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Zerbe P. Plants against cancer: towards green Taxol production through pathway discovery and metabolic engineering. ABIOTECH 2024; 5:394-402. [PMID: 39279861 PMCID: PMC11399496 DOI: 10.1007/s42994-024-00170-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/08/2024] [Indexed: 09/18/2024]
Abstract
The diversity of plant natural products presents a rich resource for accelerating drug discovery and addressing pressing human health issues. However, the challenges in accessing and cultivating source species, as well as metabolite structural complexity, and general low abundance present considerable hurdles in developing plant-derived therapeutics. Advances in high-throughput sequencing, genome assembly, gene synthesis, analytical technologies, and synthetic biology approaches, now enable us to efficiently identify and engineer enzymes and metabolic pathways for producing natural and new-to-nature therapeutics and drug candidates. This review highlights challenges and progress in plant natural product discovery and engineering by example of recent breakthroughs in identifying the missing enzymes involved in the biosynthesis of the anti-cancer agent Taxol®. These enzyme resources offer new avenues for the bio-manufacture and semi-synthesis of an old blockbuster drug.
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Affiliation(s)
- Philipp Zerbe
- Department of Plant Biology, University of California Davis, Davis, CA 95616 USA
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2
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Dulak K, Sordon S, Matera A, Wilczak A, Huszcza E, Popłoński J. Novel enzymatic route to the synthesis of C-8 hydroxyflavonoids including flavonols and isoflavones. Sci Rep 2024; 14:18217. [PMID: 39107441 PMCID: PMC11303751 DOI: 10.1038/s41598-024-68513-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 07/24/2024] [Indexed: 08/10/2024] Open
Abstract
Flavin-dependent monooxygenases (FMOs) are a valuable group of biocatalysts that can regioselectively introduce a hydroxy group for the targeted modification of biologically active compounds. Here, we present the fdeE, the FMO from Herbaspirillum seropedicae SmR1 that is a part of the naringenin degradation pathway and is active towards a wide range of flavonoids-flavanones, flavones, isoflavones, and flavonols. Bioinformatics and biochemical analysis revealed a high similarity between the analyzed enzyme and other F8H FMOs what might indicate convergent evolutionary mechanism of flavonoid degradation pathway emergence by microorganism. A simple approach with the manipulation of the reaction environment allowed the stable formation of hydroxylation products, which showed very high reactivity in both in vivo and in vitro assays. This approach resulted in an 8-hydroxyquercetin-gossypetin titer of 0.16 g/L and additionally it is a first report of production of this compound.
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Affiliation(s)
- Kinga Dulak
- Department of Food Chemistry and Biocatalysis, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - Sandra Sordon
- Department of Food Chemistry and Biocatalysis, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - Agata Matera
- Department of Food Chemistry and Biocatalysis, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - Aleksandra Wilczak
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Ewa Huszcza
- Department of Food Chemistry and Biocatalysis, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - Jarosław Popłoński
- Department of Food Chemistry and Biocatalysis, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland.
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3
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Kumari M, Checker VG, Kathpalia R, Srivastava V, Singh IK, Singh A. Metabolic engineering for enhanced terpenoid production: Leveraging new horizons with an old technique. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108511. [PMID: 38593484 DOI: 10.1016/j.plaphy.2024.108511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/06/2024] [Accepted: 03/06/2024] [Indexed: 04/11/2024]
Abstract
Terpenoids are a vast class of plant specialized metabolites (PSMs) manufactured by plants and are involved in their interactions with environment. In addition, they add health benefits to human nutrition and are widely used as pharmaceutically active compounds. However, native plants produce a limited amount of terpenes restricting metabolite yield of terpene-related metabolites. Exponential growth in the plant metabolome data and the requirement of alternative approaches for producing the desired amount of terpenoids, has redirected plant biotechnology research to plant metabolic engineering, which requires in-depth knowledge and precise expertise about dynamic plant metabolic pathways and cellular physiology. Metabolic engineering is an assuring tool for enhancing the concentration of terpenes by adopting specific strategies such as overexpression of the key genes associated with the biosynthesis of targeted metabolites, controlling the modulation of transcription factors, downregulation of competitive pathways (RNAi), co-expression of the biosynthetic pathway genes in heterologous system and other combinatorial approaches. Microorganisms, fast-growing host plants (such as Nicotiana benthamiana), and cell suspension/callus cultures have provided better means for producing valuable terpenoids. Manipulation in the biosynthetic pathways responsible for synthesis of terpenoids can provide opportunities to enhance the content of desired terpenoids and open up new avenues to enhance their production. This review deliberates the worth of metabolic engineering in medicinal plants to resolve issues associated with terpenoid production at a commercial scale. However, to bring the revolution through metabolic engineering, further implementation of genome editing, elucidation of metabolic pathways using omics approaches, system biology approaches, and synthetic biology tactics are essentially needed.
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Affiliation(s)
- Megha Kumari
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021, India; Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India
| | | | - Renu Kathpalia
- Department of Botany, Kirori Mal College, University of Delhi, Delhi, 110007, India
| | - Vikas Srivastava
- Department of Botany, School of Life Sciences, Central University of Jammu, Samba, 181143, India
| | - Indrakant Kumar Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India
| | - Archana Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021, India; Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India; Delhi School of Climate Change and Sustainability, Institution of Eminence, Maharishi Karnad Bhawan, University of Delhi, Delhi, India.
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4
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Long Y, Han X, Meng X, Xu P, Tao F. A robust yeast chassis: comprehensive characterization of a fast-growing Saccharomyces cerevisiae. mBio 2024; 15:e0319623. [PMID: 38214535 PMCID: PMC10865977 DOI: 10.1128/mbio.03196-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 12/07/2023] [Indexed: 01/13/2024] Open
Abstract
Robust chassis are critical to facilitate advances in synthetic biology. This study describes a comprehensive characterization of a new yeast isolate Saccharomyces cerevisiae XP that grows faster than commonly used research and industrial S. cerevisiae strains. The genomic, transcriptomic, and metabolomic analyses suggest that the fast growth rate is, in part, due to the efficient electron transport chain and key growth factor synthesis. A toolbox for genetic manipulation of the yeast was developed; we used it to construct l-lactic acid producers for high lactate production. The development of genetically malleable yeast strains that grow faster than currently used strains may significantly enhance the uses of S. cerevisiae in biotechnology.IMPORTANCEYeast is known as an outstanding starting strain for constructing microbial cell factories. However, its growth rate restricts its application. A yeast strain XP, which grows fast in high concentrations of sugar and acidic environments, is revealed to demonstrate the potential in industrial applications. A toolbox was also built for its genetic manipulation including gene insertion, deletion, and ploidy transformation. The knowledge of its metabolism, which could guide the designing of genetic experiments, was generated with multi-omics analyses. This novel strain along with its toolbox was then tested by constructing an l-lactic acid efficient producer, which is conducive to the development of degradable plastics. This study highlights the remarkable competence of nonconventional yeast for applications in biotechnology.
