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Jung Y, Mitsuhashi T, Kikuchi T, Fujita M. Functional Plasticity of a Viral Terpene Synthase, OILTS, that Shows Non-Specific Metal Cofactor Binding and Metal-Dependent Biosynthesis. Chemistry 2024; 30:e202304317. [PMID: 38527951 DOI: 10.1002/chem.202304317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 03/27/2024]
Abstract
OILTS is a viral class I terpene synthase found from the giant virus Orpheovirus IHUMI-LCC2. It exhibits a unique structure and demonstrates high plasticity to metal cofactors, allowing it to biosynthesize different cyclic terpene frameworks. Notably, while OILTS produces only (+)-germacrene D-4-ol with the most common cofactor, Mg2+, it also biosynthesizes a different cyclic terpene, (+)-cubebol, with Mn2+, Co2+, or Ni2+, presenting a rare instance of cofactor-dependent enzyme catalysis. This is the first report of (+)-cubebol biosynthesis, to our knowledge. In addition, OILTS can uptake Zn2+ as a cofactor, which is uncommon among ordinary terpene synthases. These findings suggest that OILTS's functional plasticity may benefit the virus in diverse host environments, highlighting potential evolutionary implications.
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Affiliation(s)
- Youngcheol Jung
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Mitsui Link Lab Kashiwanoha 1, FS CREATION, 6-6-2 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
| | - Takaaki Mitsuhashi
- Division of Advanced Molecular Science, Institute for Molecular Science (IMS), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Takashi Kikuchi
- Rigaku Corporation 3-9-12 Matsubaracho, Akishima, Tokyo, 196-8666, Japan
| | - Makoto Fujita
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Mitsui Link Lab Kashiwanoha 1, FS CREATION, 6-6-2 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
- Division of Advanced Molecular Science, Institute for Molecular Science (IMS), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
- Tokyo College, Institutes for Advanced Study, The University of Tokyo, Mitsui Link Lab Kashiwanoha 1, FS CREATION, 6-6-2 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
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Ballal A, Laurendon C, Salmon M, Vardakou M, Cheema J, Defernez M, O'Maille PE, Morozov AV. Sparse Epistatic Patterns in the Evolution of Terpene Synthases. Mol Biol Evol 2020; 37:1907-1924. [PMID: 32119077 DOI: 10.1093/molbev/msaa052] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We explore sequence determinants of enzyme activity and specificity in a major enzyme family of terpene synthases. Most enzymes in this family catalyze reactions that produce cyclic terpenes-complex hydrocarbons widely used by plants and insects in diverse biological processes such as defense, communication, and symbiosis. To analyze the molecular mechanisms of emergence of terpene cyclization, we have carried out in-depth examination of mutational space around (E)-β-farnesene synthase, an Artemisia annua enzyme which catalyzes production of a linear hydrocarbon chain. Each mutant enzyme in our synthetic libraries was characterized biochemically, and the resulting reaction rate data were used as input to the Michaelis-Menten model of enzyme kinetics, in which free energies were represented as sums of one-amino-acid contributions and two-amino-acid couplings. Our model predicts measured reaction rates with high accuracy and yields free energy landscapes characterized by relatively few coupling terms. As a result, the Michaelis-Menten free energy landscapes have simple, interpretable structure and exhibit little epistasis. We have also developed biophysical fitness models based on the assumption that highly fit enzymes have evolved to maximize the output of correct products, such as cyclic products or a specific product of interest, while minimizing the output of byproducts. This approach results in nonlinear fitness landscapes that are considerably more epistatic. Overall, our experimental and computational framework provides focused characterization of evolutionary emergence of novel enzymatic functions in the context of microevolutionary exploration of sequence space around naturally occurring enzymes.
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Affiliation(s)
- Aditya Ballal
- Department of Physics & Astronomy and Center for Quantitative Biology, Rutgers University, Piscataway, NJ
| | - Caroline Laurendon
- John Innes Centre, Department of Metabolic Biology, Norwich Research Park, Norwich, United Kingdom.,Food & Health Programme, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom
| | - Melissa Salmon
- John Innes Centre, Department of Metabolic Biology, Norwich Research Park, Norwich, United Kingdom.,Food & Health Programme, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom.,Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Maria Vardakou
- John Innes Centre, Department of Metabolic Biology, Norwich Research Park, Norwich, United Kingdom.,Food & Health Programme, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Jitender Cheema
- John Innes Centre, Department of Computational and Systems Biology, Norwich Research Park, Norwich, United Kingdom
| | - Marianne Defernez
- Core Science Resources, Quadram Institute, Norwich Research Park, Norwich, United Kingdom
| | - Paul E O'Maille
- John Innes Centre, Department of Metabolic Biology, Norwich Research Park, Norwich, United Kingdom.,Food & Health Programme, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom.,SRI International, Menlo Park, CA
| | - Alexandre V Morozov
- Department of Physics & Astronomy and Center for Quantitative Biology, Rutgers University, Piscataway, NJ
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Styles MQ, Nesbitt EA, Marr S, Hutchby M, Leak DJ. Characterization of the first naturally thermostable terpene synthases and development of strategies to improve thermostability in this family of enzymes. FEBS J 2017; 284:1700-1711. [PMID: 28371548 PMCID: PMC6849719 DOI: 10.1111/febs.14072] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/20/2017] [Accepted: 03/27/2017] [Indexed: 12/24/2022]
Abstract
The terpenoid family of natural products is being targeted for heterologous microbial production as a cheaper and more reliable alternative to extraction from plants. The key enzyme responsible for diversification of terpene structure is the class-I terpene synthase (TS), and these often require engineering to improve properties such as thermostability, robustness and catalytic activity before they are suitable for industrial use. Improving thermostability typically relies on screening a large number of mutants, as there are no naturally thermostable TSs described upon which to base rational design decisions. We have characterized the first examples of natural TSs exhibiting thermostability, which catalyse the formation of the sesquiterpene τ-muurolol at temperatures up to 78 °C. We also report an enzyme with a kcat value of 0.95 s-1 at 65 °C, the highest kcat recorded for a bacterial sesquiterpene synthase. In turn, these thermostable enzymes were used as a model to inform the rational engineering of another TS, with the same specificity but low sequence identity to the model. The newly engineered variant displayed increased thermostability and turnover. Given the high structural homology of the class-I TS domain, this approach could be generally applicable to improving the properties of other enzymes in this class. DATABASE Model data are available in the PMDB database under the accession number PM0080780.
