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Lu Z, Shen Q, Bandari NC, Evans S, McDonnell L, Liu L, Jin W, Luna-Flores CH, Collier T, Talbo G, McCubbin T, Esquirol L, Myers C, Trau M, Dumsday G, Speight R, Howard CB, Vickers CE, Peng B. LowTempGAL: a highly responsive low temperature-inducible GAL system in Saccharomyces cerevisiae. Nucleic Acids Res 2024; 52:7367-7383. [PMID: 38808673 PMCID: PMC11229376 DOI: 10.1093/nar/gkae460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 05/12/2024] [Accepted: 05/16/2024] [Indexed: 05/30/2024] Open
Abstract
Temperature is an important control factor for biologics biomanufacturing in precision fermentation. Here, we explored a highly responsive low temperature-inducible genetic system (LowTempGAL) in the model yeast Saccharomyces cerevisiae. Two temperature biosensors, a heat-inducible degron and a heat-inducible protein aggregation domain, were used to regulate the GAL activator Gal4p, rendering the leaky LowTempGAL systems. Boolean-type induction was achieved by implementing a second-layer control through low-temperature-mediated repression on GAL repressor gene GAL80, but suffered delayed response to low-temperature triggers and a weak response at 30°C. Application potentials were validated for protein and small molecule production. Proteomics analysis suggested that residual Gal80p and Gal4p insufficiency caused suboptimal induction. 'Turbo' mechanisms were engineered through incorporating a basal Gal4p expression and a galactose-independent Gal80p-supressing Gal3p mutant (Gal3Cp). Varying Gal3Cp configurations, we deployed the LowTempGAL systems capable for a rapid stringent high-level induction upon the shift from a high temperature (37-33°C) to a low temperature (≤30°C). Overall, we present a synthetic biology procedure that leverages 'leaky' biosensors to deploy highly responsive Boolean-type genetic circuits. The key lies in optimisation of the intricate layout of the multi-factor system. The LowTempGAL systems may be applicable in non-conventional yeast platforms for precision biomanufacturing.
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Affiliation(s)
- Zeyu Lu
- ARC Centre of Excellence in Synthetic Biology, Australia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Qianyi Shen
- ARC Centre of Excellence in Synthetic Biology, Australia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Naga Chandra Bandari
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Samuel Evans
- ARC Centre of Excellence in Synthetic Biology, Australia
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Liam McDonnell
- ARC Centre of Excellence in Synthetic Biology, Australia
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Lian Liu
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
- The Queensland Node of Metabolomics Australia and Proteomics Australia (Q-MAP), Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Wanli Jin
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Carlos Horacio Luna-Flores
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Thomas Collier
- ARC Centre of Excellence in Synthetic Biology, Australia
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Gert Talbo
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
- The Queensland Node of Metabolomics Australia and Proteomics Australia (Q-MAP), Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Tim McCubbin
- ARC Centre of Excellence in Synthetic Biology, Australia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lygie Esquirol
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
- Environment, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
| | - Chris Myers
- Department of Electrical, Computer, and Energy Engineering University of Colorado, Boulder, CO 80309, USA
| | - Matt Trau
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
- School of Chemistry and Molecular Biosciences (SCMB), the University of Queensland, Brisbane, QLD 4072, Australia
| | - Geoff Dumsday
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, VIC, 3169, Australia
| | - Robert Speight
- ARC Centre of Excellence in Synthetic Biology, Australia
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD 4000, Australia
- Advanced Engineering Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Black Mountain, ACT, 2601, Australia
| | - Christopher B Howard
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Claudia E Vickers
- ARC Centre of Excellence in Synthetic Biology, Australia
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Bingyin Peng
- ARC Centre of Excellence in Synthetic Biology, Australia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD 4000, Australia
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Sundaraj Y, Abdullah H, Nezhad NG, Rodrigues KF, Sabri S, Baharum SN. Cloning, Expression and Functional Characterization of a Novel α-Humulene Synthase, Responsible for the Formation of Sesquiterpene in Agarwood Originating from Aquilaria malaccensis. Curr Issues Mol Biol 2023; 45:8989-9002. [PMID: 37998741 PMCID: PMC10670791 DOI: 10.3390/cimb45110564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/04/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023] Open
