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Kwon M, Utomo JC, Park K, Pascoe CA, Chiorean S, Ngo I, Pelot KA, Pan CH, Kim SW, Zerbe P, Vederas JC, Ro DK. Cytochrome P450-Catalyzed Biosynthesis of a Dihydrofuran Neoclerodane in Magic Mint (Salvia divinorum). ACS Catal 2021. [DOI: 10.1021/acscatal.1c03691] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Moonhyuk Kwon
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N1N4, Canada
- Division of Applied Life Science (BK21 Four), ABC-RLRC, PMBBRC, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Joseph C. Utomo
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N1N4, Canada
| | - Keunwan Park
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung, 25451, Republic of Korea
| | - Cameron A. Pascoe
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr. NW, Edmonton, Alberta T6G 2G2, Canada
| | - Sorina Chiorean
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr. NW, Edmonton, Alberta T6G 2G2, Canada
| | - Iris Ngo
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N1N4, Canada
| | - Kyle A. Pelot
- Department of Plant Biology, University of California-Davis, 1 Shields Avenue, Davis, California 95616, United States
| | - Cheol-Ho Pan
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung, 25451, Republic of Korea
- Department of Biological Chemistry, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Seon-Won Kim
- Division of Applied Life Science (BK21 Four), ABC-RLRC, PMBBRC, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Philipp Zerbe
- Department of Plant Biology, University of California-Davis, 1 Shields Avenue, Davis, California 95616, United States
| | - John C. Vederas
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr. NW, Edmonton, Alberta T6G 2G2, Canada
| | - Dae-Kyun Ro
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N1N4, Canada
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Ma S, Mandalapu D, Wang S, Zhang Q. Biosynthesis of cyclopropane in natural products. Nat Prod Rep 2021; 39:926-945. [PMID: 34860231 DOI: 10.1039/d1np00065a] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Covering: 2012 to 2021Cyclopropane attracts wide interests in the fields of synthetic and pharmaceutical chemistry, and chemical biology because of its unique structural and chemical properties. This structural motif is widespread in natural products, and is usually essential for biological activities. Nature has evolved diverse strategies to access this structural motif, and increasing knowledge of the enzymes forming cyclopropane (i.e., cyclopropanases) has been revealed over the last two decades. Here, the scientific literature from the last two decades relating to cyclopropane biosynthesis is summarized, and the enzymatic cyclopropanations, according to reaction mechanism, which can be grouped into two major pathways according to whether the reaction involves an exogenous C1 unit from S-adenosylmethionine (SAM) or not, is discussed. The reactions can further be classified based on the key intermediates required prior to cyclopropane formation, which can be carbocations, carbanions, or carbon radicals. Besides the general biosynthetic pathways of the cyclopropane-containing natural products, particular emphasis is placed on the mechanism and engineering of the enzymes required for forming this unique structure motif.
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Affiliation(s)
- Suze Ma
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | | | - Shu Wang
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
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Alicandri E, Covino S, Sebastiani B, Paolacci AR, Badiani M, Manti F, Bonsignore CP, Sorgonà A, Ciaffi M. Diterpene Resin Acids and Olefins in Calabrian Pine ( Pinus nigra subsp. laricio (Poiret) Maire) Oleoresin: GC-MS Profiling of Major Diterpenoids in Different Plant Organs, Molecular Identification and Expression Analysis of Diterpene Synthase Genes. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112391. [PMID: 34834754 PMCID: PMC8622628 DOI: 10.3390/plants10112391] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/28/2021] [Accepted: 11/04/2021] [Indexed: 05/04/2023]
Abstract
A quali-quantitative analysis of diterpenoid composition in tissues obtained from different organs of Pinus nigra subsp. laricio (Poiret) Maire (Calabrian pine) was carried out. Diterpene resin acids were the most abundant diterpenoids across all the examined tissues. The same nine diterpene resin acids were always found, with the abietane type prevailing on the pimarane type, although their quantitative distribution was found to be remarkably tissue-specific. The scrutiny of the available literature revealed species specificity as well. A phylogeny-based approach allowed us to isolate four cDNAs coding for diterpene synthases in Calabrian pine, each of which belonging to one of the four groups into which the d3 clade of the plants' terpene synthases family can be divided. The deduced amino acid sequences allowed predicting that both monofunctional and bifunctional diterpene synthases are involved in the biosynthesis of diterpene resin acids in Calabrian pine. Transcript profiling revealed differential expression across the different tissues and was found to be consistent with the corresponding diterpenoid profiles. The isolation of the complete genomic sequences and the determination of their exon/intron structures allowed us to place the diterpene synthase genes from Calabrian pine on the background of current ideas on the functional evolution of diterpene synthases in Gymnosperms.
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Affiliation(s)
- Enrica Alicandri
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Loc. Feo di Vito, 89129 Reggio Calabria, Italy; (E.A.); (M.B.); (A.S.)
| | - Stefano Covino
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università della Tuscia, Via S. Camillo De Lellis, s.n.c., 01100 Viterbo, Italy; (S.C.); (A.R.P.)
| | - Bartolomeo Sebastiani
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy;
| | - Anna Rita Paolacci
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università della Tuscia, Via S. Camillo De Lellis, s.n.c., 01100 Viterbo, Italy; (S.C.); (A.R.P.)
| | - Maurizio Badiani
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Loc. Feo di Vito, 89129 Reggio Calabria, Italy; (E.A.); (M.B.); (A.S.)
| | - Francesco Manti
- Dipartimento di Patrimonio, Architettura e Urbanistica, Università Mediterranea di Reggio Calabria, Salita Melissari, 89124 Reggio Calabria, Italy; (F.M.); (C.P.B.)
| | - Carmelo Peter Bonsignore
- Dipartimento di Patrimonio, Architettura e Urbanistica, Università Mediterranea di Reggio Calabria, Salita Melissari, 89124 Reggio Calabria, Italy; (F.M.); (C.P.B.)
| | - Agostino Sorgonà
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Loc. Feo di Vito, 89129 Reggio Calabria, Italy; (E.A.); (M.B.); (A.S.)
| | - Mario Ciaffi
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università della Tuscia, Via S. Camillo De Lellis, s.n.c., 01100 Viterbo, Italy; (S.C.); (A.R.P.)
- Correspondence: ; Tel.: +39-0761-357-424; Fax: +39-0761-357-389
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Sangster JJ, Marshall JR, Turner NJ, Mangas-Sanchez J. New Trends and Future Opportunities in the Enzymatic Formation of C-C, C-N, and C-O bonds. Chembiochem 2021; 23:e202100464. [PMID: 34726813 PMCID: PMC9401909 DOI: 10.1002/cbic.202100464] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/29/2021] [Indexed: 01/04/2023]
Abstract
Organic chemistry provides society with fundamental products we use daily. Concerns about the impact that the chemical industry has over the environment is propelling major changes in the way we manufacture chemicals. Biocatalysis offers an alternative to other synthetic approaches as it employs enzymes, Nature's catalysts, to carry out chemical transformations. Enzymes are biodegradable, come from renewable sources, operate under mild reaction conditions, and display high selectivities in the processes they catalyse. As a highly multidisciplinary field, biocatalysis benefits from advances in different areas, and developments in the fields of molecular biology, bioinformatics, and chemical engineering have accelerated the extension of the range of available transformations (E. L. Bell et al., Nat. Rev. Meth. Prim. 2021, 1, 1-21). Recently, we surveyed advances in the expansion of the scope of biocatalysis via enzyme discovery and protein engineering (J. R. Marshall et al., Tetrahedron 2021, 82, 131926). Herein, we focus on novel enzymes currently available to the broad synthetic community for the construction of new C-C, C-N and C-O bonds, with the purpose of providing the non-specialist with new and alternative tools for chiral and sustainable chemical synthesis.
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Affiliation(s)
- Jack J Sangster
- Department of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - James R Marshall
- Department of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Nicholas J Turner
- Department of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Juan Mangas-Sanchez
- Institute of Chemical Synthesis and Homogeneous Catalysis, Spanish National Research Council (CSIC), Pedro Cerbuna 12, 50009, Zaragoza, Spain.,ARAID Foundation, Zaragoza, Spain
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55
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Keasling J, Garcia Martin H, Lee TS, Mukhopadhyay A, Singer SW, Sundstrom E. Microbial production of advanced biofuels. Nat Rev Microbiol 2021; 19:701-715. [PMID: 34172951 DOI: 10.1038/s41579-021-00577-w] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2021] [Indexed: 02/06/2023]
Abstract
Concerns over climate change have necessitated a rethinking of our transportation infrastructure. One possible alternative to carbon-polluting fossil fuels is biofuels produced by engineered microorganisms that use a renewable carbon source. Two biofuels, ethanol and biodiesel, have made inroads in displacing petroleum-based fuels, but their uptake has been limited by the amounts that can be used in conventional engines and by their cost. Advanced biofuels that mimic petroleum-based fuels are not limited by the amounts that can be used in existing transportation infrastructure but have had limited uptake due to costs. In this Review, we discuss engineering metabolic pathways to produce advanced biofuels, challenges with substrate and product toxicity with regard to host microorganisms and methods to engineer tolerance, and the use of functional genomics and machine learning approaches to produce advanced biofuels and prospects for reducing their costs.
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Affiliation(s)
- Jay Keasling
- Joint BioEnergy Institute, Emeryville, CA, USA. .,Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA. .,Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA. .,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Center for Biosustainability, Danish Technical University, Lyngby, Denmark. .,Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, China.
| | - Hector Garcia Martin
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,DOE Agile BioFoundry, Emeryville, CA, USA.,BCAM,Basque Center for Applied Mathematics, Bilbao, Spain.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Taek Soon Lee
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Eric Sundstrom
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Advanced Biofuels and Bioproducts Process Development Unit, Emeryville, CA, USA
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Gerasymenko I, Sheludko YV, Navarro Fuertes I, Schmidts V, Steinel L, Haumann E, Warzecha H. Engineering of a Plant Isoprenyl Diphosphate Synthase for Development of Irregular Coupling Activity. Chembiochem 2021; 23:e202100465. [PMID: 34672410 PMCID: PMC9297866 DOI: 10.1002/cbic.202100465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/20/2021] [Indexed: 11/17/2022]
Abstract
We performed mutagenesis on a regular isoprenyl diphosphate synthase (IDS), neryl diphosphate synthase from Solanum lycopersicum (SlNPPS), that has a structurally related analogue performing non‐head‐to‐tail coupling of two dimethylallyl diphosphate (DMAPP) units, lavandulyl diphosphate synthase from Lavandula x intermedia (LiLPPS). Wild‐type SlNPPS catalyses regular coupling of isopentenyl diphosphate (IPP) and DMAPP in cis‐orientation resulting in the formation of neryl diphosphate. However, if the enzyme is fed with DMAPP only, it is able to catalyse the coupling of two DMAPP units and synthesizes two irregular monoterpene diphosphates; their structures were elucidated by the NMR analysis of their dephosphorylation products. One of the alcohols is lavandulol. The second compound is the trans‐isomer of planococcol, the first example of an irregular cyclobutane monoterpene with this stereochemical configuration. The irregular activity of SlNPPS constitutes 0.4 % of its regular activity and is revealed only if the enzyme is supplied with DMAPP in the absence of IPP. The exchange of asparagine 88 for histidine considerably enhanced the non‐head‐to‐tail coupling. While still only observed in the absence of IPP, irregular activity of the mutant reaches 13.1 % of its regular activity. The obtained results prove that regular IDS are promising starting points for protein engineering aiming at the development of irregular activities and leading to novel monoterpene structures.
