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Raghavan I, Juman R, Wang ZQ. The non-mevalonate pathway requires a delicate balance of intermediates to maximize terpene production. Appl Microbiol Biotechnol 2024; 108:245. [PMID: 38421431 PMCID: PMC10904526 DOI: 10.1007/s00253-024-13077-7] [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: 05/31/2023] [Revised: 02/13/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024]
Abstract
Terpenes are valuable industrial chemicals whose demands are increasingly being met by bioengineering microbes such as E. coli. Although the bioengineering efforts commonly involve installing the mevalonate (MVA) pathway in E. coli for terpene production, the less studied methylerythritol phosphate (MEP) pathway is a more attractive target due to its higher energy efficiency and theoretical yield, despite its tight regulation. In this study, we integrated an additional copy of the entire MEP pathway into the E. coli genome for stable, marker-free terpene production. The genomically integrated strain produced more monoterpene geraniol than a plasmid-based system. The pathway genes' transcription was modulated using different promoters to produce geraniol as the reporter of the pathway flux. Pathway genes, including dxs, idi, and ispDF, expressed from a medium-strength promoter, led to the highest geraniol production. Quantifying the MEP pathway intermediates revealed that the highest geraniol producers had high levels of isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), but moderate levels of the pathway intermediates upstream of these two building blocks. A principal component analysis demonstrated that 1-deoxy-D-xylulose 5-phosphate (DXP), the product of the first enzyme of the pathway, was critical for determining the geraniol titer, whereas MEP, the product of DXP reductoisomerase (Dxr or IspC), was the least essential. This work shows that an intricate balance of the MEP pathway intermediates determines the terpene yield in engineered E. coli. The genetically stable and intermediate-balanced strains created in this study will serve as a chassis for producing various terpenes. KEY POINTS: • Genome-integrated MEP pathway afforded higher strain stability • Genome-integrated MEP pathway produced more terpene than the plasmid-based system • High monoterpene production requires a fine balance of MEP pathway intermediates.
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Affiliation(s)
- Indu Raghavan
- Department of Biological Sciences, University at Buffalo, the State University of New York, 653 Cooke Hall, Buffalo, New York, NY14260, USA
| | - Rosheena Juman
- Department of Biological Sciences, University at Buffalo, the State University of New York, 653 Cooke Hall, Buffalo, New York, NY14260, USA
| | - Zhen Q Wang
- Department of Biological Sciences, University at Buffalo, the State University of New York, 653 Cooke Hall, Buffalo, New York, NY14260, USA.
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2
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Darvishi F, Rafatiyan S, Abbaspour Motlagh Moghaddam MH, Atkinson E, Ledesma-Amaro R. Applications of synthetic yeast consortia for the production of native and non-native chemicals. Crit Rev Biotechnol 2024; 44:15-30. [PMID: 36130800 DOI: 10.1080/07388551.2022.2118569] [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: 06/03/2022] [Revised: 08/03/2022] [Accepted: 08/19/2022] [Indexed: 11/03/2022]
Abstract
The application of microbial consortia is a new approach in synthetic biology. Synthetic yeast consortia, simple or complex synthetic mixed cultures, have been used for the production of various metabolites. Cooperation between the members of a consortium and cross-feeding can be applied to create stable microbial communication. These consortia can: consume a variety of substrates, perform more complex functions, produce metabolites in high titer, rate, and yield (TRY), and show higher stability during industrial fermentations. Due to the new research context of synthetic consortia, few yeasts were used to build these consortia, including Saccharomyces cerevisiae, Pichia pastoris, and Yarrowia lipolytica. Here, application of the yeasts for design of synthetic microbial consortia and their advantages and bottlenecks for effective and robust production of valuable metabolites from bioresource, including: cellulose, xylose, glycerol and so on, have been reviewed. Key trends and challenges are also discussed for the future development of synthetic yeast consortia.
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Affiliation(s)
- Farshad Darvishi
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
- Research Center for Applied Microbiology and Microbial Biotechnology (CAMB), Alzahra University, Tehran, Iran
| | - Sajad Rafatiyan
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | | | - Eliza Atkinson
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
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3
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Johnston ML, Bonett EM, DeColli AA, Freel Meyers CL. Antibacterial Target DXP Synthase Catalyzes the Cleavage of d-Xylulose 5-Phosphate: a Study of Ketose Phosphate Binding and Ketol Transfer Reaction. Biochemistry 2022; 61:1810-1823. [PMID: 35998648 PMCID: PMC9531112 DOI: 10.1021/acs.biochem.2c00274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bacterial enzyme 1-deoxy-d-xylulose 5-phosphate synthase (DXPS) catalyzes the formation of DXP from pyruvate and d-glyceraldehyde 3-phosphate (d-GAP) in a thiamin diphosphate (ThDP)-dependent manner. In addition to its role in isoprenoid biosynthesis, DXP is required for ThDP and pyridoxal phosphate biosynthesis. Due to its function as a branch-point enzyme and its demonstrated substrate and catalytic promiscuity, we hypothesize that DXPS could be key for bacterial adaptation in the dynamic metabolic landscape during infection. Prior work in the Freel Meyers laboratory has illustrated that DXPS displays relaxed specificity toward donor and acceptor substrates and varies acceptor specificity according to the donor used. We have reported that DXPS forms dihydroxyethyl (DHE)ThDP from ketoacid or aldehyde donor substrates via decarboxylation and deprotonation, respectively. Here, we tested other DHE donors and found that DXPS cleaves d-xylulose 5-phosphate (X5P) at C2-C3, producing DHEThDP through a third mechanism involving d-GAP elimination. We interrogated DXPS-catalyzed reactions using X5P as a donor substrate and illustrated (1) production of a semi-stable enzyme-bound intermediate and (2) O2, H+, and d-erythrose 4-phosphate act as acceptor substrates, highlighting a new transketolase-like activity of DXPS. Furthermore, we examined X5P binding to DXPS and suggest that the d-GAP binding pocket plays a crucial role in X5P binding and turnover. Overall, this study reveals a ketose-cleavage reaction catalyzed by DXPS, highlighting the remarkable flexibility for donor substrate usage by DXPS compared to other C-C bond-forming enzymes.
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Affiliation(s)
- Melanie L. Johnston
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Eucolona M. Bonett
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Caren L. Freel Meyers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Basiony M, Ouyang L, Wang D, Yu J, Zhou L, Zhu M, Wang X, Feng J, Dai J, Shen Y, Zhang C, Hua Q, Yang X, Zhang L. Optimization of microbial cell factories for astaxanthin production: Biosynthesis and regulations, engineering strategies and fermentation optimization strategies. Synth Syst Biotechnol 2022; 7:689-704. [PMID: 35261927 PMCID: PMC8866108 DOI: 10.1016/j.synbio.2022.01.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/08/2021] [Accepted: 01/03/2022] [Indexed: 12/29/2022] Open
Abstract
The global market demand for natural astaxanthin is rapidly increasing owing to its safety, the potential health benefits, and the diverse applications in food and pharmaceutical industries. The major native producers of natural astaxanthin on industrial scale are the alga Haematococcus pluvialis and the yeast Xanthopyllomyces dendrorhous. However, the natural production via these native producers is facing challenges of limited yield and high cost of cultivation and extraction. Alternatively, astaxanthin production via metabolically engineered non-native microbial cell factories such as Escherichia coli, Saccharomyces cerevisiae and Yarrowia lipolytica is another promising strategy to overcome these limitations. In this review we summarize the recent scientific and biotechnological progresses on astaxanthin biosynthetic pathways, transcriptional regulations, the interrelation with lipid metabolism, engineering strategies as well as fermentation process control in major native and non-native astaxanthin producers. These progresses illuminate the prospects of producing astaxanthin by microbial cell factories on industrial scale.
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Usuda Y, Nishio Y, Nonaka G, Hara Y. Microbial Production Potential of Pantoea ananatis: From Amino Acids to Secondary Metabolites. Microorganisms 2022; 10:microorganisms10061133. [PMID: 35744651 PMCID: PMC9231021 DOI: 10.3390/microorganisms10061133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/25/2022] [Accepted: 05/27/2022] [Indexed: 11/16/2022] Open
Abstract
Pantoea ananatis, a gram-negative bacterium belonging to the Erwiniaceae family, is a well-known phytopathogen isolated from many ecological niches and plant hosts. However, this bacterium also provides us with various beneficial characteristics, such as the growth promotion of their host plants and increased crop yield. Some isolated non-pathogenic strains are promising for the microbial production of useful substances. P. ananatis AJ13355 was isolated as an acidophilic bacterium and was used as an excellent host to produce L-glutamic acid under acidic conditions. The genome sequence of P. ananatis AJ13355 was determined, and specific genome-engineering technologies were developed. As a result, P. ananatis was successfully used to construct a bacterial strain that produces cysteine, a sulfur-containing amino acid that has been difficult to produce through fermentation because of complex regulation. Furthermore, by heterologous expression including plant-derived genes, construction of a strain that produces isoprenoids such as isoprene and linalool as secondary metabolites was achieved. P. ananatis is shown to be a useful host for the production of secondary metabolites, as well as amino acids, and is expected to be used as a platform for microbial production of bioactive substances, aromatic substances, and other high-value-added substances of plant origin in the future.
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Affiliation(s)
- Yoshihiro Usuda
- Research and Business Planning Department, Ajinomoto Co., Inc., Tokyo 104-8315, Japan
- Correspondence: ; Tel.: +81-70-4361-3762; Fax: +81-3-5250-8352
| | - Yousuke Nishio
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., Kawasaki 210-8681, Japan; (Y.N.); (Y.H.)
| | - Gen Nonaka
- Ajinomoto-Genetika Research Institute, Moscow 117545, Russia;
| | - Yoshihiko Hara
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., Kawasaki 210-8681, Japan; (Y.N.); (Y.H.)
