoids in plants.
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Affiliation(s)
- Guanghong Cui
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (G.C., L.D., Z.X., G.S., J.H.S., X.Q.);State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China (G.C., B.J., L.H.);Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China (J.Q., J.S., S.C.); andDepartment of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011 (R.J.P.)
| | - Lixin Duan
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (G.C., L.D., Z.X., G.S., J.H.S., X.Q.);State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China (G.C., B.J., L.H.);Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China (J.Q., J.S., S.C.); andDepartment of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011 (R.J.P.)
| | - Baolong Jin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (G.C., L.D., Z.X., G.S., J.H.S., X.Q.);State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China (G.C., B.J., L.H.);Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China (J.Q., J.S., S.C.); andDepartment of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011 (R.J.P.)
| | - Jun Qian
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (G.C., L.D., Z.X., G.S., J.H.S., X.Q.);State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China (G.C., B.J., L.H.);Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China (J.Q., J.S., S.C.); andDepartment of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011 (R.J.P.)
| | - Zheyong Xue
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (G.C., L.D., Z.X., G.S., J.H.S., X.Q.);State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China (G.C., B.J., L.H.);Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China (J.Q., J.S., S.C.); andDepartment of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011 (R.J.P.)
| | - Guoan Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (G.C., L.D., Z.X., G.S., J.H.S., X.Q.);State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China (G.C., B.J., L.H.);Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China (J.Q., J.S., S.C.); andDepartment of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011 (R.J.P.)
| | - John Hugh Snyder
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (G.C., L.D., Z.X., G.S., J.H.S., X.Q.);State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China (G.C., B.J., L.H.);Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China (J.Q., J.S., S.C.); andDepartment of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011 (R.J.P.)
| | - Jingyuan Song
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (G.C., L.D., Z.X., G.S., J.H.S., X.Q.);State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China (G.C., B.J., L.H.);Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China (J.Q., J.S., S.C.); andDepartment of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011 (R.J.P.)
| | - Shilin Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (G.C., L.D., Z.X., G.S., J.H.S., X.Q.);State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China (G.C., B.J., L.H.);Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China (J.Q., J.S., S.C.); andDepartment of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011 (R.J.P.)
| | - Luqi Huang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (G.C., L.D., Z.X., G.S., J.H.S., X.Q.);State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China (G.C., B.J., L.H.);Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China (J.Q., J.S., S.C.); andDepartment of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011 (R.J.P.)
| | - Reuben J Peters
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (G.C., L.D., Z.X., G.S., J.H.S., X.Q.);State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China (G.C., B.J., L.H.);Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China (J.Q., J.S., S.C.); andDepartment of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011 (R.J.P.)
| | - Xiaoquan Qi
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (G.C., L.D., Z.X., G.S., J.H.S., X.Q.);State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China (G.C., B.J., L.H.);Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China (J.Q., J.S., S.C.); andDepartment of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011 (R.J.P.)
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41
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Plant diterpene synthases: exploring modularity and metabolic diversity for bioengineering. Trends Biotechnol 2015; 33:419-28. [DOI: 10.1016/j.tibtech.2015.04.006] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 04/15/2015] [Accepted: 04/16/2015] [Indexed: 11/22/2022]
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Shaw JJ, Berbasova T, Sasaki T, Jefferson-George K, Spakowicz DJ, Dunican BF, Portero CE, Narváez-Trujillo A, Strobel SA. Identification of a fungal 1,8-cineole synthase from Hypoxylon sp. with specificity determinants in common with the plant synthases. J Biol Chem 2015; 290:8511-26. [PMID: 25648891 DOI: 10.1074/jbc.m114.636159] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Terpenes are an important and diverse class of secondary metabolites widely produced by fungi. Volatile compound screening of a fungal endophyte collection revealed a number of isolates in the family Xylariaceae, producing a series of terpene molecules, including 1,8-cineole. This compound is a commercially important component of eucalyptus oil used in pharmaceutical applications and has been explored as a potential biofuel additive. The genes that produce terpene molecules, such as 1,8-cineole, have been little explored in fungi, providing an opportunity to explore the biosynthetic origin of these compounds. Through genome sequencing of cineole-producing isolate E7406B, we were able to identify 11 new terpene synthase genes. Expressing a subset of these genes in Escherichia coli allowed identification of the hyp3 gene, responsible for 1,8-cineole biosynthesis, the first monoterpene synthase discovered in fungi. In a striking example of convergent evolution, mutational analysis of this terpene synthase revealed an active site asparagine critical for water capture and specificity during cineole synthesis, the same mechanism used in an unrelated plant homologue. These studies have provided insight into the evolutionary relationship of fungal terpene synthases to those in plants and bacteria and further established fungi as a relatively untapped source of this important and diverse class of compounds.