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Affiliation(s)
- Yangdanyu Long
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao Han
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xuanlin Meng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Sun ML, Gao X, Lin L, Yang J, Ledesma-Amaro R, Ji XJ. Building Yarrowia lipolytica Cell Factories for Advanced Biomanufacturing: Challenges and Solutions. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:94-107. [PMID: 38126236 DOI: 10.1021/acs.jafc.3c07889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Microbial cell factories have shown great potential for industrial production with the benefit of being environmentally friendly and sustainable. Yarrowia lipolytica is a promising and superior non-model host for biomanufacturing due to its cumulated advantages compared to model microorganisms, such as high fluxes of metabolic precursors (acetyl-CoA and malonyl-CoA) and its naturally hydrophobic microenvironment. However, although diverse compounds have been synthesized in Y. lipolytica cell factories, most of the relevant studies have not reached the level of industrialization and commercialization due to a number of remaining challenges, including unbalanced metabolic flux, conflict between cell growth and product synthesis, and cytotoxic effects. Here, various metabolic engineering strategies for solving the challenges are summarized, which is developing fast and extremely conducive to rational design and reconstruction of robust Y. lipolytica cell factories for advanced biomanufacturing. Finally, future engineering efforts for enhancing the production efficiency of this platform strain are highlighted.
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Affiliation(s)
- Mei-Li Sun
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Xiaoxia Gao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Lu Lin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Jing Yang
- 2011 College, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Xiao-Jun Ji
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
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6
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Guo M, Lv H, Chen H, Dong S, Zhang J, Liu W, He L, Ma Y, Yu H, Chen S, Luo H. Strategies on biosynthesis and production of bioactive compounds in medicinal plants. CHINESE HERBAL MEDICINES 2024; 16:13-26. [PMID: 38375043 PMCID: PMC10874775 DOI: 10.1016/j.chmed.2023.01.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/05/2023] [Accepted: 01/26/2023] [Indexed: 02/21/2024] Open
Abstract
Medicinal plants are a valuable source of essential medicines and herbal products for healthcare and disease therapy. Compared with chemical synthesis and extraction, the biosynthesis of natural products is a very promising alternative for the successful conservation of medicinal plants, and its rapid development will greatly facilitate the conservation and sustainable utilization of medicinal plants. Here, we summarize the advances in strategies and methods concerning the biosynthesis and production of natural products of medicinal plants. The strategies and methods mainly include genetic engineering, plant cell culture engineering, metabolic engineering, and synthetic biology based on multiple "OMICS" technologies, with paradigms for the biosynthesis of terpenoids and alkaloids. We also highlight the biosynthetic approaches and discuss progress in the production of some valuable natural products, exemplifying compounds such as vindoline (alkaloid), artemisinin and paclitaxel (terpenoids), to illustrate the power of biotechnology in medicinal plants.
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Affiliation(s)
- Miaoxian Guo
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Haizhou Lv
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Hongyu Chen
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Shuting Dong
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Jianhong Zhang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Wanjing Liu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Liu He
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Yimian Ma
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Hua Yu
- Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Shilin Chen
- Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Hongmei Luo
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
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7
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Zhang Z, Wu QY, Ge Y, Huang ZY, Hong R, Li A, Xu JH, Yu HL. Hydroxylases involved in terpenoid biosynthesis: a review. BIORESOUR BIOPROCESS 2023; 10:39. [PMID: 38647640 PMCID: PMC10992849 DOI: 10.1186/s40643-023-00656-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/10/2023] [Indexed: 04/25/2024] Open
Abstract
Terpenoids are pervasive in nature and display an immense structural diversity. As the largest category of plant secondary metabolites, terpenoids have important socioeconomic value in the fields of pharmaceuticals, spices, and food manufacturing. The biosynthesis of terpenoid skeletons has made great progress, but the subsequent modifications of the terpenoid framework are poorly understood, especially for the functionalization of inert carbon skeleton usually catalyzed by hydroxylases. Hydroxylase is a class of enzymes that plays an important role in the modification of terpenoid backbone. This review article outlines the research progress in the identification, molecular modification, and functional expression of this class of enzymes in the past decade, which are profitable for the discovery, engineering, and application of more hydroxylases involved in the plant secondary metabolism.
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Affiliation(s)
- Zihan Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
| | - Qing-Yang Wu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
| | - Yue Ge
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
| | - Zheng-Yu Huang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
| | - Ran Hong
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Aitao Li
- School of Life Sciences, State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, 430062, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China.
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8
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Lautier T, Smith DJ, Yang LK, Chen X, Zhang C, Truan G, Lindley ND. β-Cryptoxanthin Production in Escherichia coli by Optimization of the Cytochrome P450 CYP97H1 Activity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4683-4695. [PMID: 36888893 DOI: 10.1021/acs.jafc.2c08970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Cytochromes P450, forming a superfamily of monooxygenases containing heme as a cofactor, show great versatility in substrate specificity. Metabolic engineering can take advantage of this feature to unlock novel metabolic pathways. However, the cytochromes P450 often show difficulty being expressed in a heterologous chassis. As a case study in the prokaryotic host Escherichia coli, the heterologous synthesis of β-cryptoxanthin was addressed. This carotenoid intermediate is difficult to produce, as its synthesis requires a monoterminal hydroxylation of β-carotene whereas most of the classic carotene hydroxylases are dihydroxylases. This study was focused on the optimization of the in vivo activity of CYP97H1, an original P450 β-carotene monohydroxylase. Engineering the N-terminal part of CYP97H1, identifying the matching redox partners, defining the optimal cellular background and adjusting the culture and induction conditions improved the production by 400 times compared to that of the initial strain, representing 2.7 mg/L β-cryptoxanthin and 20% of the total carotenoids produced.