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Fitriana HN, Lee S, Kim HS, Lee J, Lee Y, Lee JS, Park H, Ko CH, Lim SY, Lee SY. Enhanced CO 2 electroconversion of Rhodobacter sphaeroides by cobalt-phosphate complex assisted water oxidation. Bioelectrochemistry 2022; 145:108102. [PMID: 35338862 DOI: 10.1016/j.bioelechem.2022.108102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 03/10/2022] [Accepted: 03/18/2022] [Indexed: 01/02/2023]
Abstract
CO2 can be a next generation feedstock for electricity-driven bioproduction due to its abundance and availability. Microbial electrosynthesis (MES), a promising technique for CO2 electroconversion, provides an attractive route for the production of valuable products from CO2, but issues surrounding efficiency and reasonable productivity should be resolved. Improving the anode performance for water oxidation under neutral pH is one of the most important aspects to advance current MES. Here, we introduce cobalt-phosphate (Co-Pi) assisted water oxidation at the counter electrode (i.e., anode) to upgrade the MES performance at pH 7.0. We show that CO2 can be converted by photochemoautotrophic bacterium, Rhodobacter sphaeroides into organic acids and carotenoids in the MES reactor. Planktonic cells of R. sphareroides in the Co-Pi anode equipped MES reactor was ca. 1.5-fold higher than in the control condition (w/o Co-Pi). The faradaic efficiency of the Co-Pi anode equipped MES reactor was remarkably higher (58.3%) than that of the bare anode (27.8%). While the system can improve the CO2 electroconversion nonetheless there are some further optimizations are necessary.
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Affiliation(s)
- Hana Nur Fitriana
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, 61003 Gwangju, South Korea
| | - Sangmin Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, 61003 Gwangju, South Korea
| | - Hui Su Kim
- Department of Advanced Chemicals & Engineering, Chonnam National University, 61186 Gwangju, South Korea
| | - Jiye Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, 61003 Gwangju, South Korea
| | - Yurim Lee
- Interdisciplinary Program of Agriculture and Life Science, Chonnam National University, 61186 Gwangju, South Korea
| | - Jin-Suk Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, 61003 Gwangju, South Korea
| | - Hyojung Park
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, 61003 Gwangju, South Korea; Bioremediation Team, National Institute of Agricultural Sciences, 55365 Jeollabuk-do, South Korea
| | - Chang Hyun Ko
- Department of Advanced Chemicals & Engineering, Chonnam National University, 61186 Gwangju, South Korea; School of Chemical Engineering, Chonnam National University, 61186 Gwangju, South Korea
| | - Sung Yul Lim
- Department of Chemistry, Kyung Hee University, 02447 Seoul, South Korea
| | - Soo Youn Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, 61003 Gwangju, South Korea.
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7
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Chu LL. CRISPR-Cas system in microbial hosts for terpenoid production. Crit Rev Biotechnol 2022; 42:1116-1133. [PMID: 35139706 DOI: 10.1080/07388551.2021.1995318] [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: 11/03/2022]
Abstract
Terpenoids represent the largest group of secondary metabolites with variable structures and functions. Terpenoids are well known for their beneficial application in human life, such as pharmaceutical products, vitamins, hormones, anticancer drugs, cosmetics, flavors and fragrances, foods, agriculture, and biofuels. Recently, engineering microbial cells have been provided with a sustainable approach to produce terpenoids with high yields. Noticeably, the clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) system has emerged as one of the most efficient genome-editing technologies to engineer microorganisms for improving terpenoid production. In this review, we summarize the application of the CRISPR-Cas system for the production of terpenoids in microbial hosts such as Escherichia coli, Saccharomyces cerevisiae, Corynebacterium glutamicum, and Pseudomonas putida. CRISPR-Cas9 deactivated Cas9 (dCas9)-based CRISPR (CRISPRi), and the dCas9-based activator (CRISPRa) have been used in either individual or combinatorial systems to control the metabolic flux for enhancing the production of terpenoids. Finally, the prospects of using the CRISPR-Cas system in terpenoid production are also discussed.
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Affiliation(s)
- Luan Luong Chu
- Faculty of Biotechnology, Chemistry and Environmental Engineering, Phenikaa University, Hanoi, Viet Nam.,Bioresource Research Center, Phenikaa University, Hanoi, Viet Nam
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8
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Tang R, Wen Q, Li M, Zhang W, Wang Z, Yang J. Recent Advances in the Biosynthesis of Farnesene Using Metabolic Engineering. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:15468-15483. [PMID: 34905684 DOI: 10.1021/acs.jafc.1c06022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Farnesene, as an important sesquiterpene isoprenoid polymer of acetyl-CoA, is a renewable feedstock for diesel fuel, polymers, and cosmetics. It has been widely applied in agriculture, medicine, energy, and other fields. In recent years, farnesene biosynthesis is considered a green and economical approach because of its mild reaction conditions, low environmental pollution, and sustainability. Metabolic engineering has been widely applied to construct cell factories for farnesene biosynthesis. In this paper, the research progress, common problems, and strategies of farnesene biosynthesis are reviewed. They are mainly described from the perspectives of the current status of farnesene biosynthesis in different host cells, optimization of the metabolic pathway for farnesene biosynthesis, and key enzymes for farnesene biosynthesis. Furthermore, the challenges and prospects for future farnesene biosynthesis are discussed.
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Affiliation(s)
- Ruohao Tang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center of Qingdao Agricultural University. Qingdao, Shandong 266109, People's Republic of China
- Shandong Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong 266109, People's Republic of China
| | - Qifeng Wen
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center of Qingdao Agricultural University. Qingdao, Shandong 266109, People's Republic of China
- Shandong Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong 266109, People's Republic of China
| | - Meijie Li
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center of Qingdao Agricultural University. Qingdao, Shandong 266109, People's Republic of China
- Shandong Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong 266109, People's Republic of China
| | - Wei Zhang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center of Qingdao Agricultural University. Qingdao, Shandong 266109, People's Republic of China
- Shandong Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong 266109, People's Republic of China
| | - Zhaobao Wang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center of Qingdao Agricultural University. Qingdao, Shandong 266109, People's Republic of China
- Shandong Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong 266109, People's Republic of China
| | - Jianming Yang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center of Qingdao Agricultural University. Qingdao, Shandong 266109, People's Republic of China
- Shandong Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong 266109, People's Republic of China
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Hayat IF, Plan M, Ebert BE, Dumsday G, Vickers CE, Peng B. Auxin-mediated induction of GAL promoters by conditional degradation of Mig1p improves sesquiterpene production in Saccharomyces cerevisiae with engineered acetyl-CoA synthesis. Microb Biotechnol 2021; 14:2627-2642. [PMID: 34499421 PMCID: PMC8601163 DOI: 10.1111/1751-7915.13880] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/19/2021] [Accepted: 06/19/2021] [Indexed: 11/30/2022] Open
Abstract
The yeast Saccharomyces cerevisiae uses the pyruvate dehydrogenase-bypass for acetyl-CoA biosynthesis. This relatively inefficient pathway limits production potential for acetyl-CoA-derived biochemical due to carbon loss and the cost of two high-energy phosphate bonds per molecule of acetyl-CoA. Here, we attempted to improve acetyl-CoA production efficiency by introducing heterologous acetylating aldehyde dehydrogenase and phosphoketolase pathways for acetyl-CoA synthesis to enhance production of the sesquiterpene trans-nerolidol. In addition, we introduced auxin-mediated degradation of the glucose-dependent repressor Mig1p to allow induced expression of GAL promoters on glucose so that production potential on glucose could be examined. The novel genes that we used to reconstruct the heterologous acetyl-CoA pathways did not sufficiently complement the loss of endogenous acetyl-CoA pathways, indicating that superior heterologous enzymes are necessary to establish fully functional synthetic acetyl-CoA pathways and properly explore their potential for nerolidol synthesis. Notwithstanding this, nerolidol production was improved twofold to a titre of ˜ 900 mg l-1 in flask cultivation using a combination of heterologous acetyl-CoA pathways and Mig1p degradation. Conditional Mig1p depletion is presented as a valuable strategy to improve the productivities in the strains engineered with GAL promoters-controlled pathways when growing on glucose.
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Affiliation(s)
- Irfan Farabi Hayat
- Australian Institute for Bioengineering and Nanotechnology (AIBN)the University of QueenslandBrisbaneQld4072Australia
- School of Chemistry and Molecular Biosciences (SCMB)the University of QueenslandBrisbaneQld4072Australia
| | - Manuel Plan
- Australian Institute for Bioengineering and Nanotechnology (AIBN)the University of QueenslandBrisbaneQld4072Australia
| | - Birgitta E. Ebert
- Australian Institute for Bioengineering and Nanotechnology (AIBN)the University of QueenslandBrisbaneQld4072Australia
| | | | - Claudia E. Vickers
- Australian Institute for Bioengineering and Nanotechnology (AIBN)the University of QueenslandBrisbaneQld4072Australia
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organisation (CSIRO)Black MountainCanberraACT2601Australia
- ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneQld4000Australia
| | - Bingyin Peng
- Australian Institute for Bioengineering and Nanotechnology (AIBN)the University of QueenslandBrisbaneQld4072Australia
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organisation (CSIRO)Black MountainCanberraACT2601Australia
- ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneQld4000Australia
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Strategies for enhancing terpenoids accumulation in microalgae. Appl Microbiol Biotechnol 2021; 105:4919-4930. [PMID: 34125275 DOI: 10.1007/s00253-021-11368-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/17/2021] [Accepted: 05/25/2021] [Indexed: 10/21/2022]
Abstract
Terpenoids represent one of the largest class of chemicals in nature, which play important roles in food and pharmaceutical fields due to diverse biological and pharmacological activities. Microorganisms are recognized as a promising source of terpenoids due to its short growth cycle and sustainability. Importantly, microalgae can fix inorganic carbon through photosynthesis for the growth of themselves and the biosynthesis of various terpenoids. Moreover, microalgae possess effective biosynthesis pathways of terpenoids, both the eukaryotic mevalonic acid (MVA) pathway and the prokaryotic methyl-D-erythritol 4-phosphate (MEP) pathway. In recent years, various genetic engineering strategies have been applied to increase target terpenoid yields, including overexpression of the rate-limited enzymes and inhibition of the competing pathways. However, since gene-editing tools are only built in some model microalgae, fermentation strategies that are easier to be operated have been widely successful in promoting the production of terpenoids, such as changing culture conditions and addition of chemical additives. In addition, an economical and effective downstream process is also an important consideration for the industrial production of terpenoids, and the solvent extraction and the supercritical fluid extraction method are the most commonly used strategies, especially in the industrial production of β-carotene and astaxanthin from microalgae. In this review, recent advancements and novel strategies used for terpenoid production are concluded and discussed, and new insights to move the field forward are proposed. KEY POINTS: • The MEP pathway is more stoichiometrically efficient than the MVA pathway. • Advanced genetic engineering and fermentation strategies can increase terpene yield. • SFE has a higher recovery of carotenoids than solvent extraction.
