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Karim AS, Brown DM, Archuleta CM, Grannan S, Aristilde L, Goyal Y, Leonard JN, Mangan NM, Prindle A, Rocklin GJ, Tyo KJ, Zoloth L, Jewett MC, Calkins S, Kamat NP, Tullman-Ercek D, Lucks JB. Deconstructing synthetic biology across scales: a conceptual approach for training synthetic biologists. Nat Commun 2024; 15:5425. [PMID: 38926339 PMCID: PMC11208543 DOI: 10.1038/s41467-024-49626-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Synthetic biology allows us to reuse, repurpose, and reconfigure biological systems to address society's most pressing challenges. Developing biotechnologies in this way requires integrating concepts across disciplines, posing challenges to educating students with diverse expertise. We created a framework for synthetic biology training that deconstructs biotechnologies across scales-molecular, circuit/network, cell/cell-free systems, biological communities, and societal-giving students a holistic toolkit to integrate cross-disciplinary concepts towards responsible innovation of successful biotechnologies. We present this framework, lessons learned, and inclusive teaching materials to allow its adaption to train the next generation of synthetic biologists.
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Affiliation(s)
- Ashty S Karim
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA.
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA.
| | - Dylan M Brown
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Chloé M Archuleta
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Sharisse Grannan
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Independent Evaluator, Lake Geneva, WI, 53147, USA
| | - Ludmilla Aristilde
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Yogesh Goyal
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Cell and Developmental Biology, Northwestern University, Chicago, IL, 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Josh N Leonard
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Niall M Mangan
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL, 60201, USA
| | - Arthur Prindle
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, 60611, USA
| | - Gabriel J Rocklin
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Pharmacology, Northwestern University, Chicago, IL, 60611, USA
| | - Keith J Tyo
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Laurie Zoloth
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- The Divinity School, University of Chicago, Chicago, IL, 60637, USA
| | - Michael C Jewett
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Susanna Calkins
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Searle Center for Advancing Learning and Teaching, Northwestern University, Evanston, IL, 60208, USA
- Nexus for Faculty Success, Rosalind Franklin University of Medicine and Science, Chicago, IL, USA
| | - Neha P Kamat
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Biomedical Engineering Northwestern University, Evanston, IL, 60208, USA
| | - Danielle Tullman-Ercek
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Julius B Lucks
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA.
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA.
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Kramer L, Sarkar A, Foderaro T, Markley AL, Lee J, Edstrom H, Sharma S, Gill E, Traylor MJ, Fox JM. Genetically Encoded Detection of Biosynthetic Protease Inhibitors. ACS Synth Biol 2023; 12:83-94. [PMID: 36574400 PMCID: PMC10072156 DOI: 10.1021/acssynbio.2c00384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Proteases are an important class of drug targets that continue to drive inhibitor discovery. These enzymes are prone to resistance mutations, yet their promise for treating viral diseases and other disorders continues to grow. This study develops a general approach for detecting microbially synthesized protease inhibitors and uses it to screen terpenoid pathways for inhibitory compounds. The detection scheme relies on a bacterial two-hybrid (B2H) system that links protease inactivation to the transcription of a swappable reporter gene. This system, which can accomodate multiple biochemical outputs (i.e., luminescence and antibiotic resistance), permitted the facile incorporation of four disease-relevant proteases. A B2H designed to detect the inactivation of the main protease of severe acute respiratory syndrome coronavirus 2 enabled the identification of a terpenoid inhibitor of modest potency. An analysis of multiple pathways that make this terpenoid, however, suggested that its production was necessary but not sufficient to confer a survival advantage in growth-coupled assays. This finding highlights an important challenge associated with the use of genetic selection to search for inhibitors─notably, the influence of pathway toxicity─and underlines the value of including multiple pathways with overlapping product profiles in pathway screens. This study provides a detailed experimental framework for using microbes to screen libraries of biosynthetic pathways for targeted protease inhibitors.
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Affiliation(s)
- Levi Kramer
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, Colorado80303, United States
| | - Ankur Sarkar
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, Colorado80303, United States
| | - Tom Foderaro
- Think Bioscience, Inc., 1945 Colorado Avenue, Boulder, Colorado80309, United States
| | - Andrew L Markley
- Think Bioscience, Inc., 1945 Colorado Avenue, Boulder, Colorado80309, United States
| | - Jessica Lee
- Think Bioscience, Inc., 1945 Colorado Avenue, Boulder, Colorado80309, United States
| | - Hannah Edstrom
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, Colorado80303, United States
| | - Shajesh Sharma
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, Colorado80303, United States
| | - Eden Gill
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, Colorado80303, United States
| | - Matthew J Traylor
- Think Bioscience, Inc., 1945 Colorado Avenue, Boulder, Colorado80309, United States
| | - Jerome M Fox
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, Colorado80303, United States
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Fidan O, Zhan J, Ren J. Engineered production of bioactive natural products from medicinal plants. WORLD JOURNAL OF TRADITIONAL CHINESE MEDICINE 2022. [DOI: 10.4103/wjtcm.wjtcm_66_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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4
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Fidan O, Zhan J, Ren J. Engineered production of bioactive natural products from medicinal plants. WORLD JOURNAL OF TRADITIONAL CHINESE MEDICINE 2022. [DOI: 10.4103/2311-8571.336839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Xu H, Dickschat JS. Germacrene A-A Central Intermediate in Sesquiterpene Biosynthesis. Chemistry 2020; 26:17318-17341. [PMID: 32442350 PMCID: PMC7821278 DOI: 10.1002/chem.202002163] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/20/2020] [Indexed: 01/17/2023]
Abstract
This review summarises known sesquiterpenes whose biosyntheses proceed through the intermediate germacrene A. First, the occurrence and biosynthesis of germacrene A in Nature and its peculiar chemistry will be highlighted, followed by a discussion of 6-6 and 5-7 bicyclic compounds and their more complex derivatives. For each compound the absolute configuration, if it is known, and the reasoning for its assignment is presented.
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Affiliation(s)
- Houchao Xu
- Kekulé-Institute for Organic Chemistry and BiochemistryUniversity of BonnGerhard-Domagk-Straße 153121BonnGermany
| | - Jeroen S. Dickschat
- Kekulé-Institute for Organic Chemistry and BiochemistryUniversity of BonnGerhard-Domagk-Straße 153121BonnGermany
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Aguilar F, Ekramzadeh K, Scheper T, Beutel S. Whole-Cell Production of Patchouli Oil Sesquiterpenes in Escherichia coli: Metabolic Engineering and Fermentation Optimization in Solid-Liquid Phase Partitioning Cultivation. ACS OMEGA 2020; 5:32436-32446. [PMID: 33376881 PMCID: PMC7758989 DOI: 10.1021/acsomega.0c04590] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/25/2020] [Indexed: 05/27/2023]
Abstract
Patchouli oil is a major ingredient in perfumery, granting a dark-woody scent due to its main constituent (-)-patchoulol. The growing demand for patchouli oil has raised interest in the development of a biotechnological process to assure a reliable supply. Herein, we report the production of patchouli oil sesquiterpenes by metabolically engineered Escherichia coli strains, using solid-liquid phase partitioning cultivation. The (-)-patchoulol production was possible using the endogenous methylerythritol phosphate pathway and overexpressing a (-)-patchoulol synthase isoform from Pogostemon cablin but at low titers. To improve the (-)-patchoulol production, the exogenous mevalonate pathway was overexpressed in the multi-plasmid PTS + Mev strain, which increased the (-)-patchoulol titer 5-fold. Fermentation was improved further by evaluating several defined media, and optimizing the pH and temperature of culture broth, enhancing the (-)-patchoulol titer 3-fold. To augment the (-)-patchoulol recovery from fermentation, the solid-liquid phase partitioning cultivation was analyzed by screening polymeric adsorbers, where the Diaion HP20 adsorber demonstrated the highest (-)-patchoulol recovery from all tests. Fermentation was scaled-up to fed-batch bioreactors, reaching a (-)-patchoulol titer of 40.2 mg L-1 and productivity of 20.1 mg L-1 d-1. The terpene profile and aroma produced from the PTS + Mev strain were similar to the patchouli oil, comprising (-)-patchoulol as the main product, and α-bulnesene, trans-β-caryophyllene, β-patchoulene, and guaia-5,11-diene as side products. This investigation represents the first study of (-)-patchoulol production in E. coli by solid-liquid phase partitioning cultivation, which provides new insights for the development of sustainable bioprocesses for the microbial production of fragrant terpenes.