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Affiliation(s)
- Thomas Lautier
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 138669 Singapore
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
- CNRS@CREATE, 1 Create Way, #08-01 Create Tower, 138602 Singapore
| | - Derek J Smith
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 138669 Singapore
| | - Lay Kien Yang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 138669 Singapore
| | - Xixian Chen
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 138669 Singapore
| | - Congqiang Zhang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 138669 Singapore
| | - Gilles Truan
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
| | - Nic D Lindley
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 138669 Singapore
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
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9
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Yang Y, Xi D, Wu Y, Liu T. Complete biosynthesis of the phenylethanoid glycoside verbascoside. PLANT COMMUNICATIONS 2023:100592. [PMID: 36935606 PMCID: PMC10363510 DOI: 10.1016/j.xplc.2023.100592] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/02/2022] [Accepted: 03/15/2023] [Indexed: 06/18/2023]
Abstract
Verbascoside, which was first discovered in 1963, is a well-known phenylethanoid glycoside (PhG) that exhibits antioxidant, anti-inflammatory, antimicrobial, and neuroprotective activities and contributes to the therapeutic effects of many medicinal plants. However, the biosynthetic pathway of verbascoside remains to be fully elucidated. Here, we report the identification of two missing enzymes in the verbascoside biosynthesis pathway by transcriptome mining and in vitro enzymatic assays. Specifically, a BAHD acyltransferase (hydroxycinnamoyl-CoA:salidroside hydroxycinnamoyltransferase [SHCT]) was shown to catalyze the regioselective acylation of salidroside to form osmanthuside A, and a CYP98 hydroxylase (osmanthuside B 3,3'-hydroxylase [OBH]) was shown to catalyze meta-hydroxylations of the p-coumaroyl and tyrosol moieties of osmanthuside B to complete the biosynthesis of verbascoside. Because SHCTs and OBHs are found in many Lamiales species that produce verbascoside, this pathway may be general. The findings from the study provide novel insights into the formation of caffeoyl and hydroxytyrosol moieties in natural product biosynthetic pathways. In addition, with the newly acquired enzymes, we achieved heterologous production of osmanthuside B, verbascoside, and ligupurpuroside B in Escherichia coli; this work lays a foundation for sustainable production of verbascoside and other PhGs in micro-organisms.
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Affiliation(s)
- Yihan Yang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Daoyi Xi
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Yanan Wu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Tao Liu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.
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Gossart N, Berhin A, Sergeant K, Alam I, André C, Hausman JF, Boutry M, Hachez C. Engineering Nicotiana tabacum trichomes for triterpenic acid production. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 328:111573. [PMID: 36563941 DOI: 10.1016/j.plantsci.2022.111573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
In this work, we aimed at implementing the biosynthesis of triterpenic acids in Nicotiana tabacum glandular trichomes. Although endogenous genes coding for enzymes involved in such biosynthetic pathway are found in the Nicotiana tabacum genome, implementing such pathway specifically in glandular trichomes required to boost endogenous enzymatic activities. Five transgenes coding for a farnesyl-diphosphate synthase, a squalene synthase, a squalene epoxidase, a beta-amyrin synthase and a beta-amyrin 28-monooxygenase were introduced in N.tabacum, their expression being driven by pMALD1, a trichome-specific transcriptional promoter. This study aimed at testing whether sinking isoprenoid precursors localized in plastids, by exploiting potential cross-talks allowing the exchange of terpenoid pools from the chloroplast to the cytosol, could be a way to improve overall yield. By analyzing metabolites extracted from entire leaves, a low amount of ursolic acid was detected in plants expressing the five transgenes. Our study shows that the terpene biosynthetic pathway could be, in part, redirected in N.tabacum glandular trichomes with no deleterious phenotype at the whole plant level (chlorosis, dwarfism,…). In light of our results, possible ways to improve the final yield are discussed.
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Affiliation(s)
- Nicola Gossart
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Louvain-la-Neuve, Belgium
| | - Alice Berhin
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Louvain-la-Neuve, Belgium
| | - Kjell Sergeant
- Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Esch-sur-Alzette, Luxembourg
| | - Iftekhar Alam
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Louvain-la-Neuve, Belgium; Plant Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka 1349, Bangladesh
| | - Christelle André
- Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Esch-sur-Alzette, Luxembourg; The New Zealand Institute for Plant and Food Research Ltd (PFR), Private Bag 92169, Auckland, New Zealand
| | - Jean-François Hausman
- Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Esch-sur-Alzette, Luxembourg
| | - Marc Boutry
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Louvain-la-Neuve, Belgium
| | - Charles Hachez
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Louvain-la-Neuve, Belgium.
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11
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Lautier T, Smith DJ, Yang LK, Chen X, Zhang C, Truan G, Lindley ND. Cytochrome P450 Surface Domains Prevent the β-Carotene Monohydroxylase CYP97H1 of Euglena gracilis from Acting as a Dihydroxylase. Biomolecules 2023; 13:biom13020366. [PMID: 36830734 PMCID: PMC9953315 DOI: 10.3390/biom13020366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Molecular biodiversity results from branched metabolic pathways driven by enzymatic regioselectivities. An additional complexity occurs in metabolites with an internal structural symmetry, offering identical extremities to the enzymes. For example, in the terpene family, β-carotene presents two identical terminal closed-ring structures. Theses cycles can be hydroxylated by cytochrome P450s from the CYP97 family. Two sequential hydroxylations lead first to the formation of monohydroxylated β-cryptoxanthin and subsequently to that of dihydroxylated zeaxanthin. Among the CYP97 dihydroxylases, CYP97H1 from Euglena gracilis has been described as the only monohydroxylase. This study aims to determine which enzymatic domains are involved in this regioselectivity, conferring unique monohydroxylase activity on a substrate offering two identical sites for hydroxylation. We explored the effect of truncations, substitutions and domain swapping with other CYP97 members and found that CYP97H1 harbours a unique N-terminal globular domain. This CYP97H1 N-terminal domain harbours a hydrophobic patch at the entrance of the substrate channel, which is involved in the monohydroxylase activity of CYP97H1. This domain, at the surface of the enzyme, highlights the role of distal and non-catalytic domains in regulating enzyme specificity.