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11
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Rationally optimized generation of integrated Escherichia coli with stable and high yield lycopene biosynthesis from heterologous mevalonate (MVA) and lycopene expression pathways. Synth Syst Biotechnol 2021; 6:85-94. [PMID: 33997358 PMCID: PMC8091476 DOI: 10.1016/j.synbio.2021.04.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/31/2021] [Accepted: 04/07/2021] [Indexed: 11/23/2022] Open
Abstract
The stability and high productivity of heterogeneous terpenoid production in Escherichia coli expression system is one of the most key issues for its large scale industrialization. In the current study on taking lycopene biosynthesis as an example, an integrated Escherichia coli system has been generated successfully, which resulted into stable and high lycopene production. In this process, two modules of mevalonate (MVA) pathway and one module of lycopene expression pathway were completely integrated in the chromosome. Firstly, the copy number and integrated position of three modules of heterologous pathways were rationally optimized. Later, a strain DH416 equipped with heterogeneous expression pathways through chromosomal integration was efficiently derived from parental strain DH411. The evolving DH416 strain efficiently produced the lycopene level of 1.22 g/L (49.9 mg/g DCW) in a 5 L fermenter with mean productivity of 61.0 mg/L/h. Additionally, the integrated strain showed more genetic stability than the plasmid systems after successive 21st passage.
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12
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Ahmed MS, Lauersen KJ, Ikram S, Li C. Efflux Transporters' Engineering and Their Application in Microbial Production of Heterologous Metabolites. ACS Synth Biol 2021; 10:646-669. [PMID: 33751883 DOI: 10.1021/acssynbio.0c00507] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Metabolic engineering of microbial hosts for the production of heterologous metabolites and biochemicals is an enabling technology to generate meaningful quantities of desired products that may be otherwise difficult to produce by traditional means. Heterologous metabolite production can be restricted by the accumulation of toxic products within the cell. Efflux transport proteins (transporters) provide a potential solution to facilitate the export of these products, mitigate toxic effects, and enhance production. Recent investigations using knockout lines, heterologous expression, and expression profiling of transporters have revealed candidates that can enhance the export of heterologous metabolites from microbial cell systems. Transporter engineering efforts have revealed that some exhibit flexible substrate specificity and may have broader application potentials. In this Review, the major superfamilies of efflux transporters, their mechanistic modes of action, selection of appropriate efflux transporters for desired compounds, and potential transporter engineering strategies are described for potential applications in enhancing engineered microbial metabolite production. Future studies in substrate recognition, heterologous expression, and combinatorial engineering of efflux transporters will assist efforts to enhance heterologous metabolite production in microbial hosts.
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Affiliation(s)
- Muhammad Saad Ahmed
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology (BIT), Beijing 100081, P. R. China
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Abid Majeed Road, The Mall, Rawalpindi 46000, Pakistan
| | - Kyle J. Lauersen
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Kingdom of Saudi Arabia
| | - Sana Ikram
- Beijing Higher Institution Engineering Research Center for Food Additives and Ingredients, Beijing Technology & Business University (BTBU), Beijing 100048, P. R. China
| | - Chun Li
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology (BIT), Beijing 100081, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
- Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
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Carsanba E, Pintado M, Oliveira C. Fermentation Strategies for Production of Pharmaceutical Terpenoids in Engineered Yeast. Pharmaceuticals (Basel) 2021; 14:295. [PMID: 33810302 PMCID: PMC8066412 DOI: 10.3390/ph14040295] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 02/08/2023] Open
Abstract
Terpenoids, also known as isoprenoids, are a broad and diverse class of plant natural products with significant industrial and pharmaceutical importance. Many of these natural products have antitumor, anti-inflammatory, antibacterial, antiviral, and antimalarial effects, support transdermal absorption, prevent and treat cardiovascular diseases, and have hypoglycemic activities. Production of these compounds are generally carried out through extraction from their natural sources or chemical synthesis. However, these processes are generally unsustainable, produce low yield, and result in wasting of substantial resources, most of them limited. Microbial production of terpenoids provides a sustainable and environment-friendly alternative. In recent years, the yeast Saccharomyces cerevisiae has become a suitable cell factory for industrial terpenoid biosynthesis due to developments in omics studies (genomics, transcriptomics, metabolomics, proteomics), and mathematical modeling. Besides that, fermentation development has a significant importance on achieving high titer, yield, and productivity (TYP) of these compounds. Up to now, there have been many studies and reviews reporting metabolic strategies for terpene biosynthesis. However, fermentation strategies have not been yet comprehensively discussed in the literature. This review summarizes recent studies of recombinant production of pharmaceutically important terpenoids by engineered yeast, S. cerevisiae, with special focus on fermentation strategies to increase TYP in order to meet industrial demands to feed the pharmaceutical market. Factors affecting recombinant terpenoids production are reviewed (strain design and fermentation parameters) and types of fermentation process (batch, fed-batch, and continuous) are discussed.
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Affiliation(s)
- Erdem Carsanba
- Amyris BioProducts Portugal, Unipessoal, Lda. Rua Diogo Botelho 1327, 4169-005 Porto, Portugal;
- CBQF—Centro de Biotecnologia e Química Fina—Laboratório Associado, Universidade Católica Portuguesa, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal;
| | - Manuela Pintado
- CBQF—Centro de Biotecnologia e Química Fina—Laboratório Associado, Universidade Católica Portuguesa, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal;
| | - Carla Oliveira
- CBQF—Centro de Biotecnologia e Química Fina—Laboratório Associado, Universidade Católica Portuguesa, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal;
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Li ZJ, Wang YZ, Wang LR, Shi TQ, Sun XM, Huang H. Advanced Strategies for the Synthesis of Terpenoids in Yarrowia lipolytica. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:2367-2381. [PMID: 33595318 DOI: 10.1021/acs.jafc.1c00350] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Terpenoids are an important class of secondary metabolites that play an important role in food, agriculture, and other fields. Microorganisms are rapidly emerging as a promising source for the production of terpenoids. As an oleaginous yeast, Yarrowia lipolytica contains a high lipid content which indicates that it must produce high amounts of acetyl-CoA, a necessary precursor for the biosynthesis of terpenoids. Y. lipolytica has a complete eukaryotic mevalonic acid (MVA) pathway but it has not yet seen commercial use due to its low productivity. Several metabolic engineering strategies have been developed to improve the terpenoids production of Y. lipolytica, including developing the orthogonal pathway for terpenoid synthesis, increasing the catalytic efficiency of terpenoids synthases, enhancing the supply of acetyl-CoA and NADPH, expressing rate-limiting genes, and modifying the branched pathway. Moreover, most of the acetyl-CoA is used to produce lipid, so it is an effective strategy to strike a balance of precursor distribution by rewiring the lipid biosynthesis pathway. Lastly, the latest developed non-homologous end-joining strategy for improving terpenoid production is introduced. This review summarizes the status and metabolic engineering strategies of terpenoids biosynthesis in Y. lipolytica and proposes new insights to move the field forward.
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Affiliation(s)
- Zi-Jia Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Yu-Zhou Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Ling-Ru Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Xiao-Man Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, People's Republic of China
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Navale GR, Dharne MS, Shinde SS. Metabolic engineering and synthetic biology for isoprenoid production in Escherichia coli and Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2021; 105:457-475. [PMID: 33394155 DOI: 10.1007/s00253-020-11040-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/23/2020] [Accepted: 12/01/2020] [Indexed: 12/29/2022]
Abstract
Isoprenoids, often called terpenoids, are the most abundant and highly diverse family of natural organic compounds. In plants, they play a distinct role in the form of photosynthetic pigments, hormones, electron carrier, structural components of membrane, and defence. Many isoprenoids have useful applications in the pharmaceutical, nutraceutical, and chemical industries. They are synthesized by various isoprenoid synthase enzymes by several consecutive steps. Recent advancement in metabolic engineering and synthetic biology has enabled the production of these isoprenoids in the heterologous host systems like Escherichia coli and Saccharomyces cerevisiae. Both heterologous systems have been engineered for large-scale production of value-added isoprenoids. This review article will provide the detailed description of various approaches used for engineering of methyl-D-erythritol-4-phosphate (MEP) and mevalonate (MVA) pathway for synthesizing isoprene units (C5) and ultimate production of diverse isoprenoids. The review particularly highlighted the efforts taken for the production of C5-C20 isoprenoids by metabolic engineering techniques in E. coli and S. cerevisiae over a decade. The challenges and strategies are also discussed in detail for scale-up and engineering of isoprenoids in the heterologous host systems.Key points• Isoprenoids are beneficial and valuable natural products.• E. coli and S. cerevisiae are the promising host for isoprenoid biosynthesis.• Emerging techniques in synthetic biology enabled the improved production.• Need to expand the catalogue and scale-up of un-engineered isoprenoids. Metabolic engineering and synthetic biology for isoprenoid production in Escherichia coli and Saccharomyces cerevisiae.