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Affiliation(s)
- Iryna Gerasymenko
- Technische Universität Darmstadt, Plant Biotechnology and Metabolic Engineering, Schnittspahnstraße 4, 64287, Darmstadt, Germany.,Centre for Synthetic Biology, Technical University of Darmstadt, 64287, Darmstadt, Germany
| | - Yuriy V Sheludko
- Technische Universität Darmstadt, Plant Biotechnology and Metabolic Engineering, Schnittspahnstraße 4, 64287, Darmstadt, Germany.,Centre for Synthetic Biology, Technical University of Darmstadt, 64287, Darmstadt, Germany.,Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 4, 64287, Darmstadt, Germany
| | - Ismael Navarro Fuertes
- Ecología y Protección Agrícola SL, Pol. Ind. Ciutat de Carlet, 46240, Carlet, Valencia, Spain
| | - Volker Schmidts
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 4, 64287, Darmstadt, Germany
| | - Lara Steinel
- Technische Universität Darmstadt, Plant Biotechnology and Metabolic Engineering, Schnittspahnstraße 4, 64287, Darmstadt, Germany.,Centre for Synthetic Biology, Technical University of Darmstadt, 64287, Darmstadt, Germany
| | - Elisabeth Haumann
- Technische Universität Darmstadt, Plant Biotechnology and Metabolic Engineering, Schnittspahnstraße 4, 64287, Darmstadt, Germany.,Centre for Synthetic Biology, Technical University of Darmstadt, 64287, Darmstadt, Germany
| | - Heribert Warzecha
- Technische Universität Darmstadt, Plant Biotechnology and Metabolic Engineering, Schnittspahnstraße 4, 64287, Darmstadt, Germany.,Centre for Synthetic Biology, Technical University of Darmstadt, 64287, Darmstadt, Germany
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Das A, Begum K, Akhtar S, Ahmed R, Kulkarni R, Banu S. Genome-wide detection and classification of terpene synthase genes in Aquilaria agallochum. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1711-1729. [PMID: 34539112 PMCID: PMC8405786 DOI: 10.1007/s12298-021-01040-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/28/2021] [Accepted: 07/23/2021] [Indexed: 06/05/2023]
Abstract
Agarwood, one of the precious woods in the globe, is produced by Aquilaria plant species during an upshot of wounding and infection. Produced as a defence response, the dark, fragrant resin gets secreted in the plant's duramen, which is impregnated with fragrant molecules with the due course. Agarwood has gained worldwide popularity due to its high aromatic oil, fragrance, and pharmaceutical value, which makes it highly solicited by numerous industries. Predominant chemical constituents of agarwood, sesquiterpenoids, and 2-(2-phenylethyl) chromones have been scrutinized to comprehend the scientific nature of the fragrant wood and develop novel products. However, the genes involved in the biosynthesis of these aromatic compounds are still not comprehensively studied in Aquilaria. In this study, publicly available genomic and transcriptomics data of Aquilaria agallochum were integrated to identify putative functional terpene synthase genes (TPSs). The in silico study enabled us to identify ninety-six TPSs, of which thirty-nine full-length genes were systematically classified into TPS-a, TPS-b, TPS-c, TPS-e, TPS-f, and TPS-g subfamilies based on their gene structure, conserve motif, and phylogenetic comparison with TPSs from other plant species. Analysis of the cis-regulatory elements present upstream of AaTPSs revealed their association with hormone, stress and light responses. In silico expression studies detected their up-regulation in stress induced tissue. This study provides a basic understanding of terpene synthase gene repertoire in Aquilaria agallochum and unlatches opportunities for the biochemical characterization and biotechnological exploration of these genes. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01040-z.
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Affiliation(s)
- Ankur Das
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam 781014 India
| | - Khaleda Begum
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam 781014 India
| | - Suraiya Akhtar
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam 781014 India
| | - Raja Ahmed
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam 781014 India
| | - Ram Kulkarni
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune, India
| | - Sofia Banu
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam 781014 India
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58
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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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Systematic mining of fungal chimeric terpene synthases using an efficient precursor-providing yeast chassis. Proc Natl Acad Sci U S A 2021; 118:2023247118. [PMID: 34257153 PMCID: PMC8307374 DOI: 10.1073/pnas.2023247118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Chimeric terpene synthases, termed PTTSs, are a unique family of enzymes occurring only in fungi. Characterizing PTTSs is challenging due to the complex reactions they catalyze and the structural complexity of their products. Here, by devising an efficient precursor-providing yeast chassis and incorporating a high-throughput automated platform, we identified 34 active PTTSs, which was considerably more than the number of known functional PTTSs. This effective and rapid pipeline can be employed for the characterization of other PTTSs or related terpenoid biosynthetic enzymes. By systematically analyzing the presence/absence of PTTS genes together with phylogenetic analysis, the ancestral PTTS gene was inferred to have undergone duplication and functional divergence, which led to the development of two distinct cyclization mechanisms. Chimeric terpene synthases, which consist of C-terminal prenyltransferase (PT) and N-terminal class I terpene synthase (TS) domains (termed PTTSs here), is unique to fungi and produces structurally diverse di- and sesterterpenes. Prior to this study, 20 PTTSs had been functionally characterized. Our understanding of the origin and functional evolution of PTTS genes is limited. Our systematic search of sequenced fungal genomes among diverse taxa revealed that PTTS genes were restricted to Dikarya. Phylogenetic findings indicated different potential models of the origin and evolution of PTTS genes. One was that PTTS genes originated in the common Dikarya ancestor and then underwent frequent gene loss among various subsequent lineages. To understand their functional evolution, we selected 74 PTTS genes for biochemical characterization in an efficient precursor-providing yeast system employing chassis-based, robot-assisted, high-throughput automatic assembly. We found 34 PTTS genes that encoded active enzymes and collectively produced 24 di- and sesterterpenes. About half of these di- and sesterterpenes were also the products of the 20 known PTTSs, indicating functional conservation, whereas the PTTS products included the previously unknown sesterterpenes, sesterevisene (1), and sesterorbiculene (2), suggesting that a diversity of PTTS products awaits discovery. Separating functional PTTSs into two monophyletic groups implied that an early gene duplication event occurred during the evolution of the PTTS family followed by functional divergence with the characteristics of distinct cyclization mechanisms.
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Transcriptome sequencing and functional characterization of new sesquiterpene synthases from Curcuma wenyujin. Arch Biochem Biophys 2021; 709:108986. [PMID: 34252391 DOI: 10.1016/j.abb.2021.108986] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/22/2021] [Accepted: 07/08/2021] [Indexed: 12/13/2022]
Abstract
Tubers of Curcuma wenyujin are rich in essential oils, mainly various sesquiterpenes, showing antibacterial, anti-viral and anti-tumor effects. However, the molecular mechanism of C. wenyujin is deficient and related sesquiterpene synthases are still unclear. In this study, the transcriptome data of tubers and leaves from C. wenyujin were obtained and assembled into 78 092 unigenes. Of them, 244 unigenes were predicted to be involved in terpenoid biosynthesis while 131 unigenes were categorized as the "Terpenoid backbone biosynthesis" (TBB) term. Twenty-two unigenes possessed terpene synthase domain; five were predicted to be sesquiterpene synthases. Of the 208 unigenes annotated as cytochromes P450, 8 unigenes with full-length coding sequences were part of the CYP71 clade that primarily may perform hydroxylations of specialized metabolites. Furthermore, Ten DEGs related to the C5 precursor supply and sesquiterpene synthesis were validated by Real-time PCR; that showed a close correspondence with transcriptome sequence. A novel germacrene B synthase (CwGBS) and α-santalene synthase (CwSS) were identified in metabolically engineering E. coli. This study provided the first de novo transcriptome comparative analysis of leaf and tuber tissues from C. wenyujin, aiming to understand genetic mechanisms. Key genes involved in the biosynthesis of sesquiterpene will help for revealing the underlying mechanisms of C. wenyujin.
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Li RS, Zhu JH, Guo D, Li HL, Wang Y, Ding XP, Mei WL, Chen ZB, Dai HF, Peng SQ. Genome-wide identification and expression analysis of terpene synthase gene family in Aquilaria sinensis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 164:185-194. [PMID: 34004556 DOI: 10.1016/j.plaphy.2021.04.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/24/2021] [Indexed: 06/12/2023]
Abstract
Agarwood is the resinous portion of Aquilaria trees, and has been widely used as medicine and incense. Sesquiterpenes are the main chemical characteristic constituents of agarwood. Terpene synthase (TPS) is a critical enzyme responsible for biosynthesis of sesquiterpene compounds. However, limited information is available on genome-wide identification and characterization of the TPS family in Aquilaria trees. In this study, TPS gene family was identified and characterized in Aquilaria sinensis by bioinformatics methods. The expression of those genes was analyzed by RNA-seq and quantitative real-time PCR. Transcription factors regulating TPS gene expression were identified by yeast one-hybrid and dual-luciferase assay. In total, 26 AsTPS genes (AsTPS1-AsTPS26) were identified, which were classified into five subgroups. Many putative cis-elements putatively involved in stresses and phytohormones (especially jasmonic acid) were identified in the promoter regions of AsTPSs, suggesting that AsTPSs genes may be regulated by stresses and jasmonic acid. Expression analysis revealed seven TPS genes encoding sesquiterpene synthetases were induced by wounding and methyl jasmonic acid (MeJA), which may be related to sesquiterpene biosynthesis. By yeast one-hybrid screening, a ERF transcription factor AsERF1 was identified to interact with the AsTPS1 promoter. Subcellular localization analysis indicated AsERF1 was a nucleus-localized protein. Transient transfection of AsERF1 in leaves of Nicotiana benthamiana significantly enhanced the promoter activation of AsTPS1, suggesting AsERF1 may participate in sesquiterpene biosynthesis by regulating AsTPS1 expression. These data generated in this study provide a foundation for future studies on functional roles and regulation mechanisms of AsTPS in sesquiterpene biosynthesis and agarwood formation.
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Affiliation(s)
- Rong-Shuang Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China; College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163000, China
| | - Jia-Hong Zhu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Dong Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Hui-Liang Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Ying Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Xu-Po Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Wen-Li Mei
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Zhi-Bao Chen
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163000, China; College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, China; Shenzhen Research Institute, Guangdong Ocean University, Shenzhen, 518108, China.
| | - Hao-Fu Dai
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
| | - Shi-Qing Peng
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
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Liang D, Li W, Yan X, Caiyin Q, Zhao G, Qiao J. Molecular and Functional Evolution of the Spermatophyte Sesquiterpene Synthases. Int J Mol Sci 2021; 22:ijms22126348. [PMID: 34198531 PMCID: PMC8232007 DOI: 10.3390/ijms22126348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/07/2021] [Accepted: 06/10/2021] [Indexed: 12/23/2022] Open
Abstract
Sesquiterpenes are important defense and signal molecules for plants to adapt to the environment, cope with stress, and communicate with the outside world, and their evolutionary history is closely related to physiological functions. In this study, the information of plant sesquiterpene synthases (STSs) with identified functions were collected and sorted to form a dataset containing about 500 members. The phylogeny of spermatophyte functional STSs was constructed based on the structural comparative analysis to reveal the sequence–structure–function relationships. We propose the evolutionary history of plant sesquiterpene skeletons, from chain structure to small rings, followed by large rings for the first time and put forward a more detailed function-driven hypothesis. Then, the evolutionary origins and history of spermatophyte STSs are also discussed. In addition, three newly identified STSs CaSTS2, CaSTS3, and CaSTS4 were analyzed in this functional evolutionary system, and their germacrene D products were consistent with the functional prediction. This demonstrates an application of the structure-based phylogeny in predicting STS function. This work will help us to understand evolutionary patterns and dynamics of plant sesquiterpenes and STSs and screen or design STSs with specific product profiles as functional elements for synthetic biology application.