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Affiliation(s)
- Thomas Lautier
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
- Toulouse Biotechnolgy Institute, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
- CNRS@CREATE, 1 Create Way, #08-01 Create Tower, Singapore 138602, Singapore
- Correspondence: ; Tel.: +33-(0)-567048813
| | - Derek J. Smith
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
| | - Lay Kien Yang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
| | - Xixian Chen
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
| | - Congqiang Zhang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
| | - Gilles Truan
- Toulouse Biotechnolgy Institute, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
| | - Nic D Lindley
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
- Toulouse Biotechnolgy Institute, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
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12
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Zhang Y, Ma L, Su P, Huang L, Gao W. Cytochrome P450s in plant terpenoid biosynthesis: discovery, characterization and metabolic engineering. Crit Rev Biotechnol 2023; 43:1-21. [PMID: 34865579 DOI: 10.1080/07388551.2021.2003292] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
As the largest family of natural products, terpenoids play valuable roles in medicine, agriculture, cosmetics and food. However, the traditional methods that rely on direct extraction from the original plants not only produce low yields, but also result in waste of resources, and are not applicable at all to endangered species. Modern heterologous biosynthesis is considered a promising, efficient, and sustainable production method, but it relies on the premise of a complete analysis of the biosynthetic pathway of terpenoids, especially the functionalization processes involving downstream cytochrome P450s. In this review, we systematically introduce the biotech approaches used to discover and characterize plant terpenoid-related P450s in recent years. In addition, we propose corresponding metabolic engineering approaches to increase the effective expression of P450 and improve the yield of terpenoids, and also elaborate on metabolic engineering strategies and examples of heterologous biosynthesis of terpenoids in Saccharomyces cerevisiae and plant hosts. Finally, we provide perspectives for the biotech approaches to be developed for future research on terpenoid-related P450.
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Affiliation(s)
- Yifeng Zhang
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China.,School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Lin Ma
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Ping Su
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, USA
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, China
| | - Wei Gao
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China.,School of Traditional Chinese Medicine, Capital Medical University, Beijing, China.,Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China
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13
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Sethi A, Bhandawat A, Pati PK. Engineering medicinal plant-derived CYPs: a promising strategy for production of high-valued secondary metabolites. PLANTA 2022; 256:119. [PMID: 36378350 PMCID: PMC9664027 DOI: 10.1007/s00425-022-04024-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
Cytochorme P450s (CYPs) play a critical role in the catalysis of secondary metabolite biosynthetic pathways. For their commercial use, various strategies for metabolic pathway engineering using CYP as a potential target have been explored. Plants produce a vast diversity of secondary metabolites which are being used to treat various ailments and diseases. Some of these metabolites are difficult to obtain in large quantities limiting their industrial use. Cytochrome P450 enzymes (CYPs) are important catalysts in the biosynthesis of highly valued secondary metabolites, and are found in all domains of life. With the development of high-throughput sequencing and high-resolution mass spectrometry, new biosynthetic pathways and associated CYPs are being identified. In this review, we present CYPs identified from medicinal plants as a potential game changer in the metabolic engineering of secondary metabolic pathways. We present the achievements made so far in enhancing the production of important bioactivities through pathway engineering, giving some popular examples. At last, current challenges and possible strategies to overcome the limitations associated with CYP engineering to enhance the biosynthesis of target secondary metabolites are also highlighted.
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Affiliation(s)
- Anshika Sethi
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, 143 005, India
| | - Abhishek Bhandawat
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, 143 005, India
| | - Pratap Kumar Pati
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, 143 005, India.
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14
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Zhao L, Zhu Y, Jia H, Han Y, Zheng X, Wang M, Feng W. From Plant to Yeast-Advances in Biosynthesis of Artemisinin. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27206888. [PMID: 36296479 PMCID: PMC9609949 DOI: 10.3390/molecules27206888] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/28/2022]
Abstract
Malaria is a life-threatening disease. Artemisinin-based combination therapy (ACT) is the preferred choice for malaria treatment recommended by the World Health Organization. At present, the main source of artemisinin is extracted from Artemisia annua; however, the artemisinin content in A. annua is only 0.1-1%, which cannot meet global demand. Meanwhile, the chemical synthesis of artemisinin has disadvantages such as complicated steps, high cost and low yield. Therefore, the application of the synthetic biology approach to produce artemisinin in vivo has magnificent prospects. In this review, the biosynthesis pathway of artemisinin was summarized. Then we discussed the advances in the heterologous biosynthesis of artemisinin using microorganisms (Escherichia coli and Saccharomyces cerevisiae) as chassis cells. With yeast as the cell factory, the production of artemisinin was transferred from plant to yeast. Through the optimization of the fermentation process, the yield of artemisinic acid reached 25 g/L, thereby producing the semi-synthesis of artemisinin. Moreover, we reviewed the genetic engineering in A. annua to improve the artemisinin content, which included overexpressing artemisinin biosynthesis pathway genes, blocking key genes in competitive pathways, and regulating the expression of transcription factors related to artemisinin biosynthesis. Finally, the research progress of artemisinin production in other plants (Nicotiana, Physcomitrella, etc.) was discussed. The current advances in artemisinin biosynthesis may help lay the foundation for the remarkable up-regulation of artemisinin production in A. annua through gene editing or molecular design breeding in the future.
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Affiliation(s)
- Le Zhao
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
- Co-Construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan and Education Ministry of P. R. China, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Yunhao Zhu
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
- Co-Construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan and Education Ministry of P. R. China, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Haoyu Jia
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Yongguang Han
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Xiaoke Zheng
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
- Co-Construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan and Education Ministry of P. R. China, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Min Wang
- College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China
- Beijing Key Laboratory of Plant Research and Development, Beijing Technology and Business University, Beijing 100048, China
- Correspondence: (M.W.); (W.F.); Tel.: +86-134-2629-2115 (M.W.); +86-371-60190296 (W.F.)
| | - Weisheng Feng
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
- Co-Construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan and Education Ministry of P. R. China, Henan University of Chinese Medicine, Zhengzhou 450046, China
- Correspondence: (M.W.); (W.F.); Tel.: +86-134-2629-2115 (M.W.); +86-371-60190296 (W.F.)