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Affiliation(s)
- Govinda R Navale
- NCIM Resource Centre, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pashan, Pune, 411 008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 001, India
| | - Mahesh S Dharne
- NCIM Resource Centre, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pashan, Pune, 411 008, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 001, India.
| | - Sandip S Shinde
- NCIM Resource Centre, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pashan, Pune, 411 008, India. .,Department Industrial and Chemical Engineering, Institute of Chemical Technology Mumbai Marathwada Campus, Jalna, 431213, India.
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16
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Combinatorial engineering for improved menaquinone-4 biosynthesis in Bacillus subtilis. Enzyme Microb Technol 2020; 141:109652. [DOI: 10.1016/j.enzmictec.2020.109652] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/11/2020] [Accepted: 08/20/2020] [Indexed: 11/21/2022]
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Chen X, Zhang C, Lindley ND. Metabolic Engineering Strategies for Sustainable Terpenoid Flavor and Fragrance Synthesis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:10252-10264. [PMID: 31865696 DOI: 10.1021/acs.jafc.9b06203] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Terpenoids derived from plant material are widely applied in the flavor and fragrance industry. Traditional extraction methods are unsustainable, but microbial synthesis offers a promising solution to attain efficient production of natural-identical terpenoids. Overproduction of terpenoids in microbes requires careful balancing of the synthesis pathway constituents within the constraints of host cell metabolism. Advances in metabolic engineering have greatly facilitated overcoming the challenges of achieving high titers, rates, and yields (TRYs). The review summarizes recent development in the molecular biology toolbox to achieve high TRYs for terpenoid biosynthesis, mainly in the two industrial platform microorganisms: Escherichia coli and Saccharomyces cerevisiae. The biosynthetic pathways, including alternative pathway designs, are briefly introduced, followed by recently developed methodologies used for pathway, genome, and strain optimization. Integrated applications of these tools are important to achieve high "TRYs" of terpenoid production and pave the way for translating laboratory research into successful commercial manufacturing.
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Affiliation(s)
- Xixian Chen
- Biotransformation Innovation Platform, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore 138673
| | - Congqiang Zhang
- Biotransformation Innovation Platform, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore 138673
| | - Nicholas D Lindley
- Biotransformation Innovation Platform, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore 138673
- TBI, Université de Toulouse, CNRS, INRA, INSA,31077 Toulouse, France
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Röhl A, Riou T, Bockmayr A. Computing irreversible minimal cut sets in genome-scale metabolic networks via flux cone projection. Bioinformatics 2020; 35:2618-2625. [PMID: 30590390 DOI: 10.1093/bioinformatics/bty1027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 12/06/2018] [Accepted: 12/14/2018] [Indexed: 12/19/2022] Open
Abstract
MOTIVATION Minimal cut sets (MCSs) for metabolic networks are sets of reactions which, if they are removed from the network, prevent a target reaction from carrying flux. To compute MCSs different methods exist, which may fail to find sufficiently many MCSs for larger genome-scale networks. RESULTS Here we introduce irreversible minimal cut sets (iMCSs). These are MCSs that consist of irreversible reactions only. The advantage of iMCSs is that they can be computed by projecting the flux cone of the metabolic network on the set of irreversible reactions, which usually leads to a smaller cone. Using oriented matroid theory, we show how the projected cone can be computed efficiently and how this can be applied to find iMCSs even in large genome-scale networks. AVAILABILITY AND IMPLEMENTATION Software is freely available at https://sourceforge.net/projects/irreversibleminimalcutsets/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Annika Röhl
- Department of Mathematics and Computer Science, FB Mathematik und Informatik, Freie Universität Berlin, Berlin, Germany
| | - Tanguy Riou
- Department FRANCE, Ecole Centrale de Nantes, Nantes, France
| | - Alexander Bockmayr
- Department of Mathematics and Computer Science, FB Mathematik und Informatik, Freie Universität Berlin, Berlin, Germany
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Ward VCA, Chatzivasileiou AO, Stephanopoulos G. Metabolic engineering of Escherichia coli for the production of isoprenoids. FEMS Microbiol Lett 2019; 365:4953741. [PMID: 29718190 DOI: 10.1093/femsle/fny079] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 03/25/2018] [Indexed: 12/22/2022] Open
Abstract
Metabolic engineering is the practice of using directed genetic manipulations to rewire cellular metabolism primarily with the aim to transform the organism into a single-celled chemical factory. Using biological processes, we can produce more complex chemicals in a more sustainable way. This is particularly important for chemicals which are hard to synthesize using traditional chemistry. However, cells have evolved for growth and must be engineered to produce a single chemical at commercially viable levels. This review focuses on the strategies used to rewire cellular metabolism to produce chemicals using isoprenoid production in Escherichia coli as an example that illustrates many of the challenges faced in metabolic engineering.
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Affiliation(s)
- Valerie C A Ward
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Chemical Engineering, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada
| | | | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Li L, Wang X, Li X, Shi H, Wang F, Zhang Y, Li X. Combinatorial Engineering of Mevalonate Pathway and Diterpenoid Synthases in Escherichia coli for cis-Abienol Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:6523-6531. [PMID: 31117507 DOI: 10.1021/acs.jafc.9b02156] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Identification of diterpene synthase-encoding genes together with synthetic biology technology offers an opportunity for the biosynthesis of cis-abienol. The methylerythritol phosphate (MEP) and the mevalonate (MVA) pathways were both engineered for cis-abienol production in Escherichia coli, which improved the cis-abienol yield by approximately 7-fold and 31-fold, respectively, compared to the yield obtained by overexpression of the MEP pathway alone or the original MEP pathway. Furthermore, systematic optimization of cis-abienol biosynthesis was performed, such as diterpene synthase screening and two-phase cultivation. The combination of bifunctional class I/II cis-abienol synthase from Abies balsamea ( AbCAS) and class II abienol synthase from Salvia sclarea ( SsTPS2) was found to be the most effective. By using isopropyl myristate as a solvent in two-phase cultivation, cis-abienol production reached 634.7 mg/L in a fed-batch bioreactor. This work shows the possibility of E. coli utilizing glucose as a carbon source for cis-abienol biosynthesis through a modified pathway.
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Affiliation(s)
- Lei 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
| | - 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
| | - Xinyang 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
| | - Hao Shi
- Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration , Huaiyin Institute of Technology , Huaian 223003 , 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
| | - 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
| | - 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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Moser S, Pichler H. Identifying and engineering the ideal microbial terpenoid production host. Appl Microbiol Biotechnol 2019; 103:5501-5516. [PMID: 31129740 PMCID: PMC6597603 DOI: 10.1007/s00253-019-09892-y] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/03/2019] [Accepted: 05/06/2019] [Indexed: 12/11/2022]
Abstract
More than 70,000 different terpenoid structures are known so far; many of them offer highly interesting applications as pharmaceuticals, flavors and fragrances, or biofuels. Extraction of these compounds from their natural sources or chemical synthesis is—in many cases—technically challenging with low or moderate yields while wasting valuable resources. Microbial production of terpenoids offers a sustainable and environment-friendly alternative starting from simple carbon sources and, frequently, safeguards high product specificity. Here, we provide an overview on employing recombinant bacteria and yeasts for heterologous de novo production of terpenoids. Currently, Escherichia coli and Saccharomyces cerevisiae are the two best-established production hosts for terpenoids. An increasing number of studies have been successful in engineering alternative microorganisms for terpenoid biosynthesis, which we intend to highlight in this review. Moreover, we discuss the specific engineering challenges as well as recent advances for microbial production of different classes of terpenoids. Rationalizing the current stages of development for different terpenoid production hosts as well as future prospects shall provide a valuable decision basis for the selection and engineering of the cell factory(ies) for industrial production of terpenoid target molecules.
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Affiliation(s)
- Sandra Moser
- Austrian Centre of Industrial Biotechnology (acib GmbH), Petersgasse 14, 8010, Graz, Austria
- Institute of Molecular Biotechnology, NAWI Graz, BioTechMed Graz, Graz University of Technology, Petersgasse 14/2, 8010, Graz, Austria
| | - Harald Pichler
- Austrian Centre of Industrial Biotechnology (acib GmbH), Petersgasse 14, 8010, Graz, Austria.
- Institute of Molecular Biotechnology, NAWI Graz, BioTechMed Graz, Graz University of Technology, Petersgasse 14/2, 8010, Graz, Austria.
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Lund S, Hall R, Williams GJ. An Artificial Pathway for Isoprenoid Biosynthesis Decoupled from Native Hemiterpene Metabolism. ACS Synth Biol 2019; 8:232-238. [PMID: 30648856 DOI: 10.1021/acssynbio.8b00383] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Isoprenoids are constructed in nature using hemiterpene building blocks that are biosynthesized from lengthy enzymatic pathways with little opportunity to deploy precursor-directed biosynthesis. Here, an artificial alcohol-dependent hemiterpene biosynthetic pathway was designed and coupled to several isoprenoid biosynthetic systems, affording lycopene and a prenylated tryptophan in robust yields. This approach affords a potential route to diverse non-natural hemiterpenes and by extension isoprenoids modified with non-natural chemical functionality. Accordingly, the prototype chemo-enzymatic pathway is a critical first step toward the construction of engineered microbial strains for bioconversion of simple scalable building blocks into complex isoprenoid scaffolds.
