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Wang T, Sun Y, Chen Y, Ma D, Zhan R, Yang J, Yang P. Functional characterization of geranyl/farnesyl diphosphate synthase in Wurfbainia villosa and Wurfbainia longiligularis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108741. [PMID: 38772167 DOI: 10.1016/j.plaphy.2024.108741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/26/2024] [Accepted: 05/16/2024] [Indexed: 05/23/2024]
Abstract
Wurfbainia villosa and Wurfbainia longiligularis are the two primary plant sources of Fructus Amomi, a traditional Chinese medicine. Both plants are rich in volatile terpenoids, including monoterpenes and sesquiterpenes, which are the primary medicinal components of Fructus Amomi. The trans-isopentenyl diphosphate synthase (TIDS) gene family plays a key part in determining terpenoid diversity and accumulation. However, the TIDS gene family have not been identified in W. villosa and W. longiligularis. This study identified thirteen TIDS genes in W. villosa and eleven TIDS genes in W. longiligularis, which may have expanded through segmental replication events. Based on phylogenetic analysis and expression levels, eight candidate WvTIDSs and five WlTIDSs were selected for cloning. Functional characterization in vitro demonstrated that four homologous geranyl diphosphate synthases (GPPSs) (WvGPPS1, WvGPPS2, WlGPPS1, WlGPPS2) and two geranylgeranyl diphosphate synthases (GGPPSs) (WvGGPPS and WlGGPPS) were responsible for catalyzing the biosynthesis of geranyl diphosphate (GPP), whereas two farnesyl diphosphate synthases (FPPSs) (WvFPPS and WlFPPS) catalysed the biosynthesis of the farnesyl diphosphate (FPP). A comparison of six proteins with identified GPPS functions showed that WvGGPPS and WlGGPPS exhibited the highest activity levels. These findings indicate that homologous GPPS and GGPPS together promote the biosynthesis of GPP in W. villosa and W. longiligularis, thus providing sufficient precursors for the synthesis of monoterpenes and providing key genetic elements for Fructus Amomi variety improvement and molecular breeding.
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Affiliation(s)
- Tiantian Wang
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Yewen Sun
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Yuanxia Chen
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Dongming Ma
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Ruoting Zhan
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
| | - Jinfen Yang
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
| | - Peng Yang
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China; Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua, 418000, China.
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2
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Bergman ME, Kortbeek RWJ, Gutensohn M, Dudareva N. Plant terpenoid biosynthetic network and its multiple layers of regulation. Prog Lipid Res 2024; 95:101287. [PMID: 38906423 DOI: 10.1016/j.plipres.2024.101287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/23/2024]
Abstract
Terpenoids constitute one of the largest and most chemically diverse classes of primary and secondary metabolites in nature with an exceptional breadth of functional roles in plants. Biosynthesis of all terpenoids begins with the universal five‑carbon building blocks, isopentenyl diphosphate (IPP) and its allylic isomer dimethylallyl diphosphate (DMAPP), which in plants are derived from two compartmentally separated but metabolically crosstalking routes, the mevalonic acid (MVA) and methylerythritol phosphate (MEP) pathways. Here, we review the current knowledge on the terpenoid precursor pathways and highlight the critical hidden constraints as well as multiple regulatory mechanisms that coordinate and homeostatically govern carbon flux through the terpenoid biosynthetic network in plants.
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Affiliation(s)
- Matthew E Bergman
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States; Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Ruy W J Kortbeek
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States; Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Michael Gutensohn
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, United States
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States; Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States.
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3
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Luckie BA, Kashyap M, Pearson AN, Chen Y, Liu Y, Valencia LE, Carrillo Romero A, Hudson GA, Tao XB, Wu B, Petzold CJ, Keasling JD. Development of Corynebacterium glutamicum as a monoterpene production platform. Metab Eng 2024; 81:110-122. [PMID: 38056688 DOI: 10.1016/j.ymben.2023.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023]
Abstract
Monoterpenes are commonly known for their role in the flavors and fragrances industry and are also gaining attention for other uses like insect repellant and as potential renewable fuels for aviation. Corynebacterium glutamicum, a Generally Recognized as Safe microbe, has been a choice organism in industry for the annual million ton-scale bioproduction of amino acids for more than 50 years; however, efforts to produce monoterpenes in C. glutamicum have remained relatively limited. In this study, we report a further expansion of the C. glutamicum biosynthetic repertoire through the development and optimization of a mevalonate-based monoterpene platform. In the course of our plasmid design iterations, we increased flux through the mevalonate-based bypass pathway, measuring isoprenol production as a proxy for monoterpene precursor abundance and demonstrating the highest reported titers in C. glutamicum to date at 1504.6 mg/L. Our designs also evaluated the effects of backbone, promoter, and GPP synthase homolog origin on monoterpene product titers. Monoterpene production was further improved by disrupting competing pathways for isoprenoid precursor supply and by implementing a biphasic production system to prevent volatilization. With this platform, we achieved 321.1 mg/L of geranoids, 723.6 mg/L of 1,8-cineole, and 227.8 mg/L of linalool. Furthermore, we determined that C. glutamicum first oxidizes geraniol through an aldehyde intermediate before it is asymmetrically reduced to citronellol. Additionally, we demonstrate that the aldehyde reductase, AdhC, possesses additional substrate promiscuity for acyclic monoterpene aldehydes.
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Affiliation(s)
- Bridget A Luckie
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Meera Kashyap
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Allison N Pearson
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Yan Chen
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuzhong Liu
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - Luis E Valencia
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint Program in Bioengineering, University of California, Berkeley, San Francisco, CA, 94720, USA
| | - Alexander Carrillo Romero
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Graham A Hudson
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - Xavier B Tao
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Bryan Wu
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA; Joint Program in Bioengineering, University of California, Berkeley, San Francisco, CA, 94720, USA; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark; Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China.
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Huang ZY, Taizoumbe KA, Liang C, Goldfuss B, Xu JH, Dickschat JS. Spiroluchuene A Synthase: A Cyclase from Aspergillus luchuensis Forming a Spirotetracyclic Diterpene. Angew Chem Int Ed Engl 2023; 62:e202315659. [PMID: 37962519 DOI: 10.1002/anie.202315659] [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: 10/17/2023] [Revised: 11/14/2023] [Accepted: 11/14/2023] [Indexed: 11/15/2023]
Abstract
The diterpene synthase AlTS was identified from Aspergillus luchuensis. AlTS catalyses the formation of the diterpene hydrocarbon spiroluchuene A, which exhibits a novel skeleton characterised by a spirocyclic ring system. The cyclisation mechanism towards this compound was elucidated through isotopic labelling experiments in conjunction with DFT calculations and metadynamic simulations. The biosynthetic intermediate luchudiene, besides the derivative spiroluchuene B, was captured from an enzyme variant obtained through site-directed mutagenesis. With its 10-membered ring luchudiene is structurally related to germacrenes and can undergo a Cope rearrangement to luchuelemene.
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Affiliation(s)
- Zheng-Yu Huang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
| | - Kizerbo A Taizoumbe
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Chengqin Liang
- College of Pharmacy, Guilin Medical University, Guilin, 541004, China
| | - Bernd Goldfuss
- Department of Chemistry, University of Cologne, Greinstraße 4, 50939, Cologne, Germany
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
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5
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Yao L, Wu X, Jiang X, Shan M, Zhang Z, Li Y, Yang A, Li Y, Yang C. Subcellular compartmentalization in the biosynthesis and engineering of plant natural products. Biotechnol Adv 2023; 69:108258. [PMID: 37722606 DOI: 10.1016/j.biotechadv.2023.108258] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 09/20/2023]
Abstract
Plant natural products (PNPs) are specialized metabolites with diverse bioactivities. They are extensively used in the pharmaceutical, cosmeceutical and food industries. PNPs are synthesized in plant cells by enzymes that are distributed in different subcellular compartments with unique microenvironments, such as ions, co-factors and substrates. Plant metabolic engineering is an emerging and promising approach for the sustainable production of PNPs, for which the knowledge of the subcellular compartmentalization of their biosynthesis is instrumental. In this review we describe the state of the art on the role of subcellular compartments in the biosynthesis of major types of PNPs, including terpenoids, phenylpropanoids, alkaloids and glucosinolates, and highlight the efforts to target biosynthetic pathways to subcellular compartments in plants. In addition, we will discuss the challenges and strategies in the field of plant synthetic biology and subcellular engineering. We expect that newly developed methods and tools, together with the knowledge gained from the microbial chassis, will greatly advance plant metabolic engineering.
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Affiliation(s)
- Lu Yao
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Xiuming Wu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Xun Jiang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Muhammad Shan
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Zhuoxiang Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Yiting Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Aiguo Yang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Yu Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Changqing Yang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China.
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6
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Madhavan A, Arun KB, Alex D, Anoopkumar AN, Emmanual S, Chaturvedi P, Varjani S, Tiwari A, Kumar V, Reshmy R, Awasthi MK, Binod P, Aneesh EM, Sindhu R. Microbial production of nutraceuticals: Metabolic engineering interventions in phenolic compounds, poly unsaturated fatty acids and carotenoids synthesis. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2023; 60:2092-2104. [PMID: 37273565 PMCID: PMC10232702 DOI: 10.1007/s13197-022-05482-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 04/20/2022] [Accepted: 05/07/2022] [Indexed: 06/06/2023]
Abstract
Nutraceuticals have attained substantial attention due to their health-boosting or disease-prevention characteristics. Growing awareness about the potential of nutraceuticals for the prevention and management of diseases affecting human has led to an increase in the market value of nutraceuticals in several billion dollars. Nevertheless, limitations in supply and isolation complications from plants, animals or fungi, limit the large-scale production of nutraceuticals. Microbial engineering at metabolic level has been proved as an environment friendly substitute for the chemical synthesis of nutraceuticals. Extensively used microbial systems such as E. coli and S. cerevisiae have been modified as versatile cell factories for the synthesis of diverse nutraceuticals. This review describes current interventions in metabolic engineering for synthesising some of the therapeutically important nutraceuticals (phenolic compounds, polyunsaturated fatty acids and carotenoids). We focus on the interventions in enhancing product yield through engineering at gene level or pathway level.
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Affiliation(s)
- Aravind Madhavan
- Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014 India
| | - K. B. Arun
- Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014 India
| | - Deepthy Alex
- Department of Biotechnology, Mar Ivanios College, Trivandrum, Kerala 695015 India
| | - A. N. Anoopkumar
- Department of Zoology, Centre for Research in Emerging Tropical Diseases (CRET‑D), University of Calicut, Malappuram, Kerala India
| | - Shibitha Emmanual
- Department of Zoology, St. Joseph’s College, Thrissur, Kerala 680121 India
| | - Preeti Chaturvedi
- Aquatic Toxicology Laboratory, Environmental Toxicology Group, CSIR- Indian Institute for Toxicology Research (CSIR-IITR), 31 MG Marg, Lucknow, 226001 India
| | - Sunita Varjani
- Gujarat Pollution Control Board, Paryavaran Bhavan, CHH Road, Sector 10 A, Gandhinagar, Gujarat 382010 India
| | - Archana Tiwari
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Uttar Pradesh, Noida, 201301 India
| | - Vinod Kumar
- Fermentation Technology Division, CSIR- Indian Institute of Integrative Medicine (CSIR-IIIM), Jammu, J & K 180001 India
| | - R. Reshmy
- Department of Science and Humanities, Providence College of Engineering, Chengannur, Kerala 689122 India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, Kerala 695019 India
| | - Embalil Mathachan Aneesh
- Department of Zoology, Centre for Research in Emerging Tropical Diseases (CRET‑D), University of Calicut, Malappuram, Kerala India
| | - Raveendran Sindhu
- Department of Food Technology, T K M Institute of Technology, Kollam, Kerala 691505 India
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7
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Conart C, Bomzan DP, Huang XQ, Bassard JE, Paramita SN, Saint-Marcoux D, Rius-Bony A, Hivert G, Anchisi A, Schaller H, Hamama L, Magnard JL, Lipko A, Swiezewska E, Jame P, Riveill G, Hibrand-Saint Oyant L, Rohmer M, Lewinsohn E, Dudareva N, Baudino S, Caissard JC, Boachon B. A cytosolic bifunctional geranyl/farnesyl diphosphate synthase provides MVA-derived GPP for geraniol biosynthesis in rose flowers. Proc Natl Acad Sci U S A 2023; 120:e2221440120. [PMID: 37126706 PMCID: PMC10175749 DOI: 10.1073/pnas.2221440120] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/30/2023] [Indexed: 05/03/2023] Open
Abstract
Geraniol derived from essential oils of various plant species is widely used in the cosmetic and perfume industries. It is also an essential trait of the pleasant smell of rose flowers. In contrast to other monoterpenes which are produced in plastids via the methyl erythritol phosphate pathway, geraniol biosynthesis in roses relies on cytosolic NUDX1 hydrolase which dephosphorylates geranyl diphosphate (GPP). However, the metabolic origin of cytosolic GPP remains unknown. By feeding Rosa chinensis "Old Blush" flowers with pathway-specific precursors and inhibitors, combined with metabolic profiling and functional characterization of enzymes in vitro and in planta, we show that geraniol is synthesized through the cytosolic mevalonate (MVA) pathway by a bifunctional geranyl/farnesyl diphosphate synthase, RcG/FPPS1, producing both GPP and farnesyl diphosphate (FPP). The downregulation and overexpression of RcG/FPPS1 in rose petals affected not only geraniol and germacrene D emissions but also dihydro-β-ionol, the latter due to metabolic cross talk of RcG/FPPS1-dependent isoprenoid intermediates trafficking from the cytosol to plastids. Phylogenetic analysis together with functional characterization of G/FPPS orthologs revealed that the G/FPPS activity is conserved among Rosaceae species. Site-directed mutagenesis and molecular dynamic simulations enabled to identify two conserved amino acids that evolved from ancestral FPPSs and contribute to GPP/FPP product specificity. Overall, this study elucidates the origin of the cytosolic GPP for NUDX1-dependent geraniol production, provides insights into the emergence of the RcG/FPPS1 GPPS activity from the ancestral FPPSs, and shows that RcG/FPPS1 plays a key role in the biosynthesis of volatile terpenoid compounds in rose flowers.
