1
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Némethová I, Schmid D, Tiefenbacher K. Supramolecular Capsule Catalysis Enables the Exploration of Terpenoid Chemical Space Untapped by Nature. Angew Chem Int Ed Engl 2023; 62:e202218625. [PMID: 36727480 DOI: 10.1002/anie.202218625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/23/2023] [Accepted: 01/26/2023] [Indexed: 02/03/2023]
Abstract
Terpenes represent the largest and the most diverse class of natural compounds. This is remarkable as the whole variety is accessed from just a handful of highly conserved linear precursors. Modification of the cyclization precursors would enable a dramatic expansion of the accessible chemical space. However, natural enzymes do not enable us to tap into this potential, as they do not tolerate larger deviations from the prototypical substrate structure. Herein we report that supramolecular capsule catalysis enables facile access to diverse and novel terpenoid skeletons that formally can be traced back to C3-phenyl, benzyl, and homoprenyl derivatives of farnesol. Novel skeletons related to the presilphiperfolane core structure, as well as novel neoclovene derivatives were accessed efficiently in only four synthetic steps. Importantly, the products obtained carry functional groups that may be readily derivatized further.
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Affiliation(s)
- Ivana Némethová
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4002, Basel, Switzerland
| | - Dario Schmid
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4002, Basel, Switzerland
| | - Konrad Tiefenbacher
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4002, Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
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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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Abstract
The product of a terpene synthase from Streptomyces lincolnensis has been identified as the new natural product isoishwarane. The enzyme mechanism was studied by isotopic labelling experiments and site-directed mutagenesis.
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Affiliation(s)
- Houchao Xu
- Kekulé-Institut für Organische Chemie und Biochemie
- Rheinische Friedrich-Wilhelms-Universität Bonn
- 53121 Bonn
- Germany
| | - Jan Rinkel
- Kekulé-Institut für Organische Chemie und Biochemie
- Rheinische Friedrich-Wilhelms-Universität Bonn
- 53121 Bonn
- Germany
| | - Jeroen S. Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie
- Rheinische Friedrich-Wilhelms-Universität Bonn
- 53121 Bonn
- Germany
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4
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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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5
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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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6
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Zhang LL, Huang W, Zhang YY, Fan G, He J, Ren JN, Li Z, Li X, Pan SY. Genomic and Transcriptomic Study for Screening Genes Involved in the Limonene Biotransformation of Penicillium digitatum DSM 62840. Front Microbiol 2020; 11:744. [PMID: 32390984 PMCID: PMC7188761 DOI: 10.3389/fmicb.2020.00744] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/30/2020] [Indexed: 12/21/2022] Open
Abstract
α-Terpineol has been widely used in daily chemical, pharmaceutical, food, and flavor industries due to its pleasant odor with high economic value and pharmacological action. Our previous study showed that Penicillium digitatum DSM 62840 was an efficient biocatalyst for the transformation of limonene to α-terpineol. Thus, it was meaningful to explore the genome features and the gene expression differences of strain DSM 62840 during limonene biotransformation, and the detailed bioconversion pathways. In this study, the functional genes related to limonene bioconversion were investigated using genome and transcriptome sequences analysis. The results showed that the P. digitatum DSM 62840 genome was estimated to be 29.09 Mb and it encoded 9,086 protein-encoding genes. The most annotated genes were associated to some protein metabolism and energy metabolism functions. When the threshold for differentially expressed genes (DEGs) was set at twofold ratio, a total of 4,128, and 4,148 DEGs were identified in P_L_12h (limonene-treated condition) compared with P_0h (blank) and P_12h (limonene-untreated blank), respectively. Among them, the expression levels of genes involved in the biosynthesis of secondary metabolites, energy metabolism and ATP-binding cassette (ABC) transporters were significantly altered during the biotransformation. And the reliability of these results was further confirmed by quantitative real-time polymerase chain reaction (RT-qPCR). Moreover, we found that the enzyme participated in limonene biotransformation was inducible. This enzyme was located in the microsome, and it was inhibited by cytochrome P450 inhibitors. This indicated that the cytochrome P450 may be responsible for the limonene bioconversion. Several differentially expressed cytochrome P450 genes were further identified, such as PDIDSM_85260 and PDIDSM_67430, which were significantly up-regulated with limonene treatment. These genes may be responsible for converting limonene to α-terpineol. Totally, the genomic and transcriptomic data could provide valuable information in the discovery of related-genes which was involved in limonene biotransformation, pathogenicity of fungi, and investigation of metabolites and biological pathways of strain DSM 62840.
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Affiliation(s)
- Lu-Lu Zhang
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wen Huang
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ying-Ying Zhang
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Gang Fan
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jin He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jing-Nan Ren
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhi Li
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiao Li
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Si-Yi Pan
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
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7
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Drummond L, Kschowak MJ, Breitenbach J, Wolff H, Shi YM, Schrader J, Bode HB, Sandmann G, Buchhaupt M. Expanding the Isoprenoid Building Block Repertoire with an IPP Methyltransferase from Streptomyces monomycini. ACS Synth Biol 2019; 8:1303-1313. [PMID: 31059642 DOI: 10.1021/acssynbio.8b00525] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Many synthetic biology approaches aim at expanding the product diversity of enzymes or whole biosynthetic pathways. However, the chemical structure space of natural product forming routes is often restricted by the limited cellular availability of different starting intermediates. Although the terpene biosynthesis pathways are highly modular, their starting intermediates are almost exclusively the C5 units IPP and DMAPP. To amplify the possibilities of terpene biosynthesis through the modification of its building blocks, we identified and characterized a SAM-dependent methyltransferase converting IPP into a variety of C6 and C7 prenyl pyrophosphates. Heterologous expression in Escherichia coli not only extended the intracellular prenyl pyrophosphate spectrum with mono- or dimethylated IPP and DMAPP, but also enabled the biosynthesis of C11, C12, C16, and C17 prenyl pyrophosphates. We furthermore demonstrated the general high promiscuity of terpenoid biosynthesis pathways toward uncommon building blocks by the E. coli-based production of polymethylated C41, C42, and C43 carotenoids. Integration of the IPP methyltransferase in terpene synthesis pathways enables an expansion of the terpenoid structure space beyond the borders predetermined by the isoprene rule which indicates a restricted synthesis by condensation of C5 units.