Abstract
This study describes the cloning, expression and functional characterization of α-humulene synthase, responsible for the formation of the key aromatic compound α-humulene in agarwood originating from Aquilaria malaccensis. The partial sesquiterpene synthase gene from the transcriptome data of A. malaccensis was utilized for full-length gene isolation via a 3' RACE PCR. The complete gene, denoted as AmDG2, has an open reading frame (ORF) of 1671 bp and encodes for a polypeptide of 556 amino acids. In silico analysis of the protein highlighted several conserved motifs typically found in terpene synthases such as Asp-rich substrate binding (DDxxD), metal-binding residues (NSE/DTE), and cytoplasmic ER retention (RxR) motifs at their respective sites. The AmDG2 was successfully expressed in the E. coli:pET-28a(+) expression vector whereby an expected band of about 64 kDa in size was detected in the SDS-PAGE gel. In vitro enzyme assay using substrate farnesyl pyrophosphate (FPP) revealed that AmDG2 gave rise to two sesquiterpenes: α-humulene (major) and β-caryophyllene (minor), affirming its identity as α-humulene synthase. On the other hand, protein modeling performed using AlphaFold2 suggested that AmDG2 consists entirely of α-helices with short connecting loops and turns. Meanwhile, molecular docking via AutoDock Vina (Version 1.5.7) predicted that Asp307 and Asp311 act as catalytic residues in the α-humulene synthase. To our knowledge, this is the first comprehensive report on the cloning, expression and functional characterization of α-humulene synthase from agarwood originating from A. malaccensis species. These findings reveal a deeper understanding of the structure and functional properties of the α-humulene synthase and could be utilized for metabolic engineering work in the future.
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Affiliation(s)
- Yasotha Sundaraj
- Metabolomics Research Laboratory, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia;
- Faculty of Engineering and Life Sciences, Universiti Selangor (UNISEL), Bestari Jaya 45600, Selangor, Malaysia;
| | - Hasdianty Abdullah
- Faculty of Engineering and Life Sciences, Universiti Selangor (UNISEL), Bestari Jaya 45600, Selangor, Malaysia;
| | - Nima Ghahremani Nezhad
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia;
| | - Kenneth Francis Rodrigues
- Biotechnology Research Institute, Universiti Malaysia Sabah (UMS), Kota Kinabalu 88400, Sabah, Malaysia;
| | - Suriana Sabri
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia;
| | - Syarul Nataqain Baharum
- Metabolomics Research Laboratory, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia;
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3
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Chen PY, Yi YC, Wang HC, Ng IS. Heterologous Expression of Toxic White Spot Syndrome Virus (WSSV) Protein in Eengineered Escherichia coli Strains. Appl Biochem Biotechnol 2023:10.1007/s12010-023-04369-1. [PMID: 36701096 DOI: 10.1007/s12010-023-04369-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2023] [Indexed: 01/27/2023]
Abstract
Aquacultural shrimps suffer economic lost due to the white spot syndrome virus (WSSV) that is the most notorious virus for its fatality and contagion, leading to a 100% death rate on infected shrimps within 7 days. However, the infection of mechanism remains a mystery and crucial problem. To elucidate the pathogenesis of WSSV, a high abundance of protein is required to identify and characterize its functions. Therefore, the optimal WSSV355 overexpression was explored in engineered Escherichia coli strains, in particular C43(DE3) as a toxic tolerance strain remedied 40% of cell growth from BL21(DE3). Meanwhile, a trace amount of WSSV355 was observed in both strains. To optimize the codon of WSSV355 using codon adaption index (CAI), an overexpression was observed with 1.32 mg/mL in C43(DE3), while the biomass was decreased by 35%. Subsequently, the co-expression with pRARE boosted the target protein up to 1.93 mg/mL. Finally, by scaling up production of WSSV355 in the fermenter with sufficient oxygen supplied, the biomass and total and soluble protein were enhanced 67.6%, 44.9%, and 7.8% compared with that in flask condition. Herein, the current approach provides efficacious solutions to produce toxic proteins via codon usage, strain selection, and processing optimization by alleviating the burden and boosting protein production in E. coli.
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Affiliation(s)
- Po-Yen Chen
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Ying-Chen Yi
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Han-Ching Wang
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 70101, Taiwan.,International Center for the Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, 70101, Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan.