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15
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Wu QY, Huang ZY, Wang JY, Yu HL, Xu JH. Construction of an Escherichia coli cell factory to synthesize taxadien-5α-ol, the key precursor of anti-cancer drug paclitaxel. BIORESOUR BIOPROCESS 2022; 9:82. [PMID: 38647602 PMCID: PMC10992617 DOI: 10.1186/s40643-022-00569-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/01/2022] [Indexed: 11/10/2022] Open
Abstract
Paclitaxel (Taxol™), an alkaloid of diterpenoid family, is one of the most widely used anti-cancer drugs due to its effectiveness against a variety of tumors. Rather than directly extraction and chemical synthesis of paclitaxel or its intermediates from yew plants, construction of a microbial cell factory for paclitaxel biosynthesis will be more efficient and sustainable. The challenge for biosynthesis of paclitaxel lies on the insufficient precursor, such as taxadien-5α-ol. In this study, we report a recombinant Escherichia coli strain constructed with a heterologous mevalonate pathway, a taxadiene synthase from yew, and a cytochrome P450-mediated oxygenation system for the de novo production of taxadien-5α-ol, the first product of the multi-step taxadiene oxygenation metabolism. The key enzymes including taxadiene synthases and cytochrome P450 reductases were screened, and the linker for fusing taxadiene-5α-hydroxylase with its reductase partner cytochrome P450 reductase was optimized. By reducing the metabolic burden and optimizing the fermentation conditions, the final production of total oxygenated taxanes was raised up to 27 mg L-1 in a 50-mL flask cultivation, of which the yield of taxadien-5α-ol was 7.0 mg L-1, representing approximately a 12-fold and 23-fold improvements, respectively, as compared with the initial titers. The engineered MVA pathway for the overproduction of terpenoid precursors can serve as an efficient platform for the production of other valuable terpenoids.
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Affiliation(s)
- Qing-Yang Wu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, College of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Zheng-Yu Huang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, College of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Jin-Yi Wang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, College of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, College of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, College of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
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16
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Liu X, Li L, Zhao GR. Systems Metabolic Engineering of Escherichia coli Coculture for De Novo Production of Genistein. ACS Synth Biol 2022; 11:1746-1757. [PMID: 35507680 DOI: 10.1021/acssynbio.1c00590] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Genistein is a plant-derived isoflavone possessing various bioactivities to prevent aging, carcinogenesis, and neurodegenerative and inflammation diseases. As a typical complex flavonoid, its microbial production from sugar remains to be completed. Here, we use systems metabolic engineering stategies to design and develop a three-strain commensalistic Escherichia coli coculture that for the first time realized the de novo production of genistein. First, we reconstituted the naringenin module by screening and incorporating chalcone isomerase-like protein, an auxiliary component to rectify the chalcone synthase promiscuity. Furthermore, we devised and constructed the genistein module by N-terminal modifications of plant P450 enzyme 2-hydroxyisoflavanone synthase and cytochrome P450 enzyme reductase. When naringenin-producing strain was cocultivated with p-coumaric acid-overproducing strain (a phenylalanine-auxotroph), two-strain coculture worked as commensalism through a unidirectional nutrient flow, which favored the efficient production of naringenin with a titer of 206.5 mg/L from glucose. A three-strain commensalistic coculture was subsequently engineered, which produced the highest titer to date of 60.8 mg/L genistein from a glucose and glycerol mixture. The commensalistic coculture is a flexible and versatile platform for the production of flavonoids, indicating a promising future for production of complex natural products in engineered E. coli.
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Affiliation(s)
- Xue Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China
- Georgia Tech Shenzhen Institute, Tianjin University, Dashi Road 1, Nanshan District, Shenzhen 518055, China
| | - Lingling Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China
- Georgia Tech Shenzhen Institute, Tianjin University, Dashi Road 1, Nanshan District, Shenzhen 518055, China
| | - Guang-Rong Zhao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China
- Georgia Tech Shenzhen Institute, Tianjin University, Dashi Road 1, Nanshan District, Shenzhen 518055, China
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17
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Liu J, Wang X, Dai G, Zhang Y, Bian X. Microbial chassis engineering drives heterologous production of complex secondary metabolites. Biotechnol Adv 2022; 59:107966. [PMID: 35487394 DOI: 10.1016/j.biotechadv.2022.107966] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 12/27/2022]
Abstract
The cryptic secondary metabolite biosynthetic gene clusters (BGCs) far outnumber currently known secondary metabolites. Heterologous production of secondary metabolite BGCs in suitable chassis facilitates yield improvement and discovery of new-to-nature compounds. The two juxtaposed conventional model microorganisms, Escherichia coli, Saccharomyces cerevisiae, have been harnessed as microbial chassis to produce a bounty of secondary metabolites with the help of certain host engineering. In last decade, engineering non-model microbes to efficiently biosynthesize secondary metabolites has received increasing attention due to their peculiar advantages in metabolic networks and/or biosynthesis. The state-of-the-art synthetic biology tools lead the way in operating genetic manipulation in non-model microorganisms for phenotypic optimization or yields improvement of desired secondary metabolites. In this review, we firstly discuss the pros and cons of several model and non-model microbial chassis, as well as the importance of developing broader non-model microorganisms as alternative programmable heterologous hosts to satisfy the desperate needs of biosynthesis study and industrial production. Then we highlight the lately advances in the synthetic biology tools and engineering strategies for optimization of non-model microbial chassis, in particular, the successful applications for efficient heterologous production of multifarious complex secondary metabolites, e.g., polyketides, nonribosomal peptides, as well as ribosomally synthesized and post-translationally modified peptides. Lastly, emphasis is on the perspectives of chassis cells development to access the ideal cell factory in the artificial intelligence-driven genome era.
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Affiliation(s)
- Jiaqi Liu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China; Present address: Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
| | - Xue Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Guangzhi Dai
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China.