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Affiliation(s)
- Laura Drummond
- Industrial Biotechnology, DECHEMA Research Institute, Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
- Institute for Molecular Bioscience, Johann Wolfgang Goethe University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Max J. Kschowak
- Industrial Biotechnology, DECHEMA Research Institute, Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
- Institute for Molecular Bioscience, Johann Wolfgang Goethe University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Jürgen Breitenbach
- Institute for Molecular Bioscience, Johann Wolfgang Goethe University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Hendrik Wolff
- Institute for Molecular Bioscience, Johann Wolfgang Goethe University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Yi-Ming Shi
- Institute for Molecular Bioscience, Johann Wolfgang Goethe University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Jens Schrader
- Industrial Biotechnology, DECHEMA Research Institute, Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
| | - Helge B. Bode
- Institute for Molecular Bioscience, Johann Wolfgang Goethe University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Johann Wolfgang Goethe University, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
| | - Gerhard Sandmann
- Institute for Molecular Bioscience, Johann Wolfgang Goethe University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Markus Buchhaupt
- Industrial Biotechnology, DECHEMA Research Institute, Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
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8
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Liu T, Yin K, Liu C, Luo J, Crittenden J, Zhang W, Luo S, He Q, Deng Y, Liu H, Zhang D. The role of reactive oxygen species and carbonate radical in oxcarbazepine degradation via UV, UV/H 2O 2: Kinetics, mechanisms and toxicity evaluation. WATER RESEARCH 2018; 147:204-213. [PMID: 30312793 DOI: 10.1016/j.watres.2018.10.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 10/01/2018] [Accepted: 10/04/2018] [Indexed: 05/17/2023]
Abstract
Oxcarbazepine (OXC) is ubiquitous in the aqueous environment. And due to its ecotoxicological effects and potential risks to human, an effective way to eliminate OXC from aqueous environment has aroused public concerns in recent years. Radical-based reactions have been shown to be an efficient way for OXC destruction, but the reactions of OXC with reactive oxygen species (ROS) and carbonate radical (CO3•-) are still unclear. In this study, we focused the degradation of OXC and ROS, CO3•- generation mechanism, and their roles in OXC degradation via UV and UV/H2O2. The triplet state of oxcarbazepine (3OXC∗) was found to play an important role in OXC degradation via UV. And hydroxyl radicals (•OH) and singlet oxygen (1O2) were found to be the dominant ROS in OXC degradation. Superoxide radical (O2•-) did not react with OXC directly, but it may react with intermediate byproducts. Generation of CO3•- played a positive role on OXC degradation for both UV and UV/H2O2. In addition to •OH, 3OXC* also contribute to CO3•- production. The second-order rate constants of OXC with •OH and CO3•- were 1.7 × 1010 M-1 s-1 and 8.6 × 107 M-1 s-1, respectively. Potential OXC degradation mechanisms by •OH were proposed and included hydroxylation, α-ketol rearrangement, and benzylic acid rearrangement. Compared with non-selective •OH, the reactions involving CO3•- are mainly electron transfer and hydrogen abstraction. And the acute toxicity of OXC was lower after UV/H2O2 and UV/H2O2/HCO3- treatments, which was confirmed by luminescent bacterial assay (Vibrio fischeri bacterium).
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Affiliation(s)
- Tongcai Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, PR China
| | - Kai Yin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, PR China
| | - Chengbin Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, PR China
| | - Jinming Luo
- Brook Byers Institute for Sustainable Systems and School of Civil and Environmental Engineering, Georgia Institute of Technology, 828 West Peachtree Street, Atlanta, GA, 30332, United States.
| | - John Crittenden
- Brook Byers Institute for Sustainable Systems and School of Civil and Environmental Engineering, Georgia Institute of Technology, 828 West Peachtree Street, Atlanta, GA, 30332, United States
| | - Weiqiu Zhang
- Brook Byers Institute for Sustainable Systems and School of Civil and Environmental Engineering, Georgia Institute of Technology, 828 West Peachtree Street, Atlanta, GA, 30332, United States
| | - Shenglian Luo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, PR China; Department of Environmental and Chemical Engineering, Nanchang Hongkong University, Nanchang, 330063, China
| | - Qunying He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, PR China
| | - Yongxiu Deng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, PR China
| | - Hui Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, PR China
| | - Danyu Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, PR China
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9
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Ignea C, Pontini M, Motawia MS, Maffei ME, Makris AM, Kampranis SC. Synthesis of 11-carbon terpenoids in yeast using protein and metabolic engineering. Nat Chem Biol 2018; 14:1090-1098. [DOI: 10.1038/s41589-018-0166-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 10/11/2018] [Indexed: 12/12/2022]
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10
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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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11
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Abstract
![]()
The
year 2017 marks the twentieth anniversary of terpenoid cyclase
structural biology: a trio of terpenoid cyclase structures reported
together in 1997 were the first to set the foundation for understanding
the enzymes largely responsible for the exquisite chemodiversity of
more than 80000 terpenoid natural products. Terpenoid cyclases catalyze
the most complex chemical reactions in biology, in that more than
half of the substrate carbon atoms undergo changes in bonding and
hybridization during a single enzyme-catalyzed cyclization reaction.
