1
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Schwartz R, Zev S, Major DT. Mechanistic docking in terpene synthases using EnzyDock. Methods Enzymol 2024; 699:265-292. [PMID: 38942507 DOI: 10.1016/bs.mie.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Terpene Synthases (TPS) catalyze the formation of multicyclic, complex terpenes and terpenoids from linear substrates. Molecular docking is an important research tool that can further our understanding of TPS multistep mechanisms and guide enzyme design. Standard docking programs are not well suited to tackle the unique challenges of TPS, like the many chemical steps which form multiple stereo-centers, the weak dispersion interactions between the isoprenoid chain and the hydrophobic region of the active site, description of carbocation intermediates, and finding mechanistically meaningful sets of docked poses. To address these and other unique challenges, we developed the multistate, multiscale docking program EnzyDock and used it to study many TPS and other enzymes. In this review we discuss the unique challenges of TPS, the special features of EnzyDock developed to address these challenges and demonstrate its successful use in ongoing research on the bacterial TPS CotB2.
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Affiliation(s)
- Renana Schwartz
- Department of Chemistry and Institute for Nanotechnology Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Shani Zev
- Department of Chemistry and Institute for Nanotechnology Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Dan T Major
- Department of Chemistry and Institute for Nanotechnology Advanced Materials, Bar Ilan University, Ramat Gan, Israel.
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2
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Oufensou S, Dessì A, Dallocchio R, Balmas V, Azara E, Carta P, Migheli Q, Delogu G. Molecular Docking and Comparative Inhibitory Efficacy of Naturally Occurring Compounds on Vegetative Growth and Deoxynivalenol Biosynthesis in Fusarium culmorum. Toxins (Basel) 2021; 13:toxins13110759. [PMID: 34822543 PMCID: PMC8623340 DOI: 10.3390/toxins13110759] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/18/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022] Open
Abstract
The fungal pathogen Fusarium culmorum causes Fusarium head blight in cereals, resulting in yield loss and contamination of the grain by type B trichothecene mycotoxins such as deoxynivalenol (DON), and its acetylated derivatives. Synthesis of trichothecenes is driven by a trichodiene synthase (TRI5) that converts farnesyl pyrophosphate (FPP) to trichodiene. In this work, 15 naturally occurring compounds that belong to the structural phenol and hydroxylated biphenyl classes were tested in vitro and in planta (durum wheat) to determine their inhibitory activity towards TRI5. In vitro analysis highlighted the fungicidal effect of these compounds when applied at 0.25 mM. Greenhouse assays showed a strong inhibitory activity of octyl gallate 5, honokiol 13 and the combination propyl gallate 4 + thymol 7 on trichothecene biosynthesis. Docking analyses were run on the 3D model of F. culmorum TRI5 containing the inorganic pyrophosphate (PPi) or FPP. Significant ligand affinities with TRI-PPi and TRI-FPP were observed for the same sites for almost all compounds, with 1 and 2 as privileged sites. Octyl gallate 5 and honokiol 13 interacted almost exclusively with sites 1 and 2, by concurrently activating strong H-bonds with common sets of amino acids. These results open new perspectives for the targeted search of naturally occurring compounds that may find practical application in the eco-friendly control of FHB in wheat.
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Affiliation(s)
- Safa Oufensou
- Dipartimento di Agraria, Università degli Studi di Sassari, Via E. De Nicola 9, 07100 Sassari, Italy; (V.B.); (Q.M.)
- Nucleo di Ricerca sulla Desertificazione, Università degli Studi di Sassari, Via E. De Nicola 9, 07100 Sassari, Italy
- Correspondence:
| | - Alessandro Dessì
- Istituto CNR di Chimica Biomolecolare, Traversa La Crucca 3, 07100 Sassari, Italy; (A.D.); (R.D.); (E.A.); (P.C.); (G.D.)
| | - Roberto Dallocchio
- Istituto CNR di Chimica Biomolecolare, Traversa La Crucca 3, 07100 Sassari, Italy; (A.D.); (R.D.); (E.A.); (P.C.); (G.D.)
| | - Virgilio Balmas
- Dipartimento di Agraria, Università degli Studi di Sassari, Via E. De Nicola 9, 07100 Sassari, Italy; (V.B.); (Q.M.)
| | - Emanuela Azara
- Istituto CNR di Chimica Biomolecolare, Traversa La Crucca 3, 07100 Sassari, Italy; (A.D.); (R.D.); (E.A.); (P.C.); (G.D.)
| | - Paola Carta
- Istituto CNR di Chimica Biomolecolare, Traversa La Crucca 3, 07100 Sassari, Italy; (A.D.); (R.D.); (E.A.); (P.C.); (G.D.)
| | - Quirico Migheli
- Dipartimento di Agraria, Università degli Studi di Sassari, Via E. De Nicola 9, 07100 Sassari, Italy; (V.B.); (Q.M.)
- Nucleo di Ricerca sulla Desertificazione, Università degli Studi di Sassari, Via E. De Nicola 9, 07100 Sassari, Italy
| | - Giovanna Delogu
- Istituto CNR di Chimica Biomolecolare, Traversa La Crucca 3, 07100 Sassari, Italy; (A.D.); (R.D.); (E.A.); (P.C.); (G.D.)
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3
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Liang Z, Zhi H, Fang Z, Zhang P. Genetic engineering of yeast, filamentous fungi and bacteria for terpene production and applications in food industry. Food Res Int 2021; 147:110487. [PMID: 34399483 DOI: 10.1016/j.foodres.2021.110487] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/21/2021] [Accepted: 05/23/2021] [Indexed: 01/05/2023]
Abstract
Terpenes are a major class of natural aromatic compounds in grapes and wines to offer the characteristic flavor and aroma, serving as important quality traits of wine products. Saccharomyces cerevisiae represents an excellent cell factory platform for large-scale bio-based terpene production. This review describes the biosynthetic pathways of terpenes in different organisms. The metabolic engineering of S. cerevisiae for promoting terpene biosynthesis and the alternative microbial engineering platforms including filamentous fungi and Escherichia coli are also elaborated. Additionally, the potential applications of the terpene products from engineered microorganisms in food and beverage industries are also discussed. This review provides comprehensive information for an innovative supply way of terpene via microbial cell factory, which could facilitate the development and application of this technique at the industrial scale.
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Affiliation(s)
- Zijian Liang
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Hang Zhi
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Zhongxiang Fang
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Pangzhen Zhang
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3010, Australia.
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4
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Raz K, Driller R, Dimos N, Ringel M, Brück T, Loll B, Major DT. The Impression of a Nonexisting Catalytic Effect: The Role of CotB2 in Guiding the Complex Biosynthesis of Cyclooctat-9-en-7-ol. J Am Chem Soc 2020; 142:21562-21574. [PMID: 33289561 DOI: 10.1021/jacs.0c11348] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Terpene synthases generate terpenes employing diversified carbocation chemistry, including highly specific ring formations, proton and hydride transfers, and methyl as well as methylene migrations, followed by reaction quenching. In this enzyme family, the main catalytic challenge is not rate enhancement, but rather structural and reactive control of intrinsically unstable carbocations in order to guide the resulting product distribution. Here we employ multiscale modeling within classical and quantum dynamics frameworks to investigate the reaction mechanism in the diterpene synthase CotB2, commencing with the substrate geranyl geranyl diphosphate and terminating with the carbocation precursor to the final product cyclooctat-9-en-7-ol. The 11-step in-enzyme carbocation cascade is compared with the same reaction in the absence of the enzyme. Remarkably, the free energy profiles in gas phase and in CotB2 are surprisingly similar. This similarity contrasts the multitude of strong π-cation, dipole-cation, and ion-pair interactions between all intermediates in the reaction cascade and the enzyme, suggesting a remarkable balance of interactions in CotB2. We ascribe this balance to the similar magnitude of the interactions between the carbocations along the reaction coordinate and the enzyme environment. The effect of CotB2 mutations is studied using multiscale mechanistic docking, machine learning, and X-ray crystallography, pointing the way for future terpene synthase design.
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Affiliation(s)
- Keren Raz
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Ronja Driller
- Institut für Chemie und Biochemie, Strukturbiochemie, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany
| | - Nicole Dimos
- Institut für Chemie und Biochemie, Strukturbiochemie, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany
| | - Marion Ringel
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), Lichtenbergstr. 4, 85748 Garching, Germany
| | - Thomas Brück
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), Lichtenbergstr. 4, 85748 Garching, Germany
| | - Bernhard Loll
- Institut für Chemie und Biochemie, Strukturbiochemie, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany
| | - Dan Thomas Major
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
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5
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Zhuang J, Zhang F, Zhou J, Deng W, Wu R. Residue-Orientation-Dependent Dynamics and Selectivity of Active Pocket in Microbe Class I Terpene Cyclases. J Chem Inf Model 2020; 60:4985-4994. [PMID: 32786702 DOI: 10.1021/acs.jcim.0c00159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Microbe class I terpene cyclases (TPCs) are responsible for deriving numerous functionally and structurally diverse groups of terpenoid natural products. The conformational change of their active pockets from "open" state to "closed" state upon substrate binding has been clarified. However, the key structural basis relevant to this active pocket dynamics and its detailed molecular mechanism are still unclear. In this work, on the basis of the molecular dynamics (MD) on two microbe class I TPCs (SdS and bCinS), we propose that the active pocket dynamics is highly dependent on the residue orientation of two conserved structural bases R-D dyad and X-R-D triad, rather than the previously suggested flexibility of kink region. Actually, we considered that the flexibility of kink region is synchronous with the R residue orientation of the X-R-D triad, which could regulate the entrance size of active pocket and thus affect the substrate selectivity of active pocket by utilizing the promiscuity of the X-R-D triad. Furthermore, to better understand the function of the two structural bases, two intelligible models of "PPi catcher-locker" and "selector-PPi sensor-orienter" are proposed to, respectively, describe the R-D dyad and X-R-D triad and broadened to more microbe class I TPCs. These findings exhibit the dynamics of active pocket inaccessible in static crystal structures and provide useful structural basis knowledge for further design of microbe class I TPCs with different cyclization ability.