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Affiliation(s)
- Corentin Conart
- Université Jean Monnet Saint-Etienne, Centre National de la Recherche Scientifique, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales, Unité Mixte de Recherche 5079, Saint-EtienneF-42023, France
| | - Dikki Pedenla Bomzan
- Université Jean Monnet Saint-Etienne, Centre National de la Recherche Scientifique, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales, Unité Mixte de Recherche 5079, Saint-EtienneF-42023, France
| | - Xing-Qi Huang
- Department of Biochemistry, Purdue University, West Lafayette, IN47907-2063
| | - Jean-Etienne Bassard
- Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique, Unité Propre de Recherche 2357, Université de Strasbourg, Strasbourg67084, France
| | - Saretta N. Paramita
- Université Jean Monnet Saint-Etienne, Centre National de la Recherche Scientifique, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales, Unité Mixte de Recherche 5079, Saint-EtienneF-42023, France
| | - Denis Saint-Marcoux
- Université Jean Monnet Saint-Etienne, Centre National de la Recherche Scientifique, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales, Unité Mixte de Recherche 5079, Saint-EtienneF-42023, France
| | - Aurélie Rius-Bony
- Université Jean Monnet Saint-Etienne, Centre National de la Recherche Scientifique, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales, Unité Mixte de Recherche 5079, Saint-EtienneF-42023, France
| | - Gal Hivert
- Department of Vegetable Crops, Newe Ya’ar Research Center, Agricultural Research organization, The Volcani Center, Ramat Yishay30095, Israel
- Department of Vegetable Crops, The Robert Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot76100001, Israel
| | - Anthony Anchisi
- Université de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, VilleurbanneF-69100, France
| | - Hubert Schaller
- Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique, Unité Propre de Recherche 2357, Université de Strasbourg, Strasbourg67084, France
| | - Latifa Hamama
- Université d'Angers, Institut Agro, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Institut de Recherche en Horticulture et Semences, Structure Fédérative de Recherche Qualité et Santé du Végétal, Angers49000, France
| | - Jean-Louis Magnard
- Université Jean Monnet Saint-Etienne, Centre National de la Recherche Scientifique, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales, Unité Mixte de Recherche 5079, Saint-EtienneF-42023, France
| | - Agata Lipko
- Nalecz Institute of Biocybernetics and Biomedical Engineering, Polish Academy of Sciences, Warsaw02-109Poland
| | - Ewa Swiezewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw02-106Poland
| | - Patrick Jame
- Université de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, VilleurbanneF-69100, France
| | - Geneviève Riveill
- Université de Strasbourg, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Unité Mixte de Recherche 1131 Santé de la Vigne et Qualité du Vin,F-68000Colmar, France
| | - Laurence Hibrand-Saint Oyant
- Université d'Angers, Institut Agro, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Institut de Recherche en Horticulture et Semences, Structure Fédérative de Recherche Qualité et Santé du Végétal, Angers49000, France
| | - Michel Rohmer
- Institut de Chimie de Strasbourg, Université de Strasbourg/Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7177, Institut Le Bel, Strasbourg67081, France
| | - Efraim Lewinsohn
- Department of Vegetable Crops, Newe Ya’ar Research Center, Agricultural Research organization, The Volcani Center, Ramat Yishay30095, Israel
- Department of Vegetable Crops, The Robert Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot76100001, Israel
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, IN47907-2063
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN47907
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN47907-2010
| | - Sylvie Baudino
- Université Jean Monnet Saint-Etienne, Centre National de la Recherche Scientifique, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales, Unité Mixte de Recherche 5079, Saint-EtienneF-42023, France
| | - Jean-Claude Caissard
- Université Jean Monnet Saint-Etienne, Centre National de la Recherche Scientifique, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales, Unité Mixte de Recherche 5079, Saint-EtienneF-42023, France
| | - Benoît Boachon
- Université Jean Monnet Saint-Etienne, Centre National de la Recherche Scientifique, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales, Unité Mixte de Recherche 5079, Saint-EtienneF-42023, France
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8
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Pan Q, Ma X, Liang H, Liu Y, Zhou Y, Stephanopoulos G, Zhou K. Biosynthesis of geranate via isopentenol utilization pathway in Escherichia coli. Biotechnol Bioeng 2023; 120:230-238. [PMID: 36224741 PMCID: PMC10092522 DOI: 10.1002/bit.28255] [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: 07/06/2022] [Revised: 10/03/2022] [Accepted: 10/08/2022] [Indexed: 11/06/2022]
Abstract
Isoprenoids are a large family of natural products with diverse structures, which allow them to play diverse and important roles in the physiology of plants and animals. They also have important commercial uses as pharmaceuticals, flavoring agents, fragrances, and nutritional supplements. Recently, metabolic engineering has been intensively investigated and emerged as the technology of choice for the production of isoprenoids through microbial fermentation. Isoprenoid biosynthesis typically originates in plants from acetyl-coA in central carbon metabolism, however, a recent study reported an alternative pathway, the isopentenol utilization pathway (IUP), that can provide the building blocks of isoprenoid biosynthesis from affordable C5 substrates. In this study, we expressed the IUP in Escherichia coli to efficiently convert isopentenols into geranate, a valuable isoprenoid compound. We first established a geraniol-producing strain in E. coli that uses the IUP. Then, we extended the geraniol synthesis pathway to produce geranate through two oxidation reactions catalyzed by two alcohol/aldehyde dehydrogenases from Castellaniella defragrans. The geranate titer was further increased by optimizing the expression of the two dehydrogenases and also parameters of the fermentation process. The best strain produced 764 mg/L geranate in 24 h from 2 g/L isopentenols (a mixture of isoprenol and prenol). We also investigated if the dehydrogenases could accept other isoprenoid alcohols as substrates.
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Affiliation(s)
- Qiuchi Pan
- Disruptive & Sustainable Technologies for Agricultural Precision (DiSTAP), Singapore-MIT Alliance for Research and Technology, Singapore, Singapore.,Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore
| | - Xiaoqiang Ma
- Disruptive & Sustainable Technologies for Agricultural Precision (DiSTAP), Singapore-MIT Alliance for Research and Technology, Singapore, Singapore.,Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore.,Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Hong Liang
- Disruptive & Sustainable Technologies for Agricultural Precision (DiSTAP), Singapore-MIT Alliance for Research and Technology, Singapore, Singapore.,Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore
| | - Yurou Liu
- Disruptive & Sustainable Technologies for Agricultural Precision (DiSTAP), Singapore-MIT Alliance for Research and Technology, Singapore, Singapore.,Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore
| | - Ying Zhou
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore
| | - Gregory Stephanopoulos
- Disruptive & Sustainable Technologies for Agricultural Precision (DiSTAP), Singapore-MIT Alliance for Research and Technology, Singapore, Singapore.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kang Zhou
- Disruptive & Sustainable Technologies for Agricultural Precision (DiSTAP), Singapore-MIT Alliance for Research and Technology, Singapore, Singapore.,Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore
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9
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A microbial supply chain for production of the anti-cancer drug vinblastine. Nature 2022; 609:341-347. [PMID: 36045295 PMCID: PMC9452304 DOI: 10.1038/s41586-022-05157-3] [Citation(s) in RCA: 143] [Impact Index Per Article: 71.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/27/2022] [Indexed: 12/05/2022]
Abstract
Monoterpene indole alkaloids (MIAs) are a diverse family of complex plant secondary metabolites with many medicinal properties, including the essential anti-cancer therapeutics vinblastine and vincristine1. As MIAs are difficult to chemically synthesize, the world’s supply chain for vinblastine relies on low-yielding extraction and purification of the precursors vindoline and catharanthine from the plant Catharanthus roseus, which is then followed by simple in vitro chemical coupling and reduction to form vinblastine at an industrial scale2,3. Here, we demonstrate the de novo microbial biosynthesis of vindoline and catharanthine using a highly engineered yeast, and in vitro chemical coupling to vinblastine. The study showcases a very long biosynthetic pathway refactored into a microbial cell factory, including 30 enzymatic steps beyond the yeast native metabolites geranyl pyrophosphate and tryptophan to catharanthine and vindoline. In total, 56 genetic edits were performed, including expression of 34 heterologous genes from plants, as well as deletions, knock-downs and overexpression of ten yeast genes to improve precursor supplies towards de novo production of catharanthine and vindoline, from which semisynthesis to vinblastine occurs. As the vinblastine pathway is one of the longest MIA biosynthetic pathways, this study positions yeast as a scalable platform to produce more than 3,000 natural MIAs and a virtually infinite number of new-to-nature analogues. De novo microbial biosynthesis of vindoline and catharanthine using a highly engineered yeast and in vitro chemical coupling to vinblastine is carried out, positioning yeast as a scalable platform to produce many monoterpene indole alkaloids.
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10
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Park SY, Eun H, Lee MH, Lee SY. Metabolic engineering of Escherichia coli with electron channelling for the production of natural products. Nat Catal 2022. [DOI: 10.1038/s41929-022-00820-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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11
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Rinaldi MA, Ferraz CA, Scrutton NS. Alternative metabolic pathways and strategies to high-titre terpenoid production in Escherichia coli. Nat Prod Rep 2022; 39:90-118. [PMID: 34231643 PMCID: PMC8791446 DOI: 10.1039/d1np00025j] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Indexed: 12/14/2022]
Abstract
Covering: up to 2021Terpenoids are a diverse group of chemicals used in a wide range of industries. Microbial terpenoid production has the potential to displace traditional manufacturing of these compounds with renewable processes, but further titre improvements are needed to reach cost competitiveness. This review discusses strategies to increase terpenoid titres in Escherichia coli with a focus on alternative metabolic pathways. Alternative pathways can lead to improved titres by providing higher orthogonality to native metabolism that redirects carbon flux, by avoiding toxic intermediates, by bypassing highly-regulated or bottleneck steps, or by being shorter and thus more efficient and easier to manipulate. The canonical 2-C-methyl-D-erythritol 4-phosphate (MEP) and mevalonate (MVA) pathways are engineered to increase titres, sometimes using homologs from different species to address bottlenecks. Further, alternative terpenoid pathways, including additional entry points into the MEP and MVA pathways, archaeal MVA pathways, and new artificial pathways provide new tools to increase titres. Prenyl diphosphate synthases elongate terpenoid chains, and alternative homologs create orthogonal pathways and increase product diversity. Alternative sources of terpenoid synthases and modifying enzymes can also be better suited for E. coli expression. Mining the growing number of bacterial genomes for new bacterial terpenoid synthases and modifying enzymes identifies enzymes that outperform eukaryotic ones and expand microbial terpenoid production diversity. Terpenoid removal from cells is also crucial in production, and so terpenoid recovery and approaches to handle end-product toxicity increase titres. Combined, these strategies are contributing to current efforts to increase microbial terpenoid production towards commercial feasibility.