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23
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Lauersen KJ. Eukaryotic microalgae as hosts for light-driven heterologous isoprenoid production. PLANTA 2019; 249:155-180. [PMID: 30467629 DOI: 10.1007/s00425-018-3048-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 11/14/2018] [Indexed: 05/21/2023]
Abstract
Eukaryotic microalgae hold incredible metabolic potential for the sustainable production of heterologous isoprenoid products. Recent advances in algal engineering have enabled the demonstration of prominent examples of heterologous isoprenoid production. Isoprenoids, also known as terpenes or terpenoids, are the largest class of natural chemicals, with a vast diversity of structures and biological roles. Some have high-value in human-use applications, although may be found in their native contexts in low abundance or be difficult to extract and purify. Heterologous production of isoprenoid compounds in heterotrophic microbial hosts such as bacteria or yeasts has been an active area of research for some time and is now a mature technology. Eukaryotic microalgae represent sustainable alternatives to these hosts for biotechnological production processes as their cultivation can be driven by light and freely available CO2 as a carbon source. Their photosynthetic lifestyles require metabolic architectures structured towards the generation of associated isoprenoids (carotenoids, phytol) which participate in photon capture, energy dissipation, and electron transfer. Eukaryotic microalgae should, therefore, contain inherently high capacities for the generation of heterologous isoprenoid products. Although engineering strategies in eukaryotic microalgae have lagged behind the more genetically tractable bacteria and yeasts, recent advances in algal engineering concepts have demonstrated prominent examples of light-driven heterologous isoprenoid production from these photosynthetic hosts. This work seeks to provide practical insights into the choice of eukaryotic microalgae as biotechnological chassis. Recent reports of advances in algal engineering for heterologous isoprenoid production are highlighted as encouraging examples that promote their expanded use as sustainable green-cell factories. Current state of the art, limitations, and future challenges are also discussed.
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Affiliation(s)
- Kyle J Lauersen
- Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615, Bielefeld, Germany.
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24
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Liu Y, Jiang X, Cui Z, Wang Z, Qi Q, Hou J. Engineering the oleaginous yeast Yarrowia lipolytica for production of α-farnesene. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:296. [PMID: 31890024 PMCID: PMC6927232 DOI: 10.1186/s13068-019-1636-z] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 12/12/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Yarrowia lipolytica, a non-traditional oil yeast, has been widely used as a platform for lipid production. However, the production of other chemicals such as terpenoids in engineered Y. lipolytica is still low. α-Farnesene, a sesquiterpene, can be used in medicine, bioenergy and other fields, and has very high economic value. Here, we used α-farnesene as an example to explore the potential of Y. lipolytica for terpenoid production. RESULTS We constructed libraries of strains overexpressing mevalonate pathway and α-farnesene synthase genes by non-homologous end-joining (NHEJ) mediated integration into the Y. lipolytica chromosome. First, a mevalonate overproduction strain was selected by overexpressing relevant genes and changing the cofactor specificity. Based on this strain, the downstream α-farnesene synthesis pathway was overexpressed by iterative integration. Culture conditions were also optimized. A strain that produced 25.55 g/L α-farnesene was obtained. This is the highest terpenoid titer reported in Y. lipolytica. CONCLUSIONS Yarrowia lipolytica is a potentially valuable species for terpenoid production, and NHEJ-mediated modular integration is effective for expression library construction and screening of high-producer strains.
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Affiliation(s)
- Yinghang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237 People’s Republic of China
| | - Xin Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237 People’s Republic of China
| | - Zhiyong Cui
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237 People’s Republic of China
| | - Zhaoxuan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237 People’s Republic of China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237 People’s Republic of China
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237 People’s Republic of China
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Wang T, Guo J, Liu Y, Xue Z, Zhang C, Xing XH. Genome-wide screening identifies promiscuous phosphatases impairing terpenoid biosynthesis in Escherichia coli. Appl Microbiol Biotechnol 2018; 102:9771-9780. [DOI: 10.1007/s00253-018-9330-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/06/2018] [Accepted: 08/12/2018] [Indexed: 01/11/2023]
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26
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de Melo Pereira GV, de Carvalho Neto DP, Magalhães Júnior AI, Vásquez ZS, Medeiros ABP, Vandenberghe LPS, Soccol CR. Exploring the impacts of postharvest processing on the aroma formation of coffee beans - A review. Food Chem 2018; 272:441-452. [PMID: 30309567 DOI: 10.1016/j.foodchem.2018.08.061] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 08/15/2018] [Accepted: 08/16/2018] [Indexed: 12/15/2022]
Abstract
The aim of this review is to describe the volatile aroma compounds of green coffee beans and evaluate sources of variation in the formation and development of coffee aroma through postharvest processing. The findings of this survey showed that the volatile constituents of green coffee beans (e.g., alcohols, aldehydes, and alkanes) have no significant influence on the final coffee aroma composition, as only a few such compounds remain in the beans after roasting. On the other hand, microbial-derived, odor-active compounds produced during removal of the fruit mucilage layer, including esters, higher alcohols, aldehydes, and ketones, can be detected in the final coffee product. Many postharvest processing including drying and storage processes could influence the levels of coffee aroma compositions, which remain to be elucidated. Better understanding of the effect of these processes on coffee aroma composition would assist coffee producers in the optimal selection of postharvest parameters that favor the consistent production of flavorful coffee beans.
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Affiliation(s)
- Gilberto V de Melo Pereira
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná (UFPR), 19011 Curitiba, Paraná 81531-980, Brazil
| | - Dão P de Carvalho Neto
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná (UFPR), 19011 Curitiba, Paraná 81531-980, Brazil
| | - Antonio I Magalhães Júnior
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná (UFPR), 19011 Curitiba, Paraná 81531-980, Brazil
| | - Zulma S Vásquez
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná (UFPR), 19011 Curitiba, Paraná 81531-980, Brazil
| | - Adriane B P Medeiros
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná (UFPR), 19011 Curitiba, Paraná 81531-980, Brazil
| | - Luciana P S Vandenberghe
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná (UFPR), 19011 Curitiba, Paraná 81531-980, Brazil
| | - Carlos R Soccol
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná (UFPR), 19011 Curitiba, Paraná 81531-980, Brazil.
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Englund E, Shabestary K, Hudson EP, Lindberg P. Systematic overexpression study to find target enzymes enhancing production of terpenes in Synechocystis PCC 6803, using isoprene as a model compound. Metab Eng 2018; 49:164-177. [PMID: 30025762 DOI: 10.1016/j.ymben.2018.07.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 06/28/2018] [Accepted: 07/08/2018] [Indexed: 11/25/2022]
Abstract
Of the two natural metabolic pathways for making terpenoids, biotechnological utilization of the mevalonate (MVA) pathway has enabled commercial production of valuable compounds, while the more recently discovered but stoichiometrically more efficient methylerythritol phosphate (MEP) pathway is underdeveloped. We conducted a study on the overexpression of each enzyme in the MEP pathway in the unicellular cyanobacterium Synechocystis sp. PCC 6803, to identify potential targets for increasing flux towards terpenoid production, using isoprene as a reporter molecule. Results showed that the enzymes Ipi, Dxs and IspD had the biggest impact on isoprene production. By combining and creating operons out of those genes, isoprene production was increased 2-fold compared to the base strain. A genome-scale model was used to identify targets upstream of the MEP pathway that could redirect flux towards terpenoids. A total of ten reactions from the Calvin-Benson-Bassham cycle, lower glycolysis and co-factor synthesis pathways were probed for their effect on isoprene synthesis by co-expressing them with the MEP enzymes, resulting in a 60% increase in production from the best strain. Lastly, we studied two isoprene synthases with the highest reported catalytic rates. Only by expressing them together with Dxs and Ipi could we get stable strains that produced 2.8 mg/g isoprene per dry cell weight, a 40-fold improvement compared to the initial strain.
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Affiliation(s)
- Elias Englund
- Department of Chemistry - Ångström, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden; School of Biotechnology, KTH - Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Kiyan Shabestary
- School of Biotechnology, KTH - Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Elton P Hudson
- School of Biotechnology, KTH - Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Pia Lindberg
- Department of Chemistry - Ångström, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden.
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28
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Carvalho Â, Hansen EH, Kayser O, Carlsen S, Stehle F. Designing microorganisms for heterologous biosynthesis of cannabinoids. FEMS Yeast Res 2018; 17:3861260. [PMID: 28582498 PMCID: PMC5812543 DOI: 10.1093/femsyr/fox037] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 06/02/2017] [Indexed: 11/14/2022] Open
Abstract
During the last decade, the use of medical Cannabis has expanded globally and legislation is getting more liberal in many countries, facilitating the research on cannabinoids. The unique interaction of cannabinoids with the human endocannabinoid system makes these compounds an interesting target to be studied as therapeutic agents for the treatment of several medical conditions. However, currently there are important limitations in the study, production and use of cannabinoids as pharmaceutical drugs. Besides the main constituent tetrahydrocannabinolic acid, the structurally related compound cannabidiol is of high interest as drug candidate. From the more than 100 known cannabinoids reported, most can only be extracted in very low amounts and their pharmacological profile has not been determined. Today, cannabinoids are isolated from the strictly regulated Cannabis plant, and the supply of compounds with sufficient quality is a major problem. Biotechnological production could be an attractive alternative mode of production. Herein, we explore the potential use of synthetic biology as an alternative strategy for synthesis of cannabinoids in heterologous hosts. We summarize the current knowledge surrounding cannabinoids biosynthesis and present a comprehensive description of the key steps of the genuine and artificial pathway, systems biotechnology needs and platform optimization.