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18
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Hussain MH, Mohsin MZ, Zaman WQ, Yu J, Zhao X, Wei Y, Zhuang Y, Mohsin A, Guo M. Multiscale engineering of microbial cell factories: A step forward towards sustainable natural products industry. Synth Syst Biotechnol 2022; 7:586-601. [PMID: 35155840 PMCID: PMC8816652 DOI: 10.1016/j.synbio.2021.12.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/08/2021] [Accepted: 12/30/2021] [Indexed: 01/09/2023] Open
Abstract
Microbial cell factories (bacteria and fungi) are the leading producers of beneficial natural products such as lycopene, carotene, herbal medicine, and biodiesel etc. These microorganisms are considered efficient due to their effective bioprocessing strategy (monoculture- and consortial-based approach) under distinct processing conditions. Meanwhile, the advancement in genetic and process optimization techniques leads to enhanced biosynthesis of natural products that are known functional ingredients with numerous applications in the food, cosmetic and medical industries. Natural consortia and monoculture thrive in nature in a small proportion, such as wastewater, food products, and soils. In similitude to natural consortia, it is possible to engineer artificial microbial consortia and program their behaviours via synthetic biology tools. Therefore, this review summarizes the optimization of genetic and physicochemical parameters of the microbial system for improved production of natural products. Also, this review presents a brief history of natural consortium and describes the functional properties of monocultures. This review focuses on synthetic biology tools that enable new approaches to design synthetic consortia; and highlights the syntropic interactions that determine the performance and stability of synthetic consortia. In particular, the effect of processing conditions and advanced genetic techniques to improve the productibility of both monoculture and consortial based systems have been greatly emphasized. In this context, possible strategies are also discussed to give an insight into microbial engineering for improved production of natural products in the future. In summary, it is concluded that the coupling of genomic modifications with optimum physicochemical factors would be promising for producing a robust microbial cell factory that shall contribute to the increased production of natural products.
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Affiliation(s)
- Muhammad Hammad Hussain
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Muhammad Zubair Mohsin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Waqas Qamar Zaman
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology (NUST), Sector H-12, Islamabad, 44000, Pakistan
| | - Junxiong Yu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Xueli Zhao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Yanlong Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Ali Mohsin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
- Corresponding author. East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, PR China.
| | - Meijin Guo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
- Corresponding author. P.O. box 329#, East China University of Science and Technology, 130 Meilong Rd., Shanghai, 200237, PR China.
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19
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Rinaldi MA, Ferraz CA, Scrutton NS. Alternative metabolic pathways and strategies to high-titre terpenoid production in Escherichia coli. Nat Prod Rep 2022; 39:90-118. [PMID: 34231643 PMCID: PMC8791446 DOI: 10.1039/d1np00025j] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Indexed: 12/14/2022]
Abstract
Covering: up to 2021Terpenoids are a diverse group of chemicals used in a wide range of industries. Microbial terpenoid production has the potential to displace traditional manufacturing of these compounds with renewable processes, but further titre improvements are needed to reach cost competitiveness. This review discusses strategies to increase terpenoid titres in Escherichia coli with a focus on alternative metabolic pathways. Alternative pathways can lead to improved titres by providing higher orthogonality to native metabolism that redirects carbon flux, by avoiding toxic intermediates, by bypassing highly-regulated or bottleneck steps, or by being shorter and thus more efficient and easier to manipulate. The canonical 2-C-methyl-D-erythritol 4-phosphate (MEP) and mevalonate (MVA) pathways are engineered to increase titres, sometimes using homologs from different species to address bottlenecks. Further, alternative terpenoid pathways, including additional entry points into the MEP and MVA pathways, archaeal MVA pathways, and new artificial pathways provide new tools to increase titres. Prenyl diphosphate synthases elongate terpenoid chains, and alternative homologs create orthogonal pathways and increase product diversity. Alternative sources of terpenoid synthases and modifying enzymes can also be better suited for E. coli expression. Mining the growing number of bacterial genomes for new bacterial terpenoid synthases and modifying enzymes identifies enzymes that outperform eukaryotic ones and expand microbial terpenoid production diversity. Terpenoid removal from cells is also crucial in production, and so terpenoid recovery and approaches to handle end-product toxicity increase titres. Combined, these strategies are contributing to current efforts to increase microbial terpenoid production towards commercial feasibility.
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Affiliation(s)
- Mauro A Rinaldi
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Clara A Ferraz
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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20
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Carruthers DN, Lee TS. Diversifying Isoprenoid Platforms via Atypical Carbon Substrates and Non-model Microorganisms. Front Microbiol 2021; 12:791089. [PMID: 34925299 PMCID: PMC8677530 DOI: 10.3389/fmicb.2021.791089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/10/2021] [Indexed: 01/07/2023] Open
Abstract
Isoprenoid compounds are biologically ubiquitous, and their characteristic modularity has afforded products ranging from pharmaceuticals to biofuels. Isoprenoid production has been largely successful in Escherichia coli and Saccharomyces cerevisiae with metabolic engineering of the mevalonate (MVA) and methylerythritol phosphate (MEP) pathways coupled with the expression of heterologous terpene synthases. Yet conventional microbial chassis pose several major obstacles to successful commercialization including the affordability of sugar substrates at scale, precursor flux limitations, and intermediate feedback-inhibition. Now, recent studies have challenged typical isoprenoid paradigms by expanding the boundaries of terpene biosynthesis and using non-model organisms including those capable of metabolizing atypical C1 substrates. Conversely, investigations of non-model organisms have historically informed optimization in conventional microbes by tuning heterologous gene expression. Here, we review advances in isoprenoid biosynthesis with specific focus on the synergy between model and non-model organisms that may elevate the commercial viability of isoprenoid platforms by addressing the dichotomy between high titer production and inexpensive substrates.
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Affiliation(s)
- David N Carruthers
- Joint BioEnergy Institute, Emeryville, CA, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Taek Soon Lee
- Joint BioEnergy Institute, Emeryville, CA, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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21
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Simić S, Zukić E, Schmermund L, Faber K, Winkler CK, Kroutil W. Shortening Synthetic Routes to Small Molecule Active Pharmaceutical Ingredients Employing Biocatalytic Methods. Chem Rev 2021; 122:1052-1126. [PMID: 34846124 DOI: 10.1021/acs.chemrev.1c00574] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Biocatalysis, using enzymes for organic synthesis, has emerged as powerful tool for the synthesis of active pharmaceutical ingredients (APIs). The first industrial biocatalytic processes launched in the first half of the last century exploited whole-cell microorganisms where the specific enzyme at work was not known. In the meantime, novel molecular biology methods, such as efficient gene sequencing and synthesis, triggered breakthroughs in directed evolution for the rapid development of process-stable enzymes with broad substrate scope and good selectivities tailored for specific substrates. To date, enzymes are employed to enable shorter, more efficient, and more sustainable alternative routes toward (established) small molecule APIs, and are additionally used to perform standard reactions in API synthesis more efficiently. Herein, large-scale synthetic routes containing biocatalytic key steps toward >130 APIs of approved drugs and drug candidates are compared with the corresponding chemical protocols (if available) regarding the steps, reaction conditions, and scale. The review is structured according to the functional group formed in the reaction.