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Affiliation(s)
- Jeffrey J Shaw
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - Tetyana Berbasova
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - Tomoaki Sasaki
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - Kyra Jefferson-George
- the Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and
| | - Daniel J Spakowicz
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - Brian F Dunican
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - Carolina E Portero
- the Laboratorio de Biotecnología Vegetal, Pontificia Universidad Católica del Ecuador, Quito 17 01 21 84, Ecuador
| | - Alexandra Narváez-Trujillo
- the Laboratorio de Biotecnología Vegetal, Pontificia Universidad Católica del Ecuador, Quito 17 01 21 84, Ecuador
| | - Scott A Strobel
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520,
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Jackson AJ, Hershey DM, Chesnut T, Xu M, Peters RJ. Biochemical characterization of the castor bean ent-kaurene synthase(-like) family supports quantum chemical view of diterpene cyclization. PHYTOCHEMISTRY 2014; 103:13-21. [PMID: 24810014 PMCID: PMC4062354 DOI: 10.1016/j.phytochem.2014.04.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 04/04/2014] [Accepted: 04/10/2014] [Indexed: 05/20/2023]
Abstract
It has become apparent that plants have extensively diversified their arsenal of labdane-related diterpenoids (LRDs), in part via gene duplication and neo-functionalization of the ancestral ent-kaurene synthase (KS) required for gibberellin metabolism. For example, castor bean (Ricinus communis) was previously shown to produce an interesting set of biosynthetically related diterpenes, specifically ent-sandracopimaradiene, ent-beyerene, and ent-trachylobane, in addition to ent-kaurene, using four separate diterpene synthases, albeit these remain unidentified. Notably, despite mechanistic similarity of the underlying reaction to that catalyzed by KSs, ent-beyerene and ent-trachylobane synthases have not yet been identified. Given our interest in LRD biosynthesis, and the recent availability of the castor bean genome sequence, a synthetic biology approach was applied to biochemically characterize the four KS(-like) enzymes [KS(L)s] found in Ricinus communis [i.e., the RcKS(L)s]. In particular, using bacteria engineered to produce the relevant ent-copalyl diphosphate precursor and synthetic genes based on the predicted RcKS(L)s, although this ultimately required correction of a "splicing" error in one of the predicted genes, highlighting the dependence of such a synthetic biology approach on accurate gene sequences. Nevertheless, it is possible to assign each of the four RcKS(L)s to one of the previously observed diterpene synthase activities, providing access to functionally enzymes. Intriguingly, the product distribution of the RcKS(L)s seems to support the distinct diterpene synthase reaction mechanism proposed by quantum chemical calculations, rather than the classically proposed pathway.
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Affiliation(s)
- Alana J Jackson
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - David M Hershey
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Taylor Chesnut
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Meimei Xu
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Reuben J Peters
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
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Potter K, Criswell J, Zi J, Stubbs A, Peters RJ. Novel Product Chemistry from Mechanistic Analysis of
ent
‐Copalyl Diphosphate Synthases from Plant Hormone Biosynthesis. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402911] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Kevin Potter
- Dept. Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011 (USA)
| | - Jared Criswell
- Dept. Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011 (USA)
| | - Jiachen Zi
- Dept. Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011 (USA)
| | - Alisha Stubbs
- Dept. Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011 (USA)
| | - Reuben J. Peters
- Dept. Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011 (USA)
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Potter K, Criswell J, Zi J, Stubbs A, Peters RJ. Novel product chemistry from mechanistic analysis of ent-copalyl diphosphate synthases from plant hormone biosynthesis. Angew Chem Int Ed Engl 2014; 53:7198-202. [PMID: 24862907 DOI: 10.1002/anie.201402911] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/08/2014] [Indexed: 11/08/2022]
Abstract
An active-site water molecule coordinated by conserved histidine and asparagine residues seems to serve as the catalytic base in all ent-copalyl diphosphate synthases (CPSs). When these residues are substituted by alanine, the mutant CPSs produce stereochemically novel ent-8-hydroxy-CPP. Given the requisite presence of CPSs in all land plants for gibberellin phytohormone biosynthesis, such plasticity presumably underlies the observed extensive diversification of the resulting labdane-related diterpenoids.