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Affiliation(s)
- Ângela Carvalho
- Evolva Biotech A/S, Lersø Parkallé 42-44, 2100, Copenhagen, Denmark
| | | | - Oliver Kayser
- Laboratory of Technical Biochemistry, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 66, 44227 Dortmund, Germany
| | - Simon Carlsen
- Evolva Biotech A/S, Lersø Parkallé 42-44, 2100, Copenhagen, Denmark
| | - Felix Stehle
- Laboratory of Technical Biochemistry, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 66, 44227 Dortmund, Germany
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29
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Patchoulol Production with Metabolically Engineered Corynebacterium glutamicum. Genes (Basel) 2018; 9:genes9040219. [PMID: 29673223 PMCID: PMC5924561 DOI: 10.3390/genes9040219] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 04/10/2018] [Accepted: 04/16/2018] [Indexed: 12/25/2022] Open
Abstract
Patchoulol is a sesquiterpene alcohol and an important natural product for the perfume industry. Corynebacterium glutamicum is the prominent host for the fermentative production of amino acids with an average annual production volume of ~6 million tons. Due to its robustness and well established large-scale fermentation, C. glutamicum has been engineered for the production of a number of value-added compounds including terpenoids. Both C40 and C50 carotenoids, including the industrially relevant astaxanthin, and short-chain terpenes such as the sesquiterpene valencene can be produced with this organism. In this study, systematic metabolic engineering enabled construction of a patchoulol producing C. glutamicum strain by applying the following strategies: (i) construction of a farnesyl pyrophosphate-producing platform strain by combining genomic deletions with heterologous expression of ispA from Escherichia coli; (ii) prevention of carotenoid-like byproduct formation; (iii) overproduction of limiting enzymes from the 2-c-methyl-d-erythritol 4-phosphate (MEP)-pathway to increase precursor supply; and (iv) heterologous expression of the plant patchoulol synthase gene PcPS from Pogostemon cablin. Additionally, a proof of principle liter-scale fermentation with a two-phase organic overlay-culture medium system for terpenoid capture was performed. To the best of our knowledge, the patchoulol titers demonstrated here are the highest reported to date with up to 60 mg L−1 and volumetric productivities of up to 18 mg L−1 d−1.
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Schempp FM, Drummond L, Buchhaupt M, Schrader J. Microbial Cell Factories for the Production of Terpenoid Flavor and Fragrance Compounds. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:2247-2258. [PMID: 28418659 DOI: 10.1021/acs.jafc.7b00473] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Terpenoid flavor and fragrance compounds are of high interest to the aroma industry. Microbial production offers an alternative sustainable access to the desired terpenoids independent of natural sources. Genetically engineered microorganisms can be used to synthesize terpenoids from cheap and renewable resources. Due to its modular architecture, terpenoid biosynthesis is especially well suited for the microbial cell factory concept: a platform host engineered for a high flux toward the central C5 prenyl diphosphate precursors enables the production of a broad range of target terpenoids just by varying the pathway modules converting the C5 intermediates to the product of interest. In this review typical terpenoid flavor and fragrance compounds marketed or under development by biotech and aroma companies are given, and the specificities of the aroma market are discussed. The main part of this work focuses on key strategies and recent advances to engineer microbes to become efficient terpenoid producers.
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Affiliation(s)
- Florence M Schempp
- DECHEMA-Forschungsinstitut, Industrial Biotechnology , Theodor-Heuss-Allee 25 , 60486 Frankfurt am Main , Germany
| | - Laura Drummond
- DECHEMA-Forschungsinstitut, Industrial Biotechnology , Theodor-Heuss-Allee 25 , 60486 Frankfurt am Main , Germany
| | - Markus Buchhaupt
- DECHEMA-Forschungsinstitut, Industrial Biotechnology , Theodor-Heuss-Allee 25 , 60486 Frankfurt am Main , Germany
| | - Jens Schrader
- DECHEMA-Forschungsinstitut, Industrial Biotechnology , Theodor-Heuss-Allee 25 , 60486 Frankfurt am Main , Germany
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31
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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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32
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Identification of Enzymes Involved in Sesterterpene Biosynthesis in Marine Fungi. Methods Enzymol 2018; 604:441-498. [DOI: 10.1016/bs.mie.2018.04.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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33
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Biosynthesis and production of sabinene: current state and perspectives. Appl Microbiol Biotechnol 2017; 102:1535-1544. [DOI: 10.1007/s00253-017-8695-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/03/2017] [Accepted: 12/04/2017] [Indexed: 01/10/2023]
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34
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Schwarzhans JP, Luttermann T, Geier M, Kalinowski J, Friehs K. Towards systems metabolic engineering in Pichia pastoris. Biotechnol Adv 2017; 35:681-710. [DOI: 10.1016/j.biotechadv.2017.07.009] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/20/2017] [Accepted: 07/24/2017] [Indexed: 12/30/2022]
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35
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Use of CellNetAnalyzer in biotechnology and metabolic engineering. J Biotechnol 2017; 261:221-228. [DOI: 10.1016/j.jbiotec.2017.05.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 04/28/2017] [Accepted: 05/03/2017] [Indexed: 01/28/2023]
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36
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Czarnotta E, Dianat M, Korf M, Granica F, Merz J, Maury J, Baallal Jacobsen SA, Förster J, Ebert BE, Blank LM. Fermentation and purification strategies for the production of betulinic acid and its lupane-type precursors in Saccharomyces cerevisiae. Biotechnol Bioeng 2017; 114:2528-2538. [DOI: 10.1002/bit.26377] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/02/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Eik Czarnotta
- iAMB-Institute of Applied Microbiology; ABBt-Aachen Biology and Biotechnology; RWTH Aachen University; Aachen Germany
| | - Mariam Dianat
- iAMB-Institute of Applied Microbiology; ABBt-Aachen Biology and Biotechnology; RWTH Aachen University; Aachen Germany
| | - Marcel Korf
- APT-Laboratory of Plant and Process Design; Department of Biochemical and Chemical Engineering; TU Dortmund University; Dortmund Germany
| | - Fabian Granica
- APT-Laboratory of Plant and Process Design; Department of Biochemical and Chemical Engineering; TU Dortmund University; Dortmund Germany
| | - Juliane Merz
- APT-Laboratory of Plant and Process Design; Department of Biochemical and Chemical Engineering; TU Dortmund University; Dortmund Germany
| | - Jérôme Maury
- Technical University of Denmark; Novo Nordisk Foundation Center for Biosustainability; Kgs. Lyngby Denmark
| | - Simo A. Baallal Jacobsen
- Technical University of Denmark; Novo Nordisk Foundation Center for Biosustainability; Kgs. Lyngby Denmark
| | - Jochen Förster
- Technical University of Denmark; Novo Nordisk Foundation Center for Biosustainability; Kgs. Lyngby Denmark
| | - Birgitta E. Ebert
- iAMB-Institute of Applied Microbiology; ABBt-Aachen Biology and Biotechnology; RWTH Aachen University; Aachen Germany
| | - Lars M. Blank
- iAMB-Institute of Applied Microbiology; ABBt-Aachen Biology and Biotechnology; RWTH Aachen University; Aachen Germany
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37
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Lopes H, Rocha I. Genome-scale modeling of yeast: chronology, applications and critical perspectives. FEMS Yeast Res 2017; 17:3950252. [PMID: 28899034 PMCID: PMC5812505 DOI: 10.1093/femsyr/fox050] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/07/2017] [Indexed: 01/21/2023] Open
Abstract
Over the last 15 years, several genome-scale metabolic models (GSMMs) were developed for different yeast species, aiding both the elucidation of new biological processes and the shift toward a bio-based economy, through the design of in silico inspired cell factories. Here, an historical perspective of the GSMMs built over time for several yeast species is presented and the main inheritance patterns among the metabolic reconstructions are highlighted. We additionally provide a critical perspective on the overall genome-scale modeling procedure, underlining incomplete model validation and evaluation approaches and the quest for the integration of regulatory and kinetic information into yeast GSMMs. A summary of experimentally validated model-based metabolic engineering applications of yeast species is further emphasized, while the main challenges and future perspectives for the field are finally addressed.
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Affiliation(s)
- Helder Lopes
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Isabel Rocha
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
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38
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Simultaneous determination of intracellular nucleotides and coenzymes in Yarrowia lipolytica producing lipid and lycopene by capillary zone electrophoresis. J Chromatogr A 2017; 1514:120-126. [PMID: 28760603 DOI: 10.1016/j.chroma.2017.07.074] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 07/15/2017] [Accepted: 07/23/2017] [Indexed: 11/21/2022]
Abstract
Yarrowia lipolytica is an oleaginous yeast with promise in producing terpenoids such as lycopene. Though methods for analyzing primary metabolic intermediates have been established, further work is needed to better analyze nucleotides and coenzymes. Here, we presented an optimized method for the separation of nucleotides and coenzymes in Y. lipolytica using the capillary electrophoresis. The separation of twelve metabolites including four coenzymes, five nucleotides and three nucleosides was achieved within 32min using a voltage of 15kV and 70mM sodium carbonate/hydrogencarbonate buffer with 1.0% β-CD at pH 10. The results show that the concentrations of adenosine triphosphate and nicotinamide adenine dinucleotide phosphate changed significantly between lycopene producing strain and the control, indicating that these two metabolites may be closely related with lycopene production. The optimized method provides a useful approach for future metabolic analysis of fermentation process as well as industrial strain improvement.
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39
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Jozwiak A, Lipko A, Kania M, Danikiewicz W, Surmacz L, Witek A, Wojcik J, Zdanowski K, Pączkowski C, Chojnacki T, Poznanski J, Swiezewska E. Modeling of Dolichol Mass Spectra Isotopic Envelopes as a Tool to Monitor Isoprenoid Biosynthesis. PLANT PHYSIOLOGY 2017; 174:857-874. [PMID: 28385729 PMCID: PMC5462023 DOI: 10.1104/pp.17.00036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/05/2017] [Indexed: 05/27/2023]
Abstract
The cooperation of the mevalonate (MVA) and methylerythritol phosphate (MEP) pathways, operating in parallel in plants to generate isoprenoid precursors, has been studied extensively. Elucidation of the isoprenoid metabolic pathways is indispensable for the rational design of plant and microbial systems for the production of industrially valuable terpenoids. Here, we describe a new method, based on numerical modeling of mass spectra of metabolically labeled dolichols (Dols), designed to quantitatively follow the cooperation of MVA and MEP reprogrammed upon osmotic stress (sorbitol treatment) in Arabidopsis (Arabidopsis thaliana). The contribution of the MEP pathway increased significantly (reaching 100%) exclusively for the dominating Dols, while for long-chain Dols, the relative input of the MEP and MVA pathways remained unchanged, suggesting divergent sites of synthesis for dominating and long-chain Dols. The analysis of numerically modeled Dol mass spectra is a novel method to follow modulation of the concomitant activity of isoprenoid-generating pathways in plant cells; additionally, it suggests an exchange of isoprenoid intermediates between plastids and peroxisomes.