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Affiliation(s)
- Francisco Aguilar
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstr. 5, 30167 Hannover, Germany
| | - Kimia Ekramzadeh
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstr. 5, 30167 Hannover, Germany
| | - Thomas Scheper
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstr. 5, 30167 Hannover, Germany
| | - Sascha Beutel
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstr. 5, 30167 Hannover, Germany
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Pramastya H, Song Y, Elfahmi EY, Sukrasno S, Quax WJ. Positioning Bacillus subtilis as terpenoid cell factory. J Appl Microbiol 2020; 130:1839-1856. [PMID: 33098223 PMCID: PMC8247319 DOI: 10.1111/jam.14904] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/29/2020] [Accepted: 10/09/2020] [Indexed: 12/16/2022]
Abstract
Increasing demands for bioactive compounds have motivated researchers to employ micro‐organisms to produce complex natural products. Currently, Bacillus subtilis has been attracting lots of attention to be developed into terpenoids cell factories due to its generally recognized safe status and high isoprene precursor biosynthesis capacity by endogenous methylerythritol phosphate (MEP) pathway. In this review, we describe the up‐to‐date knowledge of each enzyme in MEP pathway and the subsequent steps of isomerization and condensation of C5 isoprene precursors. In addition, several representative terpene synthases expressed in B. subtilis and the engineering steps to improve corresponding terpenoids production are systematically discussed. Furthermore, the current available genetic tools are mentioned as along with promising strategies to improve terpenoids in B. subtilis, hoping to inspire future directions in metabolic engineering of B. subtilis for further terpenoid cell factory development.
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Affiliation(s)
- H Pramastya
- University of Groningen, Groningen, The Netherlands.,Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, Bandung, Indonesia
| | - Y Song
- University of Groningen, Groningen, The Netherlands
| | - E Y Elfahmi
- Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, Bandung, Indonesia
| | - S Sukrasno
- Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, Bandung, Indonesia
| | - W J Quax
- University of Groningen, Groningen, The Netherlands
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Pramastya H, Xue D, Abdallah II, Setroikromo R, Quax WJ. High level production of amorphadiene using Bacillus subtilis as an optimized terpenoid cell factory. N Biotechnol 2020; 60:159-167. [PMID: 33148534 DOI: 10.1016/j.nbt.2020.10.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/09/2023]
Abstract
The anti-malarial drug artemisinin, produced naturally in the plant Artemisia annua, experiences unstable and insufficient supply as its production relies heavily on the plant source. To meet the massive demand for this compound, metabolic engineering of microbes has been studied extensively. In this study, we focus on improving the production of amorphadiene, a crucial artemisinin precursor, in Bacillus subtilis. The expression level of the plant-derived amorphadiene synthase (ADS) was upregulated by fusion with green fluorescent protein (GFP). Furthermore, a co-expression system of ADS and a synthetic operon carrying the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway genes was established. Subsequently, farnesyl pyrophosphate synthase (FPPS), a key enzyme in formation of the sesquiterpene precursor farnesyl pyrophosphate (FPP), was expressed to supply sufficient substrate for ADS. The consecutive combination of these features yielded a B. subtilis strain expressing chromosomally integrated GFP-ADS followed by FPPS and a plasmid encoded synthetic operon showing a stepwise increased production of amorphadiene. An experimental design-aided systematic medium optimization was used to maximize the production level for the most promising engineered B. subtilis strain, resulting in an amorphadiene yield of 416 ± 15 mg/L, which is 20-fold higher than that previously reported in B. subtilis and more than double the production in Escherichia coli or Saccharomyces cerevisiae on a shake flask fermentation level.
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Affiliation(s)
- Hegar Pramastya
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, the Netherlands; Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, 40132, Bandung, Indonesia
| | - Dan Xue
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, the Netherlands
| | - Ingy I Abdallah
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, the Netherlands; Department of Pharmacognosy, Faculty of Pharmacy, Alexandria University, Egypt
| | - Rita Setroikromo
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, the Netherlands
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, the Netherlands.
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Modulating the Precursor and Terpene Synthase Supply for the Whole-Cell Biocatalytic Production of the Sesquiterpene (+)-Zizaene in a Pathway Engineered E. coli. Genes (Basel) 2019; 10:genes10060478. [PMID: 31238595 PMCID: PMC6627501 DOI: 10.3390/genes10060478] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 06/15/2019] [Accepted: 06/20/2019] [Indexed: 11/23/2022] Open
Abstract
The vetiver essential oil from Chrysopogon zizanioides contains fragrant sesquiterpenes used widely in the formulation of nearly 20% of men’s cosmetics. The growing demand and issues in the supply have raised interest in the microbial production of the sesquiterpene khusimol, the main compound of the vetiver essential oil due to its woody smell. In this study, we engineered the biosynthetic pathway for the production of (+)-zizaene, the immediate precursor of khusimol. A systematic approach of metabolic engineering in Escherichia coli was applied to modulate the critical bottlenecks of the metabolic flux towards (+)-zizaene. Initially, production of (+)-zizaene was possible with the endogenous methylerythritol phosphate pathway and the codon-optimized zizaene synthase (ZS). Raising the precursor E,E-farnesyl diphosphate supply through the mevalonate pathway improved the (+)-zizaene titers 2.7-fold, although a limitation of the ZS supply was observed. To increase the ZS supply, distinct promoters were tested for the expression of the ZS gene, which augmented 7.2-fold in the (+)-zizaene titers. Final metabolic enhancement for the ZS supply by using a multi-plasmid strain harboring multiple copies of the ZS gene improved the (+)-zizaene titers 1.3-fold. The optimization of the fermentation conditions increased the (+)-zizaene titers 2.2-fold, achieving the highest (+)-zizaene titer of 25.09 mg L−1. This study provides an alternative strategy to enhance the terpene synthase supply for the engineering of isoprenoids. Moreover, it demonstrates the development of a novel microbial platform for the sustainable production of fragrant molecules for the cosmetic industry.