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Affiliation(s)
- Jingyuan Zhuang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Fan Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Jingwei Zhou
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510405, P. R. China
| | - Wenbin Deng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Ruibo Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
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6
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Malico AA, Calzini MA, Gayen AK, Williams GJ. Synthetic biology, combinatorial biosynthesis, and chemo‑enzymatic synthesis of isoprenoids. J Ind Microbiol Biotechnol 2020; 47:675-702. [PMID: 32880770 PMCID: PMC7666032 DOI: 10.1007/s10295-020-02306-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 08/27/2020] [Indexed: 12/12/2022]
Abstract
Isoprenoids are a large class of natural products with myriad applications as bioactive and commercial compounds. Their diverse structures are derived from the biosynthetic assembly and tailoring of their scaffolds, ultimately constructed from two C5 hemiterpene building blocks. The modular logic of these platforms can be harnessed to improve titers of valuable isoprenoids in diverse hosts and to produce new-to-nature compounds. Often, this process is facilitated by the substrate or product promiscuity of the component enzymes, which can be leveraged to produce novel isoprenoids. To complement rational enhancements and even re-programming of isoprenoid biosynthesis, high-throughput approaches that rely on searching through large enzymatic libraries are being developed. This review summarizes recent advances and strategies related to isoprenoid synthetic biology, combinatorial biosynthesis, and chemo-enzymatic synthesis, focusing on the past 5 years. Emerging applications of cell-free biosynthesis and high-throughput tools are included that culminate in a discussion of the future outlook and perspective of isoprenoid biosynthetic engineering.
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Affiliation(s)
| | - Miles A Calzini
- Department of Chemistry, NC State University, Raleigh, NC, 27695, USA
| | - Anuran K Gayen
- Department of Chemistry, NC State University, Raleigh, NC, 27695, USA
| | - Gavin J Williams
- Department of Chemistry, NC State University, Raleigh, NC, 27695, USA.
- Comparative Medicine Institute, NC State University, Raleigh, NC, 27695, USA.
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7
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Raz K, Levi S, Gupta PK, Major DT. Enzymatic control of product distribution in terpene synthases: insights from multiscale simulations. Curr Opin Biotechnol 2020; 65:248-258. [PMID: 32679412 DOI: 10.1016/j.copbio.2020.06.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/03/2020] [Accepted: 06/07/2020] [Indexed: 11/25/2022]
Abstract
In this opinion, we review some recent work on terpene biosynthesis using multiscale simulation approaches, with special focus on contributions from our group. Terpene synthases generate terpenes employing rich carbocation chemistry, including highly specific ring formations, proton, hydride, methyl, and methylene migrations, followed by reaction quenching. In these enzymes, the main catalytic challenge is not rate enhancement, but rather control of intrinsically reactive carbocations and the resulting product distribution. Herein, we review multiscale simulations of selected mono-, sesqui-, and diterpene synthases. We point to the many tools adopted by terpene synthases to achieve correct substrate fold, carbocation formation, carbocation reaction environment, and reaction quenching. A better understanding of the toolbox employed by terpene synthases is expected to aid in the search for new enzymatic and biomimetic synthetic routes to natural and unnatural terpenes.
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Affiliation(s)
- Keren Raz
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Shani Levi
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Prashant Kumar Gupta
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel.
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8
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Villafana RT, Rampersad SN. Signatures of TRI5, TRI8 and TRI11 Protein Sequences of Fusarium incarnatum-equiseti Species Complex (FIESC) Indicate Differential Trichothecene Analogue Production. Toxins (Basel) 2020; 12:E386. [PMID: 32545314 PMCID: PMC7354511 DOI: 10.3390/toxins12060386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/03/2020] [Accepted: 06/07/2020] [Indexed: 11/24/2022] Open
Abstract
The variability and phylogeny among TRI5, TRI8 and TRI11 nucleotide and translated protein sequences of isolates from Trinidad belonging to Fusarium incarnatum-equiseti species complex (FIESC) were compared with FIESC reference sequences. Taxa appeared to be more divergent when DNA sequences were analyzed compared to protein sequences. Neutral and non-neutral mutations in TRI protein sequences that may correspond to variability in the function and structure of the selected TRI proteins were identified. TRI5p had the lowest amino acid diversity with zero predicted non-neutral mutations. TRI5p had potentially three protein disorder regions compared to TRI8p with five protein disorder regions. The deduced TRI11p was more conserved than TRI8p of the same strains. Amino acid substitutions that may be non-neutral to protein function were only detected in diacetoxyscirpenol (DAS) and fusarenon-X (FUS-X) producers of the reference sequence subset for TRI8p and TRI11p. The deduced TRI5 and TRI8 amino acid sequences were mapped to known 3D-structure models and indicated that variations in specific protein order/disorder regions exist in these sequences which affect the overall structural conservation of TRI proteins. Assigning single or combination non-neutral mutations to a particular toxicogenic phenotype may be more representative of potential compared to using genotypic data alone, especially in the absence of wet-lab, experimental validation.
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Affiliation(s)
| | - Sephra N. Rampersad
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago, West Indies;
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Zhang C, Chen X, Orban A, Shukal S, Birk F, Too HP, Rühl M. Agrocybe aegerita Serves As a Gateway for Identifying Sesquiterpene Biosynthetic Enzymes in Higher Fungi. ACS Chem Biol 2020; 15:1268-1277. [PMID: 32233445 DOI: 10.1021/acschembio.0c00155] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Terpenoids constitute a structurally diverse group of natural products with wide applications in the pharmaceutical, nutritional, flavor and fragrance industries. Fungi are known to produce a large variety of terpenoids, yet fungal terpene synthases remain largely unexploited. Here, we report the sesquiterpene network and gene clusters of the black poplar mushroom Agrocybe aegerita. Among 11 putative sesquiterpene synthases (STSs) identified in its genome, nine are functional, including two novel synthases producing viridiflorol and viridiflorene. On this basis, an additional 1133 STS homologues from higher fungi have been curated and used for a sequence similarity network to probe isofunctional STS groups. With the focus on two STS groups, one producing viridiflorene/viridiflorol and one Δ6-protoilludene, the isofunctionality was probed and verified. Three new Δ6-protoilludene synthases and two new viridflorene/viridiflorol synthases from five different fungi were correctly predicted. The study herein serves as a fundamental predictive framework for the discovery of fungal STSs and biosynthesis of novel terpenoids. Furthermore, it becomes clear that fungal STS function differs between the phyla Ascomycota and Basidiomycota with the latter phylum being more dominant in the overall number and variability. This study aims to encourage the scientific community to further work on fungal STS and the products, biological functions, and potential applications of this vast source of natural products.
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Affiliation(s)
- Congqiang Zhang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Xixian Chen
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Axel Orban
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Giessen, Germany
| | - Sudha Shukal
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Florian Birk
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Giessen, Germany
| | - Heng-Phon Too
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Martin Rühl
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Branch for Bioresources, Giessen, Germany
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Rinkel J, Dickschat JS. Mechanistic investigations on multiproduct β-himachalene synthase from Cryptosporangium arvum. Beilstein J Org Chem 2019; 15:1008-1019. [PMID: 31164939 PMCID: PMC6541374 DOI: 10.3762/bjoc.15.99] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 04/26/2019] [Indexed: 12/30/2022] Open
Abstract
A bacterial terpene synthase from Cryptosporangium arvum was characterised as a multiproduct β-himachalene synthase. In vitro studies showed not only a high promiscuity with respect to its numerous sesquiterpene products, including the structurally demanding terpenes longicyclene, longifolene and α-longipinene, but also to its substrates, as additional activity was observed with geranyl- and geranylgeranyl diphosphate. In-depth mechanistic investigations using isotopically labelled precursors regarding the stereochemical course of both 1,11-cyclisation and 1,3-hydride shift furnished a detailed catalytic model suggesting the molecular basis of the observed low product selectivity. The enzyme’s synthetic potential was also exploited in the preparation of sesquiterpene isotopomers, which provided insights into their EIMS fragmentation mechanisms.