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Affiliation(s)
- Adam Jozwiak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.J., A.L., L.S., A.W., J.W., K.Z., T.C., J.P., E.S.)
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland (M.K., W.D.)
- Institute of Chemistry, University of Natural Sciences and Humanities, 08-110 Siedlce, Poland (K.Z.); and
- Department of Plant Biochemistry, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland (C.P.)
| | - Agata Lipko
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.J., A.L., L.S., A.W., J.W., K.Z., T.C., J.P., E.S.)
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland (M.K., W.D.)
- Institute of Chemistry, University of Natural Sciences and Humanities, 08-110 Siedlce, Poland (K.Z.); and
- Department of Plant Biochemistry, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland (C.P.)
| | - Magdalena Kania
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.J., A.L., L.S., A.W., J.W., K.Z., T.C., J.P., E.S.)
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland (M.K., W.D.)
- Institute of Chemistry, University of Natural Sciences and Humanities, 08-110 Siedlce, Poland (K.Z.); and
- Department of Plant Biochemistry, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland (C.P.)
| | - Witold Danikiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.J., A.L., L.S., A.W., J.W., K.Z., T.C., J.P., E.S.)
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland (M.K., W.D.)
- Institute of Chemistry, University of Natural Sciences and Humanities, 08-110 Siedlce, Poland (K.Z.); and
- Department of Plant Biochemistry, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland (C.P.)
| | - Liliana Surmacz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.J., A.L., L.S., A.W., J.W., K.Z., T.C., J.P., E.S.)
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland (M.K., W.D.)
- Institute of Chemistry, University of Natural Sciences and Humanities, 08-110 Siedlce, Poland (K.Z.); and
- Department of Plant Biochemistry, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland (C.P.)
| | - Agnieszka Witek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.J., A.L., L.S., A.W., J.W., K.Z., T.C., J.P., E.S.)
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland (M.K., W.D.)
- Institute of Chemistry, University of Natural Sciences and Humanities, 08-110 Siedlce, Poland (K.Z.); and
- Department of Plant Biochemistry, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland (C.P.)
| | - Jacek Wojcik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.J., A.L., L.S., A.W., J.W., K.Z., T.C., J.P., E.S.)
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland (M.K., W.D.)
- Institute of Chemistry, University of Natural Sciences and Humanities, 08-110 Siedlce, Poland (K.Z.); and
- Department of Plant Biochemistry, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland (C.P.)
| | - Konrad Zdanowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.J., A.L., L.S., A.W., J.W., K.Z., T.C., J.P., E.S.)
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland (M.K., W.D.)
- Institute of Chemistry, University of Natural Sciences and Humanities, 08-110 Siedlce, Poland (K.Z.); and
- Department of Plant Biochemistry, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland (C.P.)
| | - Cezary Pączkowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.J., A.L., L.S., A.W., J.W., K.Z., T.C., J.P., E.S.)
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland (M.K., W.D.)
- Institute of Chemistry, University of Natural Sciences and Humanities, 08-110 Siedlce, Poland (K.Z.); and
- Department of Plant Biochemistry, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland (C.P.)
| | - Tadeusz Chojnacki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.J., A.L., L.S., A.W., J.W., K.Z., T.C., J.P., E.S.)
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland (M.K., W.D.)
- Institute of Chemistry, University of Natural Sciences and Humanities, 08-110 Siedlce, Poland (K.Z.); and
- Department of Plant Biochemistry, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland (C.P.)
| | - Jaroslaw Poznanski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.J., A.L., L.S., A.W., J.W., K.Z., T.C., J.P., E.S.);
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland (M.K., W.D.);
- Institute of Chemistry, University of Natural Sciences and Humanities, 08-110 Siedlce, Poland (K.Z.); and
- Department of Plant Biochemistry, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland (C.P.)
| | - Ewa Swiezewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.J., A.L., L.S., A.W., J.W., K.Z., T.C., J.P., E.S.);
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland (M.K., W.D.);
- Institute of Chemistry, University of Natural Sciences and Humanities, 08-110 Siedlce, Poland (K.Z.); and
- Department of Plant Biochemistry, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland (C.P.)
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40
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Metabolomic changes and metabolic responses to expression of heterologous biosynthetic genes for lycopene production in Yarrowia lipolytica. J Biotechnol 2017; 251:174-185. [DOI: 10.1016/j.jbiotec.2017.04.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 03/27/2017] [Accepted: 04/16/2017] [Indexed: 11/19/2022]
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41
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Ghosh IN, Landick R. OptSSeq: High-Throughput Sequencing Readout of Growth Enrichment Defines Optimal Gene Expression Elements for Homoethanologenesis. ACS Synth Biol 2016; 5:1519-1534. [PMID: 27404024 DOI: 10.1021/acssynbio.6b00121] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The optimization of synthetic pathways is a central challenge in metabolic engineering. OptSSeq (Optimization by Selection and Sequencing) is one approach to this challenge. OptSSeq couples selection of optimal enzyme expression levels linked to cell growth rate with high-throughput sequencing to track enrichment of gene expression elements (promoters and ribosome-binding sites) from a combinatorial library. OptSSeq yields information on both optimal and suboptimal enzyme levels, and helps identify constraints that limit maximal product formation. Here we report a proof-of-concept implementation of OptSSeq using homoethanologenesis, a two-step pathway consisting of pyruvate decarboxylase (Pdc) and alcohol dehydrogenase (Adh) that converts pyruvate to ethanol and is naturally optimized in the bacterium Zymomonas mobilis. We used OptSSeq to determine optimal gene expression elements and enzyme levels for Z. mobilis Pdc, AdhA, and AdhB expressed in Escherichia coli. By varying both expression signals and gene order, we identified an optimal solution using only Pdc and AdhB. We resolved current uncertainty about the functions of the Fe2+-dependent AdhB and Zn2+-dependent AdhA by showing that AdhB is preferred over AdhA for rapid growth in both E. coli and Z. mobilis. Finally, by comparing predictions of growth-linked metabolic flux to enzyme synthesis costs, we established that optimal E. coli homoethanologenesis was achieved by our best pdc-adhB expression cassette and that the remaining constraints lie in the E. coli metabolic network or inefficient Pdc or AdhB function in E. coli. OptSSeq is a general tool for synthetic biology to tune enzyme levels in any pathway whose optimal function can be linked to cell growth or survival.
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Affiliation(s)
- Indro Neil Ghosh
- DOE
Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin 53726, United States
| | - Robert Landick
- DOE
Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin 53726, United States
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Kirby J, Dietzel KL, Wichmann G, Chan R, Antipov E, Moss N, Baidoo EEK, Jackson P, Gaucher SP, Gottlieb S, LaBarge J, Mahatdejkul T, Hawkins KM, Muley S, Newman JD, Liu P, Keasling JD, Zhao L. Engineering a functional 1-deoxy-D-xylulose 5-phosphate (DXP) pathway in Saccharomyces cerevisiae. Metab Eng 2016; 38:494-503. [PMID: 27989805 DOI: 10.1016/j.ymben.2016.10.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/19/2016] [Accepted: 10/25/2016] [Indexed: 01/28/2023]
Abstract
Isoprenoids are used in many commercial applications and much work has gone into engineering microbial hosts for their production. Isoprenoids are produced either from acetyl-CoA via the mevalonate pathway or from pyruvate and glyceraldehyde 3-phosphate via the 1-deoxy-D-xylulose 5-phosphate (DXP) pathway. Saccharomyces cerevisiae exclusively utilizes the mevalonate pathway to synthesize native isoprenoids and in fact the alternative DXP pathway has never been found or successfully reconstructed in the eukaryotic cytosol. There are, however, several advantages to isoprenoid synthesis via the DXP pathway, such as a higher theoretical yield, and it has long been a goal to transplant the pathway into yeast. In this work, we investigate and address barriers to DXP pathway functionality in S. cerevisiae using a combination of synthetic biology, biochemistry and metabolomics. We report, for the first time, functional expression of the DXP pathway in S. cerevisiae. Under low aeration conditions, an engineered strain relying solely on the DXP pathway for isoprenoid biosynthesis achieved an endpoint biomass 80% of that of the same strain using the mevalonate pathway.
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Affiliation(s)
- James Kirby
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA 94702, USA; Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | - Kevin L Dietzel
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Gale Wichmann
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Rossana Chan
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA 94702, USA; Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | - Eugene Antipov
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Nathan Moss
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | | | - Peter Jackson
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Sara P Gaucher
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Shayin Gottlieb
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Jeremy LaBarge
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Tina Mahatdejkul
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Kristy M Hawkins
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Sheela Muley
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Jack D Newman
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Jay D Keasling
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA 94702, USA; Joint BioEnergy Institute, Emeryville, CA 94608, USA; Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA 94702, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94702, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé, DK2970 Hørsholm, Denmark
| | - Lishan Zhao
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA.