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Ahmed MS, Ikram S, Rasool A, Li C. Design and construction of short synthetic terminators for β-amyrin production in Saccharomyces cerevisiae. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.03.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Sesquiterpene Synthase-3-Hydroxy-3-Methylglutaryl Coenzyme A Synthase Fusion Protein Responsible for Hirsutene Biosynthesis in Stereum hirsutum. Appl Environ Microbiol 2018; 84:AEM.00036-18. [PMID: 29625976 DOI: 10.1128/aem.00036-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/25/2018] [Indexed: 01/09/2023] Open
Abstract
The wood-rotting mushroom Stereum hirsutum is a known producer of a large number of namesake hirsutenoids, many with important bioactivities. Hirsutenoids form a structurally diverse and distinct class of sesquiterpenoids. No genes involved in hirsutenoid biosynthesis have yet been identified or their enzymes characterized. Here, we describe the cloning and functional characterization of a hirsutene synthase as an unexpected fusion protein of a sesquiterpene synthase (STS) with a C-terminal 3-hydroxy-3-methylglutaryl-coenzyme A (3-hydroxy-3-methylglutaryl-CoA) synthase (HMGS) domain. Both the full-length fusion protein and truncated STS domain are highly product-specific 1,11-cyclizing STS enzymes with kinetic properties typical of STSs. Complementation studies in Saccharomyces cerevisiae confirmed that the HMGS domain is also functional in vivo Phylogenetic analysis shows that the hirsutene synthase domain does not form a clade with other previously characterized sesquiterpene synthases from Basidiomycota. Comparative gene structure analysis of this hirsutene synthase with characterized fungal enzymes reveals a significantly higher intron density, suggesting that this enzyme may be acquired by horizontal gene transfer. In contrast, the HMGS domain is clearly related to other fungal homologs. This STS-HMGS fusion protein is part of a biosynthetic gene cluster that includes P450s and oxidases that are expressed and could be cloned from cDNA. Finally, this unusual fusion of a terpene synthase to an HMGS domain, which is not generally recognized as a key regulatory enzyme of the mevalonate isoprenoid precursor pathway, led to the identification of additional HMGS duplications in many fungal genomes, including the localization of HMGSs in other predicted sesquiterpenoid biosynthetic gene clusters.IMPORTANCE Hirsutenoids represent a structurally diverse class of bioactive sesquiterpenoids isolated from fungi. Identification of their biosynthetic pathways will provide access to this chemodiversity for the discovery and synthesis of molecules with new bioactivities. The identification and successful cloning of the previously elusive hirsutene synthase from the S. hirsutum provide important insights and strategies for biosynthetic gene discovery in Basidiomycota. The finding of a terpene synthase-HMGS fusion, the discovery of other sesquiterpenoid biosynthetic gene clusters with dedicated HMGS genes, and HMGS gene duplications in fungal genomes give new importance to the role of HMGS as a key regulatory enzyme in isoprenoid and sterol biosynthesis that should be exploited for metabolic engineering.
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Tang X, Demiray M, Wirth T, Allemann RK. Concise synthesis of artemisinin from a farnesyl diphosphate analogue. Bioorg Med Chem 2018; 26:1314-1319. [PMID: 28404524 PMCID: PMC5930831 DOI: 10.1016/j.bmc.2017.03.068] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/23/2017] [Accepted: 03/31/2017] [Indexed: 01/04/2023]
Abstract
Artemisinin is one of the most potent anti-malaria drugs and many often-lengthy routes have been developed for its synthesis. Amorphadiene synthase, a key enzyme in the biosynthetic pathway of artemisinin, is able to convert an oxygenated farnesyl diphosphate analogue directly to dihydroartemisinic aldehyde, which can be converted to artemisinin in only four chemical steps, resulting in an efficient synthetic route to the anti-malaria drug.
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Affiliation(s)
- Xiaoping Tang
- School of Chemistry, Cardiff University, Park Place, Main Building, Cardiff CF10 3AT, UK
| | - Melodi Demiray
- School of Chemistry, Cardiff University, Park Place, Main Building, Cardiff CF10 3AT, UK
| | - Thomas Wirth
- School of Chemistry, Cardiff University, Park Place, Main Building, Cardiff CF10 3AT, UK.
| | - Rudolf K Allemann
- School of Chemistry, Cardiff University, Park Place, Main Building, Cardiff CF10 3AT, UK.
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Kotopka BJ, Li Y, Smolke CD. Synthetic biology strategies toward heterologous phytochemical production. Nat Prod Rep 2018; 35:902-920. [DOI: 10.1039/c8np00028j] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
This review summarizes the recent progress in heterologous phytochemical biosynthetic pathway reconstitution in plant, bacteria, and yeast, with a focus on the synthetic biology strategies applied in these engineering efforts.
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Affiliation(s)
| | - Yanran Li
- Department of Chemical and Environmental Engineering
- Riverside
- USA
| | - Christina D. Smolke
- Department of Bioengineering
- Stanford University
- Stanford
- USA
- Chan Zuckerberg Biohub
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Liu CL, Tian T, Alonso-Gutierrez J, Garabedian B, Wang S, Baidoo EEK, Benites V, Chen Y, Petzold CJ, Adams PD, Keasling JD, Tan T, Lee TS. Renewable production of high density jet fuel precursor sesquiterpenes from Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:285. [PMID: 30377444 PMCID: PMC6195743 DOI: 10.1186/s13068-018-1272-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 09/26/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND Aviation fuels are an important target of biofuels research due to their high market demand and competitive price. Isoprenoids have been demonstrated as good feedstocks for advanced renewable jet fuels with high energy density, high heat of combustion, and excellent cold-weather performance. In particular, sesquiterpene compounds (C15), such as farnesene and bisabolene, have been identified as promising jet fuel candidates. RESULTS In this study, we explored three sesquiterpenes-epi-isozizaene, pentalenene and α-isocomene-as novel jet fuel precursors. We performed a computational analysis to calculate the energy of combustion of these sesquiterpenes and found that their specific energies are comparable to commercial jet fuel A-1. Through heterologous MVA pathway expression and promoter engineering, we produced 727.9 mg/L epi-isozizaene, 780.3 mg/L pentalenene and 77.5 mg/L α-isocomene in Escherichia coli and 344 mg/L pentalenene in Saccharomyces cerevisiae. We also introduced a dynamic autoinduction system using previously identified FPP-responsive promoters for inducer-free production and managed to achieve comparable amounts of each compound. CONCLUSION We produced tricyclic sesquiterpenes epi-isozizaene, pentalenene and α-isocomene, promising jet fuel feedstocks at high production titers, providing novel, sustainable alternatives to petroleum-based jet fuels.
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Affiliation(s)
- Chun-Li Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 People’s Republic of China
- Joint BioEnergy Institute, 5885 Hollis Street, 4th Floor, Emeryville, CA 94608 USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Tian Tian
- Joint BioEnergy Institute, 5885 Hollis Street, 4th Floor, Emeryville, CA 94608 USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Jorge Alonso-Gutierrez
- Joint BioEnergy Institute, 5885 Hollis Street, 4th Floor, Emeryville, CA 94608 USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Brett Garabedian
- Joint BioEnergy Institute, 5885 Hollis Street, 4th Floor, Emeryville, CA 94608 USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Shuai Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 People’s Republic of China
| | - Edward E. K. Baidoo
- Joint BioEnergy Institute, 5885 Hollis Street, 4th Floor, Emeryville, CA 94608 USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Veronica Benites
- Joint BioEnergy Institute, 5885 Hollis Street, 4th Floor, Emeryville, CA 94608 USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Yan Chen
- Joint BioEnergy Institute, 5885 Hollis Street, 4th Floor, 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, 4th Floor, Emeryville, CA 94608 USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Paul D. Adams
- Joint BioEnergy Institute, 5885 Hollis Street, 4th Floor, Emeryville, CA 94608 USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Department of Bioengineering, University of California, Berkeley, CA 94720 USA
| | - Jay D. Keasling
- Joint BioEnergy Institute, 5885 Hollis Street, 4th Floor, Emeryville, CA 94608 USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Department of Bioengineering, University of California, Berkeley, 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, Lyngby, Denmark
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Tianwei Tan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 People’s Republic of China
| | - Taek Soon Lee
- Joint BioEnergy Institute, 5885 Hollis Street, 4th Floor, Emeryville, CA 94608 USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
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15
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Nybo SE, Saunders J, McCormick SP. Metabolic engineering of Escherichia coli for production of valerenadiene. J Biotechnol 2017; 262:60-66. [DOI: 10.1016/j.jbiotec.2017.10.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 10/03/2017] [Accepted: 10/04/2017] [Indexed: 01/25/2023]
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16
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Chen X, Zhang C, Zou R, Stephanopoulos G, Too HP. In Vitro Metabolic Engineering of Amorpha-4,11-diene Biosynthesis at Enhanced Rate and Specific Yield of Production. ACS Synth Biol 2017; 6:1691-1700. [PMID: 28520394 DOI: 10.1021/acssynbio.6b00377] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In vitro metabolic engineering is an alternative approach to cell-based biosynthesis. It offers unprecedented flexibility for the study of biochemical pathways, thus providing useful information for the rational design and assembly of reaction modules. Herein, we took the advantage of in vitro metabolic engineering to initially gain insight into the regulatory network of a reconstituted amorpha-4,11-diene (AD) synthetic pathway. Guided by lin-log approximation, we rapidly identified the hitherto unrecognized inhibition of adenosine triphosphate (ATP) on both farnesyl pyrophosphate synthase (FPPS) and amorpha-4,11-diene synthase (ADS). Furthermore, the byproduct, pyrophosphate (PPi), potently inhibits ADS, but not FPPS. To lower the inhibition, an ATP recycling system and pyrophosphatase were used and resulted in a significant (∼3-fold) enhancement in the rate of AD production (∼5.7 μmol L-1 min-1). A coimmobilized multienzyme reaction system was then developed to recycle the enzymes. When inhibitory metabolites concentrations were reduced, the specific enzymatic yield of AD was further enhanced (>6-fold). This study demonstrated that mitigating the accumulation of inhibitory metabolites can result in higher yields of AD production by in vitro multienzymatic reactions.