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4
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Mukherjee M, Blair RH, Wang ZQ. Machine-learning guided elucidation of contribution of individual steps in the mevalonate pathway and construction of a yeast platform strain for terpenoid production. Metab Eng 2022; 74:139-149. [DOI: 10.1016/j.ymben.2022.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 10/16/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022]
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5
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Guo Q, Li YW, Yan F, Li K, Wang YT, Ye C, Shi TQ, Huang H. Dual cytoplasmic-peroxisomal engineering for high-yield production of sesquiterpene α-humulene in Yarrowia lipolytica. Biotechnol Bioeng 2022; 119:2819-2830. [PMID: 35798689 DOI: 10.1002/bit.28176] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/24/2022] [Accepted: 07/05/2022] [Indexed: 11/06/2022]
Abstract
The sesquiterpene α-humulene is an important plant natural product, which has been used in pharmaceutical industry due to the anti-inflammatory and anticancer activities. Although phytoextraction and chemical synthesis have previously been applied into α-humulene production, the low efficiency and high costs limit the development. In this study, Y. lipolytica was engineered as the robust cell factory for sustainable α-humulene production. First, a chassis with high α-humulene output in the cytoplasm was constructed by integrating α-humulene synthases with high catalytic activity, optimizing the flux of MVA and acetyl-CoA pathways. Subsequently, the strategy of dual cytoplasmic-peroxisomal engineering was adopted in Y. lipolytica, the best strain GQ3006 generated by introducing 31 copies of 12 different genes could produce 2280.3 ± 38.2 mg/L (98.7 ± 4.2 mg/g DCW) α-humulene, a 100-fold improvement relative to the baseline strain. In order to further improve the titer, a novel strategy for downregulation of squalene biosynthesis based on Cu2+ -repressible promoters was firstly established, which significantly improved the α-humulene titer by 54.2 % to 3516.6 ± 34.3 mg/L. Finally, the engineered strain could produce 21.7 g/L α-humulene in 5-L bioreactor, 6.8-fold higher than the highest α-humulene titer reported prior to this study. Overall, system metabolic engineering strategies used in this study provide a valuable reference for highly sustainable production of terpenoids in Y. lipolytica. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Qi Guo
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
| | - Ya-Wen Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, 210046, People's Republic of China
| | - Fang Yan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, 210046, People's Republic of China
| | - Ke Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, 210046, People's Republic of China
| | - Yue-Tong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, 210046, People's Republic of China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, 210046, People's Republic of China
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, 210046, People's Republic of China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, 210046, People's Republic of China.,College of Pharmaceutical Sciences, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China.,State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
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6
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Different strategies for expression and purification of the CT26-poly-neoepitopes vaccine in Escherichia coli. Mol Biol Rep 2022; 49:859-873. [DOI: 10.1007/s11033-021-06727-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 09/28/2021] [Indexed: 11/26/2022]
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7
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Guo Q, Shi TQ, Peng QQ, Sun XM, Ji XJ, Huang H. Harnessing Yarrowia lipolytica Peroxisomes as a Subcellular Factory for α-Humulene Overproduction. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:13831-13837. [PMID: 34751575 DOI: 10.1021/acs.jafc.1c05897] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The sesquiterpene α-humulene has been shown to have anti-inflammatory and anticancer activities, which has led to its vast application potential in medicine. However, α-humulene production methods including phytoextraction and chemical synthesis currently were limited to low yield, high costs, and expensive catalysts, which cannot meet the increasing market demand. In this study, Yarrowia lipolytica was developed as a robust cell factory for α-humulene production. The peroxisome in Y. lipolytica was first engineered to boost the synthesis of the sesquiterpene α-humulene. By compartmentalization of the α-humulene biosynthesis pathway, improving ATP and acetyl-CoA supply, and optimizing the gene copy numbers of rate-limiting enzymes, the engineered strain GQ2012 could produce 3.2 g/L α-humulene in a 5 L bioreactor, the highest α-humulene titer reported so far. Our study provides a valuable reference for highly sustainable production of terpenoids by peroxisome engineering in Y. lipolytica.