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Jiménez-Díaz L, Caballero A, Pérez-Hernández N, Segura A. Microbial alkane production for jet fuel industry: motivation, state of the art and perspectives. Microb Biotechnol 2016; 10:103-124. [PMID: 27723249 PMCID: PMC5270751 DOI: 10.1111/1751-7915.12423] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 09/09/2016] [Accepted: 09/15/2016] [Indexed: 11/27/2022] Open
Abstract
Bio‐jet fuel has attracted a lot of interest in recent years and has become a focus for aircraft and engine manufacturers, oil companies, governments and researchers. Given the global concern about environmental issues and the instability of oil market, bio‐jet fuel has been identified as a promising way to reduce the greenhouse gas emissions from the aviation industry, while also promoting energy security. Although a number of bio‐jet fuel sources have been approved for manufacture, their commercialization and entry into the market is still a far way away. In this review, we provide an overview of the drivers for intensified research into bio‐jet fuel technologies, the type of chemical compounds found in bio‐jet fuel preparations and the current state of related pre‐commercial technologies. The biosynthesis of hydrocarbons is one of the most promising approaches for bio‐jet fuel production, and thus we provide a detailed analysis of recent advances in the microbial biosynthesis of hydrocarbons (with a focus on alkanes). Finally, we explore the latest developments and their implications for the future of research into bio‐jet fuel technologies.
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Affiliation(s)
- Lorena Jiménez-Díaz
- Abengoa Research, Campus Palmas Altas, C/Energía Solar, 41014, Sevilla, Spain
| | - Antonio Caballero
- Abengoa Research, Campus Palmas Altas, C/Energía Solar, 41014, Sevilla, Spain
| | | | - Ana Segura
- Abengoa Research, Campus Palmas Altas, C/Energía Solar, 41014, Sevilla, Spain.,Estación Experimental del Zaidín-CSIC, C/Profesor Albareda s/n, 18008, Granada, Spain
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Expression of Codon-Optimized Plant Glycosyltransferase UGT72B14 in Escherichia coli Enhances Salidroside Production. BIOMED RESEARCH INTERNATIONAL 2016; 2016:9845927. [PMID: 27597978 PMCID: PMC5002478 DOI: 10.1155/2016/9845927] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/18/2016] [Accepted: 07/21/2016] [Indexed: 11/18/2022]
Abstract
Salidroside, a plant secondary metabolite in Rhodiola, has been demonstrated to have several adaptogenic properties as a medicinal herb. Due to the limitation of plant source, microbial production of salidroside by expression of plant uridine diphosphate glycosyltransferase (UGT) is promising. However, glycoside production usually remains hampered by poor expression of plant UGTs in microorganisms. Herein, we achieved salidroside production by expression of Rhodiola UGT72B14 in Escherichia coli (E. coli) and codon optimization was accordingly applied. UGT72B14 expression was optimized by changing 278 nucleotides and decreasing the G+C content to 51.05% without altering the amino acid sequence. The effect of codon optimization on UGT72B14 catalysis for salidroside production was assessed both in vitro and in vivo. In vitro, salidroside production by codon-optimized UGT72B14 is enhanced because of a significantly improved protein yield (increased by 4.8-fold) and an equivalently high activity as demonstrated by similar kinetic parameters (KM and Vmax), compared to that by wild-type protein. In vivo, both batch and fed-batch cultivation using the codon-optimized gene resulted in a significant increase in salidroside production, which was up to 6.7 mg/L increasing 3.2-fold over the wild-type UGT72B14.
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Liao P, Hemmerlin A, Bach TJ, Chye ML. The potential of the mevalonate pathway for enhanced isoprenoid production. Biotechnol Adv 2016; 34:697-713. [PMID: 26995109 DOI: 10.1016/j.biotechadv.2016.03.005] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 03/12/2016] [Accepted: 03/14/2016] [Indexed: 01/03/2023]
Abstract
The cytosol-localised mevalonic acid (MVA) pathway delivers the basic isoprene unit isopentenyl diphosphate (IPP). In higher plants, this central metabolic intermediate is also synthesised by the plastid-localised methylerythritol phosphate (MEP) pathway. Both MVA and MEP pathways conspire through exchange of intermediates and regulatory interactions. Products downstream of IPP such as phytosterols, carotenoids, vitamin E, artemisinin, tanshinone and paclitaxel demonstrate antioxidant, cholesterol-reducing, anti-ageing, anticancer, antimalarial, anti-inflammatory and antibacterial activities. Other isoprenoid precursors including isoprene, isoprenol, geraniol, farnesene and farnesol are economically valuable. An update on the MVA pathway and its interaction with the MEP pathway is presented, including the improvement in the production of phytosterols and other isoprenoid derivatives. Such attempts are for instance based on the bioengineering of microbes such as Escherichia coli and Saccharomyces cerevisiae, as well as plants. The function of relevant genes in the MVA pathway that can be utilised in metabolic engineering is reviewed and future perspectives are presented.
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Affiliation(s)
- Pan Liao
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
| | - Andréa Hemmerlin
- Centre National de la Recherche Scientifique, UPR 2357, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 67083 Strasbourg, France.
| | - Thomas J Bach
- Centre National de la Recherche Scientifique, UPR 2357, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 67083 Strasbourg, France.
| | - Mee-Len Chye
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, 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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Leavell MD, McPhee DJ, Paddon CJ. Developing fermentative terpenoid production for commercial usage. Curr Opin Biotechnol 2016; 37:114-119. [DOI: 10.1016/j.copbio.2015.10.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/11/2015] [Accepted: 10/26/2015] [Indexed: 10/22/2022]
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Gruchattka E, Kayser O. In Vivo Validation of In Silico Predicted Metabolic Engineering Strategies in Yeast: Disruption of α-Ketoglutarate Dehydrogenase and Expression of ATP-Citrate Lyase for Terpenoid Production. PLoS One 2015; 10:e0144981. [PMID: 26701782 PMCID: PMC4689373 DOI: 10.1371/journal.pone.0144981] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 11/25/2015] [Indexed: 12/28/2022] Open
Abstract
Background Engineering of the central carbon metabolism of Saccharomyces cerevisiae to redirect metabolic flux towards cytosolic acetyl-CoA has become a central topic in yeast biotechnology. A cell factory with increased flux into acetyl-CoA can be used for heterologous production of terpenoids for pharmaceuticals, biofuels, fragrances, or other acetyl-CoA derived compounds. In a previous study, we identified promising metabolic engineering targets in S. cerevisiae using an in silico stoichiometric metabolic network analysis. Here, we validate selected in silico strategies in vivo. Results Patchoulol was produced by yeast via a heterologous patchoulol synthase of Pogostemon cablin. To increase the metabolic flux from acetyl-CoA towards patchoulol, a truncated HMG-CoA reductase was overexpressed and farnesyl diphosphate synthase was fused with patchoulol synthase. The highest increase in production could be achieved by modifying the carbon source; sesquiterpenoid titer increased from glucose to ethanol by a factor of 8.4. Two strategies predicted in silico were chosen for validation in this work. Disruption of α-ketoglutarate dehydrogenase gene (KGD1) was predicted to redirect the metabolic flux via the pyruvate dehydrogenase bypass towards acetyl-CoA. The metabolic flux was redirected as predicted, however, the effect was dependent on cultivation conditions and the flux was interrupted at the level of acetate. High amounts of acetate were produced. As an alternative pathway to synthesize cytosolic acetyl-CoA, ATP-citrate lyase was expressed as a polycistronic construct, however, in vivo performance of the enzyme needs to be optimized to increase terpenoid production. Conclusions Stoichiometric metabolic network analysis can be used successfully as a metabolic prediction tool. However, this study highlights that kinetics, regulation and cultivation conditions may interfere, resulting in poor in vivo performance. Main sites of regulation need to be released and improved enzymes are essential to meet the required activities for an increased product formation in vivo.
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Affiliation(s)
- Evamaria Gruchattka
- Technical Biochemistry, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 66, 44227, Dortmund, Germany
| | - Oliver Kayser
- Technical Biochemistry, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 66, 44227, Dortmund, Germany
- * E-mail:
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49
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Pearsall SM, Rowley CN, Berry A. Advances in Pathway Engineering for Natural Product Biosynthesis. ChemCatChem 2015. [DOI: 10.1002/cctc.201500602] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Sarah M. Pearsall
- Astbury Centre for Structural Molecular Biology; University of Leeds; Leeds LS2 9JT UK
| | - Christopher N. Rowley
- Astbury Centre for Structural Molecular Biology; University of Leeds; Leeds LS2 9JT UK
| | - Alan Berry
- Astbury Centre for Structural Molecular Biology; University of Leeds; Leeds LS2 9JT UK
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50
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Coutte F, Niehren J, Dhali D, John M, Versari C, Jacques P. Modeling leucine's metabolic pathway and knockout prediction improving the production of surfactin, a biosurfactant from
Bacillus subtilis. Biotechnol J 2015. [DOI: 10.1002/biot.201400541] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- François Coutte
- ProBioGEM team, Research Institute for Food and Biotechnology ‐ Charles Viollette (EA7394), University of Lille, Villeneuve d'Ascq, France
- University of Lille, Villeneuve d'Ascq, France
| | - Joachim Niehren
- BioComputing team, CRIStAL Lab (CNRS UMR9189), University of Lille, Villeneuve d'Ascq, France
- Inria Lille, Villeneuve d'Ascq, France
| | - Debarun Dhali
- ProBioGEM team, Research Institute for Food and Biotechnology ‐ Charles Viollette (EA7394), University of Lille, Villeneuve d'Ascq, France
- University of Lille, Villeneuve d'Ascq, France
| | - Mathias John
- University of Lille, Villeneuve d'Ascq, France
- BioComputing team, CRIStAL Lab (CNRS UMR9189), University of Lille, Villeneuve d'Ascq, France
| | - Cristian Versari
- University of Lille, Villeneuve d'Ascq, France
- BioComputing team, CRIStAL Lab (CNRS UMR9189), University of Lille, Villeneuve d'Ascq, France
| | - Philippe Jacques
- ProBioGEM team, Research Institute for Food and Biotechnology ‐ Charles Viollette (EA7394), University of Lille, Villeneuve d'Ascq, France
- University of Lille, Villeneuve d'Ascq, France
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