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Affiliation(s)
- Mauro A Rinaldi
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Clara A Ferraz
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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12
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Huang Y, Xie FJ, Cao X, Li MY. Research progress in biosynthesis and regulation of plant terpenoids. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2021.2020162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Ying Huang
- Department of Horticulture, College of Agriculture and Forestry Sciences, Linyi University, Linyi, Shandong, PR China
| | - Fang-Jie Xie
- Department of Horticulture, College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Xue Cao
- Department of Horticulture, College of Agriculture and Forestry Sciences, Linyi University, Linyi, Shandong, PR China
| | - Meng-Yao Li
- Department of Horticulture, College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, PR China
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13
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Zhu K, Kong J, Zhao B, Rong L, Liu S, Lu Z, Zhang C, Xiao D, Pushpanathan K, Foo JL, Wong A, Yu A. Metabolic engineering of microbes for monoterpenoid production. Biotechnol Adv 2021; 53:107837. [PMID: 34555428 DOI: 10.1016/j.biotechadv.2021.107837] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/07/2021] [Accepted: 09/14/2021] [Indexed: 12/29/2022]
Abstract
Monoterpenoids are an important class of natural products that are derived from the condensation of two five‑carbon isoprene subunits. They are widely used for flavouring, fragrances, colourants, cosmetics, fuels, chemicals, and pharmaceuticals in various industries. They can also serve as precursors for the production of many industrially important products. Currently, monoterpenoids are produced predominantly through extraction from plant sources. However, the small quantity of monoterpenoids in nature renders this method of isolation non-economically viable. Similarly impractical is the chemical synthesis of these compounds as they suffer from high energy consumption and pollutant discharge. Microbial biosynthesis, however, exists as a potential solution to these hindrances, but the transformation of cells into efficient factories remains a major impediment. Here, we critically review the recent advances in engineering microbes for monoterpenoid production, with an emphasis on categorized strategies, and discuss the challenges and perspectives to offer guidance for future engineering.
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Affiliation(s)
- Kun Zhu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin 300457, PR China.
| | - Jing Kong
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin 300457, PR China.
| | - Baixiang Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin 300457, PR China.
| | - Lanxin Rong
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin 300457, PR China.
| | - Shiqi Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin 300457, PR China.
| | - Zhihui Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin 300457, PR China.
| | - Cuiying Zhang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin 300457, PR China.
| | - Dongguang Xiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin 300457, PR China.
| | - Krithi Pushpanathan
- Chemical Engineering and Food Technology Cluster, Singapore Institute of Technology, Singapore 138683, Singapore.
| | - Jee Loon Foo
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.
| | - Adison Wong
- Chemical Engineering and Food Technology Cluster, Singapore Institute of Technology, Singapore 138683, Singapore.
| | - Aiqun Yu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin 300457, PR China.
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14
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Strictosidine synthase, an indispensable enzyme involved in the biosynthesis of terpenoid indole and β-carboline alkaloids. Chin J Nat Med 2021; 19:591-607. [PMID: 34419259 DOI: 10.1016/s1875-5364(21)60059-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Indexed: 11/21/2022]
Abstract
Terpenoid indole (TIAs) and β-carboline alkaloids (BCAs), such as suppressant reserpine, vasodilatory yohimbine, and antimalarial quinine, are natural compounds derived from strictosidine. These compounds can exert powerful pharmacological effects but be obtained from limited source in nature. the whole biosynthetic pathway of TIAs and BCAs, The Pictet-Spengler reaction catalyzed by strictosidine synthase (STR; EC: 4.3.3.2) is the rate-limiting step. Therefore, it is necessary to investigate their biosynthesis pathways, especially the role of STR, and related findings will support the biosynthetic generation of natural and unnatural compounds. This review summarizes the latest studies concerning the function of STR in TIA and BCA biosynthesis, and illustrates the compounds derived from strictosidine. The substrate specificity of STR based on its structure is also summarized. Proteins that contain six-bladed four-stranded β-propeller folds in many organisms, other than plants, are listed. The presence of these folds may lead to similar functions among organisms. The expression of STR gene can greatly influence the production of many compounds. STR is mainly applied to product various valuable drugs in plant cell suspension culture and biosynthesis in other carriers.
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15
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Wang X, Chen J, Zhang J, Zhou Y, Zhang Y, Wang F, Li X. Engineering Escherichia coli for production of geraniol by systematic synthetic biology approaches and laboratory-evolved fusion tags. Metab Eng 2021; 66:60-67. [PMID: 33865982 DOI: 10.1016/j.ymben.2021.04.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/23/2021] [Accepted: 04/11/2021] [Indexed: 12/16/2022]
Abstract
Geraniol is a valuable monoterpene extensively used in the fragrance, food, and cosmetic industries. Increasing environmental concerns and supply gaps have motivated efforts to advance the microbial production of geraniol from renewable feedstocks. In this study, we first constructed a platform geraniol Escherichia coli strain by bioprospecting the key enzymes geranyl diphosphate synthase (GPPS) and geraniol synthase (GES) and selection of a host cell background. This strategy led to a 46.4-fold increase in geraniol titer to 964.3 mg/L. We propose that the expression level of eukaryotic GES can be further optimized through fusion tag evolution engineering. To this end, we manipulated GES to maximize flux towards the targeted product geraniol from precursor geranyl diphosphate (GPP) via the utilization of fusion tags. Additionally, we developed a high-throughput screening system to monitor fusion tag variants. This common plug-and-play toolbox proved to be a robust approach for systematic modulation of protein expression and can be used to tune biosynthetic metabolic pathways. Finally, by combining a modified E1* fusion tag, we achieved 2124.1 mg/L of geraniol in shake flask cultures, which reached 27.2% of the maximum theoretical yield and was the highest titer ever reported. We propose that this strategy has set a good reference for enhancing a broader range of terpenoid production in microbial cell factories, which might open new possibilities for the bio-production of other valuable chemicals.
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Affiliation(s)
- Xun Wang
- Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-forest Biomass, Nanjing Forestry University, Nanjing, 210037, China; Jiangsu Key Laboratory of Biomass-based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing, 210037, China; College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Jiaming Chen
- Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-forest Biomass, Nanjing Forestry University, Nanjing, 210037, China; Jiangsu Key Laboratory of Biomass-based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing, 210037, China; College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Jia Zhang
- Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-forest Biomass, Nanjing Forestry University, Nanjing, 210037, China; Jiangsu Key Laboratory of Biomass-based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing, 210037, China; College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Yujunjie Zhou
- Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-forest Biomass, Nanjing Forestry University, Nanjing, 210037, China; Jiangsu Key Laboratory of Biomass-based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing, 210037, China; College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Yu Zhang
- Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-forest Biomass, Nanjing Forestry University, Nanjing, 210037, China; Jiangsu Key Laboratory of Biomass-based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing, 210037, China; College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Fei Wang
- Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-forest Biomass, Nanjing Forestry University, Nanjing, 210037, China; Jiangsu Key Laboratory of Biomass-based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing, 210037, China; College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Xun Li
- Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-forest Biomass, Nanjing Forestry University, Nanjing, 210037, China; Jiangsu Key Laboratory of Biomass-based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing, 210037, China; College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China.
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16
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Computer-Aid Directed Evolution of GPPS and PS Enzymes. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6653500. [PMID: 33791370 PMCID: PMC7994089 DOI: 10.1155/2021/6653500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/20/2021] [Accepted: 03/03/2021] [Indexed: 11/18/2022]
Abstract
Pinene, a natural active monoterpene, is widely used as a flavoring agent, perfume, medicine, and biofuel. Although genetically engineered microorganisms have successfully produced pinene, to date, the biological yield of pinene is much lower than that of semiterpenes (isoprene) and sesquiterpenes (farnesene). In addition to the low heterologous expression of geranyl pyrophosphate synthase (GPPS) and pinene synthase (PS), cytotoxicity due to accumulation of the monoterpene also limits the production of pinene in microorganisms. In this study, we attempted to use two strategies to increase the biological yield of pinene. By deleting the random coils of GPPS and PS alone or in combination, a strain with a 335% yield increase was obtained. Additionally, upon computer-guided molecular modeling and docking of GPPS with isopentenyl pyrophosphate (IPP), its substrate, the key sites located within the catalytic pocket for substrate binding, was predicted. After screening, a strain harboring the T273R mutation of GPPS was selected among a batch of mutations of the key sites with a 154% increase in pinene yield.
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Lin PC, Zhang F, Pakrasi HB. Enhanced limonene production in a fast-growing cyanobacterium through combinatorial metabolic engineering. Metab Eng Commun 2021; 12:e00164. [PMID: 33659180 PMCID: PMC7890178 DOI: 10.1016/j.mec.2021.e00164] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 01/12/2021] [Accepted: 01/19/2021] [Indexed: 12/14/2022] Open
Abstract
Terpenoids are a large and diverse group of natural products with commercial applications. Microbial production of terpenes is considered as a feasible approach for the stable supply of these complex hydrocarbons. Cyanobacteria, photosynthetic prokaryotes, are attractive hosts for sustainable bioproduction, because these autotrophs require only light and CO2 for growth. Despite cyanobacteria having been engineered to produce a variety of compounds, their productivities of terpenes are generally low. Further research is needed to determine the bottleneck reactions for enhancing terpene production in cyanobacteria. In this study, we engineered the fast-growing cyanobacterium Synechococcus elongatus UTEX 2973 to produce a commercially-used terpenoid, limonene. We identified a beneficial mutation in the gene encoding geranylgeranyl pyrophosphate synthase crtE, leading to a 2.5-fold increase in limonene production. The engineered strain produced 16.4 mg L−1 of limonene at a rate of 8.2 mg L−1 day−1, which is 8-fold higher than limonene productivities previously reported in other cyanobacterial species. Furthermore, we employed a combinatorial metabolic engineering approach to optimize genes involved in the upstream pathway of limonene biosynthesis. By modulating the expression of genes encoding the enzymes in the MEP pathway and the geranyl pyrophosphate synthase, we showed that optimization of the expression level is critical to enhance limonene production in cyanobacteria. Engineering of the fast growing cyanobacterium Synechococcus elongatus UTEX 2973 for limonene production. Identification of a beneficial mutation with 2.5-fold increase in limonene productivity. Pathway optimization for limonene biosynthesis.
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Affiliation(s)
- Po-Cheng Lin
- Department of Energy, Environmental & Chemical Engineering, Washington University, St. Louis, MO, 63130, USA
| | - Fuzhong Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University, St. Louis, MO, 63130, USA
| | - Himadri B Pakrasi
- Department of Biology, Washington University, St. Louis, MO, 63130, USA
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18
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You MK, Lee YJ, Yu JS, Ha SH. The Predicted Functional Compartmentation of Rice Terpenoid Metabolism by Trans-Prenyltransferase Structural Analysis, Expression and Localization. Int J Mol Sci 2020; 21:E8927. [PMID: 33255547 PMCID: PMC7728057 DOI: 10.3390/ijms21238927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/15/2020] [Accepted: 11/18/2020] [Indexed: 12/17/2022] Open
Abstract
Most terpenoids are derived from the basic terpene skeletons of geranyl pyrophosphate (GPP, C10), farnesyl-PP (FPP, C15) and geranylgeranyl-PP (GGPP, C20). The trans-prenyltransferases (PTs) mediate the sequential head-to-tail condensation of an isopentenyl-PP (C5) with allylic substrates. The in silico structural comparative analyses of rice trans-PTs with 136 plant trans-PT genes allowed twelve rice PTs to be identified as GGPS_LSU (OsGGPS1), homomeric G(G)PS (OsGPS) and GGPS_SSU-II (OsGRP) in Group I; two solanesyl-PP synthase (OsSPS2 and 3) and two polyprenyl-PP synthases (OsSPS1 and 4) in Group II; and five FPSs (OsFPS1, 2, 3, 4 and 5) in Group III. Additionally, several residues in "three floors" for the chain length and several essential domains for enzymatic activities specifically varied in rice, potentiating evolutionarily rice-specific biochemical functions of twelve trans-PTs. Moreover, expression profiling and localization patterns revealed their functional compartmentation in rice. Taken together, we propose the predicted topology-based working model of rice PTs with corresponding terpene metabolites: GPP/GGPPs mainly in plastoglobuli, SPPs in stroma, PPPs in cytosol, mitochondria and chloroplast and FPPs in cytosol. Our findings could be suitably applied to metabolic engineering for producing functional terpene metabolites in rice systems.