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Affiliation(s)
- Qi Guo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Qian-Qian Peng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Xiao-Man Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Xiao-Jun Ji
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
- College of Pharmaceutical Sciences, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
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Taxonomic Insights and Its Type Cyclization Correlation of Volatile Sesquiterpenes in Vitex Species and Potential Source Insecticidal Compounds: A Review. Molecules 2021; 26:molecules26216405. [PMID: 34770814 PMCID: PMC8587464 DOI: 10.3390/molecules26216405] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 11/17/2022] Open
Abstract
Sesquiterpenes (SS) are secondary metabolites formed by the bonding of 3 isoprene (C5) units. They play an important role in the defense and signaling of plants to adapt to the environment, face stress, and communicate with the outside world, and their evolutionary history is closely related to their physiological functions. This review considers their presence and extensively summarizes the 156 sesquiterpenes identified in Vitextaxa, emphasizing those with higher concentrations and frequency among species and correlating with the insecticidal activities and defensive responses reported in the literature. In addition, we classify the SS based on their chemical structures and addresses cyclization in biosynthetic origin. Most relevant sesquiterpenes of the Vitex genus are derived from the germacredienyl cation mainly via bicyclogermacrene and germacrene C, giving rise to aromadrendanes, a skeleton with the highest number of representative compounds in this genus, and 6,9-guaiadiene, respectively, indicating the production of 1.10-cyclizing sesquiterpene synthases. These enzymes can play an important role in the chemosystematics of the genus from their corresponding routes and cyclizations, constituting a new approach to chemotaxonomy. In conclusion, this review is a compilation of detailed information on the profile of sesquiterpene in the Vitex genus and, thus, points to new unexplored horizons for future research.
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Nguyen AD, Kim D, Lee EY. Unlocking the biosynthesis of sesquiterpenoids from methane via the methylerythritol phosphate pathway in methanotrophic bacteria, using α-humulene as a model compound. Metab Eng 2020; 61:69-78. [PMID: 32387228 DOI: 10.1016/j.ymben.2020.04.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/21/2020] [Accepted: 04/25/2020] [Indexed: 11/22/2022]
Abstract
Isoprenoids are an abundant and diverse class of natural products with various applications in the pharmaceutical, cosmetics and biofuel industries. A methanotroph-based biorefinery is an attractive scenario for the production of a variety of value-added compounds from methane, because methane is a promising alternative feedstock for industrial biomanufacturing. In this study, we metabolically engineered Methylotuvimicrobium alcaliphilum 20Z for de novo synthesis of a sesquiterpenoid from methane, using α-humulene as a model compound, via optimization of the native methylerythritol phosphate (MEP) pathway. Expression of codon-optimized α-humulene synthase from Zingiber zerumbet in M. alcaliphilum 20Z resulted in an initial yield of 0.04 mg/g dry cell weight. Overexpressing key enzymes (IspA, IspG, and Dxs) for debottlenecking of the MEP pathway increased α-humulene production 5.2-fold compared with the initial strain. Subsequently, redirecting the carbon flux through the Embden-Meyerhof-Parnas pathway resulted in an additional 3-fold increase in α-humulene production. Additionally, a genome-scale model using flux scanning based on enforced objective flux method was used to identify potential overexpression targets to increase flux towards isoprenoid production. Several target reactions from cofactor synthesis pathways were probed and evaluated for their effects on α-humulene synthesis, resulting in α-humulene yield up to 0.75 mg/g DCW with 18.8-fold enhancement from initial yield. This study first demonstrates production of a sesquiterpenoid from methane using methanotrophs as the biocatalyst and proposes potential strategies to enhance production of sesquiterpenoid and related isoprenoid products in engineered methanotrophic bacteria.
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Affiliation(s)
- Anh Duc Nguyen
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, 17104, South Korea
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, 17104, South Korea.
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10
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Rudolf JD, Chang CY. Terpene synthases in disguise: enzymology, structure, and opportunities of non-canonical terpene synthases. Nat Prod Rep 2020; 37:425-463. [PMID: 31650156 PMCID: PMC7101268 DOI: 10.1039/c9np00051h] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: up to July 2019 Terpene synthases (TSs) are responsible for generating much of the structural diversity found in the superfamily of terpenoid natural products. These elegant enzymes mediate complex carbocation-based cyclization and rearrangement cascades with a variety of electron-rich linear and cyclic substrates. For decades, two main classes of TSs, divided by how they generate the reaction-triggering initial carbocation, have dominated the field of terpene enzymology. Recently, several novel and unconventional TSs that perform TS-like reactions but do not resemble canonical TSs in sequence or structure have been discovered. In this review, we identify 12 families of non-canonical TSs and examine their sequences, structures, functions, and proposed mechanisms. Nature provides a wide diversity of enzymes, including prenyltransferases, methyltransferases, P450s, and NAD+-dependent dehydrogenases, as well as completely new enzymes, that utilize distinctive reaction mechanisms for TS chemistry. These unique non-canonical TSs provide immense opportunities to understand how nature evolved different tools for terpene biosynthesis by structural and mechanistic characterization while affording new probes for the discovery of novel terpenoid natural products and gene clusters via genome mining. With every new discovery, the dualistic paradigm of TSs is contradicted and the field of terpene chemistry and enzymology continues to expand.