The past two decades have witnessed structural, functional, and computational
studies illuminating the modes of substrate activation that initiate
the cyclization cascade, the management and manipulation of high-energy
carbocation intermediates that propagate the cyclization cascade,
and the chemical strategies that terminate the cyclization cascade.
The role of the terpenoid cyclase as a template for catalysis is paramount
to its function, and protein engineering can be used to reprogram
the cyclization cascade to generate alternative and commercially important
products. Here, I review key advances in terpenoid cyclase structural
and chemical biology, focusing mainly on terpenoid cyclases and related
prenyltransferases for which X-ray crystal structures have informed
and advanced our understanding of enzyme structure and function.
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Affiliation(s)
- David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
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12
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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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13
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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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14
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Structure-based virtual screening of hypothetical inhibitors of the enzyme longiborneol synthase—a potential target to reduce Fusarium head blight disease. J Mol Model 2016; 22:163. [DOI: 10.1007/s00894-016-3021-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 05/27/2016] [Indexed: 01/12/2023]
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15
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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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16
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Zhang F, Chen N, Wu R. Molecular Dynamics Simulations Elucidate Conformational Dynamics Responsible for the Cyclization Reaction in TEAS. J Chem Inf Model 2016; 56:877-85. [PMID: 27082764 DOI: 10.1021/acs.jcim.6b00091] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The Mg-dependent 5-epi-aristolochene synthase from Nicotiana tabacum (called TEAS) could catalyze the linear farnesyl pyrophosphate (FPP) substrate to form bicyclic hydrocarbon 5-epi-aristolochene. The cyclization reaction mechanism of TEAS was proposed based on static crystal structures and quantum chemistry calculations in a few previous studies, but substrate FPP binding kinetics and protein conformational dynamics responsible for the enzymatic catalysis are still unclear. Herein, by elaborative and extensive molecular dynamics simulations, the loop conformation change and several crucial residues promoting the cyclization reaction in TEAS are elucidated. It is found that the unusual noncatalytic NH2-terminal domain is essential to stabilize Helix-K and the adjoining J-K loop of the catalytic COOH-terminal domain. It is also illuminated that the induce-fit J-K/A-C loop dynamics is triggered by Y527 and the optimum substrate binding mode in a "U-shape" conformation. The U-shaped ligand binding pose is maintained well with the cooperative interaction of the three Mg(2+)-containing coordination shell and conserved residue W273. Furthermore, the conserved Arg residue pair R264/R266 and aromatic residue pair Y527/W273, whose spatial orientations are also crucial to promote the closure of the active site to a hydrophobic pocket, as well as to form π-stacking interactions with the ligand, would facilitate the carbocation migration and electrophilic attack involving the catalytic reaction. Our investigation more convincingly proves the greater roles of the protein local conformational dynamics than do hints from the static crystal structure observations. Thus, these findings can act as a guide to new protein engineering strategies on diversifying the sesquiterpene products for drug discovery.
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Affiliation(s)
- Fan Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, Guangdong, P.R. China
| | - Nanhao Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, Guangdong, P.R. China
| | - Ruibo Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, Guangdong, P.R. China
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17
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Genome of Diaporthe sp. provides insights into the potential inter-phylum transfer of a fungal sesquiterpenoid biosynthetic pathway. Fungal Biol 2016; 120:1050-1063. [PMID: 27521636 DOI: 10.1016/j.funbio.2016.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 04/01/2016] [Indexed: 02/06/2023]
Abstract
Fungi have highly active secondary metabolic pathways which enable them to produce a wealth of sesquiterpenoids that are bioactive. One example is Δ6-protoilludene, the precursor to the cytotoxic illudins, which are pharmaceutically relevant as anticancer therapeutics. To date, this valuable sesquiterpene has only been identified in members of the fungal division Basidiomycota. To explore the untapped potential of fungi belonging to the division Ascomycota in producing Δ6-protoilludene, we isolated a fungal endophyte Diaporthe sp. BR109 and show that it produces a diversity of terpenoids including Δ6-protoilludene. Using a genome sequencing and mining approach 17 putative novel sesquiterpene synthases were identified in Diaporthe sp. BR109. A phylogenetic approach was used to predict which gene encodes Δ6-protoilludene synthase, which was then confirmed experimentally. These analyses reveal that the sesquiterpene synthase and its putative sesquiterpene scaffold modifying cytochrome P450(s) may have been acquired by inter-phylum horizontal gene transfer from Basidiomycota to Ascomycota. Bioinformatic analyses indicate that inter-phylum transfer of these minimal sequiterpenoid secondary metabolic pathways may have occurred in other fungi. This work provides insights into the evolution of fungal sesquiterpenoid secondary metabolic pathways in the production of pharmaceutically relevant bioactive natural products.