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Affiliation(s)
- Min Kyoung You
- Department of Genetic Engineering and Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin 17104, Korea; (Y.J.L.); (J.S.Y.)
| | | | | | - Sun-Hwa Ha
- Department of Genetic Engineering and Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin 17104, Korea; (Y.J.L.); (J.S.Y.)
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Barsain BL, Purohit A, Kumar A, Joshi R, Hallan V, Yadav SK. PkGPPS.SSU interacts with two PkGGPPS to form heteromeric GPPS in Picrorhiza kurrooa: Molecular insights into the picroside biosynthetic pathway. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 154:115-128. [PMID: 32554175 DOI: 10.1016/j.plaphy.2020.05.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/11/2020] [Accepted: 05/24/2020] [Indexed: 06/11/2023]
Abstract
Geranyl geranyl pyrophosphate synthase (GGPPS) is known to form an integral subunit of the heteromeric GPPS (geranyl pyrophosphate synthase) complex and catalyzes the biosynthesis of monoterpene in plants. Picrorhiza kurrooa Royle ex Benth., a medicinally important high altitude plant is known for picroside biomolecules, the monoterpenoids. However, the significance of heteromeric GPPS in P. kurrooa still remains obscure. Here, transient silencing of PkGGPPS was observed to reduce picroside-I (P-I) content by more than 60% as well as picroside-II (P-II) by more than 75%. Thus, PkGGPPS was found to be involved in the biosynthesis of P-I and P-II besides other terpenoids. To unravel the mechanism, small subunit of GPPS (PkGPPS.SSU) was identified from P. kurrooa. Protein-protein interaction studies in yeast as well as bimolecular fluorescence complementation (BiFC) in planta have indicated that large subunit of GPPS PkGPPS.LSUs (PkGGPPS1 and PkGGPPS2) and PkGPPS.SSU form a heteromeric GPPS. Presence of similar conserved domains such as light responsive motifs, low temperature responsive elements (LTRE), dehydration responsive elements (DREs), W Box and MeJA responsive elements in the promoters of PkGPPS.LSU and PkGPPS.SSU documented their involvement in picroside biosynthesis. Further, the tissue specific transcript expression analysis vis-à-vis epigenetic regulation (DNA methylation) of promoters as well as coding regions of PkGPPS.LSU and PkGPPS.SSU has strongly suggested their role in picroside biosynthesis. Taken together, the newly identified PkGPPS.SSU formed the heteromeric GPPS by interacting with PkGPPS.LSUs to synthesize P-I and P-II in P. kurrooa.
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Affiliation(s)
- Bharati Lalhal Barsain
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, HP, India; Academy of Scientific and Innovative Research, New Delhi, India
| | - Anjali Purohit
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, HP, India
| | - Ajay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, HP, India; Academy of Scientific and Innovative Research, New Delhi, India
| | - Robin Joshi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, HP, India
| | - Vipin Hallan
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, HP, India; Academy of Scientific and Innovative Research, New Delhi, India.
| | - Sudesh Kumar Yadav
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, HP, India; Academy of Scientific and Innovative Research, New Delhi, India.
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Zhu QL, Zheng JL, Liu J. Transcription activation of β-carotene biosynthetic genes at the initial stage of stresses as an indicator of the increased β-carotene accumulation in isolated Dunaliella salina strain GY-H13. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2020; 222:105472. [PMID: 32203794 DOI: 10.1016/j.aquatox.2020.105472] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 06/10/2023]
Abstract
β-carotene is an efficient antioxidant and its accumulation is an oxidative response to stressors. Dunaliella salina strain GY-H13 is rich in β-carotene under environmental stresses, which was selected as material to understand the molecular mechanism underlying β-carotene biosynthesis. Seven full length cDNA sequences in β-carotene biosynthesis pathway were cloned, including geranylgeranyl pyrophosphate synthase (GGPS), phytoene synthase (PSY), phytoene desaturase (PDS), 15-cis-zeta-carotene isomerase (ZISO), zeta-carotene desaturase (ZDS), prolycopene isomerase (CRTISO), lycopene beta-cyclase (LCYb). The seven protein sequences from the strain GY-H13 showed the highest similarity with other D. salina strains. Especially, PSY, PDS and LCYb protein sequences shared 100 % identity. Phylogenetic analysis indicated all proteins from GY-H13 firstly clustered with those from other D. salina strains with a bootstrap of 100 %. Multiple alignment indicated several distinct conserved motifs such as aspartate-rich domain (ARD), dinucleotide binding domain (DBD), and carotene binding domain (CBD). These motifs are located near ligand-binding pocket, which may be required for the activity of enzyme. Expression levels of these genes and β-carotene content were measured over 24-h cycle, showing clear daily dynamics. All genes were dramatically up-regulated in the morning but the highest accumulation of β-carotene was observed at noon, suggesting a lag-effect between gene transcription and biological response. Furthermore, the accumulation of β-carotene increased under nitrogen deficiency, Cd exposure and high light and decreased under high salinity in a time-dependent manner. No gene of β-carotene biosynthesis was up-regulated by high salinity while most genes were activated by the other stresses at the beginning stage of exposure. Growth inhibition and oxidative damage were also observed under high salinity. Overall, transcription activation of β-carotene biosynthetic genes at the initial stage of stress exposure is a determinant of the increased accumulation of β-carotene in microalgae, which help their survive under harsh environments. The newly isolated D. salina strain GY-H13 would be a promising microalgae model for investigating the molecular mechanism of stress-induced β-carotene biosynthesis.
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Affiliation(s)
- Qing-Ling Zhu
- Institute of Marine Biology & Pharmacology, Ocean College, Zhejiang University, 1 Zheda Road, Dinghai District, Zhoushan, 316000, Zhejiang, PR China; College of Marine Ocean Science and Technology, Zhejiang Ocean University, Zhoushan, 316022, PR China
| | - Jia-Lang Zheng
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, PR China.
| | - Jianhua Liu
- Institute of Marine Biology & Pharmacology, Ocean College, Zhejiang University, 1 Zheda Road, Dinghai District, Zhoushan, 316000, Zhejiang, PR China; College of Marine Ocean Science and Technology, Zhejiang Ocean University, Zhoushan, 316022, PR China.
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21
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Fabris M, George J, Kuzhiumparambil U, Lawson CA, Jaramillo-Madrid AC, Abbriano RM, Vickers CE, Ralph P. Extrachromosomal Genetic Engineering of the Marine Diatom Phaeodactylum tricornutum Enables the Heterologous Production of Monoterpenoids. ACS Synth Biol 2020; 9:598-612. [PMID: 32032487 DOI: 10.1021/acssynbio.9b00455] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Geraniol is a commercially relevant plant-derived monoterpenoid that is a main component of rose essential oil and used as insect repellent. Geraniol is also a key intermediate compound in the biosynthesis of the monoterpenoid indole alkaloids (MIAs), a group of over 2000 compounds that include high-value pharmaceuticals. As plants naturally produce extremely small amounts of these molecules and their chemical synthesis is complex, industrially sourcing these compounds is costly and inefficient. Hence, microbial hosts suitable to produce MIA precursors through synthetic biology and metabolic engineering are currently being sought. Here, we evaluated the suitability of a eukaryotic microalga, the marine diatom Phaeodactylum tricornutum, for the heterologous production of monoterpenoids. Profiling of endogenous metabolism revealed that P. tricornutum, unlike other microbes employed for industrial production of terpenoids, accumulates free pools of the precursor geranyl diphosphate. To evaluate the potential for larger synthetic biology applications, we engineered P. tricornutum through extrachromosomal, episome-based expression, for the heterologous biosynthesis of the MIA intermediate geraniol. By profiling the production of geraniol resulting from various genetic and cultivation arrangements, P. tricornutum reached the maximum geraniol titer of 0.309 mg/L in phototrophic conditions. This work provides (i) a detailed analysis of P. tricornutum endogenous terpenoid metabolism, (ii) a successful demonstration of extrachromosomal expression for metabolic pathway engineering with potential gene-stacking applications, and (iii) a convincing proof-of-concept of the suitability of P. tricornutum as a novel production platform for heterologous monoterpenoids, with potential for complex pathway engineering aimed at the heterologous production of MIAs.
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Affiliation(s)
- Michele Fabris
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW 2007, Australia
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia
| | - Jestin George
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW 2007, Australia
| | | | - Caitlin A. Lawson
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW 2007, Australia
| | | | - Raffaela M. Abbriano
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW 2007, Australia
| | - Claudia E. Vickers
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Peter Ralph
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW 2007, Australia
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22
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Adal AM, Mahmoud SS. Short-chain isoprenyl diphosphate synthases of lavender (Lavandula). PLANT MOLECULAR BIOLOGY 2020; 102:517-535. [PMID: 31927660 DOI: 10.1007/s11103-020-00962-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 01/03/2020] [Indexed: 05/07/2023]
Abstract
KEY MESSAGE We reported the functional characterization of cDNAs encoding short-chain isoprenyl diphosphate synthases that control the partitioning of precursors for lavender terpenoids. Lavender essential oil is composed of regular and irregular monoterpenes, which are derived from linear precursors geranyl diphosphate (GPP) and lavandulyl diphosphate (LPP), respectively. Although this plant strongly expresses genes responsible for the biosynthesis of both monoterpene classes, it is unclear why regular monoterpenes dominate the oil. Here, we cloned and characterized Lavandula x intermedia cDNAs encoding geranyl diphosphate synthase (LiGPPS), geranylgeranyl diphosphate synthase (LiGGPPS) and farnesyl diphosphate synthase (LiFPPS). LiGPPS was heteromeric protein, consisting of a large subunit (LiGPPS.LSU) and a small subunit for which two different cDNAs (LiGPPS.SSU1 and LiGPPS.SSU2) were detected. Neither recombinant LiGPPS subunits was active by itself. However, when co-expressed in E. coli LiGPPS.LSU and LiGPPS.SSU1 formed an active heteromeric GPPS, while LiGPPS.LSU and LiGPPS.SSU2 did not form an active protein. Recombinant LiGGPPS, LiFPPS and LPP synthase (LPPS) proteins were active individually. Further, LiGPPS.SSU1 modified the activity of LiGGPPS (to produce GPP) in bacterial cells co-expressing both proteins. Given this, and previous evidence indicating that GPPS.SSU can modify the activity of GGPPS to GPPS in vitro and in plants, we hypothesized that LiGPPS.SSU1 modifies the activity of L. x intermedia LPP synthase (LiLPPS), thus accounting for the relatively low abundance of LPP-derived irregular monoterpenes in this plant. However, LiGPPS.SSU1 did not affect the activity of LiLPPS. These results, coupled to the observation that LiLPPS transcripts are more abundant than those of GPPS subunits in L. x intermedia flowers, suggest that regulatory mechanisms other than transcriptional control of LPPS regulate precursor partitioning in lavender flowers.
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Affiliation(s)
- Ayelign M Adal
- Department of Biology, University of British Columbia, Kelowna, BC, Canada
| | - Soheil S Mahmoud
- Department of Biology, University of British Columbia, Kelowna, BC, Canada.
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23
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Celedon JM, Bohlmann J. Oleoresin defenses in conifers: chemical diversity, terpene synthases and limitations of oleoresin defense under climate change. THE NEW PHYTOLOGIST 2019; 224:1444-1463. [PMID: 31179548 DOI: 10.1111/nph.15984] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/16/2019] [Indexed: 05/20/2023]
Abstract
Conifers have evolved complex oleoresin terpene defenses against herbivores and pathogens. In co-evolved bark beetles, conifer terpenes also serve chemo-ecological functions as pheromone precursors, chemical barcodes for host identification, or nutrients for insect-associated microbiomes. We highlight the genomic, molecular and biochemical underpinnings of the large chemical space of conifer oleoresin terpenes and volatiles. Conifer terpenes are predominantly the products of the conifer terpene synthase (TPS) gene family. Terpene diversity is increased by cytochromes P450 of the CYP720B class. Many conifer TPS are multiproduct enzymes. Multisubstrate CYP720B enzymes catalyse multistep oxidations. We summarise known terpenoid gene functions in various different conifer species with reference to the annotated terpenoid gene space in a spruce genome. Overall, biosynthesis of terpene diversity in conifers is achieved through a system of biochemical radiation and metabolic grids. Expression of TPS and CYP720B genes can be specific to individual cell types of constitutive or traumatic resin duct systems. Induced terpenoid transcriptomes in resin duct cells lead to dynamic changes of terpene composition and quantity to fend off herbivores and pathogens. While terpenoid defenses have contributed much to the evolutionary success of conifers, under new conditions of climate change, these defences may become inconsequential against range-expanding forest pests.