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Affiliation(s)
- Jan Rinkel
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
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11
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Flynn CM, Broz K, Jonkers W, Schmidt-Dannert C, Kistler HC. Expression of the Fusarium graminearum terpenome and involvement of the endoplasmic reticulum-derived toxisome. Fungal Genet Biol 2019; 124:78-87. [PMID: 30664933 DOI: 10.1016/j.fgb.2019.01.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/29/2018] [Accepted: 01/14/2019] [Indexed: 12/26/2022]
Abstract
The sesquiterpenoid deoxynivalenol (DON) is an important trichothecene mycotoxin produced by the cereal pathogen Fusarium graminearum. DON is synthesized in specialized subcellular structures called toxisomes. The first step in DON synthesis is catalyzed by the sesquiterpene synthase (STS), Tri5 (trichodiene synthase), resulting in the cyclization of farnesyl diphosphate (FPP) to produce the sesquiterpene trichodiene. Tri5 is one of eight putative STSs in the F. graminearum genome. To better understand the F. graminearum terpenome, the volatile and soluble fractions of fungal cultures were sampled. Stringent regulation of sesquiterpene accumulation was observed. When grown in trichothecene induction medium, the fungus produces trichothecenes as well as several volatile non-trichothecene related sesquiterpenes, whereas no volatile terpenes were detected when grown in non-inducing medium. Surprisingly, a Δtri5 deletion strain grown in inducing conditions not only ceased accumulation of trichothecenes, but also failed to produce the non-trichothecene related sesquiterpenes. To test whether Tri5 from F. graminearum may be a promiscuous STS directly producing all observed sesquiterpenes, Tri5 was cloned and expressed in E. coli and shown to produce primarily trichodiene in addition to minor, related cyclization products. Therefore, while Tri5 expression in F. graminearum is necessary for non-trichothecene sesquiterpene biosynthesis, direct catalysis by Tri5 does not explain the sesquiterpene deficient phenotype observed in the Δtri5 strain. To test whether Tri5 protein, separate from its enzymatic activity, may be required for non-trichothecene synthesis, the Tri5 locus was replaced with an enzymatically inactive, but structurally unaffected tri5N225D S229T allele. This allele restores non-trichothecene synthesis but not trichothecene synthesis. The tri5N225D S229T allele also restores toxisome structure which is lacking in the Δtri5 deletion strain. Our results indicate that the Tri5 protein, but not its enzymatic activity, is also required for the synthesis of non-trichothecene related sesquiterpenes and the formation of toxisomes. Toxisomes thus not only may be important for DON synthesis, but also for the synthesis of other sesquiterpene mycotoxins such as culmorin by F. graminearum.
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Affiliation(s)
- Christopher M Flynn
- University of Minnesota, Department of Biochemistry, Molecular Biology, and Biophysics, Saint Paul, MN, USA
| | - Karen Broz
- USDA ARS Cereal Disease Laboratory, Saint Paul, MN, USA
| | | | - Claudia Schmidt-Dannert
- University of Minnesota, Department of Biochemistry, Molecular Biology, and Biophysics, Saint Paul, MN, USA
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12
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Rinkel J, Köllner TG, Chen F, Dickschat JS. Characterisation of three terpene synthases for β-barbatene, β-araneosene and nephthenol from social amoebae. Chem Commun (Camb) 2019; 55:13255-13258. [DOI: 10.1039/c9cc07681f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Three terpene synthases from social amoebae with new functions were discovered and their mechanisms were explored.
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Affiliation(s)
- Jan Rinkel
- Kekulé-Institut für Organische Chemie und Biochemie
- Rheinische Friedrich-Wilhelms-Universität Bonn
- Gerhard-Domagk-Straße 1
- 53121 Bonn
- Germany
| | - Tobias G. Köllner
- Max Planck Institute for Chemical Ecology
- Hans-Knöll-Straße 8
- 07745 Jena
- Germany
| | - Feng Chen
- Department of Plant Sciences
- University of Tennessee
- 2431 Joe Johnson Drive
- Knoxville
- USA
| | - Jeroen S. Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie
- Rheinische Friedrich-Wilhelms-Universität Bonn
- Gerhard-Domagk-Straße 1
- 53121 Bonn
- Germany
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13
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Liu J, Zhai Y, Zhang Y, Zhu S, Liu G, Che Y. Heterologous Biosynthesis of the Fungal Sesquiterpene Trichodermol in Saccharomyces cerevisiae. Front Microbiol 2018; 9:1773. [PMID: 30127776 PMCID: PMC6087768 DOI: 10.3389/fmicb.2018.01773] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 07/16/2018] [Indexed: 01/01/2023] Open
Abstract
Trichodermol, a fungal sesquiterpene derived from the farnesyl diphosphate pathway, is the biosynthetic precursor for trichodermin, a member of the trichothecene class of fungal toxins produced mainly by the genera of Trichoderma and Fusarium. Trichodermin is a promising candidate for the development of fungicides and antitumor agents due to its significant antifungal and cytotoxic effects. It can also serve as a scaffold to generate new congeners for structure-activity relationship (SAR) study. We reconstructed the biosynthetic pathway of trichodermol in Saccharomyces cerevisiae BY4741, and investigated the effect of produced trichodermol on the host by de novo RNA sequencing (RNA-Seq) and quantitative Real-time PCR analyses. Co-expression of pESC::FgTRI5 using plasmid pLLeu-tHMGR-UPC2.1 led to trichodiene production of 683 μg L-1, while integration of only the codon-optimized FgTRI5 into the chromosome of yeast improved the production to 6,535 μg L-1. Subsequent expression of the codon-optimized cytochrome P450 monooxygenase encoding genes, TaTRI4 and TaTRI11, resulted in trichodermol, with an estimated titer of 252 μg L-1 at shake flask level. RNA-Seq and qPCR analyses revealed that the produced trichodermol downregulated the expression of the genes involved in ergosterol biosynthesis, but significantly upregulated the expression of PDR5 related to membrane transport pathway in S. cerevisiae. Collectively, we achieved the first heterologous biosynthesis of trichodermol by reconstructing its biosynthetic pathway in yeast, and the reconstructed pathway will serve as a platform to generate trichodermin analogs as potential candidates for agrochemicals and anticancer agents through further optimizations.
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Affiliation(s)
- Jianghua Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yanan Zhai
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China
| | - Yang Zhang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Shuaiming Zhu
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Gang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yongsheng Che
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China.,State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
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14
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Wang YH, Zhang F, Zhou J, Xie H, Wu R. Reply to Comment on “Substrate Folding Modes in Trichodiene Synthase: A Determinant of Chemo- and Stereoselectivity”. ACS Catal 2018. [DOI: 10.1021/acscatal.7b03906] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yong-Heng Wang
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Fan Zhang
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Jingwei Zhou
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Hujun Xie
- Department
of Applied Chemistry, Zhejiang Gongshang University, Hangzhou 310035, P. R. China
| | - Ruibo Wu
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
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15
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Burkhardt I, Dickschat JS. The absolute configuration of isochamigrene: new insights into the cyclisation mechanism of trichodiene synthase. Chem Commun (Camb) 2018; 54:3540-3542. [DOI: 10.1039/c8cc01744a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The enantioselective synthesis of isochamigrene clarified its absolute configuration and biosynthetic relation to trichodiene.
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Affiliation(s)
- Immo Burkhardt
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn
- 53121 Bonn
- Germany
| | - Jeroen S. Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn
- 53121 Bonn
- Germany
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16
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Zhang F, Wang YH, Tang X, Wu R. Catalytic promiscuity of the non-native FPP substrate in the TEAS enzyme: non-negligible flexibility of the carbocation intermediate. Phys Chem Chem Phys 2018; 20:15061-15073. [DOI: 10.1039/c8cp02262c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
By QM(DFT)/MM MD simulations, it has been revealed that the non-native substrate catalytic promiscuity of TEAS (one of the sesquiterpene cyclases) is mostly attributable to its notable conformational flexibility of the branching intermediate bisabolyl cation.
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Affiliation(s)
- Fan Zhang
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| | - Yong-Heng Wang
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| | - Xiaowen Tang
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| | - Ruibo Wu
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
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17
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Wang YH, Xie H, Zhou J, Zhang F, Wu R. Substrate Folding Modes in Trichodiene Synthase: A Determinant of Chemo- and Stereoselectivity. ACS Catal 2017. [DOI: 10.1021/acscatal.7b01462] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yong-Heng Wang
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Hujun Xie
- Department
of Applied Chemistry, Zhejiang Gongshang University, Hangzhou 310035, P. R. China
| | - Jingwei Zhou
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Fan Zhang
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Ruibo Wu
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
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18
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Eslami H, Mohtashami SK, Basmanj MT, Rahati M, Rahimi H. An in-silico insight into the substrate binding characteristics of the active site of amorpha-4, 11-diene synthase, a key enzyme in artemisinin biosynthesis. J Mol Model 2017. [PMID: 28620813 DOI: 10.1007/s00894-017-3374-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The enzyme amorphadiene synthase (ADS) conducts the first committed step in the biosynthetic conversion of the substrate farnesyl pyrophosphate (FPP) to artemisinin, which is a highly effective natural product against multidrug-resistant strains of malaria. Due to the either low abundance or low turn-over rate of the enzyme, obtaining artemisinin from both natural and synthetic sources is costly and laborious. In this in silico study, we strived to elucidate the substrate binding site specificities of the ADS, with the rational that unraveling enzyme features paves the way for enzyme engineering to increase synthesis rate. A homology model of the ADS from Artemisia annua L. was constructed based on the available crystal structure of the 5-epiaristolochene synthase (TEAS) and further analyzed with molecular dynamic simulations to determine residues forming the substrate recognition pocket. We also investigated the structural aspects of Mg2+ binding. Results revealed DDYTD and NDLMT as metal-binding motifs in the putative active site gorge, which is composed of the D and H helixes and one loop region (aa519-532). Moreover, several representative residues including Tyr519, Asp444, Trp271, Asn443, Thr399, Arg262, Val292, Gly400 and Leu405, determine the FPP binding mode and its fate in terms of stereochemistry as well as the enzyme fidelity for the specific end product. These findings lead to inferences concerning key components of the ADS catalytic cavity, and provide evidence for the spatial localization of the FPP and Mg2+. Such detailed understanding will probably help to design an improved enzyme.