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18
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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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19
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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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20
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Ignea C, Ioannou E, Georgantea P, Loupassaki S, Trikka FA, Kanellis AK, Makris AM, Roussis V, Kampranis SC. Reconstructing the chemical diversity of labdane-type diterpene biosynthesis in yeast. Metab Eng 2015; 28:91-103. [DOI: 10.1016/j.ymben.2014.12.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 11/09/2014] [Accepted: 12/02/2014] [Indexed: 01/08/2023]
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21
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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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22
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Kaiser E, Prasse C, Wagner M, Bröder K, Ternes TA. Transformation of oxcarbazepine and human metabolites of carbamazepine and oxcarbazepine in wastewater treatment and sand filters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:10208-10216. [PMID: 25137395 DOI: 10.1021/es5024493] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Carbamazepine (CBZ) and oxcarbazepine (OXC) are widely used anticonvulsants that are extensively metabolized in the human body. The pharmaceuticals and their human metabolites are present in influents and effluents of wastewater treatment plants (WWTPs), in rivers and streams, and in drinking water. In this study, the biodegradation of OXC and its main human metabolite, 10-hydroxy-CBZ (10OHCBZ), and the main human metabolite of CBZ, 10,11-dihydro-10,11-dihydroxy-CBZ (DiOHCBZ), was investigated in contact with activated sludge from a wastewater treatment plant (WWTP) and sand filter material from a waterworks. The transformation of DiOHCBZ, 10OHCBZ, and OXC led to the formation of the following main TPs: 1-(2-benzoic acid)-(1H,3H)-quinazoline-2,4-dione (BaQD), 1-(2-benzoic acid)-(1H,3H)-quinazoline-2-one (BaQM), 9-aldehyde-acridine, 9-carboxylic acid-acridine (9-CA-ADIN), hydroxyl 9-CA-ADIN, acridone (ADON), 11-keto-OXC, and 2,2'-(carbamoylazanediyl)dibenzoic acid. TP formation could be explained by three proposed transformation pathways, including reactions such as oxidation, α-ketol rearrangement, or benzylic acid rearrangement. The results highlight the fact that the TP abundances strongly depend on the concentrations spiked in the lab-scale experiments. BaQD, 9-CA-ADIN, and ADON were detected in WWTP effluents, rivers, and streams. 9-CA-ADIN was found at maximum concentrations in WWTP effluent and rivers up to 920 ± 50 ng L(-1) and 304 ± 26 ng L(-1), respectively. Even in drinking water, BaQD and 9-CA-ADIN were present at concentrations of 26 ± 2 ng L(-1) and 189 ± 3 ng L(-1), respectively.
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Affiliation(s)
- Elena Kaiser
- Federal Institute of Hydrology (BfG) , Am Mainzer Tor 1, 56068 Koblenz, Germany
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23
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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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24
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van der Kamp MW, Sirirak J, Żurek J, Allemann RK, Mulholland AJ. Conformational change and ligand binding in the aristolochene synthase catalytic cycle. Biochemistry 2013; 52:8094-105. [PMID: 24106830 DOI: 10.1021/bi400898k] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Terpene synthases are potentially useful biocatalysts for the synthesis of valuable compounds, such as anticancer drugs and antibiotics. The design of altered activities requires better knowledge of their mechanisms, for example, an understanding of the complex conformational changes that are part of their catalytic cycle, how they are coordinated, and what drives them. Crystallographic studies of the sesquiterpene synthase artistolochene synthase have led to a proposed sequence of ligand binding and conformational change but have provided only indirect insight. Here, we have performed extensive molecular dynamics simulations of multiple enzyme-ligand complexes (over 2 μs in total). The simulations provide clear evidence of what drives the conformational changes required for reaction. They support a picture in which the substrate farnesyl diphosphate binds first, followed by three magnesium ions in sequence, and, after reaction, the release of aristolochene and two magnesium ions followed by the final magnesium ion and diphosphate. Binding of farnesyl diphosphate leads to an increased level of sampling of open conformations, allowing the first two magnesium ions to bind. The closed enzyme conformation is maintained with a diphosphate moiety and two magnesium ions bound. The open-to-closed transition reduces flexibility around the active site entrance, partly through a lid closing over it. The simulations with all three magnesium ions and farnesyl diphosphate bound provide, for the first time, a realistic model of the Michaelis complex involved in reaction, which is inaccessible to experimental structural studies. These insights could help with the design of altered activities in a range of terpene synthases.
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Affiliation(s)
- Marc W van der Kamp
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Bristol BS8 1TS, U.K
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25
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Pemberton RP, Hong YJ, Tantillo DJ. Inherent dynamical preferences in carbocation rearrangements leading to terpene natural products. PURE APPL CHEM 2013. [DOI: 10.1351/pac-con-12-11-22] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
An introduction to the application of quantum chemical dynamics calculations to mechanistic problems in the field of terpene biosynthesis is provided. A bare bones introduction to the fundamentals of chemical dynamics is followed by a brief account of previous applications to terpene-forming carbocation reactions, a discussion of questions in this field that dynamics calculations may help answer, and a description of current problems to which dynamics calculations are being applied.
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26
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Faraldos JA, Gonzalez V, Li A, Yu F, Köksal M, Christianson DW, Allemann RK. Probing the mechanism of 1,4-conjugate elimination reactions catalyzed by terpene synthases. J Am Chem Soc 2012; 134:20844-8. [PMID: 23214943 DOI: 10.1021/ja311022s] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reaction mechanisms of (E)-β-farnesene synthase (EBFS) and isoprene synthase (ISPS), enzymes that catalyze a formal regiospecific 1,4-conjugate elimination of hydrogen diphosphate from (E,E)-farnesyl and dimethylallyl diphosphate (FDP and DMADP) to generate the semiochemicals (E)-β-farnesene and isoprene, respectively, were probed with substrate analogs and kinetic measurements. The results support stepwise reaction mechanisms through analogous enzyme-bound allylic cationic intermediates. For EBFS, we demonstrate that the elimination reaction can proceed via the enzyme-bound intermediate trans-nerolidyl diphosphate, while for ISPS the intermediacy of 2-methylbut-3-enyl 2-diphosphate can be inferred from the product outcome when deuterated DMADPs are used as substrates. Possible implications derived from the mechanistic details of the EBFS-catalyzed reaction for the evolution of sesquiterpene synthases are discussed.