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Affiliation(s)
- Jose M Celedon
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Jörg Bohlmann
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
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24
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Jia M, Mishra SK, Tufts S, Jernigan RL, Peters RJ. Combinatorial biosynthesis and the basis for substrate promiscuity in class I diterpene synthases. Metab Eng 2019; 55:44-58. [PMID: 31220664 DOI: 10.1016/j.ymben.2019.06.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/04/2019] [Accepted: 06/14/2019] [Indexed: 02/04/2023]
Abstract
Terpene synthases are capable of mediating complex reactions, but fundamentally simply catalyze lysis of allylic diphosphate esters with subsequent deprotonation. Even with the initially generated tertiary carbocation this offers a variety of product outcomes, and deprotonation further can be preceded by the addition of water. This is particularly evident with labdane-related diterpenes (LRDs) where such lysis follows bicyclization catalyzed by class II diterpene cyclases (DTCs) that generates preceding structural variation. Previous investigation revealed that two diterpene synthases (DTSs), one bacterial and the other plant-derived, exhibit extreme substrate promiscuity, but yet still typically produce exo-ene or tertiary alcohol LRD derivatives, respectively (i.e., demonstrating high catalytic specificity), enabling rational combinatorial biosynthesis. Here two DTSs that produce either cis or trans endo-ene LRD derivatives, also plant and bacterial (respectively), were examined for their potential analogous utility. Only the bacterial trans-endo-ene forming DTS was found to exhibit significant substrate promiscuity (with moderate catalytic specificity). This further led to investigation of the basis for substrate promiscuity, which was found to be more closely correlated with phylogenetic origin than reaction complexity. Specifically, bacterial DTSs exhibited significantly more substrate promiscuity than those from plants, presumably reflecting their distinct evolutionary context. In particular, plants typically have heavily elaborated LRD metabolism, in contrast to the rarity of such natural products in bacteria, and the lack of potential substrates presumably alleviates selective pressure against such promiscuity. Regardless of such speculation, this work provides novel biosynthetic access to almost 19 LRDs, demonstrating the power of the combinatorial approach taken here.
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Affiliation(s)
- Meirong Jia
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Sambit K Mishra
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Samuel Tufts
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Robert L Jernigan
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA, 50011, USA.
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25
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The isoprenoid alcohol pathway, a synthetic route for isoprenoid biosynthesis. Proc Natl Acad Sci U S A 2019; 116:12810-12815. [PMID: 31186357 DOI: 10.1073/pnas.1821004116] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The more than 50,000 isoprenoids found in nature are all derived from the 5-carbon diphosphates isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). Natively, IPP and DMAPP are generated by the mevalonate (MVA) and 2-C-methyl-d-erythritol-4-phosphate (MEP) pathways, which have been engineered to produce compounds with numerous applications. However, as these pathways are inherently constrained by carbon, energy inefficiencies, and their roles in native metabolism, engineering for isoprenoid biosynthesis at high flux, titer, and yield remains a challenge. To overcome these limitations, here we develop an alternative synthetic pathway termed the isoprenoid alcohol (IPA) pathway that centers around the synthesis and subsequent phosphorylation of IPAs. We first established a lower IPA pathway for the conversion of IPAs to isoprenoid pyrophosphate intermediates that enabled the production of greater than 2 g/L geraniol from prenol as well as limonene, farnesol, diaponeurosporene, and lycopene. We then designed upper IPA pathways for the generation of (iso)prenol from central carbon metabolites with the development of a route to prenol enabling its synthesis at more than 2 g/L. Using prenol as the linking intermediate further facilitated an integrated IPA pathway that resulted in the production of nearly 0.6 g/L total monoterpenoids from glycerol as the sole carbon source. The IPA pathway provides an alternative route to isoprenoids that is more energy efficient than native pathways and can serve as a platform for targeting a repertoire of isoprenoid compounds with application as high-value pharmaceuticals, commodity chemicals, and fuels.
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26
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Advances in the Metabolic Engineering of Escherichia coli for the Manufacture of Monoterpenes. Catalysts 2019. [DOI: 10.3390/catal9050433] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Monoterpenes are commonly applied as pharmaceuticals and valuable chemicals in various areas. The bioproduction of valuable monoterpenes in prokaryotic microbial hosts, such as E. coli, has progressed considerably thanks to the development of different outstanding approaches. However, the large-scale production of monoterpenes still presents considerable limitations. Thus, process development warrants further investigations. This review discusses the endogenous methylerythritol-4-phosphate-dependent pathway engineering and the exogenous mevalonate-dependent isoprenoid pathway introduction, as well as the accompanied optimization of rate-limiting enzymes, metabolic flux, and product toxicity tolerance. We suggest further studies to focus on the development of systematical, integrational, and synthetic biological strategies in light of the inter disciplines at the cutting edge. Our review provides insights into the current advances of monoterpene bioengineering and serves as a reference for future studies to promote the industrial production of valuable monoterpenes.
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27
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Zhao DD, Yuan J, Cheng Q, Qi YL, Lu K, Lai SS, Sun Q, Zhao Y, Fang L, Jin ML, Yu DC, Qiu YD, Li CJ, Chen J, Xue B. Evidence for a role of geranylgeranylation in renal angiomyolipoma and renal epithelioid angiomyolipoma. Oncol Lett 2019; 17:1523-1530. [PMID: 30675208 PMCID: PMC6341897 DOI: 10.3892/ol.2018.9808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 10/19/2018] [Indexed: 01/17/2023] Open
Abstract
Research on mevalonate kinase deficiency has revealed that it may lead to the development of renal angiomyolipomas (RAMLs). Thus, it was suspected that geranylgeranyl pyrophosphate synthase (GGPPS), a key enzyme in the mevalonate pathway, may be involved in the development of RAMLs. In the present study, the expression of GGPPS in RAMLs and renal epithelioid angiomyolipomas (REAs) was assessed, and paraffin embedded specimens from 60 patients, including 9 cases with REA and 51 cases with RAML, were examined. Immunoreactivity was evaluated semi-quantitatively according to the intensity of staining and the percentage of positively stained cells. The results indicated that GGPPS was predominantly present in the cytoplasm, and REA tissues exhibited higher expression of GGPPS in the cytoplasm compared with RAML tissues. It was also identified that GGPPS was upregulated in TSC2-null cells, and inhibition of GGPPS could induce apoptosis of TSC2-null cells by autophagy. In conclusion, the increased expression of GGPPS in RAMLs and REAs indicated that mevalonate pathways may be involved in disease progression. GGPPS may serve as a potential therapeutic target and the current results may provide a novel therapeutic strategy for RAML and lymphangioleiomyomatosis.
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Affiliation(s)
- Dan-Dan Zhao
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular Medicine and School of Medicine, Nanjing University, Nanjing, Jiangsu 210093, P.R. China.,Research Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, P.R. China
| | - Jun Yuan
- Biochemical and Environmental Engineering School of Xiaozhuang College, Nanjing 211171, P.R. China
| | - Qi Cheng
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular Medicine and School of Medicine, Nanjing University, Nanjing, Jiangsu 210093, P.R. China
| | - Ya-Ling Qi
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular Medicine and School of Medicine, Nanjing University, Nanjing, Jiangsu 210093, P.R. China
| | - Ke Lu
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular Medicine and School of Medicine, Nanjing University, Nanjing, Jiangsu 210093, P.R. China
| | - Shan-Shan Lai
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, P.R. China
| | - Qian Sun
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular Medicine and School of Medicine, Nanjing University, Nanjing, Jiangsu 210093, P.R. China
| | - Yue Zhao
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular Medicine and School of Medicine, Nanjing University, Nanjing, Jiangsu 210093, P.R. China.,Liver Disease Collaborative Research Platform of Medical School of Nanjing University, Nanjing, Jiangsu 210093, P.R. China
| | - Lei Fang
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular Medicine and School of Medicine, Nanjing University, Nanjing, Jiangsu 210093, P.R. China.,Liver Disease Collaborative Research Platform of Medical School of Nanjing University, Nanjing, Jiangsu 210093, P.R. China
| | - Mei-Ling Jin
- Pulmonary Department, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - De-Cai Yu
- Liver Disease Collaborative Research Platform of Medical School of Nanjing University, Nanjing, Jiangsu 210093, P.R. China.,Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210008, P.R. China
| | - Yu-Dong Qiu
- Liver Disease Collaborative Research Platform of Medical School of Nanjing University, Nanjing, Jiangsu 210093, P.R. China.,Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210008, P.R. China
| | - Chao-Jun Li
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular Medicine and School of Medicine, Nanjing University, Nanjing, Jiangsu 210093, P.R. China
| | - Jun Chen
- Liver Disease Collaborative Research Platform of Medical School of Nanjing University, Nanjing, Jiangsu 210093, P.R. China.,Department of Pathology, The Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210008, P.R. China
| | - Bin Xue
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular Medicine and School of Medicine, Nanjing University, Nanjing, Jiangsu 210093, P.R. China.,Liver Disease Collaborative Research Platform of Medical School of Nanjing University, Nanjing, Jiangsu 210093, P.R. China.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu 210009, P.R. China
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28
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Multidimensional heuristic process for high-yield production of astaxanthin and fragrance molecules in Escherichia coli. Nat Commun 2018; 9:1858. [PMID: 29752432 PMCID: PMC5948211 DOI: 10.1038/s41467-018-04211-x] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 04/06/2018] [Indexed: 01/09/2023] Open
Abstract
Optimization of metabolic pathways consisting of large number of genes is challenging. Multivariate modular methods (MMMs) are currently available solutions, in which reduced regulatory complexities are achieved by grouping multiple genes into modules. However, these methods work well for balancing the inter-modules but not intra-modules. In addition, application of MMMs to the 15-step heterologous route of astaxanthin biosynthesis has met with limited success. Here, we expand the solution space of MMMs and develop a multidimensional heuristic process (MHP). MHP can simultaneously balance different modules by varying promoter strength and coordinating intra-module activities by using ribosome binding sites (RBSs) and enzyme variants. Consequently, MHP increases enantiopure 3S,3′S-astaxanthin production to 184 mg l−1 day−1 or 320 mg l−1. Similarly, MHP improves the yields of nerolidol and linalool. MHP may be useful for optimizing other complex biochemical pathways. Achieving high titer yield and productivity of target chemicals in industrial organism depends on multidimensional pathway optimization. Here, the authors use a refined modular method called multidimensional heuristic process to improve production of astaxanthin, nerolidol and linalool in E. coli.
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29
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Wu W, Liu F, Davis RW. Engineering Escherichia coli for the production of terpene mixture enriched in caryophyllene and caryophyllene alcohol as potential aviation fuel compounds. Metab Eng Commun 2018; 6:13-21. [PMID: 29349039 PMCID: PMC5767561 DOI: 10.1016/j.meteno.2018.01.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 12/23/2017] [Accepted: 01/02/2018] [Indexed: 11/26/2022] Open
Abstract
Recent studies have revealed that caryophyllene and its stereoisomers not only exhibit multiple biological activities but also have desired properties as renewable candidates for ground transportation and jet fuel applications. This study presents the first significant production of caryophyllene and caryolan-1-ol by an engineered E. coli with heterologous expression of mevalonate pathway genes with a caryophyllene synthase and a caryolan-1-ol synthase. By optimizing metabolic flux and fermentation parameters, the engineered strains yielded 449 mg/L of total terpene, including 406 mg/L sesquiterpene with 100 mg/L caryophyllene and 10 mg/L caryolan-1-ol. Furthermore, a marine microalgae hydrolysate was used as the sole carbon source for the production of caryophyllene and other terpene compounds. Under the optimal fermentation conditions, 360 mg/L of total terpene, 322 mg/L of sesquiterpene, and 75 mg/L caryophyllene were obtained from the pretreated algae hydrolysates. The highest yields achieved on the biomass basis were 48 mg total terpene/g algae and 10 mg caryophyllene/g algae and the caryophyllene yield is approximately ten times higher than that from plant tissues by solvent extraction. The study provides a sustainable alternative for production of caryophyllene and its alcohol from microalgae biomass as potential candidates for next generation aviation fuels. E. coli was engineered to yield terpene enriched in caryophyllene and caryolan-1-ol. Yields were improved through metabolic flux and culture parameters optimization. Algae hydrolysate was converted to terpene at high yields using engineered strains.