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Affiliation(s)
- Habib Eslami
- Department of Pharmacology, Molecular Medicine Research Center, Hormozgan Health Institute, School of Pharmacy, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Seyed Kaveh Mohtashami
- Crop Genetic Engineering Group- Biofuel Research Team (BRT), Agricultural Biotechnology Research Institute of Iran (ABRII), Karaj, Iran
| | - Maryam Taghavi Basmanj
- Biotechnology Research Center, Molecular Medicine Department, Pasteur Institute of Iran, Tehran, Iran
| | - Maryam Rahati
- Crop Genetic Engineering Group- Biofuel Research Team (BRT), Agricultural Biotechnology Research Institute of Iran (ABRII), Karaj, Iran
| | - Hamzeh Rahimi
- Biotechnology Research Center, Molecular Medicine Department, Pasteur Institute of Iran, Tehran, Iran.
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19
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Maeda K, Nakajima Y, Motoyama T, Kondoh Y, Kawamura T, Kanamaru K, Ohsato S, Nishiuchi T, Yoshida M, Osada H, Kobayashi T, Kimura M. Identification of a trichothecene production inhibitor by chemical array and library screening using trichodiene synthase as a target protein. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2017; 138:1-7. [PMID: 28456298 DOI: 10.1016/j.pestbp.2017.03.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/20/2017] [Accepted: 03/21/2017] [Indexed: 06/07/2023]
Abstract
Trichothecene mycotoxins often accumulate in apparently normal grains of cereal crops. In an effort to develop an agricultural chemical to reduce trichothecene contamination, we screened trichothecene production inhibitors from the compounds on the chemical arrays. By using the trichodiene (TDN) synthase tagged with hexahistidine (rTRI5) as a target protein, 32 hit compounds were obtained from chemical library of the RIKEN Natural Product Depository (NPDepo) by chemical array screening. At 10μgmL-1, none of the 32 chemicals inhibited trichothecene production by Fusarium graminearum in liquid culture. Against the purified rTRI5 enzyme, however, NPD10133 [progesterone 3-(O-carboxymethyl)oxime amide-bonded to phenylalanine] showed weak inhibitory activity at 10μgmL-1 (18.7μM). For the screening of chemicals inhibiting trichothecene accumulation in liquid culture, 20 analogs of NPD10133 selected from the NPDepo chemical library were assayed. At 10μM, only NPD352 [testosterone 3-(O-carboxymethyl)oxime amide-bonded to phenylalanine methyl ester] inhibited rTRI5 activity and trichothecene production. Kinetic analysis suggested that the enzyme inhibition was of a mixed-type. The identification of NPD352 as a TDN synthase inhibitor lays the foundation for the development of a more potent inhibitor via systematic introduction of wide structural diversity on the gonane skeleton and amino acid residues.
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Affiliation(s)
- Kazuyuki Maeda
- Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan; Graduate School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Yuichi Nakajima
- Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan; Chemical Genetics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Takayuki Motoyama
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yasumitsu Kondoh
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Tatsuro Kawamura
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kyoko Kanamaru
- Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Shuichi Ohsato
- Graduate School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Takumi Nishiuchi
- Division of Functional Genomics, Advanced Science Research Centre, Kanazawa University, 13-1 Takaramachi, Kanazawa, Ishikawa 920-0934, Japan
| | - Minoru Yoshida
- Chemical Genetics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hiroyuki Osada
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Tetsuo Kobayashi
- Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Makoto Kimura
- Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
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20
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Vattekkatte A, Garms S, Boland W. Alternate Cyclization Cascade Initiated by Substrate Isomer in Multiproduct Terpene Synthase from Medicago truncatula. J Org Chem 2017; 82:2855-2861. [DOI: 10.1021/acs.joc.6b02696] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Abith Vattekkatte
- Department of Bioorganic
Chemistry, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Hans-Knöll-Strasse 8, D-07745 Jena, Germany
| | - Stefan Garms
- Department of Bioorganic
Chemistry, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Hans-Knöll-Strasse 8, D-07745 Jena, Germany
| | - Wilhelm Boland
- Department of Bioorganic
Chemistry, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Hans-Knöll-Strasse 8, D-07745 Jena, Germany
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21
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Dixit M, Weitman M, Gao J, Major DT. Chemical Control in the Battle against Fidelity in Promiscuous Natural Product Biosynthesis: The Case of Trichodiene Synthase. ACS Catal 2017; 7:812-818. [PMID: 29399379 PMCID: PMC5793923 DOI: 10.1021/acscatal.6b02584] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Terpene cyclases catalyze the highly stereospecific molding of polyisoprenes into terpenes, which are precursors to most known natural compounds. The isoprenoids are formed via intricate chemical cascades employing rich, yet highly erratic, carbocation chemistry. It is currently not well understood how these biocatalysts achieve chemical control. Here, we illustrate the catalytic control exerted by trichodiene synthase, and in particular, we discover two features that could be general catalytic tools adopted by other terpenoid cyclases. First, to avoid formation of byproducts, the enzyme raises the energy of bisabolyl carbocation, which is a general mechanistic branching point in many sesquiterpene cyclases, resulting in an essentially concerted cyclization cascade. Second, we identify a sulfur-carbocation dative bonding interaction that anchors the bisabolyl cation in a reactive conformation, avoiding tumbling and premature deprotonation. Specifically, Met73 acts as a chameleon, shifting from an initial sulfur-π interaction in the Michaelis complex to a sulfur-carbocation complex during catalysis.
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Affiliation(s)
- Mudit Dixit
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Michal Weitman
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Jiali Gao
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Theoretical Chemistry Institute, Jilin University, Changchun 130023, P.R. China
| | - Dan T. Major
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
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22
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Zhang F, Chen N, Zhou J, Wu R. Protonation-Dependent Diphosphate Cleavage in FPP Cyclases and Synthases. ACS Catal 2016. [DOI: 10.1021/acscatal.6b02096] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Fan Zhang
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People’s Republic of China
| | - Nanhao Chen
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People’s Republic of China
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Jingwei Zhou
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People’s Republic of China
| | - Ruibo Wu
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People’s Republic of China
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23
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Lin Z, Chen D, Liu W. Biosynthesis-based artificial evolution of microbial natural products. Sci China Chem 2016. [DOI: 10.1007/s11426-016-0062-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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24
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Pani G, Dessì A, Dallocchio R, Scherm B, Azara E, Delogu G, Migheli Q. Natural Phenolic Inhibitors of Trichothecene Biosynthesis by the Wheat Fungal Pathogen Fusarium culmorum: A Computational Insight into the Structure-Activity Relationship. PLoS One 2016; 11:e0157316. [PMID: 27294666 PMCID: PMC4905666 DOI: 10.1371/journal.pone.0157316] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 05/29/2016] [Indexed: 02/02/2023] Open
Abstract
A model of the trichodiene synthase (TRI5) of the wheat fungal pathogen and type-B trichothecene producer Fusarium culmorum was developed based on homology modelling with the crystallized protein of F. sporotrichioides. Eight phenolic molecules, namely ferulic acid 1, apocynin 2, propyl gallate 3, eugenol 4, Me-dehydrozingerone 5, eugenol dimer 6, magnolol 7, and ellagic acid 8, were selected for their ability to inhibit trichothecene production and/or fungal vegetative growth in F. culmorum. The chemical structures of phenols were constructed and partially optimised based on Molecular Mechanics (MM) studies and energy minimisation by Density Functional Theory (DFT). Docking analysis of the phenolic molecules was run on the 3D model of F. culmorum TRI5. Experimental biological activity, molecular descriptors and interacting-structures obtained from computational analysis were compared. Besides the catalytic domain, three privileged sites in the interaction with the inhibitory molecules were identified on the protein surface. The TRI5-ligand interactions highlighted in this study represent a powerful tool to the identification of new Fusarium-targeted molecules with potential as trichothecene inhibitors.
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Affiliation(s)
- Giovanna Pani
- Dipartimento di Agraria and Unità di Ricerca Istituto Nazionale di Biostrutture e Biosistemi, Università degli Studi di Sassari, Viale Italia 39, I-07100, Sassari, Italy
| | - Alessandro Dessì
- Istituto CNR di Chimica Biomolecolare, Traversa La Crucca 3, I-07100, Sassari, Italy
| | - Roberto Dallocchio
- Istituto CNR di Chimica Biomolecolare, Traversa La Crucca 3, I-07100, Sassari, Italy
| | - Barbara Scherm
- Dipartimento di Agraria and Unità di Ricerca Istituto Nazionale di Biostrutture e Biosistemi, Università degli Studi di Sassari, Viale Italia 39, I-07100, Sassari, Italy
| | - Emanuela Azara
- Istituto CNR di Chimica Biomolecolare, Traversa La Crucca 3, I-07100, Sassari, Italy
| | - Giovanna Delogu
- Istituto CNR di Chimica Biomolecolare, Traversa La Crucca 3, I-07100, Sassari, Italy
| | - Quirico Migheli
- Dipartimento di Agraria and Unità di Ricerca Istituto Nazionale di Biostrutture e Biosistemi, Università degli Studi di Sassari, Viale Italia 39, I-07100, Sassari, Italy
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25
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Pearsall SM, Rowley CN, Berry A. Advances in Pathway Engineering for Natural Product Biosynthesis. ChemCatChem 2015. [DOI: 10.1002/cctc.201500602] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Sarah M. Pearsall
- Astbury Centre for Structural Molecular Biology; University of Leeds; Leeds LS2 9JT UK
| | - Christopher N. Rowley
- Astbury Centre for Structural Molecular Biology; University of Leeds; Leeds LS2 9JT UK
| | - Alan Berry
- Astbury Centre for Structural Molecular Biology; University of Leeds; Leeds LS2 9JT UK
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26
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Quin MB, Michel SN, Schmidt-Dannert C. Moonlighting Metals: Insights into Regulation of Cyclization Pathways in Fungal Δ(6) -Protoilludene Sesquiterpene Synthases. Chembiochem 2015; 16:2191-9. [PMID: 26239156 DOI: 10.1002/cbic.201500308] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Indexed: 01/30/2023]
Abstract
Fungal 1,11 cyclizing sesquiterpene synthases are product specific under typical reaction conditions. However, in vivo expression of certain Δ(6)-protoilludene synthases results in dual 1,11 and 1,10 cyclization. To determine the factors regulating this mechanistic variation, in-depth in vitro characterization of Δ(6)-protoilludene synthases was conducted. Divalent metal ions determine cyclization specificity and this product variability. Promiscuity in metal binding is mediated by secondary metal-binding sites away from the conserved D(D/E)XX(D/E) motif in sesquiterpene synthases. Phylogenetic analysis revealed a divergent evolution of Basidiomycota trans-humulyl cation producing sesquiterpene synthases, results that indicate a wider diversity in function than previously predicted. This study provides key insights into the function and evolution of 1,11 cyclizing fungal sesquiterpene synthases.