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Affiliation(s)
- Kevin Potter
- Dept. Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011 (USA)
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Zi J, Mafu S, Peters RJ. To gibberellins and beyond! Surveying the evolution of (di)terpenoid metabolism. ANNUAL REVIEW OF PLANT BIOLOGY 2014; 65:259-86. [PMID: 24471837 PMCID: PMC4118669 DOI: 10.1146/annurev-arplant-050213-035705] [Citation(s) in RCA: 186] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The diterpenoids are classically defined by their composition--four isoprenyl units (20 carbons)--and are generally derived from [E,E,E]-geranylgeranyl diphosphate (GGPP). Such metabolism seems to be ancient and has been extensively diversified, with ∼12,000 diterpenoid natural products known. Particularly notable are the gibberellin phytohormones, whose requisite biosynthesis has provided a genetic reservoir that gave rise to not only a large superfamily of ∼7,000 diterpenoids but also, to some degree, all plant terpenoid natural products. This review focuses on the diterpenoids, particularly the defining biosynthetic characteristics of the major superfamilies defined by the cyclization and/or rearrangement of GGPP catalyzed by diterpene synthases/cyclases, although it also includes some discussion of the important subsequent elaboration in the few cases where sufficient molecular genetic information is available. It additionally addresses the array of biological activity providing the selective pressures that drive the observed gene family expansion and diversification, along with biosynthetic gene clustering.
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47
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Schmidt-Dannert C. Biosynthesis of terpenoid natural products in fungi. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 148:19-61. [PMID: 25414054 DOI: 10.1007/10_2014_283] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Tens of thousands of terpenoid natural products have been isolated from plants and microbial sources. Higher fungi (Ascomycota and Basidiomycota) are known to produce an array of well-known terpenoid natural products, including mycotoxins, antibiotics, antitumor compounds, and phytohormones. Except for a few well-studied fungal biosynthetic pathways, the majority of genes and biosynthetic pathways responsible for the biosynthesis of a small number of these secondary metabolites have only been discovered and characterized in the past 5-10 years. This chapter provides a comprehensive overview of the current knowledge on fungal terpenoid biosynthesis from biochemical, genetic, and genomic viewpoints. Enzymes involved in synthesizing, transferring, and cyclizing the prenyl chains that form the hydrocarbon scaffolds of fungal terpenoid natural products are systematically discussed. Genomic information and functional evidence suggest differences between the terpenome of the two major fungal phyla--the Ascomycota and Basidiomycota--which will be illustrated for each group of terpenoid natural products.