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Affiliation(s)
- Weihua Wu
- Department of Biomass Science & Conversion Technologies, Sandia National Laboratories, 7011 East Avenue, Livermore, CA, USA
| | - Fang Liu
- Department of Biomass Science & Conversion Technologies, Sandia National Laboratories, 7011 East Avenue, Livermore, CA, USA
| | - Ryan W Davis
- Department of Biomass Science & Conversion Technologies, Sandia National Laboratories, 7011 East Avenue, Livermore, CA, USA
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30
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Metabolic engineering of the pentose phosphate pathway for enhanced limonene production in the cyanobacterium Synechocysti s sp. PCC 6803. Sci Rep 2017; 7:17503. [PMID: 29235513 PMCID: PMC5727528 DOI: 10.1038/s41598-017-17831-y] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 11/30/2017] [Indexed: 11/08/2022] Open
Abstract
Isoprenoids are diverse natural compounds, which have various applications as pharmaceuticals, fragrances, and solvents. The low yield of isoprenoids in plants makes them difficult for cost-effective production, and chemical synthesis of complex isoprenoids is impractical. Microbial production of isoprenoids has been considered as a promising approach to increase the yield. In this study, we engineered the model cyanobacterium Synechocystis sp. PCC 6803 for sustainable production of a commercially valuable isoprenoid, limonene. Limonene synthases from the plants Mentha spicata and Citrus limon were expressed in cyanobacteria for limonene production. Production of limonene was two-fold higher with limonene synthase from M. spicata than that from C. limon. To enhance isoprenoid production, computational strain design was conducted by applying the OptForce strain design algorithm on Synechocystis 6803. Based on the metabolic interventions suggested by this algorithm, genes (ribose 5-phosphate isomerase and ribulose 5-phosphate 3-epimerase) in the pentose phosphate pathway were overexpressed, and a geranyl diphosphate synthase from the plant Abies grandis was expressed to optimize the limonene biosynthetic pathway. The optimized strain produced 6.7 mg/L of limonene, a 2.3-fold improvement in productivity. Thus, this study presents a feasible strategy to engineer cyanobacteria for photosynthetic production of isoprenoids.
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31
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Mendez-Perez D, Alonso-Gutierrez J, Hu Q, Molinas M, Baidoo EEK, Wang G, Chan LJG, Adams PD, Petzold CJ, Keasling JD, Lee TS. Production of jet fuel precursor monoterpenoids from engineered Escherichia coli. Biotechnol Bioeng 2017; 114:1703-1712. [PMID: 28369701 DOI: 10.1002/bit.26296] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 02/04/2017] [Accepted: 03/24/2017] [Indexed: 12/27/2022]
Abstract
Monoterpenes (C10 isoprenoids) are the main components of essential oils and are possible precursors for many commodity chemicals and high energy density fuels. Monoterpenes are synthesized from geranyl diphosphate (GPP), which is also the precursor for the biosynthesis of farnesyl diphosphate (FPP). FPP biosynthesis diverts the carbon flux from monoterpene production to C15 products and quinone biosynthesis. In this study, we tested a chromosomal mutation of Escherichia coli's native FPP synthase (IspA) to improve GPP availability for the production of monoterpenes using a heterologous mevalonate pathway. Monoterpene production at high levels required not only optimization of GPP production but also a basal level of FPP to maintain growth. The optimized strains produced two jet fuel precursor monoterpenoids 1,8-cineole and linalool at the titer of 653 mg/L and 505 mg/L, respectively, in batch cultures with 1% glucose. The engineered strains developed in this work provide useful resources for the production of high-value monoterpenes. Biotechnol. Bioeng. 2017;114: 1703-1712. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Daniel Mendez-Perez
- Joint BioEnergy Institute (JBEI), 5885 Hollis Street, 4th floor, Emeryville, California, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Jorge Alonso-Gutierrez
- Joint BioEnergy Institute (JBEI), 5885 Hollis Street, 4th floor, Emeryville, California, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Qijun Hu
- Joint BioEnergy Institute (JBEI), 5885 Hollis Street, 4th floor, Emeryville, California, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Margaux Molinas
- Joint BioEnergy Institute (JBEI), 5885 Hollis Street, 4th floor, Emeryville, California, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Edward E K Baidoo
- Joint BioEnergy Institute (JBEI), 5885 Hollis Street, 4th floor, Emeryville, California, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - George Wang
- Joint BioEnergy Institute (JBEI), 5885 Hollis Street, 4th floor, Emeryville, California, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Leanne J G Chan
- Joint BioEnergy Institute (JBEI), 5885 Hollis Street, 4th floor, Emeryville, California, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Paul D Adams
- Joint BioEnergy Institute (JBEI), 5885 Hollis Street, 4th floor, Emeryville, California, 94608, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Christopher J Petzold
- Joint BioEnergy Institute (JBEI), 5885 Hollis Street, 4th floor, Emeryville, California, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Jay D Keasling
- Joint BioEnergy Institute (JBEI), 5885 Hollis Street, 4th floor, Emeryville, California, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Horsholm, Denmark.,Department of Chemical & Biomolecular Engineering, University of California, Berkeley, California.,Department of Bioengineering, University of California, Berkeley, California
| | - Taek S Lee
- Joint BioEnergy Institute (JBEI), 5885 Hollis Street, 4th floor, Emeryville, California, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
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Champagne A, Boutry M. A comprehensive proteome map of glandular trichomes of hop (Humulus lupulus
L.) female cones: Identification of biosynthetic pathways of the major terpenoid-related compounds and possible transport proteins. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600411] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 01/23/2017] [Accepted: 02/09/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Antoine Champagne
- Institut des Sciences de la Vie; Université catholique de Louvain; Louvain-la-Neuve Belgium
| | - Marc Boutry
- Institut des Sciences de la Vie; Université catholique de Louvain; Louvain-la-Neuve Belgium
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Hu Z, Tang B, Wu Q, Zheng J, Leng P, Zhang K. Transcriptome Sequencing Analysis Reveals a Difference in Monoterpene Biosynthesis between Scented Lilium 'Siberia' and Unscented Lilium 'Novano'. FRONTIERS IN PLANT SCIENCE 2017; 8:1351. [PMID: 28824685 PMCID: PMC5543080 DOI: 10.3389/fpls.2017.01351] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/19/2017] [Indexed: 05/08/2023]
Abstract
Lilium is a world famous fragrant bulb flower with high ornamental and economic values, and significant differences in fragrance are found among different Lilium genotypes. In order to explore the mechanism underlying the different fragrances, the floral scents of Lilium 'Sibeia', with a strong fragrance, and Lilium 'Novano', with a very faint fragrance, were collected in vivo using a dynamic headspace technique. These scents were identified using automated thermal desorption-gas chromatography/mass spectrometry (ATD-GC/MS) at different flowering stages. We used RNA-Seq technique to determine the petal transcriptome at the full-bloom stage and analyzed differentially expressed genes (DEGs) to investigate the molecular mechanism of floral scent biosynthesis. The results showed that a significantly higher amount of Lilium 'Siberia' floral scent was released compared with Lilium 'Novano'. Moreover, monoterpenes played a dominant role in the floral scent of Lilium 'Siberia'; therefore, it is believed that the different emissions of monoterpenes mainly contributed to the difference in the floral scent between the two Lilium genotypes. Transcriptome sequencing analysis indicated that ~29.24 Gb of raw data were generated and assembled into 124,233 unigenes, of which 35,749 unigenes were annotated. Through a comparison of gene expression between these two Lilium genotypes, 6,496 DEGs were identified. The genes in the terpenoid backbone biosynthesis pathway showed significantly different expression levels. The gene expressions of 1-deoxy-D-xylulose 5-phosphate synthase (DXS), 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR), 4-hydroxy-3-methylbut-2-enyl diphosphate synthase (HDS), 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HDR), isopentenyl diphosphate isomerase (IDI), and geranyl diphosphate synthase (GPS/GGPS), were upregulated in Lilium 'Siberia' compared to Lilium 'Novano', and two monoterpene synthase genes, ocimene synthase gene (OCS) and myrcene synthase gene (MYS), were also expressed at higher levels in the tepals of Lilium 'Siberia', which was consistent with the monoterpene release amounts. We demonstrated that the high activation levels of the pathways contributed to monoterpene biosynthesis in Lilium 'Siberia' resulting in high accumulations and emissions of monoterpenes, which led to the difference in fragrance between these two Lilium genotypes.
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Affiliation(s)
- Zenghui Hu
- College of Landscape Architecture, Beijing University of AgricultureBeijing, China
- Beijing Collaborative Innovation Center for Eco-environmental Improvement with Forestry and Fruit TreesBeijing, China
| | - Biao Tang
- College of Landscape Architecture, Beijing University of AgricultureBeijing, China
| | - Qi Wu
- College of Landscape Architecture, Beijing University of AgricultureBeijing, China
| | - Jian Zheng
- College of Landscape Architecture, Beijing University of AgricultureBeijing, China
- Beijing Collaborative Innovation Center for Eco-environmental Improvement with Forestry and Fruit TreesBeijing, China
| | - Pingsheng Leng
- College of Landscape Architecture, Beijing University of AgricultureBeijing, China
- Beijing Collaborative Innovation Center for Eco-environmental Improvement with Forestry and Fruit TreesBeijing, China
- *Correspondence: Pingsheng Leng
| | - Kezhong Zhang
- College of Landscape Architecture, Beijing University of AgricultureBeijing, China
- Beijing Collaborative Innovation Center for Eco-environmental Improvement with Forestry and Fruit TreesBeijing, China
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Enhanced limonene production in cyanobacteria reveals photosynthesis limitations. Proc Natl Acad Sci U S A 2016; 113:14225-14230. [PMID: 27911807 DOI: 10.1073/pnas.1613340113] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Terpenes are the major secondary metabolites produced by plants, and have diverse industrial applications as pharmaceuticals, fragrance, solvents, and biofuels. Cyanobacteria are equipped with efficient carbon fixation mechanism, and are ideal cell factories to produce various fuel and chemical products. Past efforts to produce terpenes in photosynthetic organisms have gained only limited success. Here we engineered the cyanobacterium Synechococcus elongatus PCC 7942 to efficiently produce limonene through modeling guided study. Computational modeling of limonene flux in response to photosynthetic output has revealed the downstream terpene synthase as a key metabolic flux-controlling node in the MEP (2-C-methyl-d-erythritol 4-phosphate) pathway-derived terpene biosynthesis. By enhancing the downstream limonene carbon sink, we achieved over 100-fold increase in limonene productivity, in contrast to the marginal increase achieved through stepwise metabolic engineering. The establishment of a strong limonene flux revealed potential synergy between photosynthate output and terpene biosynthesis, leading to enhanced carbon flux into the MEP pathway. Moreover, we show that enhanced limonene flux would lead to NADPH accumulation, and slow down photosynthesis electron flow. Fine-tuning ATP/NADPH toward terpene biosynthesis could be a key parameter to adapt photosynthesis to support biofuel/bioproduct production in cyanobacteria.
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Kishimoto S, Sato M, Tsunematsu Y, Watanabe K. Evaluation of Biosynthetic Pathway and Engineered Biosynthesis of Alkaloids. Molecules 2016; 21:E1078. [PMID: 27548127 PMCID: PMC6274189 DOI: 10.3390/molecules21081078] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 08/15/2016] [Accepted: 08/15/2016] [Indexed: 01/13/2023] Open
Abstract
Varieties of alkaloids are known to be produced by various organisms, including bacteria, fungi and plants, as secondary metabolites that exhibit useful bioactivities. However, understanding of how those metabolites are biosynthesized still remains limited, because most of these compounds are isolated from plants and at a trace level of production. In this review, we focus on recent efforts in identifying the genes responsible for the biosynthesis of those nitrogen-containing natural products and elucidating the mechanisms involved in the biosynthetic processes. The alkaloids discussed in this review are ditryptophenaline (dimeric diketopiperazine alkaloid), saframycin (tetrahydroisoquinoline alkaloid), strictosidine (monoterpene indole alkaloid), ergotamine (ergot alkaloid) and opiates (benzylisoquinoline and morphinan alkaloid). This review also discusses the engineered biosynthesis of these compounds, primarily through heterologous reconstitution of target biosynthetic pathways in suitable hosts, such as Escherichia coli, Saccharomyces cerevisiae and Aspergillus nidulans. Those heterologous biosynthetic systems can be used to confirm the functions of the isolated genes, economically scale up the production of the alkaloids for commercial distributions and engineer the biosynthetic pathways to produce valuable analogs of the alkaloids. In particular, extensive involvement of oxidation reactions catalyzed by oxidoreductases, such as cytochrome P450s, during the secondary metabolite biosynthesis is discussed in details.