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Affiliation(s)
- Maureen B Quin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN, 55108, USA
| | - Stephen N Michel
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN, 55108, USA
| | - Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN, 55108, USA.
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27
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Kumari I, Chaudhary N, Sandhu P, Ahmed M, Akhter Y. Structural and mechanistic analysis of engineered trichodiene synthase enzymes from Trichoderma harzianum: towards higher catalytic activities empowering sustainable agriculture. J Biomol Struct Dyn 2015. [PMID: 26207800 DOI: 10.1080/07391102.2015.1073632] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Trichoderma spp. are well-known bioagents for the plant growth promotion and pathogen suppression. The beneficial activities of the fungus Trichoderma spp. are attributed to their ability to produce and secrete certain secondary metabolites such as trichodermin that belongs to trichothecene family of molecules. The initial steps of trichodermin biosynthetic pathway in Trichoderma are similar to the trichothecenes from Fusarium sporotrichioides. Trichodiene synthase (TS) encoded by tri5 gene in Trichoderma catalyses the conversion of farnesyl pyrophosphate to trichodiene as reported earlier. In this study, we have carried out a comprehensive comparative sequence and structural analysis of the TS, which revealed the conserved residues involved in catalytic activity of the protein. In silico, modelled tertiary structure of TS protein showed stable structural behaviour during simulations. Two single-substitution mutants, i.e. D109E, D248Y and one double-substitution mutant (D109E and D248Y) of TS with potentially higher activities are screened out. The mutant proteins showed more stability than the wild type, an increased number of electrostatic interactions and better binding energies with the ligand, which further elucidates the amino acid residues involved in the reaction mechanism. These results will lead to devise strategies for higher TS activity to ultimately enhance the trichodermin production by Trichoderma spp. for its better exploitation in the sustainable agricultural practices.
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Affiliation(s)
- Indu Kumari
- a School of Earth and Environmental Sciences, Central University of Himachal Pradesh , District-Kangra, Shahpur , Himachal Pradesh 176206 , India
| | - Nitika Chaudhary
- a School of Earth and Environmental Sciences, Central University of Himachal Pradesh , District-Kangra, Shahpur , Himachal Pradesh 176206 , India
| | - Padmani Sandhu
- b School of Life Sciences, Central University of Himachal Pradesh , District-Kangra, Shahpur , Himachal Pradesh 176206 , India
| | - Mushtaq Ahmed
- a School of Earth and Environmental Sciences, Central University of Himachal Pradesh , District-Kangra, Shahpur , Himachal Pradesh 176206 , India
| | - Yusuf Akhter
- b School of Life Sciences, Central University of Himachal Pradesh , District-Kangra, Shahpur , Himachal Pradesh 176206 , India
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28
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Lauchli R, Pitzer J, Kitto RZ, Kalbarczyk KZ, Rabe KS. Improved selectivity of an engineered multi-product terpene synthase. Org Biomol Chem 2015; 12:4013-20. [PMID: 24809278 DOI: 10.1039/c4ob00479e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mutation of the sesquiterpene synthase Cop2 was conducted with a high-throughput screen for the cyclization activity using a non-natural substrate. A mutant of Cop2 was identified that contained three amino acid substitutions. This mutant, 17H2, converted the natural substrate FPP into germacrene D-4-ol with 77% selectivity. This selectivity is in contrast to that of the parent enzyme in which germacrene D-4-ol is produced as 29% and α-cadinol is produced as 46% of the product mixture. The mutations were shown to each contribute to this selectivity, and a homology model suggested that the mutations lie near to the active site though would be unlikely to be targeted for mutation by rational methods. Kinetic comparisons show that 17H2 maintains a kcat/KM of 0.62 mM(-1) s(-1), which is nearly identical to that of the parent Cop2, which had a kcat/KM of 0.58 mM(-1) s(-1).
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Affiliation(s)
- Ryan Lauchli
- California Institute of Technology, Division of Chemistry & Chemical Engineering, 1200 E. California Blvd., Pasadena CA 91125, USA
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29
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Shaw JJ, Berbasova T, Sasaki T, Jefferson-George K, Spakowicz DJ, Dunican BF, Portero CE, Narváez-Trujillo A, Strobel SA. Identification of a fungal 1,8-cineole synthase from Hypoxylon sp. with specificity determinants in common with the plant synthases. J Biol Chem 2015; 290:8511-26. [PMID: 25648891 DOI: 10.1074/jbc.m114.636159] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Terpenes are an important and diverse class of secondary metabolites widely produced by fungi. Volatile compound screening of a fungal endophyte collection revealed a number of isolates in the family Xylariaceae, producing a series of terpene molecules, including 1,8-cineole. This compound is a commercially important component of eucalyptus oil used in pharmaceutical applications and has been explored as a potential biofuel additive. The genes that produce terpene molecules, such as 1,8-cineole, have been little explored in fungi, providing an opportunity to explore the biosynthetic origin of these compounds. Through genome sequencing of cineole-producing isolate E7406B, we were able to identify 11 new terpene synthase genes. Expressing a subset of these genes in Escherichia coli allowed identification of the hyp3 gene, responsible for 1,8-cineole biosynthesis, the first monoterpene synthase discovered in fungi. In a striking example of convergent evolution, mutational analysis of this terpene synthase revealed an active site asparagine critical for water capture and specificity during cineole synthesis, the same mechanism used in an unrelated plant homologue. These studies have provided insight into the evolutionary relationship of fungal terpene synthases to those in plants and bacteria and further established fungi as a relatively untapped source of this important and diverse class of compounds.
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Affiliation(s)
- Jeffrey J Shaw
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - Tetyana Berbasova
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - Tomoaki Sasaki
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - Kyra Jefferson-George
- the Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and
| | - Daniel J Spakowicz
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - Brian F Dunican
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - Carolina E Portero
- the Laboratorio de Biotecnología Vegetal, Pontificia Universidad Católica del Ecuador, Quito 17 01 21 84, Ecuador
| | - Alexandra Narváez-Trujillo
- the Laboratorio de Biotecnología Vegetal, Pontificia Universidad Católica del Ecuador, Quito 17 01 21 84, Ecuador
| | - Scott A Strobel
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520,
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30
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Abstract
Fungi (Ascomycota and Basidiomycota) are prolific producers of structurally diverse terpenoid compounds. Classes of terpenoids identified in fungi include the sesqui-, di- and triterpenoids. Biosynthetic pathways and enzymes to terpenoids from each of these classes have been described. These typically involve the scaffold generating terpene synthases and cyclases, and scaffold tailoring enzymes such as e.g. cytochrome P450 monoxygenases, NAD(P)+ and flavin dependent oxidoreductases, and various group transferases that generate the final bioactive structures. The biosynthesis of several sesquiterpenoid mycotoxins and bioactive diterpenoids has been well-studied in Ascomycota (e.g. filamentous fungi). Little is known about the terpenoid biosynthetic pathways in Basidiomycota (e.g. mushroom forming fungi), although they produce a huge diversity of terpenoid natural products. Specifically, many trans-humulyl cation derived sesquiterpenoid natural products with potent bioactivities have been isolated. Biosynthetic gene clusters responsible for the production of trans-humulyl cation derived protoilludanes, and other sesquiterpenoids, can be rapidly identified by genome sequencing and bioinformatic methods. Genome mining combined with heterologous biosynthetic pathway refactoring has the potential to facilitate discovery and production of pharmaceutically relevant fungal terpenoids.