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Affiliation(s)
- Dongmei Liang
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (D.L.); (W.L.); (X.Y.); (Q.C.); (G.Z.)
- Key Laboratory of Systems Bioengineering, Tianjin University, Ministry of Education, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Weiguo Li
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (D.L.); (W.L.); (X.Y.); (Q.C.); (G.Z.)
- Key Laboratory of Systems Bioengineering, Tianjin University, Ministry of Education, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Xiaoguang Yan
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (D.L.); (W.L.); (X.Y.); (Q.C.); (G.Z.)
- Key Laboratory of Systems Bioengineering, Tianjin University, Ministry of Education, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Qinggele Caiyin
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (D.L.); (W.L.); (X.Y.); (Q.C.); (G.Z.)
- Key Laboratory of Systems Bioengineering, Tianjin University, Ministry of Education, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Guangrong Zhao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (D.L.); (W.L.); (X.Y.); (Q.C.); (G.Z.)
- Key Laboratory of Systems Bioengineering, Tianjin University, Ministry of Education, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Jianjun Qiao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (D.L.); (W.L.); (X.Y.); (Q.C.); (G.Z.)
- Key Laboratory of Systems Bioengineering, Tianjin University, Ministry of Education, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology, Tianjin University, Ministry of Education, Tianjin 300072, China
- Correspondence: ; Tel.: +86-22-8740-2107
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Chen R, Bu Y, Ren J, Pelot KA, Hu X, Diao Y, Chen W, Zerbe P, Zhang L. Discovery and modulation of diterpenoid metabolism improves glandular trichome formation, artemisinin production and stress resilience in Artemisia annua. THE NEW PHYTOLOGIST 2021; 230:2387-2403. [PMID: 33740256 DOI: 10.1111/nph.17351] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 03/11/2021] [Indexed: 05/27/2023]
Abstract
Plants synthesize diverse diterpenoids with numerous functions in organ development and stress resistance. However, the role of diterpenoids in glandular trichome (GT) development and GT-localized biosynthesis in plants remains unknown. Here, the identification of 10 diterpene synthases (diTPSs) revealed the diversity of diterpenoid biosynthesis in Artemisia annua. Protein-protein interactions (PPIs) between AaKSL1 and AaCPS2 in the plastids highlighted their potential functions in modulating metabolic flux to gibberellins (GAs) or ent-isopimara-7,15-diene-derived metabolites (IDMs) through metabolic engineering. A phenotypic analysis of transgenic plants suggested a complex repertoire of diterpenoids in Artemisia annua with important roles in GT formation, artemisinin accumulation and stress resilience. Metabolic engineering of diterpenoids simultaneously increased the artemisinin yield and stress resistance. Transcriptome and metabolic profiling suggested that bioactive GA4 /GA1 promote GT formation. Collectively, these results expand our knowledge of diterpenoids and show the potential of diterpenoids to simultaneously improve both the GT-localized metabolite yield and stress resistance, in planta.
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Affiliation(s)
- Ruibing Chen
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai, 200433, China
| | - Yuejuan Bu
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai, 200433, China
| | - Junze Ren
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai, 200433, China
| | - Kyle A Pelot
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
| | - Xiangyang Hu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Yong Diao
- School of Medicine, Huaqiao University, Quanzhou, 362021, China
| | - Wansheng Chen
- Department of Pharmacy, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Philipp Zerbe
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
| | - Lei Zhang
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai, 200433, China
- Biomedical Innovation R&D Center, School of Medicine, Shanghai University, Shanghai, 200444, China
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Hurgobin B, Tamiru‐Oli M, Welling MT, Doblin MS, Bacic A, Whelan J, Lewsey MG. Recent advances in Cannabis sativa genomics research. THE NEW PHYTOLOGIST 2021; 230:73-89. [PMID: 33283274 PMCID: PMC7986631 DOI: 10.1111/nph.17140] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/27/2020] [Indexed: 05/06/2023]
Abstract
Cannabis (Cannabis sativa L.) is one of the oldest cultivated plants purported to have unique medicinal properties. However, scientific research of cannabis has been restricted by the Single Convention on Narcotic Drugs of 1961, an international treaty that prohibits the production and supply of narcotic drugs except under license. Legislation governing cannabis cultivation for research, medicinal and even recreational purposes has been relaxed recently in certain jurisdictions. As a result, there is now potential to accelerate cultivar development of this multi-use and potentially medically useful plant species by application of modern genomics technologies. Whilst genomics has been pivotal to our understanding of the basic biology and molecular mechanisms controlling key traits in several crop species, much work is needed for cannabis. In this review we provide a comprehensive summary of key cannabis genomics resources and their applications. We also discuss prospective applications of existing and emerging genomics technologies for accelerating the genetic improvement of cannabis.
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Affiliation(s)
- Bhavna Hurgobin
- La Trobe Institute for Agriculture and FoodDepartment of Animal, Plant and Soil SciencesSchool of Life SciencesLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
- Australian Research Council Research Hub for Medicinal AgricultureLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
| | - Muluneh Tamiru‐Oli
- La Trobe Institute for Agriculture and FoodDepartment of Animal, Plant and Soil SciencesSchool of Life SciencesLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
- Australian Research Council Research Hub for Medicinal AgricultureLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
| | - Matthew T. Welling
- La Trobe Institute for Agriculture and FoodDepartment of Animal, Plant and Soil SciencesSchool of Life SciencesLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
- Australian Research Council Research Hub for Medicinal AgricultureLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
| | - Monika S. Doblin
- La Trobe Institute for Agriculture and FoodDepartment of Animal, Plant and Soil SciencesSchool of Life SciencesLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
- Australian Research Council Research Hub for Medicinal AgricultureLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
| | - Antony Bacic
- La Trobe Institute for Agriculture and FoodDepartment of Animal, Plant and Soil SciencesSchool of Life SciencesLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
- Australian Research Council Research Hub for Medicinal AgricultureLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
| | - James Whelan
- La Trobe Institute for Agriculture and FoodDepartment of Animal, Plant and Soil SciencesSchool of Life SciencesLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
- Australian Research Council Research Hub for Medicinal AgricultureLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
- Australian Research Council Centre of Excellence for Plant Energy BiologyLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
| | - Mathew G. Lewsey
- La Trobe Institute for Agriculture and FoodDepartment of Animal, Plant and Soil SciencesSchool of Life SciencesLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
- Australian Research Council Research Hub for Medicinal AgricultureLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
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Brown R, Jia M, Peters RJ. A pair of threonines mark ent-kaurene synthases for phytohormone biosynthesis. PHYTOCHEMISTRY 2021; 184:112672. [PMID: 33524857 PMCID: PMC7990685 DOI: 10.1016/j.phytochem.2021.112672] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/06/2021] [Accepted: 01/13/2021] [Indexed: 05/27/2023]
Abstract
All land plants (embryophytes) must contain an ent-kaurene synthase (KS), as the ability to produce this olefin from ent-copalyl diphosphate (ent-CPP) is required for phytohormone biosynthesis. These KSs have frequently given rise to other class I diterpene synthases that catalyze distinct reactions for more specialized plant metabolism. Indeed, the prevalence of such gene duplication and neofunctionalization has obscured phylogenetic assignment of function. Here a pair of threonines is found to be conserved in all land plant KS involved in phytohormone biosynthesis, and their role in enzyme function investigated. Surprisingly, these threonines are not required, nor even particularly important for efficient production of ent-kaurene from ent-CPP. In addition, these threonines do not seem to affect protein structure or stability. Moreover, the absence of codon bias and positioning within an intron do not support a role in transcription or translation either. Despite their lack of apparent function, this pair of threonines are nevertheless completely conserved in all embryophyte KS from phytohormone biosynthesis. Thus, regardless of exact role, this serves as a diagnostic mark for such KS, enabling more confident distinction of these critical enzymes.
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Affiliation(s)
- Reid Brown
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA, 50011, United States
| | - Meirong Jia
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA, 50011, United States
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA, 50011, United States.
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Ma LT, Wang CH, Hon CY, Lee YR, Chu FH. Discovery and characterization of diterpene synthases in Chamaecyparis formosensis Matsum. which participated in an unprecedented diterpenoid biosynthesis route in conifer. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 304:110790. [PMID: 33568294 DOI: 10.1016/j.plantsci.2020.110790] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/24/2020] [Accepted: 12/06/2020] [Indexed: 05/20/2023]
Abstract
Chamaecyparis formosensis Matsum. is an endemic and precious coniferous species of Taiwan, and is known for a high abundance of specialized metabolites, which contributes to the excellent timber durability. Several terpenoids were identified and isolated from C. formosensis wood and needles, and exhibit anti-fungal and anti-bacterial bioactivities, which may participate in plant defense against pathogens. In various identified compounds, not only cadinene and ferruginol, were identified in C. formosensis extracts but also unique diterpenoids, which include pisferal, totarol, and derivates of isoabienol. To understand the biosynthesis of these specific diterpenoids, we conducted a series of functional characterization of the C. formosensis diterpene synthases (CfdiTPSs), which participate in skeleton formation and differentiation of diterpenes. In this study, we identified eight diTPSs from C. formosensis transcriptome, and they all contain either class I or class II motif, which indicates they are all monofunctional enzymes. These candidates consist of three class II diTPSs and five class I diTPSs, and after conducting in vivo and in vitro assays, class II diTPS CfCPS1 was characterized as a (+)-copalyl diphosphate synthase ((+)-CPS), and class I diTPSs CfKSL1 could further convert (+)-copalyl diphosphate ((+)-CPP) to levopimaradiene. Meanwhile, CfKSL1 also accepted labda-13-en-8-ol diphosphate (LPP) as substrate and formed monoyl oxide. Another class I diTPS, CfKSL4, exhibits a strong enzymatic ability of isoabienol synthase, which is firstly reported in conifer. This finding provides potential participants in the biosynthesis of unique diterpenoids, and with this knowledge, we can further expand our understanding of diterpenoid metabolism in Cupressaceae and their potential role in plant defense.
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Affiliation(s)
- Li-Ting Ma
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, 10617, Taiwan
| | - Chang-Hsin Wang
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, 10617, Taiwan
| | - Chong-Yao Hon
- 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
| | - Fang-Hua Chu
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, 10617, Taiwan.