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Affiliation(s)
- Xixian Chen
- Chemical
and Pharmaceutical Engineering, Singapore-MIT Alliance, Singapore 138602
- Biotransformation
Innovation Platform, Agency for Science Technology and Research, Singapore 138632
| | - Congqiang Zhang
- Chemical
and Pharmaceutical Engineering, Singapore-MIT Alliance, Singapore 138602
- Biotransformation
Innovation Platform, Agency for Science Technology and Research, Singapore 138632
| | - Ruiyang Zou
- Chemical
and Pharmaceutical Engineering, Singapore-MIT Alliance, Singapore 138602
| | - Gregory Stephanopoulos
- Chemical
and Pharmaceutical Engineering, Singapore-MIT Alliance, Singapore 138602
- Department
of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States of America
| | - Heng-Phon Too
- Chemical
and Pharmaceutical Engineering, Singapore-MIT Alliance, Singapore 138602
- Department
of Biochemistry, National University of Singapore, Singapore 119077
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17
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Rai A, Saito K, Yamazaki M. Integrated omics analysis of specialized metabolism in medicinal plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:764-787. [PMID: 28109168 DOI: 10.1111/tpj.13485] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 01/10/2017] [Accepted: 01/11/2017] [Indexed: 05/19/2023]
Abstract
Medicinal plants are a rich source of highly diverse specialized metabolites with important pharmacological properties. Until recently, plant biologists were limited in their ability to explore the biosynthetic pathways of these metabolites, mainly due to the scarcity of plant genomics resources. However, recent advances in high-throughput large-scale analytical methods have enabled plant biologists to discover biosynthetic pathways for important plant-based medicinal metabolites. The reduced cost of generating omics datasets and the development of computational tools for their analysis and integration have led to the elucidation of biosynthetic pathways of several bioactive metabolites of plant origin. These discoveries have inspired synthetic biology approaches to develop microbial systems to produce bioactive metabolites originating from plants, an alternative sustainable source of medicinally important chemicals. Since the demand for medicinal compounds are increasing with the world's population, understanding the complete biosynthesis of specialized metabolites becomes important to identify or develop reliable sources in the future. Here, we review the contributions of major omics approaches and their integration to our understanding of the biosynthetic pathways of bioactive metabolites. We briefly discuss different approaches for integrating omics datasets to extract biologically relevant knowledge and the application of omics datasets in the construction and reconstruction of metabolic models.
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Affiliation(s)
- Amit Rai
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
| | - Kazuki Saito
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
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18
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Huibin Z, Liu H, Aboulnaga E, Liu H, Cheng T, Xian M. Microbial Production of Isoprene: Opportunities and Challenges. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807833.ch16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Zou Huibin
- Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences, CAS Key Laboratory of Bio-based Materials; No. 189 Songling Road Qingdao 266101 China
- Qingdao University of Science and Technology; College of Chemical Engineering; No. 53 Zhengzhou Road Qingdao 266042 China
| | - Hui Liu
- Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences, CAS Key Laboratory of Bio-based Materials; No. 189 Songling Road Qingdao 266101 China
| | - Elhussiny Aboulnaga
- Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences, CAS Key Laboratory of Bio-based Materials; No. 189 Songling Road Qingdao 266101 China
- Mansoura University; Faculty of Agriculture; No. 60 Elgomhouria St. Mansoura 35516 Egypt
| | - Huizhou Liu
- Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences, CAS Key Laboratory of Bio-based Materials; No. 189 Songling Road Qingdao 266101 China
| | - Tao Cheng
- Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences, CAS Key Laboratory of Bio-based Materials; No. 189 Songling Road Qingdao 266101 China
| | - Mo Xian
- Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences, CAS Key Laboratory of Bio-based Materials; No. 189 Songling Road Qingdao 266101 China
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19
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Rasool A, Zhang G, Li Z, Li C. Engineering of the terpenoid pathway in Saccharomyces cerevisiae co-overproduces squalene and the non-terpenoid compound oleic acid. Chem Eng Sci 2016. [DOI: 10.1016/j.ces.2016.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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20
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Rasool A, Ahmed MS, Li C. Overproduction of squalene synergistically downregulates ethanol production in Saccharomyces cerevisiae. Chem Eng Sci 2016. [DOI: 10.1016/j.ces.2016.06.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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21
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Banerjee A, Preiser AL, Sharkey TD. Engineering of Recombinant Poplar Deoxy-D-Xylulose-5-Phosphate Synthase (PtDXS) by Site-Directed Mutagenesis Improves Its Activity. PLoS One 2016; 11:e0161534. [PMID: 27548482 PMCID: PMC4993486 DOI: 10.1371/journal.pone.0161534] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 08/08/2016] [Indexed: 12/28/2022] Open
Abstract
Deoxyxylulose 5-phosphate synthase (DXS), a thiamine diphosphate (ThDP) dependent enzyme, plays a regulatory role in the methylerythritol 4-phosphate (MEP) pathway. Isopentenyl diphosphate (IDP) and dimethylallyl diphosphate (DMADP), the end products of this pathway, inhibit DXS by competing with ThDP. Feedback inhibition of DXS by IDP and DMADP constitutes a significant metabolic regulation of this pathway. The aim of this work was to experimentally test the effect of key residues of recombinant poplar DXS (PtDXS) in binding both ThDP and IDP. This work also described the engineering of PtDXS to improve the enzymatic activity by reducing its inhibition by IDP and DMADP. We have designed and tested modifications of PtDXS in an attempt to reduce inhibition by IDP. This could possibly be valuable by removing a feedback that limits the usefulness of the MEP pathway in biotechnological applications. Both ThDP and IDP use similar interactions for binding at the active site of the enzyme, however, ThDP being a larger molecule has more anchoring sites at the active site of the enzyme as compared to the inhibitors. A predicted enzyme structure was examined to find ligand-enzyme interactions, which are relatively more important for inhibitor-enzyme binding than ThDP-enzyme binding, followed by their modifications so that the binding of the inhibitors can be selectively affected compared to ThDP. Two alanine residues important for binding ThDP and the inhibitors were mutated to glycine. In two of the cases, both the IDP inhibition and the overall activity were increased. In another case, both the IDP inhibition and the overall activity were reduced. This provides proof of concept that it is possible to reduce the feedback from IDP on DXS activity.