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Affiliation(s)
| | | | - Scott Marr
- Department of Biology and Biochemistry, University of Bath, UK
| | | | - David J Leak
- Department of Biology and Biochemistry, University of Bath, UK
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Thapa HR, Naik MT, Okada S, Takada K, Molnár I, Xu Y, Devarenne TP. A squalene synthase-like enzyme initiates production of tetraterpenoid hydrocarbons in Botryococcus braunii Race L. Nat Commun 2016; 7:11198. [PMID: 27050299 PMCID: PMC4823828 DOI: 10.1038/ncomms11198] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 02/29/2016] [Indexed: 12/24/2022] Open
Abstract
The green microalga Botryococcus braunii is considered a promising biofuel feedstock producer due to its prodigious accumulation of hydrocarbon oils that can be converted into fuels. B. braunii Race L produces the C40 tetraterpenoid hydrocarbon lycopadiene via an uncharacterized biosynthetic pathway. Structural similarities suggest this pathway follows a biosynthetic mechanism analogous to that of C30 squalene. Confirming this hypothesis, the current study identifies C20 geranylgeranyl diphosphate (GGPP) as a precursor for lycopaoctaene biosynthesis, the first committed intermediate in the production of lycopadiene. Two squalene synthase (SS)-like complementary DNAs are identified in race L with one encoding a true SS and the other encoding an enzyme with lycopaoctaene synthase (LOS) activity. Interestingly, LOS uses alternative C15 and C20 prenyl diphosphate substrates to produce combinatorial hybrid hydrocarbons, but almost exclusively uses GGPP in vivo. This discovery highlights how SS enzyme diversification results in the production of specialized tetraterpenoid oils in race L of B. braunii. The green microalga Botryococcus braunii is a promising biofuel producer due to its ability to produce large amounts of hydrocarbon oils that can be converted into fuels. Here the authors implicate lycopaoctaene synthase, a squalene synthases-like enzyme, in the first step towards the biosynthesis of the C40 tetraterpenoid hydrocarbon lycopadiene.
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Affiliation(s)
- Hem R Thapa
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
| | - Mandar T Naik
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA.,Biomolecular NMR Laboratory, Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
| | - Shigeru Okada
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo, Tokyo 113-8657, Japan.,Japan Science and Technology Agency-Core Research for Evolutional Science and Technology (CREST), Gobancho, Chiyoda, Tokyo 102-0076, Japan
| | - Kentaro Takada
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo, Tokyo 113-8657, Japan.,Japan Science and Technology Agency-Core Research for Evolutional Science and Technology (CREST), Gobancho, Chiyoda, Tokyo 102-0076, Japan
| | - István Molnár
- Natural Products Center, School of Natural Resources and the Environment, The University of Arizona, Tucson, Arizona 85739, USA
| | - Yuquan Xu
- Natural Products Center, School of Natural Resources and the Environment, The University of Arizona, Tucson, Arizona 85739, USA.,Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Timothy P Devarenne
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
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Vardakou M, Salmon M, Faraldos JA, O’Maille PE. Comparative analysis and validation of the malachite green assay for the high throughput biochemical characterization of terpene synthases. MethodsX 2014; 1:187-96. [PMID: 26150952 PMCID: PMC4472957 DOI: 10.1016/j.mex.2014.08.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 08/15/2014] [Indexed: 11/21/2022] Open
Abstract
Terpenes are the largest group of natural products with important and diverse biological roles, while of tremendous economic value as fragrances, flavours and pharmaceutical agents. Class-I terpene synthases (TPSs), the dominant type of TPS enzymes, catalyze the conversion of prenyl diphosphates to often structurally diverse bioactive terpene hydrocarbons, and inorganic pyrophosphate (PPi). To measure their kinetic properties, current bio-analytical methods typically rely on the direct detection of hydrocarbon products by radioactivity measurements or gas chromatography-mass spectrometry (GC-MS). In this study we employed an established, rapid colorimetric assay, the pyrophosphate/malachite green assay (MG), as an alternative means for the biochemical characterization of class I TPSs activity.•We describe the adaptation of the MG assay for turnover and catalytic efficiency measurements of TPSs.•We validate the method by direct comparison with established assays. The agreement of k cat/K M among methods makes this adaptation optimal for rapid evaluation of TPSs.•We demonstrate the application of the MG assay for the high-throughput screening of TPS gene libraries.
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Affiliation(s)
- Maria Vardakou
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Melissa Salmon
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Juan A. Faraldos
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Paul E. O’Maille
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
- Food and Health Programme, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, United Kingdom
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