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Durairaj J, Melillo E, Bouwmeester HJ, Beekwilder J, de Ridder D, van Dijk ADJ. Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases. PLoS Comput Biol 2021; 17:e1008197. [PMID: 33750949 PMCID: PMC8016262 DOI: 10.1371/journal.pcbi.1008197] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 04/01/2021] [Accepted: 02/15/2021] [Indexed: 12/19/2022] Open
Abstract
Sesquiterpene synthases (STSs) catalyze the formation of a large class of plant volatiles called sesquiterpenes. While thousands of putative STS sequences from diverse plant species are available, only a small number of them have been functionally characterized. Sequence identity-based screening for desired enzymes, often used in biotechnological applications, is difficult to apply here as STS sequence similarity is strongly affected by species. This calls for more sophisticated computational methods for functionality prediction. We investigate the specificity of precursor cation formation in these elusive enzymes. By inspecting multi-product STSs, we demonstrate that STSs have a strong selectivity towards one precursor cation. We use a machine learning approach combining sequence and structure information to accurately predict precursor cation specificity for STSs across all plant species. We combine this with a co-evolutionary analysis on the wealth of uncharacterized putative STS sequences, to pinpoint residues and distant functional contacts influencing cation formation and reaction pathway selection. These structural factors can be used to predict and engineer enzymes with specific functions, as we demonstrate by predicting and characterizing two novel STSs from Citrus bergamia.
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Affiliation(s)
- Janani Durairaj
- Bioinformatics Group, Department of Plant Sciences, Wageningen University and Research, Wageningen, The Netherlands
| | | | - Harro J. Bouwmeester
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Jules Beekwilder
- Bioscience, Wageningen Plant Research, Wageningen University and Research, Wageningen, The Netherlands
- Laboratory of Plant Physiology, Department of Plant Sciences, Wageningen University and Research, Wageningen, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Department of Plant Sciences, Wageningen University and Research, Wageningen, The Netherlands
| | - Aalt D. J. van Dijk
- Bioinformatics Group, Department of Plant Sciences, Wageningen University and Research, Wageningen, The Netherlands
- Biometris, Department of Plant Sciences, Wageningen University and Research, Wageningen, The Netherlands
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Yan X, Li W, Liang D, Zhao G, Caiyin Q, Qiao J. Comparative transcriptome analysis of sesquiterpene biosynthesis and functional characterization of sesquiterpene synthases in Leonurus sibiricus L. PLANTA 2021; 253:71. [PMID: 33604817 DOI: 10.1007/s00425-021-03586-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
Two sesquiterpene synthases were identified through comparative transcriptome analysis of Leonurus sibiricus. LsSqTPS2 could produce high titer of δ-cadinene in vivo which suggests the terpene specificity of L. sibiricus. Leonurus sibiricus L., a medicinal herb, is widely used in China due to its pharmacological activities. Cadinene type sesquiterpenes, one of major bioactive components mainly present in aerial parts of L. sibiricus, showed antibacterial, anti-inflammatory, antioxidant and antiproliferative properties. However, there is no report about the sesquiterpene biosynthesis in L. sibiricus. This study identified L. sibiricus sesquiterpene synthases (LsSqTPSs) through comparative transcriptome analysis of L. sibiricus leaf and root samples using the BGISEQ-500 sequencing technique. A total of 83,244 unigenes were obtained with an average length of 1025 bp. Among them, 50,356 unigenes (60.49%) acquired annotations according to the BLAST searching results. A total of 68 differentially expressed genes (DEGs) were potentially involved in the sesquiterpene biosynthesis. Furthermore, four candidate DEGs encoding LsSqTPSs were characterized. The enzymatic characterization in engineered yeast showed that LsSqTPS1 produced α-farnesene as the single product and LsSqTPS2 mainly produced 76.23 mg/L of δ-cadinene, which constituted the major component of L. sibiricus leaf essential oil. This work contributes to the investigation of sesquiterpene biosynthesis in L. sibiricus.
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Affiliation(s)
- Xiaoguang Yan
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Weiguo Li
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Dongmei Liang
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Guangrong Zhao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Qinggele Caiyin
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China.
| | - Jianjun Qiao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China.
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.
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Zhang W, Guo J, Wang Z, Li Y, Meng X, Shen Y, Liu W. Improved production of germacrene A, a direct precursor of ß-elemene, in engineered Saccharomyces cerevisiae by expressing a cyanobacterial germacrene A synthase. Microb Cell Fact 2021; 20:7. [PMID: 33413372 PMCID: PMC7791714 DOI: 10.1186/s12934-020-01500-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/19/2020] [Indexed: 11/25/2022] Open
Abstract
Background The sesquiterpene germacrene A is a direct precursor of ß-elemene that is a major component of the Chinese medicinal herb Curcuma wenyujin with prominent antitumor activity. The microbial platform for germacrene A production was previously established in Saccharomyces cerevisiae using the germacrene A synthase (LTC2) of Lactuca sativa. Results We evaluated the performance of LTC2 (LsGAS) as well as nine other identified or putative germacrene A synthases from different sources for the production of germacrene A. AvGAS, a synthase of Anabaena variabilis, was found to be the most efficient in germacrene A production in yeast. AvGAS expression alone in S. cerevisiae CEN.PK2-1D already resulted in a substantial production of germacrene A while LTC2 expression did not. Further metabolic engineering the yeast using known strategies including overexpression of tHMGR1 and repression of squalene synthesis pathway led to an 11-fold increase in germacrene A production. Site-directed mutagenesis of AvGAS revealed that while changes of several residues located within the active site cavity severely compromised germacrene A production, substitution of Phe23 located on the lateral surface with tryptophan or valine led to a 35.2% and 21.8% increase in germacrene A production, respectively. Finally, the highest production titer of germacrene A reached 309.8 mg/L in shake-flask batch culture. Conclusions Our study highlights the potential of applying bacterial sesquiterpene synthases with improved performance by mutagenesis engineering in producing germacrene A.
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Affiliation(s)
- Weixin Zhang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Junqi Guo
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Zheng Wang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Yanwei Li
- Environment Research Institute, Shandong University, Qingdao, 266237, People's Republic of China
| | - Xiangfeng Meng
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Yu Shen
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China.
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70
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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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71
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Wang L, Liang J, Xie X, Liu J, Shen Q, Li L, Wang Q. Direct formation of the sesquiterpeonid ether liguloxide by a terpene synthase in Senecio scandens. PLANT MOLECULAR BIOLOGY 2021; 105:55-64. [PMID: 32915351 DOI: 10.1007/s11103-020-01068-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/01/2020] [Indexed: 06/11/2023]
Abstract
SsLOS directly catalyzed formation of the sesquiterpenoid ether liguloxide in the medicinal plant Senecio scandens. Terpene synthases determine the diversity of terpene skeletons and corresponding terpenoid natural products. Oxygenated groups introduced in catalysis of terpene synthases are important for solubility, potential bioactivity and further elaboration of terpenoids. Here we identified one terpene synthase, SsLOS, in the Chinese medicinal plant Senecio scandens. SsLOS acted as the sesquiterpene synthase and utilized (E,E)-farnesyl diphosphate as the substrate to produce a blend of sesquiterpenoids. GC-MS analysis and NMR structure identification demonstrated that SsLOS directly produced the sesquiterpenoid ether, liguloxide, as well as its alcoholic isomer, 6-epi-guaia-2(3)-en-11-ol. Homology modeling and site-directed mutagenesis were combined to explore the catalytic mechanism of SsLOS. A few key residues were identified in the active site and hedycaryol was identified as the neutral intermediate of SsLOS catalysis. The plausible catalytic mechanism was proposed as well. Altogether, SsLOS was identified and characterized as the sesquiterpenoid ether synthase, which is the second terpenoid ether synthase after 1,8-cineol synthase, suggesting some insights for the universal mechanism of terpene synthases using the water molecule in the catalytic cavity.
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Affiliation(s)
- Liping Wang
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jin Liang
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xin Xie
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiang Liu
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, China
| | - Qinqin Shen
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lixia Li
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiang Wang
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China.
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, China.
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72
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Ronnebaum TA, Gardner SM, Christianson DW. An Aromatic Cluster in the Active Site of epi-Isozizaene Synthase Is an Electrostatic Toggle for Divergent Terpene Cyclization Pathways. Biochemistry 2020; 59:4744-4754. [PMID: 33270439 DOI: 10.1021/acs.biochem.0c00876] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The sesquiterpene cyclase epi-isozizaene synthase (EIZS) catalyzes the cyclization of farnesyl diphosphate to form the tricyclic precursor of the antibiotic albaflavenone. The hydrophobic active site is largely defined by aromatic residues that direct a multistep reaction sequence through multiple carbocation intermediates. The previous substitution of polar residues for a key aromatic residue, F96, converts EIZS into a high-fidelity sesquisabinene synthase: the F96S, F96M, and F96Q variants generate 78%, 91%, and 97% sesquisabinene A, respectively. Here, we report high-resolution X-ray crystal structures of two of these reprogrammed cyclases. The structures of the F96M EIZS-Mg2+3-risedronate and F96M EIZS-Mg2+3-inorganic pyrophosphate-benzyltriethylammonium cation complexes reveal structural changes in the F96 aromatic cluster that redirect the cyclization pathway leading from the bisabolyl carbocation intermediate in catalysis. The structure of the F96S EIZS-Mg2+3-neridronate complex reveals a partially occupied inhibitor and an enzyme active site caught in transition between open and closed states. Finally, three structures of wild-type EIZS complexed with the bisphosphonate inhibitors neridronate, pamidronate, and risedronate provide a foundation for understanding binding differences between wild-type and variant enzymes. These structures provide new insight regarding active site flexibility, particularly with regard to the potential for subtle expansion and contraction to accommodate ligands of varying sizes as well as bound water molecules. Additionally, these structures highlight the importance of conformational changes in the F96 aromatic cluster that could influence cation-π interactions with carbocation intermediates in catalysis.
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Affiliation(s)
- Trey A Ronnebaum
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Sarah M Gardner
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
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73
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You MK, Lee YJ, Yu JS, Ha SH. The Predicted Functional Compartmentation of Rice Terpenoid Metabolism by Trans-Prenyltransferase Structural Analysis, Expression and Localization. Int J Mol Sci 2020; 21:E8927. [PMID: 33255547 PMCID: PMC7728057 DOI: 10.3390/ijms21238927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/15/2020] [Accepted: 11/18/2020] [Indexed: 12/17/2022] Open
Abstract
Most terpenoids are derived from the basic terpene skeletons of geranyl pyrophosphate (GPP, C10), farnesyl-PP (FPP, C15) and geranylgeranyl-PP (GGPP, C20). The trans-prenyltransferases (PTs) mediate the sequential head-to-tail condensation of an isopentenyl-PP (C5) with allylic substrates. The in silico structural comparative analyses of rice trans-PTs with 136 plant trans-PT genes allowed twelve rice PTs to be identified as GGPS_LSU (OsGGPS1), homomeric G(G)PS (OsGPS) and GGPS_SSU-II (OsGRP) in Group I; two solanesyl-PP synthase (OsSPS2 and 3) and two polyprenyl-PP synthases (OsSPS1 and 4) in Group II; and five FPSs (OsFPS1, 2, 3, 4 and 5) in Group III. Additionally, several residues in "three floors" for the chain length and several essential domains for enzymatic activities specifically varied in rice, potentiating evolutionarily rice-specific biochemical functions of twelve trans-PTs. Moreover, expression profiling and localization patterns revealed their functional compartmentation in rice. Taken together, we propose the predicted topology-based working model of rice PTs with corresponding terpene metabolites: GPP/GGPPs mainly in plastoglobuli, SPPs in stroma, PPPs in cytosol, mitochondria and chloroplast and FPPs in cytosol. Our findings could be suitably applied to metabolic engineering for producing functional terpene metabolites in rice systems.