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Affiliation(s)
- Shinji Kishimoto
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan.
| | - Michio Sato
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan.
| | - Yuta Tsunematsu
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan.
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan.
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Xi J, Rossi L, Lin X, Xie DY. Overexpression of a synthetic insect-plant geranyl pyrophosphate synthase gene in Camelina sativa alters plant growth and terpene biosynthesis. PLANTA 2016; 244:215-30. [PMID: 27023458 DOI: 10.1007/s00425-016-2504-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 03/17/2016] [Indexed: 05/18/2023]
Abstract
A novel plastidial homodimeric insect-plant geranyl pyrophosphate synthase gene is synthesized from three different cDNA origins. Its overexpression in Camelina sativa effectively alters plant development and terpenoid metabolism. Geranyl pyrophosphate synthase (GPPS) converts one isopentenyl pyrophosphate and dimethylallyl pyrophosphate to GPP. Here, we report a synthetic insect-plant GPPS gene and effects of its overexpression on plant growth and terpenoid metabolism of Camelina sativa. We synthesized a 1353-bp cDNA, namely PTP-MpGPPS. This synthetic cDNA was composed of a 1086-bp cDNA fragment encoding a small GPPS isomer of the aphid Myzus persicae (Mp), 240-bp Arabidopsis thaliana cDNA fragment encoding a plastidial transit peptide (PTP), and a 27-bp short cDNA fragment encoding a human influenza hemagglutinin tag peptide. Structural modeling showed that the deduced protein was a homodimeric prenyltransferase. Confocal microscopy analysis demonstrated that the PTP-MpGPPS fused with green florescent protein was localized in the plastids. The synthetic PTP-MpGPPS cDNA driven by 2 × 35S promoters was introduced into Camelina (Camelina sativa) by Agrobacterium-mediated transformation and its overexpression in transgenic plants were demonstrated by western blot. T2 and T3 progeny of transgenic plants developed larger leaves, grew more and longer internodes, and flowered earlier than wild-type plants. Metabolic analysis showed that the levels of beta-amyrin and campesterol were higher in tissues of transgenic plants than in those of wild-type plants. Fast isoprene sensor analysis demonstrated that transgenic Camelina plants emitted significantly less isoprene than wild-type plants. In addition, transcriptional analyses revealed that the expression levels of gibberellic acid and brassinosteroids-responsive genes were higher in transgenic plants than in wild-type plants. Taken together, these data demonstrated that this novel synthetic insect-plant GPPS cDNA was effective to improve growth traits and alter terpenoid metabolism of Camelina.
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Affiliation(s)
- Jing Xi
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Lorenzo Rossi
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Xiuli Lin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - De-Yu Xie
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA.
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Campbell A, Bauchart P, Gold ND, Zhu Y, De Luca V, Martin VJJ. Engineering of a Nepetalactol-Producing Platform Strain of Saccharomyces cerevisiae for the Production of Plant Seco-Iridoids. ACS Synth Biol 2016; 5:405-14. [PMID: 26981892 DOI: 10.1021/acssynbio.5b00289] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The monoterpene indole alkaloids (MIAs) are a valuable family of chemicals that include the anticancer drugs vinblastine and vincristine. These compounds are of global significance-appearing on the World Health Organization's list of model essential medicines-but remain exorbitantly priced due to low in planta levels. Chemical synthesis and genetic manipulation of MIA producing plants such as Catharanthus roseus have so far failed to find a solution to this problem. Synthetic biology holds a potential answer, by building the pathway into more tractable organisms such as Saccharomyces cerevisiae. Recent work has taken the first steps in this direction by producing small amounts of the intermediate strictosidine in yeast. In order to help improve on these titers, we aimed to optimize the early biosynthetic steps of the MIA pathway to the metabolite nepetalactol. We combined a number of strategies to create a base strain producing 11.4 mg/L of the precursor geraniol. We also show production of the critical intermediate 10-hydroxygeraniol and demonstrate nepetalactol production in vitro. Lastly we demonstrate that activity of the iridoid synthase toward the intermediates geraniol and 10-hydroxygeraniol results in the synthesis of the nonproductive intermediates citronellol and 10-hydroxycitronellol. This discovery has serious implications for the reconstruction of the MIA in heterologous organisms.
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Affiliation(s)
- Alex Campbell
- Department
of Biology, Centre for Structural and Functional Genomics, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Philippe Bauchart
- Department
of Biology, Centre for Structural and Functional Genomics, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Nicholas D. Gold
- Department
of Biology, Centre for Structural and Functional Genomics, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Yun Zhu
- Department
of Biology, Centre for Structural and Functional Genomics, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Vincenzo De Luca
- Department
of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario L2S 3A1, Canada
| | - Vincent J. J. Martin
- Department
of Biology, Centre for Structural and Functional Genomics, Concordia University, Montréal, Québec H4B 1R6, Canada
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Yang J, Nie Q. Engineering Escherichia coli to convert acetic acid to β-caryophyllene. Microb Cell Fact 2016; 15:74. [PMID: 27149950 PMCID: PMC4857421 DOI: 10.1186/s12934-016-0475-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/27/2016] [Indexed: 12/02/2022] Open
Abstract
Background Under aerobic conditions, acetic acid is the major byproduct produced by E. coli during the fermentation. And acetic acid is detrimental to cell growth as it destroys transmembrane pH gradients. Hence, how to reduce the production of acetic acid and how to utilize it as a feedstock are of intriguing interest. In this study, we provided an evidence to produce β-caryophyllene by the engineered E. coli using acetic acid as the only carbon source. Results Firstly, to construct the robust acetate-utilizing strain, acetyl-CoA synthases from three different sources were introduced and screened in the E. coli. Secondly, to establish the engineered strains converting acetic acid to β-caryophyllene, acetyl-CoA synthase (ACS), β-caryophyllene synthase (QHS1) and geranyl diphosphate synthase (GPPS2) were co-expressed in the E. coli cells. Thirdly, to further enhance β-caryophyllene production from acetic acid, the heterologous MVA pathway was introduced into the cells. What’s more, acetoacetyl-CoA synthase (AACS) was also expressed in the cells to increase the precursor acetoacetyl-CoA and accordingly resulted in the increase of β-caryophyllene. The final genetically modified strain, YJM67, could accumulate the production of biomass and β-caryophyllene up to 12.6 and 1.05 g/L during 72 h, respectively, with a specific productivity of 1.15 mg h−1 g−1 dry cells, and the conversion efficiency of acetic acid to β-caryophyllene (gram to gram) reached 2.1 %. The yield of β-caryophyllene on acetic acid of this strain also reached approximately 5.6 % of the theoretical yield. Conclusions In the present study, a novel biosynthetic pathway for β-caryophyllene has been investigated by means of conversion of acetic acid to β-caryophyllene using an engineered Escherichia coli. This was the first successful attempt in β-caryophyllene production by E. coli using acetic acid as the only carbon source. Therefore, we have provided a new metabolic engineering tool for β-caryophyllene synthesis.
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Affiliation(s)
- Jianming Yang
- Key Lab of Plant Biotechnology in Universities of Shandong Province; College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China. .,Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, No.700 Changcheng Road, Chengyang District, Qingdao, 266109, China.
| | - Qingjuan Nie
- Foreign Languages School, Qingdao Agricultural University, Qingdao, 266109, China
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Jongedijk E, Cankar K, Buchhaupt M, Schrader J, Bouwmeester H, Beekwilder J. Biotechnological production of limonene in microorganisms. Appl Microbiol Biotechnol 2016; 100:2927-38. [PMID: 26915992 PMCID: PMC4786606 DOI: 10.1007/s00253-016-7337-7] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 01/17/2016] [Accepted: 01/18/2016] [Indexed: 11/25/2022]
Abstract
This mini review describes novel, biotechnology-based, ways of producing the monoterpene limonene. Limonene is applied in relatively highly priced products, such as fragrances, and also has applications with lower value but large production volume, such as biomaterials. Limonene is currently produced as a side product from the citrus juice industry, but the availability and quality are fluctuating and may be insufficient for novel bulk applications. Therefore, complementary microbial production of limonene would be interesting. Since limonene can be derivatized to high-value compounds, microbial platforms also have a great potential beyond just producing limonene. In this review, we discuss the ins and outs of microbial limonene production in comparison with plant-based and chemical production. Achievements and specific challenges for microbial production of limonene are discussed, especially in the light of bulk applications such as biomaterials.
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Affiliation(s)
- Esmer Jongedijk
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708, PB, The Netherlands
| | - Katarina Cankar
- Plant Research International, PO Box 16, 6700, AA, Wageningen, The Netherlands
| | - Markus Buchhaupt
- DECHEMA Research Institute, Biochemical Engineering, Theodor Heuss-Allee 25, 60486, Frankfurt am Main, Germany
| | - Jens Schrader
- DECHEMA Research Institute, Biochemical Engineering, Theodor Heuss-Allee 25, 60486, Frankfurt am Main, Germany
| | - Harro Bouwmeester
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708, PB, The Netherlands
| | - Jules Beekwilder
- Plant Research International, PO Box 16, 6700, AA, Wageningen, The Netherlands.
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Wu W, Tran W, Taatjes CA, Alonso-Gutierrez J, Lee TS, Gladden JM. Rapid Discovery and Functional Characterization of Terpene Synthases from Four Endophytic Xylariaceae. PLoS One 2016; 11:e0146983. [PMID: 26885833 PMCID: PMC4757406 DOI: 10.1371/journal.pone.0146983] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/23/2015] [Indexed: 01/20/2023] Open
Abstract
Endophytic fungi are ubiquitous plant endosymbionts that establish complex and poorly understood relationships with their host organisms. Many endophytic fungi are known to produce a wide spectrum of volatile organic compounds (VOCs) with potential energy applications, which have been described as "mycodiesel". Many of these mycodiesel hydrocarbons are terpenes, a chemically diverse class of compounds produced by many plants, fungi, and bacteria. Due to their high energy densities, terpenes, such as pinene and bisabolene, are actively being investigated as potential "drop-in" biofuels for replacing diesel and aviation fuel. In this study, we rapidly discovered and characterized 26 terpene synthases (TPSs) derived from four endophytic fungi known to produce mycodiesel hydrocarbons. The TPS genes were expressed in an E. coli strain harboring a heterologous mevalonate pathway designed to enhance terpene production, and their product profiles were determined using Solid Phase Micro-Extraction (SPME) and GC-MS. Out of the 26 TPS's profiled, 12 TPS's were functional, with the majority of them exhibiting both monoterpene and sesquiterpene synthase activity.
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Affiliation(s)
- Weihua Wu
- Biomass Science & Conversion Technologies, Sandia National Laboratories, Livermore, California, United States of America
| | - William Tran
- Biomass Science & Conversion Technologies, Sandia National Laboratories, Livermore, California, United States of America
| | - Craig A. Taatjes
- Combustion Chemistry Department, Sandia National Laboratories, Livermore, California, United States of America
| | - Jorge Alonso-Gutierrez
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Joint BioEnergy Institute, Emeryville, California, United States of America
| | - Taek Soon Lee
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Joint BioEnergy Institute, Emeryville, California, United States of America
| | - John M. Gladden
- Biomass Science & Conversion Technologies, Sandia National Laboratories, Livermore, California, United States of America
- Joint BioEnergy Institute, Emeryville, California, United States of America
- * E-mail: ;
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Improving monoterpene geraniol production through geranyl diphosphate synthesis regulation in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2016; 100:4561-71. [PMID: 26883346 DOI: 10.1007/s00253-016-7375-1] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 01/05/2016] [Accepted: 02/02/2016] [Indexed: 10/22/2022]
Abstract
Monoterpenes have wide applications in the food, cosmetics, and medicine industries and have recently received increased attention as advanced biofuels. However, compared with sesquiterpenes, monoterpene production is still lagging in Saccharomyces cerevisiae. In this study, geraniol, a valuable acyclic monoterpene alcohol, was synthesized in S. cerevisiae. We evaluated three geraniol synthases in S. cerevisiae, and the geraniol synthase Valeriana officinalis (tVoGES), which lacked a plastid-targeting peptide, yielded the highest geraniol production. To improve geraniol production, synthesis of the precursor geranyl diphosphate (GPP) was regulated by comparing three specific GPP synthase genes derived from different plants and the endogenous farnesyl diphosphate synthase gene variants ERG20 (G) (ERG20 (K197G) ) and ERG20 (WW) (ERG20 (F96W-N127W) ), and controlling endogenous ERG20 expression, coupled with increasing the expression of the mevalonate pathway by co-overexpressing IDI1, tHMG1, and UPC2-1. The results showed that overexpressing ERG20 (WW) and strengthening the mevalonate pathway significantly improved geraniol production, while expressing heterologous GPP synthase genes or down-regulating endogenous ERG20 expression did not show positive effect. In addition, we constructed an Erg20p(F96W-N127W)-tVoGES fusion protein, and geraniol production reached 66.2 mg/L after optimizing the amino acid linker and the order of the proteins. The best strain yielded 293 mg/L geraniol in a fed-batch cultivation, a sevenfold improvement over the highest titer previously reported in an engineered S. cerevisiae strain. Finally, we showed that the toxicity of geraniol limited its production. The platform developed here can be readily used to synthesize other monoterpenes.