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Affiliation(s)
- Maureen B Quin
- University of Minnesota, Dept. of Biochemistry, Molecular Biology and Biophysics, 1479 Gortner Avenue, St. Paul, MN 55108, USA
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31
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Janke R, Görner C, Hirte M, Brück T, Loll B. The first structure of a bacterial diterpene cyclase: CotB2. ACTA ACUST UNITED AC 2014; 70:1528-37. [PMID: 24914964 DOI: 10.1107/s1399004714005513] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 03/11/2014] [Indexed: 02/05/2023]
Abstract
Sesquiterpenes and diterpenes are a diverse class of secondary metabolites that are predominantly derived from plants and some prokaryotes. The properties of these natural products encompass antitumor, antibiotic and even insecticidal activities. Therefore, they are interesting commercial targets for the chemical and pharmaceutical industries. Owing to their structural complexity, these compounds are more efficiently accessed by metabolic engineering of microbial systems than by chemical synthesis. This work presents the first crystal structure of a bacterial diterpene cyclase, CotB2 from the soil bacterium Streptomyces melanosporofaciens, at 1.64 Å resolution. CotB2 is a diterpene cyclase that catalyzes the cyclization of the linear geranylgeranyl diphosphate to the tricyclic cyclooctat-9-en-7-ol. The subsequent oxidation of cyclooctat-9-en-7-ol by two cytochrome P450 monooxygenases leads to bioactive cyclooctatin. Plasticity residues that decorate the active site of CotB2 have been mutated, resulting in alternative monocyclic, dicyclic and tricyclic compounds that show bioactivity. These new compounds shed new light on diterpene cyclase reaction mechanisms. Furthermore, the product of mutant CotB2(W288G) produced the new antibiotic compound (1R,3E,7E,11S,12S)-3,7,18-dolabellatriene, which acts specifically against multidrug-resistant Staphylococcus aureus. This opens a sustainable route for the industrial-scale production of this bioactive compound.
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Affiliation(s)
- Ronja Janke
- Institut für Chemie und Biochemie, Abteilung Strukturbiochemie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Christian Görner
- Fachgebiet Industrielle Biokatalyse, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Max Hirte
- Fachgebiet Industrielle Biokatalyse, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Thomas Brück
- Fachgebiet Industrielle Biokatalyse, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Bernhard Loll
- Institut für Chemie und Biochemie, Abteilung Strukturbiochemie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
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A high-throughput colorimetric screening assay for terpene synthase activity based on substrate consumption. PLoS One 2014; 9:e93317. [PMID: 24681801 PMCID: PMC3969365 DOI: 10.1371/journal.pone.0093317] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 03/03/2014] [Indexed: 11/25/2022] Open
Abstract
Terpene synthases catalyze the formation of a variety of terpene chemical structures. Systematic mutagenesis studies have been effective in providing insights into the characteristic and complex mechanisms of C-C bond formations and in exploring the enzymatic potential for inventing new chemical structures. In addition, there is growing demand to increase terpene synthase activity in heterologous hosts, given the maturation of metabolic engineering and host breeding for terpenoid synthesis. We have developed a simple screening method for the cellular activities of terpene synthases by scoring their substrate consumption based on the color loss of the cell harboring carotenoid pathways. We demonstrate that this method can be used to detect activities of various terpene synthase or prenyltransferase genes in a high-throughput manner, irrespective of the product type, enabling the mutation analysis and directed evolution of terpene synthases. We also report the possibility for substrate-specific screening system of terpene synthases by taking advantage of the substrate-size specificity of C30 and C40 carotenoid pathways.
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33
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Wawrzyn GT, Quin MB, Choudhary S, López-Gallego F, Schmidt-Dannert C. Draft genome of Omphalotus olearius provides a predictive framework for sesquiterpenoid natural product biosynthesis in Basidiomycota. ACTA ACUST UNITED AC 2014; 19:772-83. [PMID: 22726691 DOI: 10.1016/j.chembiol.2012.05.012] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 05/08/2012] [Accepted: 05/15/2012] [Indexed: 02/06/2023]
Abstract
The secondary metabolome of Basidiomycota represents a largely uncharacterized source of pharmaceutically relevant natural products. Terpenoids are the primary class of bioactive compounds isolated from mushrooms. The Jack O'Lantern mushroom Omphalotus olearius was identified 50 years ago as a prolific producer of anticancer illudin sesquiterpenoids; however, to date there have been exceptionally few studies into the biosynthesis of these important compounds. Here, we report the draft genome sequence of O. olearius, which reveals a diverse network of sesquiterpene synthases and two metabolic gene clusters associated with illudin biosynthesis. Characterization of the sesquiterpene synthases enabled a comprehensive survey of all currently available Basidiomycota genomes, thereby creating a predictive resource for terpenoid natural product biosynthesis in these organisms. Our results will facilitate discovery and biosynthetic production of unique pharmaceutically relevant bioactive compounds from Basidiomycota.
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Affiliation(s)
- Grayson T Wawrzyn
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
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34
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Li R, Chou WKW, Himmelberger JA, Litwin KM, Harris GG, Cane DE, Christianson DW. Reprogramming the chemodiversity of terpenoid cyclization by remolding the active site contour of epi-isozizaene synthase. Biochemistry 2014; 53:1155-68. [PMID: 24517311 PMCID: PMC3985761 DOI: 10.1021/bi401643u] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The class I terpenoid cyclase epi-isozizaene synthase (EIZS) utilizes the universal achiral isoprenoid substrate, farnesyl diphosphate, to generate epi-isozizaene as the predominant sesquiterpene cyclization product and at least five minor sesquiterpene products, making EIZS an ideal platform for the exploration of fidelity and promiscuity in a terpenoid cyclization reaction. The hydrophobic active site contour of EIZS serves as a template that enforces a single substrate conformation, and chaperones subsequently formed carbocation intermediates through a well-defined mechanistic sequence. Here, we have used the crystal structure of EIZS as a guide to systematically remold the hydrophobic active site contour in a library of 26 site-specific mutants. Remolded cyclization templates reprogram the reaction cascade not only by reproportioning products generated by the wild-type enzyme but also by generating completely new products of diverse structure. Specifically, we have tripled the overall number of characterized products generated by EIZS. Moreover, we have converted EIZS into six different sesquiterpene synthases: F96A EIZS is an (E)-β-farnesene synthase, F96W EIZS is a zizaene synthase, F95H EIZS is a β-curcumene synthase, F95M EIZS is a β-acoradiene synthase, F198L EIZS is a β-cedrene synthase, and F96V EIZS and W203F EIZS are (Z)-γ-bisabolene synthases. Active site aromatic residues appear to be hot spots for reprogramming the cyclization cascade by manipulating the stability and conformation of critical carbocation intermediates. A majority of mutant enzymes exhibit only relatively modest 2-100-fold losses of catalytic activity, suggesting that residues responsible for triggering substrate ionization readily tolerate mutations deeper in the active site cavity.
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Affiliation(s)
- Ruiqiong Li
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , Philadelphia, Pennsylvania 19104-6323, United States
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35
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Hong YJ, Tantillo DJ. Branching Out from the Bisabolyl Cation. Unifying Mechanistic Pathways to Barbatene, Bazzanene, Chamigrene, Chamipinene, Cumacrene, Cuprenene, Dunniene, Isobazzanene, Iso-γ-bisabolene, Isochamigrene, Laurene, Microbiotene, Sesquithujene, Sesquisabinene, Thujopsene, Trichodiene, and Widdradiene Sesquiterpenes. J Am Chem Soc 2014; 136:2450-63. [DOI: 10.1021/ja4106489] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Young J. Hong
- Department
of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Dean J. Tantillo
- Department
of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
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36
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Schmidt-Dannert C. Biosynthesis of terpenoid natural products in fungi. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 148:19-61. [PMID: 25414054 DOI: 10.1007/10_2014_283] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Tens of thousands of terpenoid natural products have been isolated from plants and microbial sources. Higher fungi (Ascomycota and Basidiomycota) are known to produce an array of well-known terpenoid natural products, including mycotoxins, antibiotics, antitumor compounds, and phytohormones. Except for a few well-studied fungal biosynthetic pathways, the majority of genes and biosynthetic pathways responsible for the biosynthesis of a small number of these secondary metabolites have only been discovered and characterized in the past 5-10 years. This chapter provides a comprehensive overview of the current knowledge on fungal terpenoid biosynthesis from biochemical, genetic, and genomic viewpoints. Enzymes involved in synthesizing, transferring, and cyclizing the prenyl chains that form the hydrocarbon scaffolds of fungal terpenoid natural products are systematically discussed. Genomic information and functional evidence suggest differences between the terpenome of the two major fungal phyla--the Ascomycota and Basidiomycota--which will be illustrated for each group of terpenoid natural products.