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Affiliation(s)
- Min Kyoung You
- Department of Genetic Engineering and Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin 17104, Korea; (Y.J.L.); (J.S.Y.)
| | | | | | - Sun-Hwa Ha
- Department of Genetic Engineering and Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin 17104, Korea; (Y.J.L.); (J.S.Y.)
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74
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Zhang Y, Prach LM, O'Brien TE, DiMaio F, Prigozhin DM, Corn JE, Alber T, Siegel JB, Tantillo DJ. Crystal Structure and Mechanistic Molecular Modeling Studies of Mycobacterium tuberculosis Diterpene Cyclase Rv3377c. Biochemistry 2020; 59:4507-4515. [PMID: 33182997 DOI: 10.1021/acs.biochem.0c00762] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Terpenes make up the largest class of natural products, with extensive chemical and structural diversity. Diterpenes, mostly isolated from plants and rarely prokaryotes, exhibit a variety of important biological activities and valuable applications, including providing antitumor and antibiotic pharmaceuticals. These natural products are constructed by terpene synthases, a class of enzymes that catalyze one of the most complex chemical reactions in biology: converting simple acyclic oligo-isoprenyl diphosphate substrates to complex polycyclic products via carbocation intermediates. Here we obtained the second ever crystal structure of a class II diterpene synthase from bacteria, tuberculosinol pyrophosphate synthase (i.e., Halimadienyl diphosphate synthase, MtHPS, or Rv3377c) from Mycobacterium tuberculosis (Mtb). This enzyme transforms (E,E,E)-geranylgeranyl diphosphate into tuberculosinol pyrophosphate (Halimadienyl diphosphate). Rv3377c is part of the Mtb diterpene pathway along with Rv3378c, which converts tuberculosinol pyrophosphate to 1-tuberculosinyl adenosine (1-TbAd). This pathway was shown to exist only in virulent Mycobacterium species, but not in closely related avirulent species, and was proposed to be involved in phagolysosome maturation arrest. To gain further insight into the reaction pathway and the mechanistically relevant enzyme substrate binding orientation, electronic structure calculation and docking studies of reaction intermediates were carried out. Results reveal a plausible binding mode of the substrate that can provide the information to guide future drug design and anti-infective therapies of this biosynthetic pathway.
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Affiliation(s)
- Yue Zhang
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Lisa M Prach
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
| | - Terrence E O'Brien
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Daniil M Prigozhin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jacob E Corn
- Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Tom Alber
- Department of Molecular & Cell Biology and QB3 Institute, University of California, Berkeley, California 94720, 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
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75
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Marín-Valls R, Hernández K, Bolte M, Parella T, Joglar J, Bujons J, Clapés P. Biocatalytic Construction of Quaternary Centers by Aldol Addition of 3,3-Disubstituted 2-Oxoacid Derivatives to Aldehydes. J Am Chem Soc 2020; 142:19754-19762. [PMID: 33147013 DOI: 10.1021/jacs.0c09994] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The congested nature of quaternary carbons hinders their preparation, most notably when stereocontrol is required. Here we report a biocatalytic method for the creation of quaternary carbon centers with broad substrate scope, leading to different compound classes bearing this structural feature. The key step comprises the aldol addition of 3,3-disubstituted 2-oxoacids to aldehydes catalyzed by metal dependent 3-methyl-2-oxobutanoate hydroxymethyltransferase from E. coli (KPHMT) and variants thereof. The 3,3,3-trisubstituted 2-oxoacids thus produced were converted into 2-oxolactones and 3-hydroxy acids and directly to ulosonic acid derivatives, all bearing gem-dialkyl, gem-cycloalkyl, and spirocyclic quaternary centers. In addition, some of these reactions use a single enantiomer from racemic nucleophiles to afford stereopure quaternary carbons. The notable substrate tolerance and stereocontrol of these enzymes are indicative of their potential for the synthesis of structurally intricate molecules.
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Affiliation(s)
- Roser Marín-Valls
- Biological Chemistry Department, Instituto de Química Avanzada de Cataluña, IQAC-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Karel Hernández
- Biological Chemistry Department, Instituto de Química Avanzada de Cataluña, IQAC-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Michael Bolte
- Institut für Anorganische Chemie, J.-W.-Goethe-Universität, Frankfurt/Main, Germany
| | - Teodor Parella
- Servei de Ressonancia Magnetica Nuclear, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Jesús Joglar
- Biological Chemistry Department, Instituto de Química Avanzada de Cataluña, IQAC-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Jordi Bujons
- Biological Chemistry Department, Instituto de Química Avanzada de Cataluña, IQAC-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Pere Clapés
- Biological Chemistry Department, Instituto de Química Avanzada de Cataluña, IQAC-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
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76
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Beaupre BA, Moran GR. N5 Is the New C4a: Biochemical Functionalization of Reduced Flavins at the N5 Position. Front Mol Biosci 2020; 7:598912. [PMID: 33195440 PMCID: PMC7662398 DOI: 10.3389/fmolb.2020.598912] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/05/2020] [Indexed: 12/31/2022] Open
Abstract
For three decades the C4a-position of reduced flavins was the known site for covalency within flavoenzymes. The reactivity of this position of the reduced isoalloxazine ring with the dioxygen ground-state triplet established the C4a as a site capable of one-electron chemistry. Within the last two decades new types of reduced flavin reactivity have been documented. These studies reveal that the N5 position is also a protean site of reactivity, that is capable of nucleophilic attack to form covalent bonds with substrates. In addition, though the precise mechanism of dioxygen reactivity is yet to be definitively demonstrated, it is clear that the N5 position is directly involved in substrate oxygenation in some enzymes. In this review we document the lineage of discoveries that identified five unique modes of N5 reactivity that collectively illustrate the versatility of this position of the reduced isoalloxazine ring.
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Affiliation(s)
- Brett A Beaupre
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
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77
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Vicente I, Baroncelli R, Morán-Diez ME, Bernardi R, Puntoni G, Hermosa R, Monte E, Vannacci G, Sarrocco S. Combined Comparative Genomics and Gene Expression Analyses Provide Insights into the Terpene Synthases Inventory in Trichoderma. Microorganisms 2020; 8:E1603. [PMID: 33081019 PMCID: PMC7603203 DOI: 10.3390/microorganisms8101603] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/09/2020] [Accepted: 10/16/2020] [Indexed: 12/11/2022] Open
Abstract
Trichoderma is a fungal genus comprising species used as biocontrol agents in crop plant protection and with high value for industry. The beneficial effects of these species are supported by the secondary metabolites they produce. Terpenoid compounds are key players in the interaction of Trichoderma spp. with the environment and with their fungal and plant hosts; however, most of the terpene synthase (TS) genes involved in their biosynthesis have yet not been characterized. Here, we combined comparative genomics of TSs of 21 strains belonging to 17 Trichoderma spp., and gene expression studies on TSs using T. gamsii T6085 as a model. An overview of the diversity within the TS-gene family and the regulation of TS genes is provided. We identified 15 groups of TSs, and the presence of clade-specific enzymes revealed a variety of terpenoid chemotypes evolved to cover different ecological demands. We propose that functional differentiation of gene family members is the driver for the high number of TS genes found in the genomes of Trichoderma. Expression studies provide a picture in which different TS genes are regulated in many ways, which is a strong indication of different biological functions.
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Affiliation(s)
- Isabel Vicente
- Department of Agriculture, Food and Environment, University of Pisa, 56124 Pisa, Italy; (R.B.); (G.P.); (G.V.); (S.S.)
- Department of Microbiology and Genetics, Spanish-Portuguese Institute for Agricultural Research (CIALE), University of Salamanca, Campus Villamayor, 37185 Salamanca, Spain; (R.B.); (M.E.M.-D.); (R.H.); (E.M.)
| | - Riccardo Baroncelli
- Department of Microbiology and Genetics, Spanish-Portuguese Institute for Agricultural Research (CIALE), University of Salamanca, Campus Villamayor, 37185 Salamanca, Spain; (R.B.); (M.E.M.-D.); (R.H.); (E.M.)
| | - María Eugenia Morán-Diez
- Department of Microbiology and Genetics, Spanish-Portuguese Institute for Agricultural Research (CIALE), University of Salamanca, Campus Villamayor, 37185 Salamanca, Spain; (R.B.); (M.E.M.-D.); (R.H.); (E.M.)
| | - Rodolfo Bernardi
- Department of Agriculture, Food and Environment, University of Pisa, 56124 Pisa, Italy; (R.B.); (G.P.); (G.V.); (S.S.)
| | - Grazia Puntoni
- Department of Agriculture, Food and Environment, University of Pisa, 56124 Pisa, Italy; (R.B.); (G.P.); (G.V.); (S.S.)
| | - Rosa Hermosa
- Department of Microbiology and Genetics, Spanish-Portuguese Institute for Agricultural Research (CIALE), University of Salamanca, Campus Villamayor, 37185 Salamanca, Spain; (R.B.); (M.E.M.-D.); (R.H.); (E.M.)
| | - Enrique Monte
- Department of Microbiology and Genetics, Spanish-Portuguese Institute for Agricultural Research (CIALE), University of Salamanca, Campus Villamayor, 37185 Salamanca, Spain; (R.B.); (M.E.M.-D.); (R.H.); (E.M.)
| | - Giovanni Vannacci
- Department of Agriculture, Food and Environment, University of Pisa, 56124 Pisa, Italy; (R.B.); (G.P.); (G.V.); (S.S.)
| | - Sabrina Sarrocco
- Department of Agriculture, Food and Environment, University of Pisa, 56124 Pisa, Italy; (R.B.); (G.P.); (G.V.); (S.S.)
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78
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Tang X, Zhang F, Zeng T, Li W, Yin S, Wu R. Enzymatic Plasticity Inspired by the Diterpene Cyclase CotB2. ACS Chem Biol 2020; 15:2820-2832. [PMID: 32986400 DOI: 10.1021/acschembio.0c00645] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzymatic plasticity, as a modern term referring to the functional conversion of an enzyme, is significant for enzymatic activity redesign. The bacterial diterpene cyclase CotB2 is a typical plastic enzyme by which its native form precisely conducts a chemical reaction while its mutants diversify the catalytic functions drastically. Many efforts have been made to disclose the mysteries of CotB2 enzyme catalysis. However, the catalytic details and regulatory mechanism toward the precise chemo- and stereoselectivity are still elusive. In this work, multiscale simulations are employed to illuminate the biocyclization mechanisms of the linear substrate into the final product cyclooctat-9-en-7-ol with a 5-8-5 fused ring scaffold, and the derailment products arising from the premature quenching of reactive carbocation intermediates are also discussed. The two major regulatory factors, local electrostatic stabilization effects from aromatic residues or polar residue in pocket and global features of active site including pocket-contour and pocket-hydrophobicity, are responsible for the enzymatic plasticity of CotB2. Further comparative studies of representative Euphorbiaceae and fungal diterpene cyclase (RcCS and PaFS) show a correlation between pocket plasticity and product diversity, which inspires a tentative enzyme product prediction and the rational diterpene cyclases' reengineering in the future.