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Affiliation(s)
- Juan A Faraldos
- School of Chemistry and Cardiff Catalysis Institute, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
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27
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Yoosuf-Aly Z, Faraldos JA, Miller DJ, Allemann RK. Chemoenzymatic synthesis of the alarm pheromone (+)-verbenone from geranyl diphosphate. Chem Commun (Camb) 2012; 48:7040-2. [PMID: 22684271 DOI: 10.1039/c2cc32883f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The enzyme-guided asymmetric synthesis of (+)-verbenone from geranyl diphosphate in a simple two-step, one pot transformation highlights the potential of chemoenzymatic procedures for the generation of high-value terpenoids.
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Affiliation(s)
- Zulfa Yoosuf-Aly
- School of Chemistry and Cardiff Catalysis Institute, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, United Kingdom
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28
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Köksal M, Chou WKW, Cane DE, Christianson DW. Structure of 2-methylisoborneol synthase from Streptomyces coelicolor and implications for the cyclization of a noncanonical C-methylated monoterpenoid substrate. Biochemistry 2012; 51:3011-20. [PMID: 22455514 DOI: 10.1021/bi201827a] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The crystal structure of 2-methylisoborneol synthase (MIBS) from Streptomyces coelicolor A3(2) has been determined in complex with substrate analogues geranyl-S-thiolodiphosphate and 2-fluorogeranyl diphosphate at 1.80 and 1.95 Å resolution, respectively. This terpenoid cyclase catalyzes the cyclization of the naturally occurring, noncanonical C-methylated isoprenoid substrate, 2-methylgeranyl diphosphate, to form the bicyclic product 2-methylisoborneol, a volatile C(11) homoterpene alcohol with an earthy, musty odor. While MIBS adopts the tertiary structure of a class I terpenoid cyclase, its dimeric quaternary structure differs from that previously observed in dimeric terpenoid cyclases from plants and fungi. The quaternary structure of MIBS is nonetheless similar in some respects to that of dimeric farnesyl diphosphate synthase, which is not a cyclase. The structures of MIBS complexed with substrate analogues provide insights regarding differences in the catalytic mechanism of MIBS and the mechanisms of (+)-bornyl diphosphate synthase and endo-fenchol synthase, plant cyclases that convert geranyl diphosphate into products with closely related bicyclic bornyl skeletons, but distinct structures and stereochemistries.
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Affiliation(s)
- Mustafa Köksal
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, USA
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29
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Köksal M, Chou WKW, Cane DE, Christianson DW. Structure of geranyl diphosphate C-methyltransferase from Streptomyces coelicolor and implications for the mechanism of isoprenoid modification. Biochemistry 2012; 51:3003-10. [PMID: 22455498 DOI: 10.1021/bi300109c] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Geranyl diphosphate C-methyltransferase (GPPMT) from Streptomyces coelicolor A3(2) is the first methyltransferase discovered that modifies an acyclic isoprenoid diphosphate, geranyl diphosphate (GPP), to yield a noncanonical acyclic allylic diphosphate product, 2-methylgeranyl diphosphate, which serves as the substrate for a subsequent cyclization reaction catalyzed by a terpenoid cyclase, methylisoborneol synthase. Here, we report the crystal structures of GPPMT in complex with GPP or the substrate analogue geranyl S-thiolodiphosphate (GSPP) along with S-adenosyl-L-homocysteine in the cofactor binding site, resulting from in situ demethylation of S-adenosyl-L-methionine, at 2.05 or 1.82 Å resolution, respectively. These structures suggest that both GPP and GSPP can undergo catalytic methylation in crystalline GPPMT, followed by dissociation of the isoprenoid product. S-Adenosyl-L-homocysteine remains bound in the active site, however, and does not exchange with a fresh molecule of cofactor S-adenosyl-L-methionine. These structures provide important clues about the molecular mechanism of the reaction, especially with regard to the face of the 2,3 double bond of GPP that is methylated as well as the stabilization of the resulting carbocation intermediate through cation-π interactions.