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Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Chin-Yuan Chang
- Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan, Republic of China
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11
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Modulating the Precursor and Terpene Synthase Supply for the Whole-Cell Biocatalytic Production of the Sesquiterpene (+)-Zizaene in a Pathway Engineered E. coli. Genes (Basel) 2019; 10:genes10060478. [PMID: 31238595 PMCID: PMC6627501 DOI: 10.3390/genes10060478] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 06/15/2019] [Accepted: 06/20/2019] [Indexed: 11/23/2022] Open
Abstract
The vetiver essential oil from Chrysopogon zizanioides contains fragrant sesquiterpenes used widely in the formulation of nearly 20% of men’s cosmetics. The growing demand and issues in the supply have raised interest in the microbial production of the sesquiterpene khusimol, the main compound of the vetiver essential oil due to its woody smell. In this study, we engineered the biosynthetic pathway for the production of (+)-zizaene, the immediate precursor of khusimol. A systematic approach of metabolic engineering in Escherichia coli was applied to modulate the critical bottlenecks of the metabolic flux towards (+)-zizaene. Initially, production of (+)-zizaene was possible with the endogenous methylerythritol phosphate pathway and the codon-optimized zizaene synthase (ZS). Raising the precursor E,E-farnesyl diphosphate supply through the mevalonate pathway improved the (+)-zizaene titers 2.7-fold, although a limitation of the ZS supply was observed. To increase the ZS supply, distinct promoters were tested for the expression of the ZS gene, which augmented 7.2-fold in the (+)-zizaene titers. Final metabolic enhancement for the ZS supply by using a multi-plasmid strain harboring multiple copies of the ZS gene improved the (+)-zizaene titers 1.3-fold. The optimization of the fermentation conditions increased the (+)-zizaene titers 2.2-fold, achieving the highest (+)-zizaene titer of 25.09 mg L−1. This study provides an alternative strategy to enhance the terpene synthase supply for the engineering of isoprenoids. Moreover, it demonstrates the development of a novel microbial platform for the sustainable production of fragrant molecules for the cosmetic industry.
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12
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Alemdar S, König JC, Seidel K, Kirschning A, Scheper T, Beutel S. Substrate specificity of α-humulene synthase from Zingiber zerumbet
Smith and determination of kinetic constants by a spectrophotometric assay. Eng Life Sci 2018; 18:654-658. [DOI: 10.1002/elsc.201800019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/10/2018] [Accepted: 05/24/2018] [Indexed: 11/08/2022] Open
Affiliation(s)
- Semra Alemdar
- Institute of Technical Chemistry; Leibniz Universität Hannover; Hannover Germany
| | - Jan Christoph König
- Institute of Technical Chemistry; Leibniz Universität Hannover; Hannover Germany
| | - Katja Seidel
- Institute of Organic Chemistry; Leibniz Universität Hannover; Hannover Germany
| | - Andreas Kirschning
- Institute of Organic Chemistry; Leibniz Universität Hannover; Hannover Germany
| | - Thomas Scheper
- Institute of Technical Chemistry; Leibniz Universität Hannover; Hannover Germany
| | - Sascha Beutel
- Institute of Technical Chemistry; Leibniz Universität Hannover; Hannover Germany
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13
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Rusdi NA, Goh HH, Sabri S, Ramzi AB, Mohd Noor N, Baharum SN. Functional Characterisation of New Sesquiterpene Synthase from the Malaysian Herbal Plant, Polygonum Minus. Molecules 2018; 23:E1370. [PMID: 29882808 PMCID: PMC6100370 DOI: 10.3390/molecules23061370] [Citation(s) in RCA: 8] [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: 03/23/2018] [Revised: 05/29/2018] [Accepted: 05/31/2018] [Indexed: 11/16/2022] Open