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Affiliation(s)
- Xiaowen Tang
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Department of Medicinal Chemistry, School of Pharmacy, Qingdao University, Qingdao 266021, China
| | - Fan Zhang
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Tao Zeng
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Wei Li
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Sheng Yin
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Ruibo Wu
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
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Chen Q, Li J, Liu Z, Mitsuhashi T, Zhang Y, Liu H, Ma Y, He J, Shinada T, Sato T, Wang Y, Liu H, Abe I, Zhang P, Wang G. Molecular Basis for Sesterterpene Diversity Produced by Plant Terpene Synthases. PLANT COMMUNICATIONS 2020; 1:100051. [PMID: 33367256 PMCID: PMC7747971 DOI: 10.1016/j.xplc.2020.100051] [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: 03/20/2020] [Revised: 04/10/2020] [Accepted: 04/26/2020] [Indexed: 05/04/2023]
Abstract
Class I terpene synthase (TPS) generates bioactive terpenoids with diverse backbones. Sesterterpene synthase (sester-TPS, C25), a branch of class I TPSs, was recently identified in Brassicaceae. However, the catalytic mechanisms of sester-TPSs are not fully understood. Here, we first identified three nonclustered functional sester-TPSs (AtTPS06, AtTPS22, and AtTPS29) in Arabidopsis thaliana. AtTPS06 utilizes a type-B cyclization mechanism, whereas most other sester-TPSs produce various sesterterpene backbones via a type-A cyclization mechanism. We then determined the crystal structure of the AtTPS18-FSPP complex to explore the cyclization mechanism of plant sester-TPSs. We used structural comparisons and site-directed mutagenesis to further elucidate the mechanism: (1) mainly due to the outward shift of helix G, plant sester-TPSs have a larger catalytic pocket than do mono-, sesqui-, and di-TPSs to accommodate GFPP; (2) type-A sester-TPSs have more aromatic residues (five or six) in their catalytic pocket than classic TPSs (two or three), which also determines whether the type-A or type-B cyclization mechanism is active; and (3) the other residues responsible for product fidelity are determined by interconversion of AtTPS18 and its close homologs. Altogether, this study improves our understanding of the catalytic mechanism of plant sester-TPS, which ultimately enables the rational engineering of sesterterpenoids for future applications.
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Affiliation(s)
- Qingwen Chen
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxu Li
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhixi Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Takaaki Mitsuhashi
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuting Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Haili Liu
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yihua Ma
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Juan He
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Tetsuro Shinada
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Tsutomu Sato
- Department of Applied Biological Chemistry, Faculty of Agriculture, Graduate School of Science and Technology, Niigata University, 8050 Ikarashi-2, Niigata 950-2181, Japan
| | - Yong Wang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hongwei Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- Corresponding author
| | - Guodong Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100039, China
- Corresponding author
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80
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Booth JK, Yuen MMS, Jancsik S, Madilao LL, Page JE, Bohlmann J. Terpene Synthases and Terpene Variation in Cannabis sativa. PLANT PHYSIOLOGY 2020; 184:130-147. [PMID: 32591428 PMCID: PMC7479917 DOI: 10.1104/pp.20.00593] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 06/12/2020] [Indexed: 05/22/2023]
Abstract
Cannabis (Cannabis sativa) resin is the foundation of a multibillion dollar medicinal and recreational plant bioproducts industry. Major components of the cannabis resin are the cannabinoids and terpenes. Variations of cannabis terpene profiles contribute much to the different flavor and fragrance phenotypes that affect consumer preferences. A major problem in the cannabis industry is the lack of proper metabolic characterization of many of the existing cultivars, combined with sometimes incorrect cultivar labeling. We characterized foliar terpene profiles of plants grown from 32 seed sources and found large variation both within and between sets of plants labeled as the same cultivar. We selected five plants representing different cultivars with contrasting terpene profiles for clonal propagation, floral metabolite profiling, and trichome-specific transcriptome sequencing. Sequence analysis of these five cultivars and the reference genome of cv Purple Kush revealed a total of 33 different cannabis terpene synthase (CsTPS) genes, as well as variations of the CsTPS gene family and differential expression of terpenoid and cannabinoid pathway genes between cultivars. Our annotation of the cv Purple Kush reference genome identified 19 complete CsTPS gene models, and tandem arrays of isoprenoid and cannabinoid biosynthetic genes. An updated phylogeny of the CsTPS gene family showed three cannabis-specific clades, including a clade of sesquiterpene synthases within the TPS-b subfamily that typically contains mostly monoterpene synthases. The CsTPSs described and functionally characterized here include 13 that had not been previously characterized and that collectively explain a diverse range of cannabis terpenes.
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Affiliation(s)
- Judith K Booth
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Macaire M S Yuen
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Sharon Jancsik
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Lufiani L Madilao
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Jonathan E Page
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
- Aurora Cannabis, Vancouver, British Columbia, Canada V6B 3J5
| | - Jörg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
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81
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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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82
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Lemke C, Whitham O, Peters RJ. Magnesium-specific ring expansion/contraction catalysed by the class II diterpene cyclase from pleuromutilin biosynthesis. Org Biomol Chem 2020; 18:5586-5588. [PMID: 32672326 PMCID: PMC7430159 DOI: 10.1039/d0ob01422b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The class II diterpene cyclase (DTC) from pleuromutilin biosynthesis uniquely mediates 'A' ring contraction of the initially formed decalin bicycle, yielding mutildienyl diphosphate (MPP). Catalysis requires a divalent metal cation co-factor. Intriguingly, selectively with magnesium, this DTC catalyzes ring expansion/contraction between MPP and halimadienyl diphosphate, providing some catalytic insight.
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Affiliation(s)
- Cody Lemke
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA.
| | - Owen Whitham
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA.
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA.
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83
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Hu T, Zhou J, Tong Y, Su P, Li X, Liu Y, Liu N, Wu X, Zhang Y, Wang J, Gao L, Tu L, Lu Y, Jiang Z, Zhou YJ, Gao W, Huang L. Engineering chimeric diterpene synthases and isoprenoid biosynthetic pathways enables high-level production of miltiradiene in yeast. Metab Eng 2020; 60:87-96. [DOI: 10.1016/j.ymben.2020.03.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 02/25/2020] [Accepted: 03/29/2020] [Indexed: 12/18/2022]
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84
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Stepanova R, Inagi H, Sugawara K, Asada K, Nishi T, Ueda D, Yasuno Y, Shinada T, Miki K, Fujihashi M, Sato T. Characterization of Class IB Terpene Synthase: The First Crystal Structure Bound with a Substrate Surrogate. ACS Chem Biol 2020; 15:1517-1525. [PMID: 32227910 DOI: 10.1021/acschembio.0c00145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Terpene synthases (TS) are classified into two broad types, Class I and II, based on the chemical strategy for initial carbocation formation and motif sequences of the catalytic site. We have recently identified a new class of enzymes, Class IB, showing the acceptability of long (C20-C35) prenyl-diphosphates as substrates and no amino acid sequence homology with known TS. Conversion of long prenyl-diphosphates such as heptaprenyl-diphosphate (C35) is unusual and has never been reported for Class I and II enzymes. Therefore, the characterization of Class IB enzymes is crucial to understand the reaction mechanism of the extensive terpene synthesis. Here, we report the crystal structure bound with a substrate surrogate and biochemical analysis of a Class IB TS, using the enzyme from Bacillus alcalophilus (BalTS). The structure analysis revealed that the diphosphate part of the substrate is located around the two characteristic Asp-rich motifs, and the hydrophobic tail is accommodated in a unique hydrophobic long tunnel, where the C35 prenyl-diphosphate, the longest substrate of BalTS, can be accepted. Biochemical analyses of BalTS showed that the enzymatic property, such as Mg2+ dependency, is similar to those of Class I enzymes. In addition, a new cyclic terpene was identified from BalTS reaction products. Mutational analysis revealed that five of the six Asp residues in the Asp-rich motifs and two His residues are essential for the formation of the cyclic skeleton. These results provided a clue to consider the application of the unusual large terpene synthesis by Class IB enzymes.
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Affiliation(s)
- Rafaella Stepanova
- Department of Applied Biological Chemistry, Faculty of Agriculture, and Graduate School of Science and Technology, Niigata University, 8050 Ikarashi-2, Niigata 950-2181, Japan
| | - Hayato Inagi
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kei Sugawara
- Department of Applied Biological Chemistry, Faculty of Agriculture, and Graduate School of Science and Technology, Niigata University, 8050 Ikarashi-2, Niigata 950-2181, Japan
| | - Kazuya Asada
- Department of Applied Biological Chemistry, Faculty of Agriculture, and Graduate School of Science and Technology, Niigata University, 8050 Ikarashi-2, Niigata 950-2181, Japan
| | - Tomoyuki Nishi
- Department of Applied Biological Chemistry, Faculty of Agriculture, and Graduate School of Science and Technology, Niigata University, 8050 Ikarashi-2, Niigata 950-2181, Japan
| | - Daijiro Ueda
- Department of Applied Biological Chemistry, Faculty of Agriculture, and Graduate School of Science and Technology, Niigata University, 8050 Ikarashi-2, Niigata 950-2181, Japan
| | - Yoko Yasuno
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Tetsuro Shinada
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masahiro Fujihashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Tsutomu Sato
- Department of Applied Biological Chemistry, Faculty of Agriculture, and Graduate School of Science and Technology, Niigata University, 8050 Ikarashi-2, Niigata 950-2181, Japan
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85
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Zhou F, Pichersky E. The complete functional characterisation of the terpene synthase family in tomato. THE NEW PHYTOLOGIST 2020; 226:1341-1360. [PMID: 31943222 PMCID: PMC7422722 DOI: 10.1111/nph.16431] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/05/2020] [Indexed: 05/14/2023]
Abstract
Analysis of the updated reference tomato genome found 34 full-length TPS genes and 18 TPS pseudogenes. Biochemical analysis has now identified the catalytic activities of all enzymes encoded by the 34 TPS genes: one isoprene synthase, 10 exclusively or predominantly monoterpene synthases, 17 sesquiterpene synthases and six diterpene synthases. Among the monoterpene and sesquiterpene and diterpene synthases, some use trans-prenyl diphosphates, some use cis-prenyl diphosphates and some use both. The isoprene synthase is cytosolic; six monoterpene synthases are plastidic, and four are cytosolic; the sesquiterpene synthases are almost all cytosolic, with the exception of one found in the mitochondria; and three diterpene synthases are found in the plastids, one in the cytosol and two in the mitochondria. New trans-prenyltransferases (TPTs) were characterised; together with previously characterised TPTs and cis-prenyltransferases (CPTs), tomato plants can make all cis and trans C10 , C15 and C20 prenyl diphosphates. Every type of plant tissue examined expresses some TPS genes and some TPTs and CPTs. Phylogenetic comparison of the TPS genes from tomato and Arabidopsis shows expansions in each clade of the TPS gene family in each lineage (and inferred losses), accompanied by changes in subcellular localisations and substrate specificities.