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Affiliation(s)
- Mustafa Köksal
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, USA
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30
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Faraldos JA, Miller DJ, González V, Yoosuf-Aly Z, Cascón O, Li A, Allemann RK. A 1,6-ring closure mechanism for (+)-δ-cadinene synthase? J Am Chem Soc 2012; 134:5900-8. [PMID: 22397618 DOI: 10.1021/ja211820p] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Recombinant (+)-δ-cadinene synthase (DCS) from Gossypium arboreum catalyzes the metal-dependent cyclization of (E,E)-farnesyl diphosphate (FDP) to the cadinane sesquiterpene δ-cadinene, the parent hydrocarbon of cotton phytoalexins such as gossypol. In contrast to some other sesquiterpene cyclases, DCS carries out this transformation with >98% fidelity but, as a consequence, leaves no mechanistic traces of its mode of action. The formation of (+)-δ-cadinene has been shown to occur via the enzyme-bound intermediate (3R)-nerolidyl diphosphate (NDP), which in turn has been postulated to be converted to cis-germacradienyl cation after a 1,10-cyclization. A subsequent 1,3-hydride shift would then relocate the carbocation within the transient macrocycle to expedite a second cyclization that yields the cadinenyl cation with the correct cis stereochemistry found in (+)-δ-cadinene. An elegant 1,10-mechanistic pathway that avoids the formation of (3R)-NDP has also been suggested. In this alternative scenario, the final cadinenyl cation is proposed to be formed through the intermediacy of trans, trans-germacradienyl cation and germacrene D. In addition, an alternative 1,6-ring closure mechanism via the bisabolyl cation has previously been envisioned. We report here a detailed investigation of the catalytic mechanism of DCS using a variety of mechanistic probes including, among others, deuterated and fluorinated FDPs. Farnesyl diphosphate analogues with fluorine at C2 and C10 acted as inhibitors of DCS, but intriguingly, after prolonged overnight incubations, they yielded 2F-germacrene(s) and a 10F-humulene, respectively. The observed 1,10-, and to a lesser extent, 1,11-cyclization activity of DCS with these fluorinated substrates is consistent with the postulated macrocyclization mechanism(s) en route to (+)-δ-cadinene. On the other hand, mechanistic results from incubations of DCS with 6F-FPP, (2Z,6E)-FDP, neryl diphosphate, 6,7-dihydro-FDP, and NDP seem to be in better agreement with the potential involvement of the alternative biosynthetic 1,6-ring closure pathway. In particular, the strong inhibition of DCS by 6F-FDP, coupled to the exclusive bisabolyl- and terpinyl-derived product profiles observed for the DCS-catalyzed turnover of (2Z,6E)-farnesyl and neryl diphosphates, suggested the intermediacy of α-bisabolyl cation. DCS incubations with enantiomerically pure [1-(2)H(1)](1R)-FDP revealed that the putative bisabolyl-derived 1,6-pathway proceeds through (3R)-nerolidyl diphosphate (NDP), is consistent with previous deuterium-labeling studies, and accounts for the cis stereochemistry characteristic of cadinenyl-derived sesquiterpenes. While the results reported here do not unambiguously rule in favor of 1,6- or 1,10-cyclization, they demonstrate the mechanistic versatility inherent to DCS and highlight the possible existence of multiple mechanistic pathways.
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Affiliation(s)
- Juan A Faraldos
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
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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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Cascón O, Touchet S, Miller DJ, Gonzalez V, Faraldos JA, Allemann RK. Chemoenzymatic preparation of germacrene analogues. Chem Commun (Camb) 2012; 48:9702-4. [DOI: 10.1039/c2cc35542f] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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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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Hong YJ, Tantillo DJ. How Many Secondary Carbocations Are Involved in the Biosynthesis of Avermitilol? Org Lett 2011; 13:1294-7. [DOI: 10.1021/ol103079v] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [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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Doud EH, Perlstein DL, Wolpert M, Cane DE, Walker S. Two distinct mechanisms for TIM barrel prenyltransferases in bacteria. J Am Chem Soc 2011; 133:1270-3. [PMID: 21214173 PMCID: PMC3033458 DOI: 10.1021/ja109578b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The reactions of two bacterial TIM barrel prenyltransferases (PTs), MoeO5 and PcrB, were explored. MoeO5, the enzyme responsible for the first step in moenomycin biosynthesis, catalyzes the transfer of farnesyl to 3-phosphoglyceric acid (3PG) to give a product containing a cis-allylic double bond. We show that this reaction involves isomerization to a nerolidyl pyrophosphate intermediate followed by bond rotation prior to attack by the nucleophile. This mechanism is unprecedented for a prenyltransferase that catalyzes an intermolecular coupling. We also show that PcrB transfers geranyl and geranylgeranyl groups to glycerol-1-phosphate (G1P), making it the first known bacterial enzyme to use G1P as a substrate. Unlike MoeO5, PcrB catalyzes prenyl transfer without isomerization to give products that retain the trans-allylic bond of the prenyl donors. The TIM barrel family of PTs is unique in including enzymes that catalyze prenyl transfer by distinctly different reaction mechanisms.
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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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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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Noel JP, Dellas N, Faraldos JA, Zhao M, Hess BA, Smentek L, Coates RM, O’Maille PE. Structural elucidation of cisoid and transoid cyclization pathways of a sesquiterpene synthase using 2-fluorofarnesyl diphosphates. ACS Chem Biol 2010; 5:377-92. [PMID: 20175559 PMCID: PMC2860371 DOI: 10.1021/cb900295g] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Accepted: 02/22/2010] [Indexed: 11/29/2022]
Abstract
Sesquiterpene skeletal complexity in nature originates from the enzyme-catalyzed ionization of (trans,trans)-farnesyl diphosphate (FPP) (1a) and subsequent cyclization along either 2,3-transoid or 2,3-cisoid farnesyl cation pathways. Tobacco 5-epi-aristolochene synthase (TEAS), a transoid synthase, produces cisoid products as a component of its minor product spectrum. To investigate the cryptic cisoid cyclization pathway in TEAS, we employed (cis,trans)-FPP (1b) as an alternative substrate. Strikingly, TEAS was catalytically robust in the enzymatic conversion of (cis,trans)-FPP (1b) to exclusively (>/=99.5%) cisoid products. Further, crystallographic characterization of wild-type TEAS and a catalytically promiscuous mutant (M4 TEAS) with 2-fluoro analogues of both all-trans FPP (1a) and (cis,trans)-FPP (1b) revealed binding modes consistent with preorganization of the farnesyl chain. These results provide a structural glimpse into both cisoid and transoid cyclization pathways efficiently templated by a single enzyme active site, consistent with the recently elucidated stereochemistry of the cisoid products. Further, computational studies using density functional theory calculations reveal concerted, highly asynchronous cyclization pathways leading to the major cisoid cyclization products. The implications of these discoveries for expanded sesquiterpene diversity in nature are discussed.