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Affiliation(s)
- Stefan Simić
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Erna Zukić
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Luca Schmermund
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Kurt Faber
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Christoph K Winkler
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Wolfgang Kroutil
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria.,Field of Excellence BioHealth─University of Graz, 8010 Graz, Austria.,BioTechMed Graz, 8010 Graz, Austria
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22
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Amorpha-4,11-diene synthase: a key enzyme in artemisinin biosynthesis and engineering. ABIOTECH 2021; 2:276-288. [PMID: 36303880 PMCID: PMC9590458 DOI: 10.1007/s42994-021-00058-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 07/16/2021] [Indexed: 10/20/2022]
Abstract
Amorpha-4,11-diene synthase (ADS) catalyzes the first committed step in the artemisinin biosynthetic pathway, which is the first catalytic reaction enzymatically and genetically characterized in artemisinin biosynthesis. The advent of ADS in Artemisia annua is considered crucial for the emergence of the specialized artemisinin biosynthetic pathway in the species. Microbial production of amorpha-4,11-diene is a breakthrough in metabolic engineering and synthetic biology. Recently, numerous new techniques have been used in ADS engineering; for example, assessing the substrate promiscuity of ADS to chemoenzymatically produce artemisinin. In this review, we discuss the discovery and catalytic mechanism of ADS, its application in metabolic engineering and synthetic biology, as well as the role of sesquiterpene synthases in the evolutionary origin of artemisinin.
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23
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Zhang G, Wang H, Zhang Z, Verstrepen KJ, Wang Q, Dai Z. Metabolic engineering of Yarrowia lipolytica for terpenoids production: advances and perspectives. Crit Rev Biotechnol 2021; 42:618-633. [PMID: 34325575 DOI: 10.1080/07388551.2021.1947183] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Terpenoids are a large family of natural products with diversified structures and functions that are widely used in the food, pharmaceutical, cosmetic, and agricultural fields. However, the traditional methods of terpenoids production such as plant extraction and chemical synthesis are inefficient due to the complex processes, high energy consumption, and low yields. With progress in metabolic engineering and synthetic biology, microbial cell factories provide an interesting alternative for the sustainable production of terpenoids. The non-conventional yeast, Yarrowia lipolytica, is a promising host for terpenoid biosynthesis due to its inherent mevalonate pathway, high fluxes of acetyl-CoA and NADPH, and the naturally hydrophobic microenvironment. In this review, we highlight progress in the engineering of Y. lipolytica as terpenoid biomanufacturing factories, describing the different terpenoid biosynthetic pathways and summarizing various metabolic engineering strategies, including progress in genetic manipulation, dynamic regulation, organelle engineering, and terpene synthase variants.
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Affiliation(s)
- Ge Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,TIB-VIB Joint Center of Synthetic Biology, National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Huan Wang
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing, China
| | - Ze Zhang
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing, China
| | - Kevin J Verstrepen
- TIB-VIB Joint Center of Synthetic Biology, National Center of Technology Innovation for Synthetic Biology, Tianjin, China.,VIB-KU Leuven Center for Microbiology and KU Leuven Laboratory for Genetics and Genomics, Department M2S, Leuven, Belgium
| | - Qinhong Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,TIB-VIB Joint Center of Synthetic Biology, National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Zongjie Dai
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,TIB-VIB Joint Center of Synthetic Biology, National Center of Technology Innovation for Synthetic Biology, Tianjin, China
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24
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Luo ZW, Ahn JH, Chae TU, Choi SY, Park SY, Choi Y, Kim J, Prabowo CPS, Lee JA, Yang D, Han T, Xu H, Lee SY. Metabolic Engineering of
Escherichia
coli. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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25
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Moore SJ, Hleba YB, Bischoff S, Bell D, Polizzi KM, Freemont PS. Refactoring of a synthetic raspberry ketone pathway with EcoFlex. Microb Cell Fact 2021; 20:116. [PMID: 34112158 PMCID: PMC8193874 DOI: 10.1186/s12934-021-01604-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/31/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND A key focus of synthetic biology is to develop microbial or cell-free based biobased routes to value-added chemicals such as fragrances. Originally, we developed the EcoFlex system, a Golden Gate toolkit, to study genes/pathways flexibly using Escherichia coli heterologous expression. In this current work, we sought to use EcoFlex to optimise a synthetic raspberry ketone biosynthetic pathway. Raspberry ketone is a high-value (~ £20,000 kg-1) fine chemical farmed from raspberry (Rubeus rubrum) fruit. RESULTS By applying a synthetic biology led design-build-test-learn cycle approach, we refactor the raspberry ketone pathway from a low level of productivity (0.2 mg/L), to achieve a 65-fold (12.9 mg/L) improvement in production. We perform this optimisation at the prototype level (using microtiter plate cultures) with E. coli DH10β, as a routine cloning host. The use of E. coli DH10β facilitates the Golden Gate cloning process for the screening of combinatorial libraries. In addition, we also newly establish a novel colour-based phenotypic screen to identify productive clones quickly from solid/liquid culture. CONCLUSIONS Our findings provide a stable raspberry ketone pathway that relies upon a natural feedstock (L-tyrosine) and uses only constitutive promoters to control gene expression. In conclusion we demonstrate the capability of EcoFlex for fine-tuning a model fine chemical pathway and provide a range of newly characterised promoter tools gene expression in E. coli.
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Affiliation(s)
- Simon J Moore
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, UK.,Department Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, UK.,School of Biosciences, University of Kent, CT2 7NJ, Canterbury, England
| | - Yonek B Hleba
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, UK.,Department Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, UK
| | - Sarah Bischoff
- School of Biosciences, University of Kent, CT2 7NJ, Canterbury, England
| | - David Bell
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, UK.,Department Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, UK
| | - Karen M Polizzi
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, UK. .,Department of Life Sciences, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, UK. .,Department of Chemical Engineering, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, UK.
| | - Paul S Freemont
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, UK. .,Department Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, UK. .,The London Biofoundry, Imperial College Translation & Innovation Hub, White City Campus, 80 Wood Lane, London, W12 0BZ, UK. .,Dementia Research Institute Care Research and Technology Centre, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK.