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Liu Z, Zhou J, Wu R, Xu J. Mechanism of Assembling Isoprenoid Building Blocks 1. Elucidation of the Structural Motifs for Substrate Binding in Geranyl Pyrophosphate Synthase. J Chem Theory Comput 2015; 10:5057-67. [PMID: 26584386 DOI: 10.1021/ct500607n] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Terpenes (isoprenoids) represent the most functionally and structurally diverse group of natural products. Terpenes are assembled from two building blocks, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP or DPP), by prenyltransferases (PTSs). Geranyl pyrophosphate synthase (GPPS) is the enzyme that assembles DPP and IPP in the first step of chain elongation during isoprenoid biosynthesis. The mechanism by which GPPS assembles the terpene precursor remains unknown; elucidating this mechanism will help in development of new technology to generate novel natural product-like scaffolds. With classic and QM/MM MD simulations, an "open-closed" conformation change of the catalytic pocket was observed in the GPPS active site at its large subunit (LSU), and a critical salt bridge between Asp91(in loop 1) and Lys239(in loop 2) was identified. The salt bridge is responsible for opening or closing the catalytic pocket. Meanwhile, the small subunit (SSU) regulates the size and shape of the hydrophobic pocket to flexibly host substrates with different shapes and sizes (DPP/GPP/FPP, C5/C10/C15). Further QM/MM MD simulations were carried out to explore the binding modes for the different substrates catalyzed by GPPS. Our simulations suggest that the key residues (Asp91, Lys239, and Gln156) are good candidates for site-directed mutagenesis and may help in protein engineering.
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Affiliation(s)
- Zhihong Liu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University , 132 East Circle at University City, Guangzhou 510006, China
| | - Jingwei Zhou
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University , 132 East Circle at University City, Guangzhou 510006, China
| | - Ruibo Wu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University , 132 East Circle at University City, Guangzhou 510006, China
| | - Jun Xu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University , 132 East Circle at University City, Guangzhou 510006, China
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Warren RL, Keeling CI, Yuen MMS, Raymond A, Taylor GA, Vandervalk BP, Mohamadi H, Paulino D, Chiu R, Jackman SD, Robertson G, Yang C, Boyle B, Hoffmann M, Weigel D, Nelson DR, Ritland C, Isabel N, Jaquish B, Yanchuk A, Bousquet J, Jones SJM, MacKay J, Birol I, Bohlmann J. Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:189-212. [PMID: 26017574 DOI: 10.1111/tpj.12886] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 05/15/2015] [Indexed: 05/21/2023]
Abstract
White spruce (Picea glauca), a gymnosperm tree, has been established as one of the models for conifer genomics. We describe the draft genome assemblies of two white spruce genotypes, PG29 and WS77111, innovative tools for the assembly of very large genomes, and the conifer genomics resources developed in this process. The two white spruce genotypes originate from distant geographic regions of western (PG29) and eastern (WS77111) North America, and represent elite trees in two Canadian tree-breeding programs. We present an update (V3 and V4) for a previously reported PG29 V2 draft genome assembly and introduce a second white spruce genome assembly for genotype WS77111. Assemblies of the PG29 and WS77111 genomes confirm the reconstructed white spruce genome size in the 20 Gbp range, and show broad synteny. Using the PG29 V3 assembly and additional white spruce genomics and transcriptomics resources, we performed MAKER-P annotation and meticulous expert annotation of very large gene families of conifer defense metabolism, the terpene synthases and cytochrome P450s. We also comprehensively annotated the white spruce mevalonate, methylerythritol phosphate and phenylpropanoid pathways. These analyses highlighted the large extent of gene and pseudogene duplications in a conifer genome, in particular for genes of secondary (i.e. specialized) metabolism, and the potential for gain and loss of function for defense and adaptation.
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Affiliation(s)
- René L Warren
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Christopher I Keeling
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Macaire Man Saint Yuen
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Anthony Raymond
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Greg A Taylor
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Benjamin P Vandervalk
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Hamid Mohamadi
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Daniel Paulino
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Readman Chiu
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Shaun D Jackman
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Gordon Robertson
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Chen Yang
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Brian Boyle
- Department of Wood and Forest Sciences, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Margarete Hoffmann
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076, Tübingen, Germany
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076, Tübingen, Germany
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Carol Ritland
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Nathalie Isabel
- Natural Resources Canada, Laurentian Forestry Centre, Québec, QC, G1V 4C7, Canada
| | - Barry Jaquish
- British Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, BC, V8W 9C2, Canada
| | - Alvin Yanchuk
- British Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, BC, V8W 9C2, Canada
| | - Jean Bousquet
- Department of Wood and Forest Sciences, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Steven J M Jones
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
- School of Computing Science, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - John MacKay
- Department of Wood and Forest Sciences, Université Laval, Québec, QC, G1V 0A6, Canada
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Inanc Birol
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
- School of Computing Science, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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Zhou J, Wang X, Kuang M, Wang L, Luo HB, Mo Y, Wu R. Protonation-Triggered Carbon-Chain Elongation in Geranyl Pyrophosphate Synthase (GPPS). ACS Catal 2015. [DOI: 10.1021/acscatal.5b00947] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jingwei Zhou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Xiaoming Wang
- Program in Public Health, College of Healthy Sciences, University of California—Irvine, Irvine, California 92697,United States
| | - Ming Kuang
- Institute of Chinese Medical Sciences, Guangdong Pharmaceutical University, Guangzhou 510006, P.R. China
| | - Laiyou Wang
- Institute of Chinese Medical Sciences, Guangdong Pharmaceutical University, Guangzhou 510006, P.R. China
| | - Hai-Bin Luo
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Yirong Mo
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008, United States
| | - Ruibo Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R. China
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45
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Principal component analysis of proteomics (PCAP) as a tool to direct metabolic engineering. Metab Eng 2015; 28:123-133. [DOI: 10.1016/j.ymben.2014.11.011] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 11/04/2014] [Accepted: 11/11/2014] [Indexed: 11/20/2022]
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Abstract
The monoterpene indole alkaloids are a large group of plant-derived specialized metabolites, many of which have valuable pharmaceutical or biological activity. There are ∼3,000 monoterpene indole alkaloids produced by thousands of plant species in numerous families. The diverse chemical structures found in this metabolite class originate from strictosidine, which is the last common biosynthetic intermediate for all monoterpene indole alkaloid enzymatic pathways. Reconstitution of biosynthetic pathways in a heterologous host is a promising strategy for rapid and inexpensive production of complex molecules that are found in plants. Here, we demonstrate how strictosidine can be produced de novo in a Saccharomyces cerevisiae host from 14 known monoterpene indole alkaloid pathway genes, along with an additional seven genes and three gene deletions that enhance secondary metabolism. This system provides an important resource for developing the production of more complex plant-derived alkaloids, engineering of nonnatural derivatives, identification of bottlenecks in monoterpene indole alkaloid biosynthesis, and discovery of new pathway genes in a convenient yeast host.
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Yang J, Guo L. Biosynthesis of β-carotene in engineered E. coli using the MEP and MVA pathways. Microb Cell Fact 2014; 13:160. [PMID: 25403509 PMCID: PMC4239400 DOI: 10.1186/s12934-014-0160-x] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 10/31/2014] [Indexed: 01/28/2023] Open
Abstract
Background β-carotene is a carotenoid compound that has been widely used not only in the industrial production of pharmaceuticals but also as nutraceuticals, animal feed additives, functional cosmetics, and food colorants. Currently, more than 90% of commercial β-carotene is produced by chemical synthesis. Due to the growing public concern over food safety, the use of chemically synthesized β-carotene as food additives or functional cosmetic agents has been severely controlled in recent years. This has reignited the enthusiasm for seeking natural β-carotene in large-scale fermentative production by microorganisms. Results To increase β-carotene production by improving the isopentenyl pyrophosphate (IPP) and geranyl diphospate (GPP) concentration in the cell, the optimized MEP (methylerythritol 4-phosphate) pathway containing 1-deoxy-D-xylulose-5-phosphate synthase (DXS) and isopentenyl pyrophosphate isomerase (FNI) from Bacillus subtilis, geranyl diphosphate synthase (GPPS2) from Abies grandis have been co-expressed in an engineered E. coli strain. To further enhance the production of β-carotene, the hybrid MVA (mevalonate) pathway has been introduced into an engineered E. coli strain, co-expressed with the optimized MEP pathway and GPPS2. The final genetically modified strain, YJM49, can accumulate 122.4±6.2 mg/L β-carotene in flask culture, approximately 113-fold and 1.7 times greater than strain YJM39, which carries the native MEP pathway, and YJM45, which harbors the MVA pathway and the native MEP pathway, respectively. Subsequently, the fermentation process was optimized to enhance β-carotene production with a maximum titer of 256.8±10.4 mg/L. Finally, the fed-batch fermentation of β-carotene was evaluated using the optimized culture conditions. After induction for 56 h, the final engineered strain YJM49 accumulated 3.2 g/L β-carotene with a volumetric productivity of 0.37 mg/(L · h · OD600) in aerobic fed-batch fermentation, and the conversion efficiency of glycerol to β-carotene (gram to gram) reached 2.76%. Conclusions In this paper, by using metabolic engineering techniques, the more efficient biosynthetic pathway of β-carotene was successfully assembled in E. coli BL21(DE3) with the optimized MEP (methylerythritol 4-phosphate) pathway, the gene for GPPS2 from Abies grandis, the hybrid MVA (mevalonate) pathway and β-carotene synthesis genes from Erwinia herbicola. Electronic supplementary material The online version of this article (doi:10.1186/s12934-014-0160-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jianming Yang
- Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, No.700 Changcheng Road, Chengyang District, Qingdao, 266109, China.
| | - Lizhong Guo
- Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, No.700 Changcheng Road, Chengyang District, Qingdao, 266109, China.
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Microbial Synthesis of the Forskolin Precursor Manoyl Oxide in an Enantiomerically Pure Form. Appl Environ Microbiol 2014; 80:7258-65. [PMID: 25239892 DOI: 10.1128/aem.02301-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 09/11/2014] [Indexed: 11/20/2022] Open
Abstract
Forskolin is a promising medicinal compound belonging to a plethora of specialized plant metabolites that constitute a rich source of bioactive high-value compounds. A major obstacle for exploitation of plant metabolites is that they often are produced in small amounts and in plants difficult to cultivate. This may result in insufficient and unreliable supply leading to fluctuating and high sales prices. Hence, substantial efforts and resources have been invested in developing sustainable and reliable supply routes based on microbial cell factories. Here, we report microbial synthesis of (13R)-manoyl oxide, a proposed intermediate in the biosynthesis of forskolin and other medically important labdane-type terpenoids. Process optimization enabled synthesis of enantiomerically pure (13R)-manoyl oxide as the sole metabolite, providing a pure compound in just two steps with a yield of 10 mg/liter. The work presented here demonstrates the value of a standardized bioengineering pipeline and the large potential of microbial cell factories as sources for sustainable synthesis of complex biochemicals.
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50
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Du FL, Yu HL, Xu JH, Li CX. Enhanced limonene production by optimizing the expression of limonene biosynthesis and MEP pathway genes in E. coli. BIORESOUR BIOPROCESS 2014. [DOI: 10.1186/s40643-014-0010-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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