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Affiliation(s)
- Fei Zhou
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMI48109USA
| | - Eran Pichersky
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMI48109USA
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86
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Smit SJ, Vivier MA, Young PR. Comparative (Within Species) Genomics of the Vitis vinifera L. Terpene Synthase Family to Explore the Impact of Genotypic Variation Using Phased Diploid Genomes. Front Genet 2020; 11:421. [PMID: 32431727 PMCID: PMC7216305 DOI: 10.3389/fgene.2020.00421] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/03/2020] [Indexed: 01/20/2023] Open
Abstract
The Vitis vinifera L. terpene synthase (VviTPS) family was comprehensively annotated on the phased diploid genomes of three closely related cultivars: Cabernet Sauvignon, Carménère and Chardonnay. VviTPS gene regions were grouped to chromosomes, with the haplotig assemblies used to identify allelic variants. Functional predictions of the VviTPS subfamilies were performed using enzyme active site phylogenies resulting in the putative identification of the initial substrate and cyclization mechanism of VviTPS enzymes. Subsequent groupings into conserved catalytic mechanisms was coupled with an analysis of cultivar-specific gene duplications, resulting in the identification of conserved and unique VviTPS clusters. These findings are presented as a collection of interactive networks where any VviTPS of interest can be queried through BLAST, allowing for a rapid identification of VviTPS-subfamily, enzyme mechanism and degree of connectivity (i.e., extent of duplication). The comparative genomic analyses presented expands our understanding of the VviTPS family and provides numerous new gene models from three diploid genomes.
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Affiliation(s)
| | | | - Philip Richard Young
- South African Grape and Wine Research Institute, Department of Viticulture and Oenology, Stellenbosch University, Stellenbosch, South Africa
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87
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Srividya N, Lange I, Lange BM. Determinants of Enantiospecificity in Limonene Synthases. Biochemistry 2020; 59:1661-1664. [PMID: 32293167 DOI: 10.1021/acs.biochem.0c00206] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Monoterpene synthases catalyze the first committed step in the biosynthesis of monoterpenes and are in part responsible for the enormous structural diversity among this class of metabolites. Here, we explore the structure-function relationships underlying the formation of limonene enantiomers in limonene synthases that bind geranyl diphosphate as a common substrate. On the basis of analyses that consider both crystal structure data and amino acid sequence divergence, we identified candidate active site residues with potential roles in catalyzing reactions that involve accommodating reaction intermediates of opposite enantiomeric series. We demonstrate that spearmint (-)-limonene synthase [which generates >99% (-)-limonene over (+)-limonene] can be converted into a mutant enzyme, by exchanging four residues (C321S, N345I, I453V, and M458V), which produces (+)-limonene with reversed enantiospecificity [80% (+)-limonene and 3% (-)-limonene; the remainder are mostly bicyclic monoterpenes]. This study provides the foundation for a more in-depth understanding of the formation of enantiomeric series of monoterpenes, which can have vastly different olfactory properties.
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Affiliation(s)
- Narayanan Srividya
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340, United States
| | - Iris Lange
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340, United States
| | - B Markus Lange
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340, United States
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88
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Rudolf JD, Chang CY. Terpene synthases in disguise: enzymology, structure, and opportunities of non-canonical terpene synthases. Nat Prod Rep 2020; 37:425-463. [PMID: 31650156 PMCID: PMC7101268 DOI: 10.1039/c9np00051h] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: up to July 2019 Terpene synthases (TSs) are responsible for generating much of the structural diversity found in the superfamily of terpenoid natural products. These elegant enzymes mediate complex carbocation-based cyclization and rearrangement cascades with a variety of electron-rich linear and cyclic substrates. For decades, two main classes of TSs, divided by how they generate the reaction-triggering initial carbocation, have dominated the field of terpene enzymology. Recently, several novel and unconventional TSs that perform TS-like reactions but do not resemble canonical TSs in sequence or structure have been discovered. In this review, we identify 12 families of non-canonical TSs and examine their sequences, structures, functions, and proposed mechanisms. Nature provides a wide diversity of enzymes, including prenyltransferases, methyltransferases, P450s, and NAD+-dependent dehydrogenases, as well as completely new enzymes, that utilize distinctive reaction mechanisms for TS chemistry. These unique non-canonical TSs provide immense opportunities to understand how nature evolved different tools for terpene biosynthesis by structural and mechanistic characterization while affording new probes for the discovery of novel terpenoid natural products and gene clusters via genome mining. With every new discovery, the dualistic paradigm of TSs is contradicted and the field of terpene chemistry and enzymology continues to expand.
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Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Chin-Yuan Chang
- Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan, Republic of China
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89
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Sui Y, Wisniewski M, Droby S, Piombo E, Wu X, Yue J. Genome Sequence, Assembly, and Characterization of the Antagonistic Yeast Candida oleophila Used as a Biocontrol Agent Against Post-harvest Diseases. Front Microbiol 2020; 11:295. [PMID: 32158440 PMCID: PMC7052047 DOI: 10.3389/fmicb.2020.00295] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 02/10/2020] [Indexed: 11/29/2022] Open
Abstract
Candida oleophila is an effective biocontrol agent used to control post-harvest diseases of fruits and vegetables. C. oleophila I-182 was the active agent used in the first-generation yeast-based commercial product, Aspire®, for post-harvest disease management. Several action modes, like competition for nutrients and space, induction of pathogenesis-related genes in host tissues, and production of extracellular lytic enzymes, have been demonstrated for the biological control activity exhibited by C. oleophila through which it inhibits post-harvest pathogens. In the present study, the whole genome of C. oleophila I-182 was sequenced using PacBio and Illumina shotgun sequencing technologies, yielding an estimated genome size of 14.73 Mb. The genome size is similar in length to that of the model yeast strain Saccharomyces cerevisiae S288c. Based on the assembled genome, protein-coding sequences were identified and annotated. The predicted genes were further assigned with gene ontology terms and clustered in special functional groups. A comparative analysis of C. oleophila proteome with the proteomes of 11 representative yeasts revealed 2 unique and 124 expanded families of proteins in C. oleophila. Availability of the genome sequence will facilitate a better understanding the properties of biocontrol yeasts at the molecular level.
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Affiliation(s)
- Yuan Sui
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, College of Forestry and Life Science, Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, China
| | - Michael Wisniewski
- U.S. Department of Agriculture-Agricultural Research Service, Kearneysville, WV, United States
| | - Samir Droby
- Department of Postharvest Science, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel
| | - Edoardo Piombo
- Department of Agricultural, Forestry and Food Sciences, University of Turin, Turin, Italy
| | - Xuehong Wu
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Junyang Yue
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
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90
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On the Evolution and Functional Diversity of Terpene Synthases in the Pinus Species: A Review. J Mol Evol 2020; 88:253-283. [PMID: 32036402 DOI: 10.1007/s00239-020-09930-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/17/2020] [Indexed: 02/02/2023]
Abstract
In the biosynthesis of terpenoids, the ample catalytic versatility of terpene synthases (TPS) allows the formation of thousands of different molecules. A steadily increasing number of sequenced plant genomes invariably show that the TPS gene family is medium to large in size, comprising from 30 to 100 functional members. In conifers, TPSs belonging to the gymnosperm-specific TPS-d subfamily produce a complex mixture of mono-, sesqui-, and diterpenoid specialized metabolites, which are found in volatile emissions and oleoresin secretions. Such substances are involved in the defence against pathogens and herbivores and can help to protect against abiotic stress. Oleoresin terpenoids can be also profitably used in a number of different fields, from traditional and modern medicine to fine chemicals, fragrances, and flavours, and, in the last years, in biorefinery too. In the present work, after summarizing the current views on the biosynthesis and biological functions of terpenoids, recent advances on the evolution and functional diversification of plant TPSs are reviewed, with a focus on gymnosperms. In such context, an extensive characterization and phylogeny of all the known TPSs from different Pinus species is reported, which, for such genus, can be seen as the first effort to explore the evolutionary history of the large family of TPS genes involved in specialized metabolism. Finally, an approach is described in which the phylogeny of TPSs in Pinus spp. has been exploited to isolate for the first time mono-TPS sequences from Pinus nigra subsp. laricio, an ecologically important endemic pine in the Mediterranean area.
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91
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Zhang J, Zhang Y, Xing J, Yu H, Zhang R, Chen Y, Zhang D, Yin P, Tian X, Wang Q, Duan L, Zhang M, Peters RJ, Li Z. Introducing selective agrochemical manipulation of gibberellin metabolism into a cereal crop. NATURE PLANTS 2020; 6:67-72. [PMID: 32015514 PMCID: PMC7194013 DOI: 10.1038/s41477-019-0582-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 12/17/2019] [Indexed: 05/26/2023]
Abstract
Use of growth retardants enables post-planting optimization of vegetative growth, which is particularly important given ongoing climate change. Mepiquat chloride is an economical and safe retardant widely applied in cotton farming, but it is not uniformly effective. Here, identification of its molecular target as the ent-copalyl diphosphate synthase that initiates gibberellin biosynthesis enabled the introduction of selective agrochemical inhibition, leaving intact more specialized metabolism important for resistance to biotic and abiotic stresses.
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Affiliation(s)
- Juan Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Yushi Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jiapeng Xing
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Haiyue Yu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Rui Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yiyao Chen
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, China
| | - Delin Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agriculture University, Wuhan, China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agriculture University, Wuhan, China
| | - Xiaoli Tian
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Qiang Wang
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, China
| | - Liusheng Duan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Mingcai Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA.
| | - Zhaohu Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China.
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China.
- College of Plant Science and Technology, Huazhong Agriculture University, Wuhan, China.
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92
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Subramanian M, Marudhamuthu M. Hitherto Unknown Terpene Synthase Organization in Taxol-Producing Endophytic Bacteria Isolated from Marine Macroalgae. Curr Microbiol 2020; 77:918-923. [PMID: 31970484 DOI: 10.1007/s00284-020-01878-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/07/2020] [Indexed: 11/27/2022]
Abstract
Taxol is a successful anti-cancer drug, which extensively studied in Taxus spp. However, microbial endophytes also reported as taxol producers, and especially fungal endophytes extensively studied for the taxol biosynthesis pathway. Although it was well considered, the taxol biosynthesis pathway remains undisclosed since its discovery in bacteria. To decipher this gap, we isolated and identified the endophytic bacteria such as Bacillus flexus strain DMTMMB08, Bacillus licheniformis strain DMTMMB10, and Oceanobacillus picturae strain DMTMMB24, which are unprecedented for taxol production. Subsequently, the genome annotation of these bacteria exhibited the isoprene biosynthesis pathway and terpene synthase profile. Feasibly, this is the very first report on taxol-producing endophytic bacteria from the non-Taxus host and solitary investigation on its genome analysis. The genomic insight into the bacterial system for taxol biosynthesis leads to understanding the terpene synthesis and evolution. This piece of work could expand our perception of the diversity of terpenes and their related natural products.
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Affiliation(s)
- Mugesh Subramanian
- Department of Microbial Technology, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamilnadu, India
| | - Murugan Marudhamuthu
- Department of Microbial Technology, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamilnadu, India.
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93
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Jin Y, Zhang Q, Zhang Y, Duan C. Electron transfer in the confined environments of metal–organic coordination supramolecular systems. Chem Soc Rev 2020; 49:5561-5600. [DOI: 10.1039/c9cs00917e] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In this review, we overview regulatory factors and diverse applications of electron transfer in confined environments of supramolecular host–guest systems.