Abstract
Polygonum minus (syn. Persicaria minor) is a herbal plant that is well known for producing sesquiterpenes, which contribute to its flavour and fragrance. This study describes the cloning and functional characterisation of PmSTPS1 and PmSTPS2, two sesquiterpene synthase genes that were identified from P. minus transcriptome data mining. The full-length sequences of the PmSTPS1 and PmSTPS2 genes were expressed in the E. coli pQE-2 expression vector. The sizes of PmSTPS1 and PmSTPS2 were 1098 bp and 1967 bp, respectively, with open reading frames (ORF) of 1047 and 1695 bp and encoding polypeptides of 348 and 564 amino acids, respectively. The proteins consist of three conserved motifs, namely, Asp-rich substrate binding (DDxxD), metal binding residues (NSE/DTE), and cytoplasmic ER retention (RxR), as well as the terpene synthase family N-terminal domain and C-terminal metal-binding domain. From the in vitro enzyme assays, using the farnesyl pyrophosphate (FPP) substrate, the PmSTPS1 enzyme produced multiple acyclic sesquiterpenes of β-farnesene, α-farnesene, and farnesol, while the PmSTPS2 enzyme produced an additional nerolidol as a final product. The results confirmed the roles of PmSTPS1 and PmSTPS2 in the biosynthesis pathway of P. minus, to produce aromatic sesquiterpenes.
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Affiliation(s)
- Nor Azizun Rusdi
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi 43600 UKM, Selangor, Malaysia.
- Institutes for Tropical Biology and Conservation, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia.
| | - Hoe-Han Goh
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi 43600 UKM, Selangor, Malaysia.
| | - Suriana Sabri
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang 43400, Malaysia.
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang 43400, Malaysia.
| | - Ahmad Bazli Ramzi
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi 43600 UKM, Selangor, Malaysia.
| | - Normah Mohd Noor
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi 43600 UKM, Selangor, Malaysia.
| | - Syarul Nataqain Baharum
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi 43600 UKM, Selangor, Malaysia.
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14
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Three previously unrecognised classes of biosynthetic enzymes revealed during the production of xenovulene A. Nat Commun 2018; 9:1963. [PMID: 29773797 PMCID: PMC5958101 DOI: 10.1038/s41467-018-04364-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 04/25/2018] [Indexed: 01/28/2023] Open
Abstract
Xenovulene A is a complex fungal meroterpenoid, produced by the organism hitherto known as Acremonium strictum IMI 501407, for which limited biosynthetic evidence exists. Here, we generate a draft genome and show that the producing organism is previously unknown and should be renamed as Sarocladium schorii. A biosynthetic gene cluster is discovered which bears resemblance to those involved in the biosynthesis of fungal tropolones, with additional genes of unknown function. Heterologous reconstruction of the entire pathway in Aspergillus oryzae allows the chemical steps of biosynthesis to be dissected. The pathway shows very limited similarity to the biosynthesis of other fungal meroterpenoids. The pathway features: the initial formation of tropolone intermediates; the likely involvement of a hetero Diels–Alder enzyme; a terpene cyclase with no significant sequence homology to any known terpene cyclase and two enzymes catalysing oxidative-ring contractions. Xenovulene A is a fungal compound that has the potential to be used as an antidepressant. Here, the authors unravel the pathway leading to its formation in fungi and discover a new class of enzymes, which accounts for some unusual chemistry in the synthesis of xenovulene.