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Affiliation(s)
- Aparajita Banerjee
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States of America
| | - Alyssa L. Preiser
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States of America
| | - Thomas D. Sharkey
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States of America
- * E-mail:
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22
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Xiao H, Zhong JJ. Production of Useful Terpenoids by Higher-Fungus Cell Factory and Synthetic Biology Approaches. Trends Biotechnol 2016; 34:242-255. [DOI: 10.1016/j.tibtech.2015.12.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/01/2015] [Accepted: 12/15/2015] [Indexed: 01/11/2023]
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23
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Sun X, Shen X, Jain R, Lin Y, Wang J, Sun J, Wang J, Yan Y, Yuan Q. Synthesis of chemicals by metabolic engineering of microbes. Chem Soc Rev 2016; 44:3760-85. [PMID: 25940754 DOI: 10.1039/c5cs00159e] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metabolic engineering is a powerful tool for the sustainable production of chemicals. Over the years, the exploration of microbial, animal and plant metabolism has generated a wealth of valuable genetic information. The prudent application of this knowledge on cellular metabolism and biochemistry has enabled the construction of novel metabolic pathways that do not exist in nature or enhance existing ones. The hand in hand development of computational technology, protein science and genetic manipulation tools has formed the basis of powerful emerging technologies that make the production of green chemicals and fuels a reality. Microbial production of chemicals is more feasible compared to plant and animal systems, due to simpler genetic make-up and amenable growth rates. Here, we summarize the recent progress in the synthesis of biofuels, value added chemicals, pharmaceuticals and nutraceuticals via metabolic engineering of microbes.
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Affiliation(s)
- Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15#, Beisanhuan East Road, Chaoyang District, Beijing 100029, China.
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24
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Gallego-Jara J, de Diego T, del Real Á, Écija-Conesa A, Manjón A, Cánovas M. Lycopene overproduction and in situ extraction in organic-aqueous culture systems using a metabolically engineered Escherichia coli. AMB Express 2015; 5:65. [PMID: 26395597 PMCID: PMC4579157 DOI: 10.1186/s13568-015-0150-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/03/2015] [Indexed: 11/10/2022] Open
Abstract
Lycopene is an import
ant compound with an increasing industrial value. However, there is still no biotechnological process to obtain it. In this study, a semi-continuous system for lycopene extraction from recombinant Escherichia coli BL21 cells is proposed. A two-phase culture mode using organic solvents was found to maximize lycopene production through in situ extraction from cells. Within the reactor, three phases were formed during the process: an aqueous phase containing the recombinant E. coli, an interphase, and an organic phase. Lycopene was extracted from the cells to both the interphase and the organic phase and, consequently, thus enhancing its production. Maximum lycopene production (74.71 ± 3.74 mg L−1) was obtained for an octane-aqueous culture system using the E. coli BL21LF strain, a process that doubled the level obtained in the control aqueous culture. Study of the interphase by transmission electron microscopy (TEM) showed the proteo-lipidic nature and the high storage capacity of lycopene. Moreover, a cell viability test by flow cytometry (CF) after 24 h of culture indicated that 24 % of the population could be re-used. Therefore, a batch series reactor was designed for semi-continuous lycopene extraction. After five cycles of operation (120 h), lycopene production was similar to that obtained in the control aqueous medium. A final specific lycopene yield of up to 49.70 ± 2.48 mg g−1 was reached at 24 h, which represents to the highest titer to date. In conclusion, the aqueous-organic semi-continuous culture system proposed is the first designed for lycopene extraction, representing an important breakthrough in the development of a competitive biotechnological process for lycopene production and extraction.
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25
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Jambunathan P, Zhang K. Combining biological and chemical approaches for green synthesis of chemicals. Curr Opin Chem Eng 2015. [DOI: 10.1016/j.coche.2015.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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26
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Tippmann S, Scalcinati G, Siewers V, Nielsen J. Production of farnesene and santalene by Saccharomyces cerevisiae using fed-batch cultivations with RQ-controlled feed. Biotechnol Bioeng 2015; 113:72-81. [PMID: 26108688 DOI: 10.1002/bit.25683] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 06/15/2015] [Indexed: 11/11/2022]
Abstract
Terpenes have various applications as fragrances, cosmetics and fuels. One of the most prominent examples is the sesquiterpene farnesene, which can be used as diesel substitute in its hydrogenated form farnesane. Recent metabolic engineering efforts have enabled efficient production of several terpenes in Saccharomyces cerevisiae and Escherichia coli. Plant terpene synthases take on an essential function for sesquiterpene production as they catalyze the specific conversion of the universal precursor farnesyl diphosphate (FPP) to the sesquiterpene of interest and thereby impose limitations on the overall productivity. Using farnesene as a case study, we chose three terpene synthases with distinct plant origins and compared their applicability for farnesene production in the yeast S. cerevisiae. Differences regarding the efficiency of these enzymes were observed in shake flask cultivation with maximal final titers of 4 mg/L using α-farnesene synthase from Malus domestica. By employing two existing platform strains optimized for sesquiterpene production, final titers could be raised up 170 mg/L in fed-batch fermentations with RQ-controlled exponential feeding. Based on these experiments, the difference between the selected synthases was not significant. Lastly, the same fermentation setup was used to compare these results to production of the fragrance sesquiterpene santalene, and almost equivalent titers were obtained with 163 mg/L, using the highest producing strain expressing a santalene synthase from Clausena lansium. However, a reduction of the product yield on biomass by 50% could indicate a higher catalytic efficiency of the farnesene synthase.
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Affiliation(s)
- Stefan Tippmann
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96, Gothenburg, Sweden
| | - Gionata Scalcinati
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96, Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96, Gothenburg, Sweden. .,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96, Gothenburg, Sweden. .,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2970, H, ø, rsholm, Denmark.
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27
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Abstract
This review article focuses mainly on the scientific developments concerning the enzyme-mediated synthesis of sesquiterpenes which have been reported in the academic and patent literature during the last twenty years. Nevertheless, this is not a comprehensive description of every single biotransformation involving sesquiterpenes. Only synthetic approaches that have represented a new and innovative perspective from a scientific standpoint are reported. More specifically, the review describes in depth how the use of metabolic engineering of the microbial biotransformations and of the isolated enzymes were exploited in order to perform chemo- and stereoselective chemical transformations of interest for sesquiterpenes synthesis.
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Affiliation(s)
- Stefano Serra
- C.N.R., Istituto di Chimica del Riconoscimento Molecolare; Via L. Mancinelli 7, 20131 Milano, Italy
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28
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Song AA, Ong Abdullah J, Abdullah MP, Shafee N, Othman R, Noor NM, Rahim RA. Engineering the lactococcal mevalonate pathway for increased sesquiterpene production. FEMS Microbiol Lett 2014; 355:177-84. [DOI: 10.1111/1574-6968.12469] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 05/09/2014] [Accepted: 05/11/2014] [Indexed: 11/29/2022] Open
Affiliation(s)
- Adelene A. Song
- Department of Cell and Molecular Biology; Faculty of Biotechnology and Biomolecular Sciences; Universiti Putra Malaysia; Serdang Selangor Darul Ehsan Malaysia
| | - Janna Ong Abdullah
- Department of Microbiology; Faculty of Biotechnology and Biomolecular Sciences; Universiti Putra Malaysia; Serdang Selangor Darul Ehsan Malaysia
| | - Mohd. P. Abdullah
- Department of Cell and Molecular Biology; Faculty of Biotechnology and Biomolecular Sciences; Universiti Putra Malaysia; Serdang Selangor Darul Ehsan Malaysia
| | - Norazizah Shafee
- Department of Microbiology; Faculty of Biotechnology and Biomolecular Sciences; Universiti Putra Malaysia; Serdang Selangor Darul Ehsan Malaysia
| | - Roohaida Othman
- Institute of Systems Biology; Universiti Kebangsaan Malaysia; Bangi Selangor Darul Ehsan Malaysia
- School of Biosciences and Biotechnology; Faculty of Science and Technology; Universiti Kebangsaan Malaysia; Bangi Selangor Darul Ehsan Malaysia
| | - Normah Mohd. Noor
- Institute of Systems Biology; Universiti Kebangsaan Malaysia; Bangi Selangor Darul Ehsan Malaysia
| | - Raha A. Rahim
- Department of Cell and Molecular Biology; Faculty of Biotechnology and Biomolecular Sciences; Universiti Putra Malaysia; Serdang Selangor Darul Ehsan Malaysia
- Institute of Bioscience; Universiti Putra Malaysia; Serdang Selangor Darul Ehsan Malaysia
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29
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Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development. Nat Rev Microbiol 2014; 12:355-67. [DOI: 10.1038/nrmicro3240] [Citation(s) in RCA: 461] [Impact Index Per Article: 46.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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30
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A high-throughput colorimetric screening assay for terpene synthase activity based on substrate consumption. PLoS One 2014; 9:e93317. [PMID: 24681801 PMCID: PMC3969365 DOI: 10.1371/journal.pone.0093317] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 03/03/2014] [Indexed: 11/25/2022] Open
Abstract
Terpene synthases catalyze the formation of a variety of terpene chemical structures. Systematic mutagenesis studies have been effective in providing insights into the characteristic and complex mechanisms of C-C bond formations and in exploring the enzymatic potential for inventing new chemical structures. In addition, there is growing demand to increase terpene synthase activity in heterologous hosts, given the maturation of metabolic engineering and host breeding for terpenoid synthesis. We have developed a simple screening method for the cellular activities of terpene synthases by scoring their substrate consumption based on the color loss of the cell harboring carotenoid pathways. We demonstrate that this method can be used to detect activities of various terpene synthase or prenyltransferase genes in a high-throughput manner, irrespective of the product type, enabling the mutation analysis and directed evolution of terpene synthases. We also report the possibility for substrate-specific screening system of terpene synthases by taking advantage of the substrate-size specificity of C30 and C40 carotenoid pathways.