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Affiliation(s)
- Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minneapolis, MN, 55108, USA,
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37
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Scherm B, Balmas V, Spanu F, Pani G, Delogu G, Pasquali M, Migheli Q. Fusarium culmorum: causal agent of foot and root rot and head blight on wheat. MOLECULAR PLANT PATHOLOGY 2013; 14:323-41. [PMID: 23279114 PMCID: PMC6638779 DOI: 10.1111/mpp.12011] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
UNLABELLED Fusarium culmorum is a ubiquitous soil-borne fungus able to cause foot and root rot and Fusarium head blight on different small-grain cereals, in particular wheat and barley. It causes significant yield and quality losses and results in contamination of the grain with mycotoxins. This review summarizes recent research activities related to F. culmorum, including studies into its population diversity, mycotoxin biosynthesis, mechanisms of pathogenesis and resistance, the development of diagnostic tools and preliminary genome sequence surveys. We also propose potential research areas that may expand our basic understanding of the wheat-F. culmorum interaction and assist in the management of the disease caused by this pathogen. TAXONOMY Fusarium culmorum (W.G. Smith) Sacc. Kingdom Fungi; Phylum Ascomycota; Subphylum Pezizomycotina; Class Sordariomycetes; Subclass Hypocreomycetidae; Order Hypocreales; Family Nectriaceae; Genus Fusarium. DISEASE SYMPTOMS Foot and root rot (also known as Fusarium crown rot): seedling blight with death of the plant before or after emergence; brown discoloration on roots and coleoptiles of the infected seedlings; brown discoloration on subcrown internodes and on the first two/three internodes of the main stem; tiller abortion; formation of whiteheads with shrivelled white grains; Fusarium head blight: prematurely bleached spikelets or blighting of the entire head, which remains empty or contains shrunken dark kernels. IDENTIFICATION AND DETECTION: Morphological identification is based on the shape of the macroconidia formed on sporodochia on carnation leaf agar. The conidiophores are branched monophialides, short and wide. The macroconidia are relatively short and stout with an apical cell blunt or slightly papillate; the basal cell is foot-shaped or just notched. Macroconidia are thick-walled and curved, usually 3-5 septate, and mostly measuring 30-50 × 5.0-7.5 μm. Microconidia are absent. Oval to globose chlamydospores are formed, intercalary in the hyphae, solitary, in chains or in clumps; they are also formed from macroconidia. The colony grows very rapidly (1.6-2.2 cm/day) on potato dextrose agar (PDA) at the optimum temperature of 25 °C. The mycelium on PDA is floccose, whitish, light yellow or red. The pigment on the reverse plate on PDA varies from greyish-rose, carmine red or burgundy. A wide array of polymerase chain reaction (PCR) and real-time PCR tools, as well as complementary methods, which are summarised in the first two tables, have been developed for the detection and/or quantification of F. culmorum in culture and in naturally infected plant tissue. HOST RANGE Fusarium culmorum has a wide range of host plants, mainly cereals, such as wheat, barley, oats, rye, corn, sorghum and various grasses. In addition, it has been isolated from sugar beet, flax, carnation, bean, pea, asparagus, red clover, hop, leeks, Norway spruce, strawberry and potato tuber. Fusarium culmorum has also been associated with dermatitis on marram grass planters in the Netherlands, although its role as a causal agent of skin lesions appears questionable. It is also isolated as a symbiont able to confer resistance to abiotic stress, and has been proposed as a potential biocontrol agent to control the aquatic weed Hydrilla spp. USEFUL WEBSITES http://isolate.fusariumdb.org/; http://sppadbase.ipp.cnr.it/; http://www.broad.mit.edu/annotation/genome/fusarium_group/MultiHome.html; http://www.fgsc.net/Fusarium/fushome.htm; http://plantpath.psu.edu/facilities/fusarium-research-center; http://www.phi-base.org/; http://www.uniprot.org/; http://www.cabi.org/; http://www.indexfungorum.org/
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Affiliation(s)
- Barbara Scherm
- Dipartimento di Agraria-Sezione di Patologia Vegetale ed Entomologia and Centro Interdisciplinare per lo Sviluppo della Ricerca Biotecnologica e per lo Studio della Biodiversità della Sardegna e dell'Area Mediterranea, Università degli Studi di Sassari, Via E. De Nicola 9, I-07100 Sassari, Italy
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38
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Lauchli R, Rabe KS, Kalbarczyk KZ, Tata A, Heel T, Kitto RZ, Arnold FH. High-throughput screening for terpene-synthase-cyclization activity and directed evolution of a terpene synthase. Angew Chem Int Ed Engl 2013; 52:5571-4. [PMID: 23532864 DOI: 10.1002/anie.201301362] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Indexed: 12/30/2022]
Affiliation(s)
- Ryan Lauchli
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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39
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Lauchli R, Rabe KS, Kalbarczyk KZ, Tata A, Heel T, Kitto RZ, Arnold FH. High-Throughput Screening for Terpene-Synthase-Cyclization Activity and Directed Evolution of a Terpene Synthase. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201301362] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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40
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Gao Y, Honzatko RB, Peters RJ. Terpenoid synthase structures: a so far incomplete view of complex catalysis. Nat Prod Rep 2012; 29:1153-75. [PMID: 22907771 PMCID: PMC3448952 DOI: 10.1039/c2np20059g] [Citation(s) in RCA: 244] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The complexity of terpenoid natural products has drawn significant interest, particularly since their common (poly)isoprenyl origins were discovered. Notably, much of this complexity is derived from the highly variable cyclized and/or rearranged nature of the observed hydrocarbon skeletal structures. Indeed, at least in some cases it is difficult to immediately recognize their derivation from poly-isoprenyl precursors. Nevertheless, these diverse structures are formed by sequential elongation to acyclic precursors, most often with subsequent cyclization and/or rearrangement. Strikingly, the reactions used to assemble and diversify terpenoid backbones share a common carbocationic driven mechanism, although the means by which the initial carbocation is generated does vary. High-resolution crystal structures have been obtained for at least representative examples from each of the various types of enzymes involved in producing terpenoid hydrocarbon backbones. However, while this has certainly led to some insights into the enzymatic structure-function relationships underlying the elongation and simpler cyclization reactions, our understanding of the more complex cyclization and/or rearrangement reactions remains limited. Accordingly, selected examples are discussed here to demonstrate our current understanding, its limits, and potential ways forward.
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Affiliation(s)
- Yang Gao
- Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Richard B. Honzatko
- Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Reuben J. Peters
- Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, IA 50011, USA
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41
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Garms S, Chen F, Boland W, Gershenzon J, Köllner TG. A single amino acid determines the site of deprotonation in the active center of sesquiterpene synthases SbTPS1 and SbTPS2 from Sorghum bicolor. PHYTOCHEMISTRY 2012; 75:6-13. [PMID: 22226036 DOI: 10.1016/j.phytochem.2011.12.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 12/05/2011] [Accepted: 12/09/2011] [Indexed: 05/31/2023]
Abstract
The multitude of terpene carbon skeletons found in nature is formed by enzymes known as terpene synthases (TPSs). These proteins are often multiproduct enzymes converting a single prenyl diphosphate substrate into a mixture of terpene products. The recently identified sesquiterpene synthases SbTPS1 and SbTPS2 from Sorghum bicolor produce terpene blends containing the same products, but in different proportions. A single amino acid in the active site was reported to determine the different product specificities of SbTPS1 and SbTPS2. In this study we examined the reaction mechanism of the Sorghum TPSs. Feeding experiments with deuterium-labeled substrates and chiral analysis of the enzyme products zingiberene, β-sesquiphellandrene and β-bisabolene revealed that the reactions catalyzed by both enzymes proceeded via (S)-nerolidyl diphosphate and the cyclic (6S)-bisabol-7-yl and (6R)-bisabol-1-yl cation intermediates. The site of deprotonation of the final cation was shown to be the only catalytic difference between SbTPS1 and SbTPS2. Docking of the (6R)-bisabol-1-yl cation into structural models of SbTPS1 and SbTPS2 indicated a potential role of initially cleaved pyrophosphate group as a proton acceptor.
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Affiliation(s)
- Stefan Garms
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, D-07745 Jena, Germany
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42
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Miller DJ, Allemann RK. Sesquiterpene synthases: Passive catalysts or active players? Nat Prod Rep 2012; 29:60-71. [DOI: 10.1039/c1np00060h] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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43
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Garrett SR, Morris RJ, O'Maille PE. Steady-state kinetic characterization of sesquiterpene synthases by gas chromatography-mass spectroscopy. Methods Enzymol 2012; 515:3-19. [PMID: 22999167 DOI: 10.1016/b978-0-12-394290-6.00001-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Sesquiterpene synthases produce a wide variety of structurally diverse hydrocarbon products from a single substrate: farnesyl pyrophosphate. Each enzyme will often produce a multitude of products for which the kinetic efficiency is traditionally measured using a radioactivity assay. Here, we introduce a gas chromatography-mass spectroscopy-based assay to measure the formation of a single abundant product from which the kinetic parameters of the enzyme in question can be elucidated. We present an accounting of experimental components and considerations, such as solution conditions and instrument parameters, necessary to perform a standardized vial assay experiment. Further, we outline pilot experiments to establish analyte quantification and the linear range of enzyme concentration versus reaction velocity. Finally, we describe a protocol for a steady-state kinetics experiment, and the processing of experimental data to produce a Michaelis-Menten plot enabling one to derive kinetic parameters.
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Affiliation(s)
- Steven R Garrett
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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44
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Wawrzyn GT, Bloch SE, Schmidt-Dannert C. Discovery and characterization of terpenoid biosynthetic pathways of fungi. Methods Enzymol 2012; 515:83-105. [PMID: 22999171 DOI: 10.1016/b978-0-12-394290-6.00005-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fungi produce a myriad of terpenoids with a broad range of biological activities, many of which can be adapted to human use. This requires knowledge of the enzymes responsible for the biosynthesis of these compounds. Herein, we describe strategies for identification and characterization of putative biosynthetic genes, structural examination of important pathway enzymes with a focus on altering activity, and identification of biosynthetic clusters, and genome mining for yet-to-be-discovered pathways. Fungi are a particularly attractive class of organism for terpenoid pathway discovery, as they often cluster their biosynthetic genes. The affordability of genome sequencing and the relatively small size of fungal genomes further simplify this process. While only a select few fungal strains are genetically tractable, many terpenoid biosynthetic genes are functional in Escherichia coli and Saccharomyces cerevisiae, allowing easy characterization. Identification of new terpenoid biosynthetic pathways has the potential to uncover new pharmaceutical compounds and establish new strategies for metabolic engineering.