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Affiliation(s)
- Yunhe Jin
- State Key Laboratory of Fine Chemicals
- Zhang Dayu School of Chemistry
- Dalian University of Technology
- Dalian 116024
- China
| | - Qingqing Zhang
- State Key Laboratory of Fine Chemicals
- Zhang Dayu School of Chemistry
- Dalian University of Technology
- Dalian 116024
- China
| | - Yongqiang Zhang
- State Key Laboratory of Fine Chemicals
- Zhang Dayu School of Chemistry
- Dalian University of Technology
- Dalian 116024
- China
| | - Chunying Duan
- State Key Laboratory of Fine Chemicals
- Zhang Dayu School of Chemistry
- Dalian University of Technology
- Dalian 116024
- China
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94
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Li M, Hou F, Wu T, Jiang X, Li F, Liu H, Xian M, Zhang H. Recent advances of metabolic engineering strategies in natural isoprenoid production using cell factories. Nat Prod Rep 2020; 37:80-99. [DOI: 10.1039/c9np00016j] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
This review covers the strategies mostly developed in the last three years for microbial production of isoprenoid, classified according to the engineering targets.
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Affiliation(s)
- Meijie Li
- Key Laboratory of Biobased Materials
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- P. R. China
| | - Feifei Hou
- Key Laboratory of Biobased Materials
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- P. R. China
| | - Tong Wu
- Key Laboratory of Biobased Materials
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- P. R. China
| | - Xinglin Jiang
- The Novo Nordisk Foundation Center for Biosustainability
- Technical University of Denmark
- Lyngby
- Denmark
| | - Fuli Li
- Key Laboratory of Biobased Materials
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- P. R. China
| | - Haobao Liu
- Ministry of Agriculture Key Laboratory for Tobacco Biology and Processing
- Tobacco Research Institute
- Chinese Academy of Agricultural Sciences
- Qingdao
- P. R. China
| | - Mo Xian
- Key Laboratory of Biobased Materials
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- P. R. China
| | - Haibo Zhang
- Key Laboratory of Biobased Materials
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- P. R. China
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95
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Chen H, Köllner TG, Li G, Wei G, Chen X, Zeng D, Qian Q, Chen F. Combinatorial Evolution of a Terpene Synthase Gene Cluster Explains Terpene Variations in Oryza. PLANT PHYSIOLOGY 2020; 182:480-492. [PMID: 31712306 PMCID: PMC6945850 DOI: 10.1104/pp.19.00948] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/28/2019] [Indexed: 05/21/2023]
Abstract
Terpenes are specialized metabolites ubiquitously produced by plants via the action of terpene synthases (TPSs). There are enormous variations in the types and amounts of terpenes produced by individual species. To understand the mechanisms responsible for such vast diversity, here we investigated the origin and evolution of a cluster of tandemly arrayed TPS genes in Oryza In the Oryza species analyzed, TPS genes occur as a three-TPS cluster, a two-TPS cluster, and a single TPS gene in five, one, and one species, respectively. Phylogenetic analysis revealed the origins of the two-TPS and three-TPS clusters and the role of species-specific losses of TPS genes. Within the three-TPS clusters, one orthologous group exhibited conserved catalytic activities. The other two groups, both of which contained pseudogenes and/or nonfunctional genes, exhibited distinct profiles of terpene products. Sequence and structural analyses combined with functional validation identified several amino acids in the active site that are critical for catalytic activity divergence of the three orthologous groups. In the five Oryza species containing the three-TPS cluster, their functional TPS genes showed both conserved and species-specific expression patterns in insect-damaged and untreated plants. Emission patterns of volatile terpenes from each species were largely consistent with the expression of their respective TPS genes and the catalytic activities of the encoded enzymes. This study indicates the importance of combinatorial evolution of TPS genes in determining terpene variations among individual species, which includes gene duplication, retention/loss/degradation of duplicated genes, varying selection pressure, retention/divergence in catalytic activities, and divergence in expression regulation.
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Affiliation(s)
- Hao Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996
| | - Tobias G Köllner
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - Guanglin Li
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996
| | - Guo Wei
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996
| | - Xinlu Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996
| | - Dali Zeng
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Qian Qian
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Feng Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996
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96
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Zahedifar M, Pouramiri B, Ezzati Ghadi F, Razavi R, Ramzani Ghara A. Unexpected regio- and stereoselective [4 + 3] cycloaddition reaction of azomethine ylides with benzylidene thiazolidinediones: synthesis of pharmacologically active spiroindoline oxazepine derivatives and theoretical study. Mol Divers 2019; 25:29-43. [PMID: 31865545 DOI: 10.1007/s11030-019-10022-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 12/04/2019] [Indexed: 11/28/2022]
Abstract
An unexpected regio- and stereoselective [4 + 3] cycloaddition reaction of azomethine ylides with 5-benzylidenethiazolidine-2,4-diones has been successfully developed for the synthesis of the novel pharmacologically active 4',5'-dihydro-3'H-spiro[indoline-3,2'-[1, 3] oxazepin]-2-one derivatives in basic condition. Easy purification, high yield, short experimental time and operational simplicity are specific advantages of this protocol. Furthermore, all the synthesized compounds have been evaluated for antioxidant and antibacterial activities. According to the results, most of the synthesized compounds exhibited DPPH radical scavenging activity and nine of them showed antibacterial properties. The reaction mechanism and 1H NMR spectrum have been evaluated by B3LYP/6311G method.
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Affiliation(s)
- Mahboobeh Zahedifar
- Department of Chemistry, Faculty of Science, University of Jiroft, Jiroft, 7867161167, Iran.
| | - Behjat Pouramiri
- Student Research Committee, Jiroft University of Medical Science, Jiroft, Iran
| | - Fereshteh Ezzati Ghadi
- Department of Biology, Faculty of Science, University of Jiroft, Jiroft, 7867161167, Iran
| | - Razieh Razavi
- Department of Chemistry, Faculty of Science, University of Jiroft, Jiroft, 7867161167, Iran
| | - Abdollah Ramzani Ghara
- Department of Biology, Faculty of Science, University of Jiroft, Jiroft, 7867161167, Iran
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97
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Celedon JM, Bohlmann J. Oleoresin defenses in conifers: chemical diversity, terpene synthases and limitations of oleoresin defense under climate change. THE NEW PHYTOLOGIST 2019; 224:1444-1463. [PMID: 31179548 DOI: 10.1111/nph.15984] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/16/2019] [Indexed: 05/20/2023]
Abstract
Conifers have evolved complex oleoresin terpene defenses against herbivores and pathogens. In co-evolved bark beetles, conifer terpenes also serve chemo-ecological functions as pheromone precursors, chemical barcodes for host identification, or nutrients for insect-associated microbiomes. We highlight the genomic, molecular and biochemical underpinnings of the large chemical space of conifer oleoresin terpenes and volatiles. Conifer terpenes are predominantly the products of the conifer terpene synthase (TPS) gene family. Terpene diversity is increased by cytochromes P450 of the CYP720B class. Many conifer TPS are multiproduct enzymes. Multisubstrate CYP720B enzymes catalyse multistep oxidations. We summarise known terpenoid gene functions in various different conifer species with reference to the annotated terpenoid gene space in a spruce genome. Overall, biosynthesis of terpene diversity in conifers is achieved through a system of biochemical radiation and metabolic grids. Expression of TPS and CYP720B genes can be specific to individual cell types of constitutive or traumatic resin duct systems. Induced terpenoid transcriptomes in resin duct cells lead to dynamic changes of terpene composition and quantity to fend off herbivores and pathogens. While terpenoid defenses have contributed much to the evolutionary success of conifers, under new conditions of climate change, these defences may become inconsequential against range-expanding forest pests.
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Affiliation(s)
- Jose M Celedon
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Jörg Bohlmann
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
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98
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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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99
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Helfrich EJN, Lin GM, Voigt CA, Clardy J. Bacterial terpene biosynthesis: challenges and opportunities for pathway engineering. Beilstein J Org Chem 2019; 15:2889-2906. [PMID: 31839835 PMCID: PMC6902898 DOI: 10.3762/bjoc.15.283] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/01/2019] [Indexed: 12/27/2022] Open
Abstract
Terpenoids are the largest and structurally most diverse class of natural products. They possess potent and specific biological activity in multiple assays and against diseases, including cancer and malaria as notable examples. Although the number of characterized terpenoid molecules is huge, our knowledge of how they are biosynthesized is limited, particularly when compared to the well-studied thiotemplate assembly lines. Bacteria have only recently been recognized as having the genetic potential to biosynthesize a large number of complex terpenoids, but our current ability to associate genetic potential with molecular structure is severely restricted. The canonical terpene biosynthetic pathway uses a single enzyme to form a cyclized hydrocarbon backbone followed by modifications with a suite of tailoring enzymes that can generate dozens of different products from a single backbone. This functional promiscuity of terpene biosynthetic pathways renders terpene biosynthesis susceptible to rational pathway engineering using the latest developments in the field of synthetic biology. These engineered pathways will not only facilitate the rational creation of both known and novel terpenoids, their development will deepen our understanding of a significant branch of biosynthesis. The biosynthetic insights gained will likely empower a greater degree of engineering proficiency for non-natural terpene biosynthetic pathways and pave the way towards the biotechnological production of high value terpenoids.
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Affiliation(s)
- Eric J N Helfrich
- Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, Boston, United States
| | - Geng-Min Lin
- Massachusetts Institute of Technology, Department of Biological Engineering, Cambridge, United States
| | - Christopher A Voigt
- Massachusetts Institute of Technology, Department of Biological Engineering, Cambridge, United States
| | - Jon Clardy
- Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, Boston, United States
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100
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Lacey HJ, Gilchrist CLM, Crombie A, Kalaitzis JA, Vuong D, Rutledge PJ, Turner P, Pitt JI, Lacey E, Chooi YH, Piggott AM. Nanangenines: drimane sesquiterpenoids as the dominant metabolite cohort of a novel Australian fungus, Aspergillus nanangensis. Beilstein J Org Chem 2019; 15:2631-2643. [PMID: 31807198 PMCID: PMC6880815 DOI: 10.3762/bjoc.15.256] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/14/2019] [Indexed: 12/22/2022] Open
Abstract
Chemical investigation of an undescribed Australian fungus, Aspergillus nanangensis, led to the identification of the nanangenines - a family of seven new and three previously reported drimane sesquiterpenoids. The structures of the nanangenines were elucidated by detailed spectroscopic analysis supported by single crystal X-ray diffraction studies. The compounds were assayed for in vitro activity against bacteria, fungi, mammalian cells and plants. Bioinformatics analysis, including comparative analysis with other acyl drimenol-producing Aspergilli, led to the identification of a putative nanangenine biosynthetic gene cluster that corresponds to the proposed biosynthetic pathway for nanangenines.
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Affiliation(s)
- Heather J Lacey
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
- School of Chemistry, The University of Sydney, NSW 2006, Australia
| | - Cameron L M Gilchrist
- School of Molecular Sciences, The University of Western Australia, WA 6009, Australia
| | - Andrew Crombie
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
| | - John A Kalaitzis
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
- Department of Molecular Sciences, Macquarie University, NSW 2109, Australia
| | - Daniel Vuong
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
| | - Peter J Rutledge
- School of Chemistry, The University of Sydney, NSW 2006, Australia
| | - Peter Turner
- School of Chemistry, The University of Sydney, NSW 2006, Australia
| | - John I Pitt
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
| | - Ernest Lacey
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
- Department of Molecular Sciences, Macquarie University, NSW 2109, Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, WA 6009, Australia
| | - Andrew M Piggott
- Department of Molecular Sciences, Macquarie University, NSW 2109, Australia
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