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Affiliation(s)
- Joseph P. Noel
- Howard Hughes Medical Institute
- The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology & Proteomics, 10010 Torrey Pines Road, La Jolla, California 92037
| | - Nikki Dellas
- The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology & Proteomics, 10010 Torrey Pines Road, La Jolla, California 92037
- Department of Chemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093
| | - Juan A. Faraldos
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Marylin Zhao
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - B. Andes Hess
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235
| | - Lidia Smentek
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235
- Institute of Physics, Nicolaus Copernicus University, 87-100 Toruń, Poland
| | - Robert M. Coates
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Paul E. O’Maille
- Howard Hughes Medical Institute
- The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology & Proteomics, 10010 Torrey Pines Road, La Jolla, California 92037
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Aaron JA, Lin X, Cane DE, Christianson DW. Structure of epi-isozizaene synthase from Streptomyces coelicolor A3(2), a platform for new terpenoid cyclization templates. Biochemistry 2010; 49:1787-97. [PMID: 20131801 PMCID: PMC2840623 DOI: 10.1021/bi902088z] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The X-ray crystal structure of recombinant epi-isozizaene synthase (EIZS), a sesquiterpene cyclase from Streptomyces coelicolor A3(2), has been determined at 1.60 A resolution. Specifically, the structure of wild-type EIZS is that of its closed conformation in complex with three Mg(2+) ions, inorganic pyrophosphate (PP(i)), and the benzyltriethylammonium cation (BTAC). Additionally, the structure of D99N EIZS has been determined in an open, ligand-free conformation at 1.90 A resolution. Comparison of these two structures provides the first view of conformational changes required for substrate binding and catalysis in a bacterial terpenoid cyclase. Moreover, the binding interactions of BTAC may mimic those of a carbocation intermediate in catalysis. Accordingly, the aromatic rings of F95, F96, and F198 appear to be well-oriented to stabilize carbocation intermediates in the cyclization cascade through cation-pi interactions. Mutagenesis of aromatic residues in the enzyme active site results in the production of alternative sesquiterpene product arrays due to altered modes of stabilization of carbocation intermediates as well as altered templates for the cyclization of farnesyl diphosphate. Accordingly, the 1.64 A resolution crystal structure of F198A EIZS in a complex with three Mg(2+) ions, PP(i), and BTAC reveals an alternative binding orientation of BTAC; alternative binding orientations of a carbocation intermediate could lead to the formation of alternative products. Finally, the crystal structure of wild-type EIZS in a complex with four Hg(2+) ions has been determined at 1.90 A resolution, showing that metal binding triggers a significant conformational change of helix G to cap the active site.
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Affiliation(s)
- Julie A. Aaron
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323
| | - Xin Lin
- Department of Chemistry, Box H, Brown University, Providence, RI 02912-9108
| | - David E. Cane
- Department of Chemistry, Box H, Brown University, Providence, RI 02912-9108,To whom correspondence should be addressed. D.W.C.: telephone: (215) 898-5714; fax: (215) 573-2201; . D.E.C.: telephone: (401) 863-3588; fax: (401) 863-9368;
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323,To whom correspondence should be addressed. D.W.C.: telephone: (215) 898-5714; fax: (215) 573-2201; . D.E.C.: telephone: (401) 863-3588; fax: (401) 863-9368;
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Lin X, Cane DE. Biosynthesis of the sesquiterpene antibiotic albaflavenone in Streptomyces coelicolor. Mechanism and stereochemistry of the enzymatic formation of epi-isozizaene. J Am Chem Soc 2009; 131:6332-3. [PMID: 19385616 DOI: 10.1021/ja901313v] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Epi-isozizaene synthase from Streptomyces coelicolor catalyzes the multistep cyclization of farnesyl diphosphate (2, FPP) to the tricyclic sesquiterpene hydrocarbon (+)-epi-isozizaene (3), which is converted in turn to the antibiotic albaflavenone (1) in a two-step, cytochrome P450-catalyzed oxidation. Competitive incubation of deuterated and nondeuterated samples of (3S)-NPP and (3RS)-NPP followed by GC-MS analysis of the degree of deuteration in the resulting labeled epi-isozizaene established that (3R)-NPP is the natural cyclization intermediate. Incubation of (3RS)-(Z)-[1-(2)H]NPP (4b) with epi-isozizaene synthase gave [11(anti)-(2)H]epi-isozizaene (3b), indicating that the S(N)' cyclization of 4 involves the predicted anti stereochemistry, consistent with the inference from earlier experiments with chirally deuterated FPP. Incubation of separate samples of [12,12,12-(2)H(3)]FPP (2d) and [13,13,13-(2)H(3)]FPP (2e) gave epi-isozizaenes 3d and 3e, thereby establishing the stereochemical course of the cyclization of the proposed intermediate acorenyl cation 6, as well as the stereochemistry of the successive 1,2-methyl migration and deprotonation that generate the final product. Further insights into the mechanism and the role of the enzyme came from site-directed mutagenesis of active site residues in two universally conserved Mg(2+)-binding domains and the identification of six minor sesquiterpene products 9-13 and 15 produced by the wild-type and mutant proteins. The aberrant products are believed to result from derailment and premature quenching of the normal intermediates of the cationic cyclization cascade.