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Affiliation(s)
- Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minneapolis, MN, 55108, USA,
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Zerbe P, Hamberger B, Yuen MM, Chiang A, Sandhu HK, Madilao LL, Nguyen A, Hamberger B, Bach SS, Bohlmann J. Gene discovery of modular diterpene metabolism in nonmodel systems. PLANT PHYSIOLOGY 2013; 162:1073-91. [PMID: 23613273 PMCID: PMC3668041 DOI: 10.1104/pp.113.218347] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 04/21/2013] [Indexed: 05/18/2023]
Abstract
Plants produce over 10,000 different diterpenes of specialized (secondary) metabolism, and fewer diterpenes of general (primary) metabolism. Specialized diterpenes may have functions in ecological interactions of plants with other organisms and also benefit humanity as pharmaceuticals, fragrances, resins, and other industrial bioproducts. Examples of high-value diterpenes are taxol and forskolin pharmaceuticals or ambroxide fragrances. Yields and purity of diterpenes obtained from natural sources or by chemical synthesis are often insufficient for large-volume or high-end applications. Improvement of agricultural or biotechnological diterpene production requires knowledge of biosynthetic genes and enzymes. However, specialized diterpene pathways are extremely diverse across the plant kingdom, and most specialized diterpenes are taxonomically restricted to a few plant species, genera, or families. Consequently, there is no single reference system to guide gene discovery and rapid annotation of specialized diterpene pathways. Functional diversification of genes and plasticity of enzyme functions of these pathways further complicate correct annotation. To address this challenge, we used a set of 10 different plant species to develop a general strategy for diterpene gene discovery in nonmodel systems. The approach combines metabolite-guided transcriptome resources, custom diterpene synthase (diTPS) and cytochrome P450 reference gene databases, phylogenies, and, as shown for select diTPSs, single and coupled enzyme assays using microbial and plant expression systems. In the 10 species, we identified 46 new diTPS candidates and over 400 putatively terpenoid-related P450s in a resource of nearly 1 million predicted transcripts of diterpene-accumulating tissues. Phylogenetic patterns of lineage-specific blooms of genes guided functional characterization.
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Rational engineering of plasticity residues of sesquiterpene synthases from Artemisia annua: product specificity and catalytic efficiency. Biochem J 2013; 451:417-26. [DOI: 10.1042/bj20130041] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Most TPSs (terpene synthases) contain plasticity residues that are responsible for diversified terpene products and functional evolution, which provide a potential for improving catalytic efficiency. Artemisinin, a sesquiterpene lactone from Artemisia annua L., is widely used for malaria treatment and progress has been made in engineering the production of artemisinin or its precursors. In the present paper, we report a new sesquiterpene synthase from A. annua, AaBOS (A. annua α-bisabolol synthase), which has high sequence identity with AaADS (A. annua amorpha-4,11-diene synthase), a key enzyme in artemisinin biosynthesis. Comparative analysis of the two enzymes by domain-swapping and structure-based mutagenesis led to the identification of several plasticity residues, whose alteration changed the product profile of AaBOS to include γ-humulene as the major product. To elucidate the underlying mechanisms, we solved the crystal structures of AaBOS and a γ-humulene-producing AaBOS mutant (termed AaBOS-M2). Among the plasticity residues, position 399, located in the substrate-binding pocket, is crucial for both enzymes. In AaBOS, substitution of threonine for leucine (AaBOSL339T) is required for γ-humulene production; whereas in AaADS, replacing the threonine residue with serine (AaADST399S) resulted in a substantial increase in the activity of amorpha-4,11-diene production, probably as a result of accelerated product release. The present study demonstrates that substitution of plasticity residues has potential for improving catalytic efficiency of the enzyme.
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Hammer SC, Syrén PO, Seitz M, Nestl BM, Hauer B. Squalene hopene cyclases: highly promiscuous and evolvable catalysts for stereoselective CC and CX bond formation. Curr Opin Chem Biol 2013; 17:293-300. [PMID: 23485581 DOI: 10.1016/j.cbpa.2013.01.016] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 01/20/2013] [Accepted: 01/23/2013] [Indexed: 11/18/2022]
Abstract
We review here how the inherent promiscuous nature, as well as the evolvability of terpene cyclase enzymes enables new applications in chemistry. We mainly focus on squalene hopene cyclases, class II triterpene synthases that use a proton-initiated cationic polycyclization cascade to form carbopolycyclic products. We highlight recent findings to demonstrate that these enzymes are capable of activating different functionalities other than the traditional terminal isoprene C=C-group as well as being compatible with a wide range of nucleophiles beyond the 'ene-functionality'. Thus, squalene hopene cyclases demonstrate a great potential to be used as a toolbox for general Brønsted acid catalysis.
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Affiliation(s)
- Stephan C Hammer
- Institute of Technical Biochemistry, Universitaet Stuttgart, Allmandring 31, D-70569 Stuttgart, Germany
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