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15
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Alemdar S, König JC, Hartwig S, Frister T, Scheper T, Beutel S. Bioproduction of α-humulene in metabolically engineered Escherichia coli and application in zerumbone synthesis. Eng Life Sci 2017; 17:900-907. [PMID: 32624838 DOI: 10.1002/elsc.201700043] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 06/02/2017] [Accepted: 06/06/2017] [Indexed: 01/09/2023] Open
Abstract
Zerumbone is a sesquiterpene ketone with potent anti-cancerogenic activities, produced in several ginger species of the Zingiberaceae familiy. We have investigated the biotechnological production of α-humulene, a precursor of zerumbone. By implementing a heterologous mevalonate pathway in combination with the α-humulene synthase expression, we effectively synthesized α-humulene from glucose in Escherichia coli. In this study, we developed a practical and efficient in situ separation method for α-humulene by comparison of extractive and adsorptive strategies. By the in situ adsorption of the product to the hydrophobic resin Amberlite® XAD4 we were able to increase α-humulene yield by 2310% to 60.2 mg/L. Furthermore we present an easy applicable, short subsequent chemical process for the conversion of α-humulene to zerumbone by using transition metal catalysis. To reduce process steps, the chemical reaction was carried out in the same solvent as the eluting solvent that was used to elute α-humulene from the adsorbent resin. By allylic oxidation of α-humulene with manganeseII chloride as a catalyst and tert.-butylhydroperoxide as an oxidizing agent we were able to synthetize zerumbone with a selectivity of 51.6%. Product and byproducts of the oxidation reaction were identified by GC-MS.
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Affiliation(s)
- Semra Alemdar
- Leibniz University Hannover Institute of Technical Chemistry Hannover Germany
| | - Jan C König
- Leibniz University Hannover Institute of Technical Chemistry Hannover Germany
| | - Steffen Hartwig
- Leibniz University Hannover Institute of Technical Chemistry Hannover Germany
| | - Thore Frister
- Leibniz University Hannover Institute of Technical Chemistry Hannover Germany
| | - Thomas Scheper
- Leibniz University Hannover Institute of Technical Chemistry Hannover Germany
| | - Sascha Beutel
- Leibniz University Hannover Institute of Technical Chemistry Hannover Germany
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16
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Jayaramaiah RH, Anand A, Beedkar SD, Dholakia BB, Punekar SA, Kalunke RM, Gade WN, Thulasiram HV, Giri AP. Functional characterization and transient expression manipulation of a new sesquiterpene synthase involved in β-caryophyllene accumulation in Ocimum. Biochem Biophys Res Commun 2016; 473:265-271. [PMID: 27005818 DOI: 10.1016/j.bbrc.2016.03.090] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 03/18/2016] [Indexed: 01/12/2023]
Abstract
The genus Ocimum has a unique blend of diverse secondary metabolites, with major proportion of terpenoids including mono- and sesquiterpenes. Although, β-Caryophyllene, bicyclic sesquiterpene, is one of the major terpene found in Ocimum species and known to possess several biological activities, not much is known about its biosynthesis in Ocimum. Here, we describe isolation and characterization of β-caryophyllene synthase gene from Ocimum kilimandscharicum Gürke (OkBCS- GenBank accession no. KP226502). The open reading frame of 1629 bp encoded a protein of 542 amino acids with molecular mass of 63.6 kDa and pI value of 5.66. The deduced amino acid sequence revealed 50-70% similarity with known sesquiterpene synthases from angiosperms. Recombinant OkBCS converted farnesyl diphosphate to β-caryophyllene as a major product (94%) and 6% α-humulene. Expression variation of OkBCS well corroborated with β-caryophyllene levels in different tissues from five Ocimum species. OkBCS transcript revealed higher expression in leaves and flowers. Further, agro-infiltration based transient expression manipulation with OkBCS over-expression and silencing confirmed its role in β-caryophyllene biosynthesis. These findings may potentially be further utilized to improve plant defense against insect pests.
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Affiliation(s)
- Ramesha H Jayaramaiah
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune 411008, Maharashtra, India
| | - Atul Anand
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune 411008, Maharashtra, India; Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune 411008, Maharashtra, India
| | - Supriya D Beedkar
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune 411008, Maharashtra, India; Department of Biotechnology, Savitribai Phule Pune University, Pune 411007, Maharashtra, India
| | - Bhushan B Dholakia
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune 411008, Maharashtra, India
| | - Sachin A Punekar
- Biospheres, Eshwari, 52/403, Lakshminagar, Parvati, Pune 411 009, Maharashtra, India
| | - Raviraj M Kalunke
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune 411008, Maharashtra, India
| | - Wasudeo N Gade
- Department of Biotechnology, Savitribai Phule Pune University, Pune 411007, Maharashtra, India
| | - Hirekodathakallu V Thulasiram
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune 411008, Maharashtra, India; CSIR- Institute of Genomics and Integrative Biology, Mall Road, New Delhi 110007, India.
| | - Ashok P Giri
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune 411008, Maharashtra, India.
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