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Affiliation(s)
- Xin Lin
- Department of Chemistry, Box H, Brown University, Providence, Rhode Island 02912-9108, USA
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41
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Hong YJ, Tantillo DJ. Consequences of Conformational Preorganization in Sesquiterpene Biosynthesis: Theoretical Studies on the Formation of the Bisabolene, Curcumene, Acoradiene, Zizaene, Cedrene, Duprezianene, and Sesquithuriferol Sesquiterpenes. J Am Chem Soc 2009; 131:7999-8015. [DOI: 10.1021/ja9005332] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Young J. Hong
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616
| | - Dean J. Tantillo
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616
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42
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Hong YJ, Tantillo DJ. Modes of inactivation of trichodiene synthase by a cyclopropane-containing farnesyldiphosphate analog. Org Biomol Chem 2009; 7:4101-9. [DOI: 10.1039/b908738a] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Shishova EY, Yu F, Miller DJ, Faraldos JA, Zhao Y, Coates RM, Allemann RK, Cane DE, Christianson DW. X-ray crystallographic studies of substrate binding to aristolochene synthase suggest a metal ion binding sequence for catalysis. J Biol Chem 2008; 283:15431-9. [PMID: 18385128 DOI: 10.1074/jbc.m800659200] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The universal sesquiterpene precursor, farnesyl diphosphate (FPP), is cyclized in an Mg(2+)-dependent reaction catalyzed by the tetrameric aristolochene synthase from Aspergillus terreus to form the bicyclic hydrocarbon aristolochene and a pyrophosphate anion (PP(i)) coproduct. The 2.1-A resolution crystal structure determined from crystals soaked with FPP reveals the binding of intact FPP to monomers A-C, and the binding of PP(i) and Mg(2+)(B) to monomer D. The 1.89-A resolution structure of the complex with 2-fluorofarnesyl diphosphate (2F-FPP) reveals 2F-FPP binding to all subunits of the tetramer, with Mg(2+)(B)accompanying the binding of this analogue only in monomer D. All monomers adopt open activesite conformations in these complexes, but slight structural changes in monomers C and D of each complex reflect the very initial stages of a conformational transition to the closed state. Finally, the 2.4-A resolution structure of the complex with 12,13-difluorofarnesyl diphosphate (DF-FPP) reveals the binding of intact DF-FPP to monomers A-C in the open conformation and the binding of PP(i), Mg(2+)(B), and Mg(2+)(C) to monomer D in a predominantly closed conformation. Taken together, these structures provide 12 independent "snapshots" of substrate or product complexes that suggest a possible sequence for metal ion binding and conformational changes required for catalysis.
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Affiliation(s)
- Ekaterina Y Shishova
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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Unearthing the roots of the terpenome. Curr Opin Chem Biol 2008; 12:141-50. [PMID: 18249199 DOI: 10.1016/j.cbpa.2007.12.008] [Citation(s) in RCA: 229] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Accepted: 12/27/2007] [Indexed: 11/22/2022]
Abstract
Although terpenoid synthases catalyze the most complex reactions in biology, these enzymes appear to play little role in the chemistry of catalysis other than to trigger the ionization and chaperone the conformation of flexible isoprenoid substrates and carbocation intermediates through multistep reaction cascades. Fidelity and promiscuity in this chemistry (whether a terpenoid synthase generates one or several products), depends on the permissiveness of the active site template in chaperoning each step of an isoprenoid coupling or cyclization reaction. Structure-guided mutagenesis studies of terpenoid synthases such as farnesyl diphosphate synthase, 5-epi-aristolochene synthase, and gamma-humulene synthase suggest that the vast diversity of terpenoid natural products is rooted in the facile evolution of alpha-helical folds shared by terpenoid synthases in all forms of life.
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45
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Vedula LS, Jiang J, Zakharian T, Cane DE, Christianson DW. Structural and mechanistic analysis of trichodiene synthase using site-directed mutagenesis: probing the catalytic function of tyrosine-295 and the asparagine-225/serine-229/glutamate-233-Mg2+B motif. Arch Biochem Biophys 2008; 469:184-94. [PMID: 17996718 PMCID: PMC2329581 DOI: 10.1016/j.abb.2007.10.015] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2007] [Revised: 10/15/2007] [Accepted: 10/17/2007] [Indexed: 11/15/2022]
Abstract
Trichodiene synthase from Fusarium sporotrichioides contains two metal ion-binding motifs required for the cyclization of farnesyl diphosphate: the "aspartate-rich" motif D(100)DXX(D/E) that coordinates to Mg2+A and Mg2+C, and the "NSE/DTE" motif N(225)DXXSXXXE that chelates Mg2+B (boldface indicates metal ion ligands). Here, we report steady-state kinetic parameters, product array analyses, and X-ray crystal structures of trichodiene synthase mutants in which the fungal NSE motif is progressively converted into a plant-like DDXXTXXXE motif, resulting in a degradation in both steady-state kinetic parameters and product specificity. Each catalytically active mutant generates a different distribution of sesquiterpene products, and three newly detected sesquiterpenes are identified. In addition, the kinetic and structural properties of the Y295F mutant of trichodiene synthase were found to be similar to those of the wild-type enzyme, thereby ruling out a proposed role for Y295 in catalysis.
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Affiliation(s)
- L. Sangeetha Vedula
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
| | - Jiaoyang Jiang
- Department of Chemistry, Brown University, Providence, Rhode Island 02912-9108, USA
| | - Tatiana Zakharian
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
| | - David E. Cane
- Department of Chemistry, Brown University, Providence, Rhode Island 02912-9108, USA
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
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