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31
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Bution ML, Molina G, Abrahão MR, Pastore GM. Genetic and metabolic engineering of microorganisms for the development of new flavor compounds from terpenic substrates. Crit Rev Biotechnol 2014; 35:313-25. [DOI: 10.3109/07388551.2013.855161] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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32
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Statistical experimental design guided optimization of a one-pot biphasic multienzyme total synthesis of amorpha-4,11-diene. PLoS One 2013; 8:e79650. [PMID: 24278153 PMCID: PMC3835790 DOI: 10.1371/journal.pone.0079650] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 10/04/2013] [Indexed: 01/20/2023] Open
Abstract
In vitro synthesis of chemicals and pharmaceuticals using enzymes is of considerable interest as these biocatalysts facilitate a wide variety of reactions under mild conditions with excellent regio-, chemo- and stereoselectivities. A significant challenge in a multi-enzymatic reaction is the need to optimize the various steps involved simultaneously so as to obtain high-yield of a product. In this study, statistical experimental design was used to guide the optimization of a total synthesis of amorpha-4,11-diene (AD) using multienzymes in the mevalonate pathway. A combinatorial approach guided by Taguchi orthogonal array design identified the local optimum enzymatic activity ratio for Erg12:Erg8:Erg19:Idi:IspA to be 100∶100∶1∶25∶5, with a constant concentration of amorpha-4,11-diene synthase (Ads, 100 mg/L). The model also identified an unexpected inhibitory effect of farnesyl pyrophosphate synthase (IspA), where the activity was negatively correlated with AD yield. This was due to the precipitation of farnesyl pyrophosphate (FPP), the product of IspA. Response surface methodology was then used to optimize IspA and Ads activities simultaneously so as to minimize the accumulation of FPP and the result showed that Ads to be a critical factor. By increasing the concentration of Ads, a complete conversion (∼100%) of mevalonic acid (MVA) to AD was achieved. Monovalent ions and pH were effective means of enhancing the specific Ads activity and specific AD yield significantly. The results from this study represent the first in vitro reconstitution of the mevalonate pathway for the production of an isoprenoid and the approaches developed herein may be used to produce other isopentenyl pyrophosphate (IPP)/dimethylallyl pyrophosphate (DMAPP) based products.
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33
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Zhao L, Chang WC, Xiao Y, Liu HW, Liu P. Methylerythritol phosphate pathway of isoprenoid biosynthesis. Annu Rev Biochem 2013; 82:497-530. [PMID: 23746261 DOI: 10.1146/annurev-biochem-052010-100934] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Isoprenoids are a class of natural products with more than 55,000 members. All isoprenoids are constructed from two precursors, isopentenyl diphosphate and its isomer dimethylallyl diphosphate. Two of the most important discoveries in isoprenoid biosynthetic studies in recent years are the elucidation of a second isoprenoid biosynthetic pathway [the methylerythritol phosphate (MEP) pathway] and a modified mevalonic acid (MVA) pathway. In this review, we summarize mechanistic insights on the MEP pathway enzymes. Because many isoprenoids have important biological activities, the need to produce them in sufficient quantities for downstream research efforts or commercial application is apparent. Recent advances in both MVA and MEP pathway-based synthetic biology are also illustrated by reviewing the landmark work of artemisinic acid and taxadien-5α-ol production through microbial fermentations.
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Affiliation(s)
- Lishan Zhao
- Amyris, Inc., Emeryville, California 94608, USA.
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34
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Dahl RH, Zhang F, Alonso-Gutierrez J, Baidoo E, Batth TS, Redding-Johanson AM, Petzold CJ, Mukhopadhyay A, Lee TS, Adams PD, Keasling JD. Engineering dynamic pathway regulation using stress-response promoters. Nat Biotechnol 2013; 31:1039-46. [DOI: 10.1038/nbt.2689] [Citation(s) in RCA: 352] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Accepted: 08/09/2013] [Indexed: 12/20/2022]
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35
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Özaydın B, Burd H, Lee TS, Keasling JD. Carotenoid-based phenotypic screen of the yeast deletion collection reveals new genes with roles in isoprenoid production. Metab Eng 2013; 15:174-83. [DOI: 10.1016/j.ymben.2012.07.010] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 07/17/2012] [Accepted: 07/23/2012] [Indexed: 10/28/2022]
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Song AAL, Abdullah JO, Abdullah MP, Shafee N, Othman R, Tan EF, Noor NM, Raha AR. Overexpressing 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) in the lactococcal mevalonate pathway for heterologous plant sesquiterpene production. PLoS One 2012; 7:e52444. [PMID: 23300671 PMCID: PMC3530464 DOI: 10.1371/journal.pone.0052444] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 11/13/2012] [Indexed: 12/02/2022] Open
Abstract
Isoprenoids are a large and diverse group of metabolites with interesting properties such as flavour, fragrance and therapeutic properties. They are produced via two pathways, the mevalonate pathway or the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway. While plants are the richest source of isoprenoids, they are not the most efficient producers. Escherichia coli and yeasts have been extensively studied as heterologous hosts for plant isoprenoids production. In the current study, we describe the usage of the food grade Lactococcus lactis as a potential heterologous host for the production of sesquiterpenes from a local herbaceous Malaysian plant, Persicaria minor (synonym Polygonum minus). A sesquiterpene synthase gene from P. minor was successfully cloned and expressed in L. lactis. The expressed protein was identified to be a β-sesquiphellandrene synthase as it was demonstrated to be functional in producing β-sesquiphellandrene at 85.4% of the total sesquiterpenes produced based on in vitro enzymatic assays. The recombinant L. lactis strain developed in this study was also capable of producing β-sesquiphellandrene in vivo without exogenous substrates supplementation. In addition, overexpression of the strain’s endogenous 3-hydroxy-3-methylglutaryl coenzyme-A reductase (HMGR), an established rate-limiting enzyme in the eukaryotic mevalonate pathway, increased the production level of β-sesquiphellandrene by 1.25–1.60 fold. The highest amount achieved was 33 nM at 2 h post-induction.