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Affiliation(s)
- Grayson T Wawrzyn
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota, USA
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Dickschat JS, Brock NL, Citron CA, Tudzynski B. Biosynthesis of sesquiterpenes by the fungus Fusarium verticillioides. Chembiochem 2011; 12:2088-95. [PMID: 21748838 DOI: 10.1002/cbic.201100268] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Indexed: 11/06/2022]
Abstract
The volatiles of the fungus Fusarium verticillioides were analysed by GC-MS. Sesquiterpenes dominated, with trichodiene as the principle component. Several other sesquiterpenes were detected in low amounts that were unambiguously identified from their mass spectra and retention indices. The absolute configurations of (R)-β-bisabolene, (R)-cuparene, (+)-β-barbatene, (-)-α-cedrene, (+)-β-cedrene, and (+)-α-funebrene originating from different key cationic intermediates, were determined by chiral GC-MS and proved to be related to the trichodiene stereostructure. The unusual compound (E)-iso-γ-bisabolene was also found corroborating a previously suggested mechanism for the cyclisation of the bisabolyl to the cuprenyl cation that is based on quantum mechanical calculations (Y. J. Hong, D. J. Tantillo, Org. Lett. 2006, 8, 4601-4604). These analyses resulted in a revised biosynthesis scheme to trichodiene and the side products of the responsible terpene cyclase, trichodiene synthase, an enzyme that is well characterised from Fusarium sporotrichioides. Feeding studies with several deuterated mevalonolactone isotopomers unravelled stereochemical aspects of the late cyclisations towards trichodiene.
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Affiliation(s)
- Jeroen S Dickschat
- Institut für Organische Chemie, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany.
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Engels B, Heinig U, Grothe T, Stadler M, Jennewein S. Cloning and characterization of an Armillaria gallica cDNA encoding protoilludene synthase, which catalyzes the first committed step in the synthesis of antimicrobial melleolides. J Biol Chem 2010; 286:6871-8. [PMID: 21148562 PMCID: PMC3044942 DOI: 10.1074/jbc.m110.165845] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Melleolides and related fungal sesquiterpenoid aryl esters are antimicrobial and cytotoxic natural products derived from cultures of the Homobasidiomycetes genus Armillaria. The initial step in the biosynthesis of all melleolides involves cyclization of the universal sesquiterpene precursor farnesyl diphosphate to produce protoilludene, a reaction catalyzed by protoilludene synthase. We achieved the partial purification of protoilludene synthase from a mycelial culture of Armillaria gallica and found that 6-protoilludene was its exclusive reaction product. Therefore, a further isomerization reaction is necessary to convert the 6–7 double bond into the 7–8 double bond found in melleolides. We expressed an A. gallica protoilludene synthase cDNA in Escherichia coli, and this also led to the exclusive production of 6-protoilludene. Sequence comparison of the isolated sesquiterpene synthase revealed a distant relationship to other fungal terpene synthases. The isolation of the genomic sequence identified the 6-protoilludene synthase to be present as a single copy gene in the genome of A. gallica, possessing an open reading frame interrupted with eight introns.
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Affiliation(s)
- Benedikt Engels
- Fraunhofer Institut für Molekularbiologie und Angewandte Ökologie, Forckenbeckstrasse 6, 52074 Aachen, Germany
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Overexpression of the trichodiene synthase gene tri5 increases trichodermin production and antimicrobial activity in Trichoderma brevicompactum. Fungal Genet Biol 2010; 48:285-96. [PMID: 21145409 DOI: 10.1016/j.fgb.2010.11.012] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 11/06/2010] [Accepted: 11/25/2010] [Indexed: 11/20/2022]
Abstract
Trichoderma brevicompactum produces trichodermin, a simple trichothecene-type toxin that shares the first steps of the sesquiterpene biosynthetic pathway with other phytotoxic trichothecenes from Fusarium spp. Trichodiene synthase catalyses the conversion of farnesyl pyrophosphate to trichodiene and it is encoded by the tri5 gene that was cloned and analysed functionally by homologous overexpression in T. brevicompactum. tri5 expression was up-regulated in media with glucose, H(2)O(2) or glycerol. tri5 repression was observed in cultures supplemented with the antioxidants ferulic acid and tyrosol. Acetone extracts of tri5-overexpressing transformants displayed higher antifungal activity than those from the wild-type. Chromatographic and spectroscopic analyses revealed that tri5 overexpression led to an increased production of trichodermin and tyrosol. Agar diffusion assays with these two purified metabolites from the tri5-overexpressing transformant T. brevicompactum Tb41tri5 showed that only trichodermin had antifungal activity against Saccharomyces cerevisiae, Kluyveromyces marxianus, Candida albicans, Candida glabrata, Candida tropicalis and Aspergillus fumigatus, in most cases such activity being higher than that observed for amphotericin B and hygromycin. Our results point to the significant role of tri5 in the production of trichodermin and in the antifungal activity of T. brevicompactum.
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López-Gallego F, Wawrzyn G, Schmidt-Dannert C. Selectivity of fungal sesquiterpene synthases: role of the active site's H-1 alpha loop in catalysis. Appl Environ Microbiol 2010; 76:7723-33. [PMID: 20889795 PMCID: PMC2988597 DOI: 10.1128/aem.01811-10] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 09/22/2010] [Indexed: 11/20/2022] Open
Abstract
Sesquiterpene synthases are responsible for the cyclization of farnesyl pyrophosphate into a myriad of structurally diverse compounds with various biological activities. We examine here the role of the conserved active site H-α1 loop in catalysis in three previously characterized fungal sesquiterpene synthases. The H-α1 loops of Cop3, Cop4, and Cop6 from Coprinus cinereus were altered by site-directed mutagenesis and the resultant product profiles were analyzed by gas chromatography-mass spectrometry and compared to the wild-type enzymes. In addition, we examine the effect of swapping the H-α1 loop from the promiscuous enzyme Cop4 with the more selective Cop6 and the effect of acidic or basic conditions on loop mutations in Cop4. Directed mutations of the H-α1 loop had a marked effect on the product profile of Cop3 and Cop4, while little to no change was shown in Cop6. Swapping of the Cop4 and Cop6 loops with one another was again shown to influence the product profile of Cop4, while the product profile of Cop6 remained identical to the wild-type enzyme. The loop mutations in Cop4 also implicate specific residues responsible for the pH sensitivity of the enzyme. These results affirm the role of the H-α1 loop in catalysis and provide a potential target to increase the product diversity of terpene synthases.
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Affiliation(s)
- Fernando López-Gallego
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108
| | - GraysonT. Wawrzyn
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108
| | - Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108
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Garms S, Köllner TG, Boland W. A multiproduct terpene synthase from Medicago truncatula generates cadalane sesquiterpenes via two different mechanisms. J Org Chem 2010; 75:5590-600. [PMID: 20704432 DOI: 10.1021/jo100917c] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Terpene synthases are responsible for a large diversity of terpene carbon skeletons found in nature. The multiproduct sesquiterpene synthase MtTPS5 isolated from Medicago truncatula produces 27 products from farnesyl diphosphate (1, FDP). In this paper, we report the reaction steps involved in the formation of these products using incubation experiments with deuterium-containing substrates; we determined the absolute configuration of individual products to establish the stereochemical course of the reaction cascade and the initial conformation of the cycling substrate. Additional labeling experiments conducted with deuterium oxide showed that cadalane sesquiterpenes are mainly produced via the protonation of the neutral intermediate germacrene D (5). These findings provide an alternative route to the general accepted pathway via nerolidyl diphosphate (2, NDP) en route to sesquiterpenes with a cadalane skeleton. Mutational analysis of the enzyme demonstrated that a tyrosine residue is important for the protonation process.
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Affiliation(s)
- Stefan Garms
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
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Lopez-Gallego F, Agger SA, Abate-Pella D, Distefano MD, Schmidt-Dannert C. Sesquiterpene synthases Cop4 and Cop6 from Coprinus cinereus: catalytic promiscuity and cyclization of farnesyl pyrophosphate geometric isomers. Chembiochem 2010; 11:1093-106. [PMID: 20419721 DOI: 10.1002/cbic.200900671] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Sesquiterpene synthases catalyze with different catalytic fidelity the cyclization of farnesyl pyrophosphate (FPP) into hundreds of known compounds with diverse structures and stereochemistries. Two sesquiterpene synthases, Cop4 and Cop6, were previously isolated from Coprinus cinereus as part of a fungal genome survey. This study investigates the reaction mechanism and catalytic fidelity of the two enzymes. Cyclization of all-trans-FPP ((E,E)-FPP) was compared to the cyclization of the cis-trans isomer of FPP ((Z,E)-FPP) as a surrogate for the secondary cisoid neryl cation intermediate generated by sesquiterpene synthases, which are capable of isomerizing the C2--C3 pi bond of all-trans-FPP. Cop6 is a "high-fidelity" alpha-cuprenene synthase that retains its fidelity under various conditions tested. Cop4 is a catalytically promiscuous enzyme that cyclizes (E,E)-FPP into multiple products, including (-)-germacrene D and cubebol. Changing the pH of the reaction drastically alters the fidelity of Cop4 and makes it a highly selective enzyme. Cyclization of (Z,E)-FPP by Cop4 and Cop6 yields products that are very different from those obtained with (E,E)-FPP. Conversion of (E,E)-FPP proceeds via a (6R)-beta-bisabolyl carbocation in the case of Cop6 and an (E,E)-germacradienyl carbocation in the case of Cop4. However, (Z,E)-FPP is cyclized via a (6S)-beta-bisabolene carbocation by both enzymes. Structural modeling suggests that differences in the active site and the loop that covers the active site of the two enzymes might explain their different catalytic fidelities.
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