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Affiliation(s)
- Adelene Ai-Lian Song
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor Darul Ehsan, Malaysia
| | - Janna Ong Abdullah
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor Darul Ehsan, Malaysia
| | - Mohd. Puad Abdullah
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor Darul Ehsan, Malaysia
| | - Norazizah Shafee
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor Darul Ehsan, Malaysia
| | - Roohaida Othman
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor Darul Ehsan, Malaysia
| | - Ee-Fun Tan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor Darul Ehsan, Malaysia
| | - Normah Mohd. Noor
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor Darul Ehsan, Malaysia
| | - Abdul Rahim Raha
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor Darul Ehsan, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor Darul Ehsan, Malaysia
- * E-mail:
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Kampranis SC, Makris AM. Developing a yeast cell factory for the production of terpenoids. Comput Struct Biotechnol J 2012; 3:e201210006. [PMID: 24688666 PMCID: PMC3962098 DOI: 10.5936/csbj.201210006] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 10/25/2012] [Accepted: 10/25/2012] [Indexed: 12/21/2022] Open
Abstract
Technological developments over the past century have made microbes the work-horses of large scale industrial production processes. Current efforts focus on the metabolic engineering of microbial strains to produce high levels of desirable end-products. The arsenal of the contemporary metabolic engineer contains tools that allow either targeted rational interventions or global screens that combine classical approaches with –omics technologies. Production of terpenoids in S. cerevisiae presents a characteristic example of contemporary biotechnology that integrates all the variety of novel approaches used in metabolic engineering. Terpenoids have attracted significant interest as pharmaceuticals, flavour and fragrance additives, and, more recently, biofuels. The ongoing metabolic engineering efforts, combined with the continuously increasing number of terpene biosynthetic enzymes discovered will enable the economical and environmentally friendly production of a wide range of compounds.
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Affiliation(s)
| | - Antonios M Makris
- Institute of Applied Biosciences/ CERTH, P.O. Box 60361, Thermi 57001, Thessaloniki, Greece
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Berthelot K, Estevez Y, Deffieux A, Peruch F. Isopentenyl diphosphate isomerase: A checkpoint to isoprenoid biosynthesis. Biochimie 2012; 94:1621-34. [DOI: 10.1016/j.biochi.2012.03.021] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 03/27/2012] [Indexed: 11/25/2022]
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Synthetic biology and the development of tools for metabolic engineering. Metab Eng 2012; 14:189-95. [DOI: 10.1016/j.ymben.2012.01.004] [Citation(s) in RCA: 321] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 01/24/2012] [Indexed: 12/21/2022]
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Functional expression of an orchid fragrance gene in Lactococcus lactis. Int J Mol Sci 2012; 13:1582-1597. [PMID: 22408409 PMCID: PMC3291978 DOI: 10.3390/ijms13021582] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 11/30/2011] [Accepted: 12/20/2011] [Indexed: 11/16/2022] Open
Abstract
Vanda Mimi Palmer (VMP), an orchid hybrid of Vanda tesselata and Vanda Tan Chay Yan is a highly scented tropical orchid which blooms all year round. Previous studies revealed that VMP produces a variety of isoprenoid volatiles during daylight. Isoprenoids are well known to contribute significantly to the scent of most fragrant plants. They are a large group of secondary metabolites which may possess valuable characteristics such as flavor, fragrance and toxicity and are produced via two pathways, the mevalonate (MVA) pathway or/and the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway. In this study, a sesquiterpene synthase gene denoted VMPSTS, previously isolated from a floral cDNA library of VMP was cloned and expressed in Lactococcus lactis to characterize the functionality of the protein. L. lactis, a food grade bacterium which utilizes the mevalonate pathway for isoprenoid production was found to be a suitable host for the characterization of plant terpene synthases. Through recombinant expression of VMPSTS, it was revealed that VMPSTS produced multiple sesquiterpenes and germacrene D dominates its profile.
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Wang C, Yoon SH, Jang HJ, Chung YR, Kim JY, Choi ES, Kim SW. Metabolic engineering of Escherichia coli for α-farnesene production. Metab Eng 2011; 13:648-55. [DOI: 10.1016/j.ymben.2011.08.001] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 07/02/2011] [Accepted: 08/15/2011] [Indexed: 11/25/2022]
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Increase of lycopene production by supplementing auxiliary carbon sources in metabolically engineered Escherichia coli. Appl Microbiol Biotechnol 2011; 90:489-97. [DOI: 10.1007/s00253-011-3091-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Revised: 12/15/2010] [Accepted: 01/03/2011] [Indexed: 10/18/2022]
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Zhang H, Boghigian BA, Armando J, Pfeifer BA. Methods and options for the heterologous production of complex natural products. Nat Prod Rep 2011; 28:125-51. [PMID: 21060956 PMCID: PMC9896020 DOI: 10.1039/c0np00037j] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This review will detail the motivations, experimental approaches, and growing list of successful cases associated with the heterologous production of complex natural products.
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Affiliation(s)
- Haoran Zhang
- Department of Chemical & Biological Engineering, Science & Technology Center, Tufts University, Medford, MA 02155, USA.
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Wang C, Yoon SH, Shah AA, Chung YR, Kim JY, Choi ES, Keasling JD, Kim SW. Farnesol production from Escherichia coli by harnessing the exogenous mevalonate pathway. Biotechnol Bioeng 2010; 107:421-9. [PMID: 20552672 DOI: 10.1002/bit.22831] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Farnesol (FOH) production has been carried out in metabolically engineered Escherichia coli. FOH is formed through the depyrophosphorylation of farnesyl pyrophosphate (FPP), which is synthesized from isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) by FPP synthase. In order to increase FPP synthesis, E. coli was metabolically engineered to overexpress ispA and to utilize the foreign mevalonate (MVA) pathway for the efficient synthesis of IPP and DMAPP. Two-phase culture using a decane overlay of the culture broth was applied to reduce volatile loss of FOH produced during culture and to extract FOH from the culture broth. A FOH production of 135.5 mg/L was obtained from the recombinant E. coli harboring the pTispA and pSNA plasmids for ispA overexpression and MVA pathway utilization, respectively. It is interesting to observe that a large amount of FOH could be produced from E. coli without FOH synthase by the augmentation of FPP synthesis. Introduction of the exogenous MVA pathway enabled the dramatic production of FOH by E. coli while no detectable FOH production was observed in the endogenous MEP pathway-only control.
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Affiliation(s)
- Chonglong Wang
- Division of Applied Life Sciences (BK21 Program), EB-NCRC and PMBBRC, Gyeongsang National University, Jinju 660-701, Korea
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Kim SW, Kim JB, Ryu JM, Jung JK, Kim JH. High-level production of lycopene in metabolically engineered E. coli. Process Biochem 2009. [DOI: 10.1016/j.procbio.2009.04.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Martin CH, Nielsen DR, Solomon KV, Prather KLJ. Synthetic metabolism: engineering biology at the protein and pathway scales. ACTA ACUST UNITED AC 2009; 16:277-86. [PMID: 19318209 DOI: 10.1016/j.chembiol.2009.01.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Revised: 01/21/2009] [Accepted: 01/22/2009] [Indexed: 11/25/2022]
Abstract
Biocatalysis has become a powerful tool for the synthesis of high-value compounds, particularly so in the case of highly functionalized and/or stereoactive products. Nature has supplied thousands of enzymes and assembled them into numerous metabolic pathways. Although these native pathways can be use to produce natural bioproducts, there are many valuable and useful compounds that have no known natural biochemical route. Consequently, there is a need for both unnatural metabolic pathways and novel enzymatic activities upon which these pathways can be built. Here, we review the theoretical and experimental strategies for engineering synthetic metabolic pathways at the protein and pathway scales, and highlight the challenges that this subfield of synthetic biology currently faces.
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Affiliation(s)
- Collin H Martin
- Department of Chemical Engineering, Synthetic Biology Engineering Research Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Harris DM, van der Krogt ZA, Klaassen P, Raamsdonk LM, Hage S, van den Berg MA, Bovenberg RAL, Pronk JT, Daran JM. Exploring and dissecting genome-wide gene expression responses of Penicillium chrysogenum to phenylacetic acid consumption and penicillinG production. BMC Genomics 2009; 10:75. [PMID: 19203396 PMCID: PMC2657799 DOI: 10.1186/1471-2164-10-75] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Accepted: 02/10/2009] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Since the discovery of the antibacterial activity of penicillin by Fleming 80 years ago, improvements of penicillin titer were essentially achieved by classical strain improvement through mutagenesis and screening. The recent sequencing of Penicillium chrysogenum strain Wisconsin1255-54 and the availability of genomics tools such as DNA-microarray offer new perspective. RESULTS In studies on beta-lactam production by P. chrysogenum, addition and omission of a side-chain precursor is commonly used to generate producing and non-producing scenarios. To dissect effects of penicillinG production and of its side-chain precursor phenylacetic acid (PAA), a derivative of a penicillinG high-producing strain without a functional penicillin-biosynthesis gene cluster was constructed. In glucose-limited chemostat cultures of the high-producing and cluster-free strains, PAA addition caused a small reduction of the biomass yield, consistent with PAA acting as a weak-organic-acid uncoupler. Microarray-based analysis on chemostat cultures of the high-producing and cluster-free strains, grown in the presence and absence of PAA, showed that: (i) Absence of a penicillin gene cluster resulted in transcriptional upregulation of a gene cluster putatively involved in production of the secondary metabolite aristolochene and its derivatives, (ii) The homogentisate pathway for PAA catabolism is strongly transcriptionally upregulated in PAA-supplemented cultures (iii) Several genes involved in nitrogen and sulfur metabolism were transcriptionally upregulated under penicillinG producing conditions only, suggesting a drain of amino-acid precursor pools. Furthermore, the number of candidate genes for penicillin transporters was strongly reduced, thus enabling a focusing of functional analysis studies. CONCLUSION This study demonstrates the usefulness of combinatorial transcriptome analysis in chemostat cultures to dissect effects of biological and process parameters on gene expression regulation. This study provides for the first time clear-cut target genes for metabolic engineering, beyond the three genes of the beta-lactam pathway.
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Affiliation(s)
- Diana M Harris
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Zita A van der Krogt
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Paul Klaassen
- DSM Anti-Infectives, DAI/INNO (624-0270), Postbus 425, 2600 AK, Delft, The Netherlands
| | - Leonie M Raamsdonk
- DSM Anti-Infectives, DAI/INNO (624-0270), Postbus 425, 2600 AK, Delft, The Netherlands
| | - Susanne Hage
- DSM Anti-Infectives, DAI/INNO (624-0270), Postbus 425, 2600 AK, Delft, The Netherlands
| | - Marco A van den Berg
- DSM Anti-Infectives, DAI/INNO (624-0270), Postbus 425, 2600 AK, Delft, The Netherlands
| | - Roel AL Bovenberg
- DSM Anti-Infectives, DAI/INNO (624-0270), Postbus 425, 2600 AK, Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands
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Yoon SH, Lee SH, Das A, Ryu HK, Jang HJ, Kim JY, Oh DK, Keasling JD, Kim SW. Combinatorial expression of bacterial whole mevalonate pathway for the production of beta-carotene in E. coli. J Biotechnol 2009; 140:218-26. [PMID: 19428716 DOI: 10.1016/j.jbiotec.2009.01.008] [Citation(s) in RCA: 158] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Revised: 01/07/2009] [Accepted: 01/16/2009] [Indexed: 12/18/2022]
Abstract
The increased synthesis of building blocks of IPP (isopentenyl diphosphate) and DMAPP (dimethylallyl diphosphate) through metabolic engineering is a way to enhance the production of carotenoids. Using E. coli as a host, IPP and DMAPP supply can be increased significantly through the introduction of foreign MVA (mevalonate) pathway into it. The MVA pathway is split into two parts with the top and bottom portions supplying mevalonate from acetyl-CoA, and IPP and DMAPP from mevalonate, respectively. The bottom portions of MVA pathway from Streptococcus pneumonia, Enterococcus faecalis, Staphylococcus aureus, Streptococcus pyogenes and Saccharomyces cerevisiae were compared with exogenous mevalonate supplementation for beta-carotene production in recombinant Escherichia coli harboring beta-carotene synthesis genes. The E. coli harboring the bottom MVA pathway of S. pneumoniae produced the highest amount of beta-carotene. The top portions of MVA pathway were also compared and the top MVA pathway of E. faecalis was found out to be the most efficient for mevalonate production in E. coli. The whole MVA pathway was constructed by combining the bottom and top portions of MVA pathway of S. pneumoniae and E. faecalis, respectively. The recombinant E. coli harboring the whole MVA pathway and beta-carotene synthesis genes produced high amount of beta-carotene even without exogenous mevalonate supplementation. When comparing various E. coli strains - MG1655, DH5alpha, S17-1, XL1-Blue and BL21 - the DH5alpha was found to be the best beta-carotene producer. Using glycerol as the carbon source for beta-carotene production was found to be superior to glucose, galactose, xylose and maltose. The recombinant E. coli DH5alpha harboring the whole MVA pathway and beta-carotene synthesis genes produced beta-carotene of 465mg/L at glycerol concentration of 2% (w/v).
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Affiliation(s)
- Sang-Hwal Yoon
- Division of Applied Life Science (BK21), EB-NCRC and PMBBRC, Gyeongsang National University, Jinju 660-701, Republic of Korea
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Lee SY, Kim HU, Park JH, Park JM, Kim TY. Metabolic engineering of microorganisms: general strategies and drug production. Drug Discov Today 2008; 14:78-88. [PMID: 18775509 DOI: 10.1016/j.drudis.2008.08.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Revised: 07/29/2008] [Accepted: 08/04/2008] [Indexed: 01/11/2023]
Abstract
Many drugs and drug precursors found in natural organisms are rather difficult to synthesize chemically and to extract in large amounts. Metabolic engineering is playing an increasingly important role in the production of these drugs and drug precursors. This is typically achieved by establishing new metabolic pathways leading to the product formation, and enforcing or removing the existing metabolic pathways toward enhanced product formation. Recent advances in system biology and synthetic biology are allowing us to perform metabolic engineering at the whole cell level, thus enabling optimal design of a microorganism for the efficient production of drugs and drug precursors. In this review, we describe the general strategies for the metabolic engineering of microorganisms for the production of drugs and drug precursors. As successful examples of metabolic engineering, the approaches taken toward strain development for the production of artemisinin, an antimalarial drug, and benzylisoquinoline alkaloids, a family of antibacterial and anticancer drugs, are described in detail. Also, systems metabolic engineering of Escherichia coli for the production of L-valine, an important drug precursor, is showcased as an important strategy of future metabolic engineering effort.
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Affiliation(s)
- Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering, Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, KAIST, Daejeon 305-701, Korea.
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Yoshikuni Y, Dietrich JA, Nowroozi FF, Babbitt PC, Keasling JD. Redesigning enzymes based on adaptive evolution for optimal function in synthetic metabolic pathways. ACTA ACUST UNITED AC 2008; 15:607-18. [PMID: 18559271 DOI: 10.1016/j.chembiol.2008.05.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2007] [Revised: 04/29/2008] [Accepted: 05/02/2008] [Indexed: 01/09/2023]
Abstract
Nature has balanced most metabolic pathways such that no one enzyme in the pathway controls the flux through that pathway. However, unnatural or nonnative, constructed metabolic pathways may have limited product flux due to unfavorable in vivo properties of one or more enzymes in the pathway. One such example is the mevalonate-based isoprenoid biosynthetic pathway that we previously reconstructed in Escherichia coli. We have used a probable mechanism of adaptive evolution to engineer the in vivo properties of two enzymes (3-hydroxy-3-methylglutaryl-CoA reductase [tHMGR] and many terpene synthases) in this pathway and thereby eliminate or minimize the bottleneck created by these inefficient or nonfunctional enzymes. Here, we demonstrate how we significantly improved the productivity (by approximately 1000 fold) of this reconstructed biosynthetic pathway using this strategy. We anticipate that this strategy will find broad applicability in the functional construction (or reconstruction) of biological pathways in heterologous hosts.
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Affiliation(s)
- Yasuo Yoshikuni
- UCSF/UCB Joint Graduate Group in Bioengineering, University of California at Berkeley, Berkeley, CA 94720, USA
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