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26
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When Carotenoid Biosynthesis Genes Met Escherichia coli : The Early Days and These Days. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021. [PMID: 33783740 DOI: 10.1007/978-981-15-7360-6_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Nowadays, carotenoid biosynthetic pathways are sufficiently elucidated at gene levels in bacteria, fungi, and higher plants. Also, in pathway engineering for isoprenoid (terpene) production, carotenoids have been one of the most studied targets. However, in 1988 when the author started carotenoid research, almost no carotenoid biosynthesis genes were identified. It was because carotenogenic enzymes are easily inactivated when extracted from their organism sources, indicating that their purification and the subsequent cloning of the corresponding genes were infeasible or difficult. On the other hand, natural product chemistry of carotenoids had advanced a great deal. Thus, those days, carotenoid biosynthetic pathways had been proposed based mainly on the chemical structures of carotenoids without findings on relevant enzymes and genes. This chapter shows what happened on carotenoid research, when carotenoid biosynthesis genes met non-carotenogenic Escherichia coli around 1990, followed by subsequent developments.
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27
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Zhou A, Zhou K, Li Y. Rational design strategies for functional reconstitution of plant cytochrome P450s in microbial systems. CURRENT OPINION IN PLANT BIOLOGY 2021; 60:102005. [PMID: 33647811 PMCID: PMC8435529 DOI: 10.1016/j.pbi.2021.102005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/07/2021] [Accepted: 01/17/2021] [Indexed: 05/08/2023]
Abstract
Plant natural products (NPs) are of pharmaceutical and agricultural significance, yet the low abundance is largely impeding the broad investigation and utilization. Microbial bioproduction is a promising alternative sourcing to plant NPs. Cytochrome P450s (CYPs) play an essential role in plant secondary metabolism, and functional reconstitution of plant CYPs in the microbial system is one of the major challenges in establishing efficient microbial plant NP bioproduction. In this review, we briefly summarized the recent progress in rational engineering strategies for enhanced activity of plant CYPs in Escherichia coli and Saccharomyces cerevisiae, two commonly used microbial hosts. We believe that in-depth foundational investigations on the native microenvironment of plant CYPs are necessary to adapt the microbial systems for more efficient functional reconstitution of plant CYPs.
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Affiliation(s)
- Anqi Zhou
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521, USA
| | - Kang Zhou
- Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore; Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore.
| | - Yanran Li
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521, USA.
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28
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Ma C, Zhang K, Zhang X, Liu G, Zhu T, Che Q, Li D, Zhang G. Heterologous expression and metabolic engineering tools for improving terpenoids production. Curr Opin Biotechnol 2021; 69:281-289. [PMID: 33770560 DOI: 10.1016/j.copbio.2021.02.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 02/06/2023]
Abstract
Terpenoids, also referred to as isoprenoids, are the largest group of natural compounds which have contributed significantly to the pharmaceutical industry. The challenges in producing bioactive terpenoids from their original host or by organic synthesis methods spurred the endeavors of producing terpenoids in heterologous host. Modern advances utilizing synthetic biology and biological engineering tools have provided a variety of pharmaceutical terpenoids in large-scale and with diversified structures. In this review, we will summarize the progress in production of typical terpenoids skeletons using heterologous expression method assisted by metabolic engineering techniques, with the purpose of enlightening further efforts in developing advanced cell factories for producing terpenoid based pharmaceuticals.
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Affiliation(s)
- Chuanteng Ma
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, People's Republic of China
| | - Kaijin Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, People's Republic of China
| | - Xianyan Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, People's Republic of China
| | - Guowei Liu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, People's Republic of China
| | - Tianjiao Zhu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, People's Republic of China
| | - Qian Che
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, People's Republic of China
| | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, People's Republic of China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao, People's Republic of China
| | - Guojian Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, People's Republic of China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao, People's Republic of China.
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29
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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: 36] [Impact Index Per Article: 12.0] [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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30
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Wang X, Pereira JH, Tsutakawa S, Fang X, Adams PD, Mukhopadhyay A, Lee TS. Efficient production of oxidized terpenoids via engineering fusion proteins of terpene synthase and cytochrome P450. Metab Eng 2021; 64:41-51. [PMID: 33482331 DOI: 10.1016/j.ymben.2021.01.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 12/08/2020] [Accepted: 01/11/2021] [Indexed: 12/18/2022]
Abstract
The functionalization of terpenes using cytochrome P450 enzymes is a versatile route to the production of useful derivatives that can be further converted to value-added products. Many terpenes are hydrophobic and volatile making their availability as a substrate for P450 enzymes significantly limited during microbial production. In this study, we developed a strategy to improve the accessibility of terpene molecules for the P450 reaction by linking terpene synthase and P450 together. As a model system, fusion proteins of 1,8-cineole synthase (CS) and P450cin were investigated and it showed an improved hydroxylation of the monoterpenoid 1,8-cineole up to 5.4-fold. Structural analysis of the CS-P450cin fusion proteins by SEC-SAXS indicated a dimer formation with preferred orientations of the active sites of the two domains. We also applied the enzyme fusion strategy to the oxidation of a sesquiterpene epi-isozizaene and the fusion enzymes significantly improved albaflavenol production in engineered E. coli. From the analysis of positive and negative examples of the fusion strategy, we proposed key factors in structure-based prediction and evaluation of fusion enzymes. Developing fusion enzymes for terpene synthase and P450 presents an efficient strategy toward oxidation of hydrophobic terpene compounds. This strategy could be widely applicable to improve the biosynthetic titer of the functionalized products from hydrophobic terpene intermediates.
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Affiliation(s)
- Xi Wang
- Joint BioEnergy Institute (JBEI), 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jose Henrique Pereira
- Joint BioEnergy Institute (JBEI), 5885 Hollis St., Emeryville, CA, 94608, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Susan Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Xinyue Fang
- Joint BioEnergy Institute (JBEI), 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Department of Molecular & Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Paul D Adams
- Joint BioEnergy Institute (JBEI), 5885 Hollis St., Emeryville, CA, 94608, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute (JBEI), 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Taek Soon Lee
- Joint BioEnergy Institute (JBEI), 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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31
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Wang S, Liu Z, Wang X, Sun T, Zou L. Cloning and characterization of a phosphomevalonate kinase gene from Sanghuangporus baumii. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1938678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Shixin Wang
- Department of Forest Conservation, College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, PR China
| | - Zengcai Liu
- Department of Forest Conservation, College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, PR China
| | - Xutong Wang
- Department of Forest Conservation, College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, PR China
| | - Tingting Sun
- Department of Food Engineering, College of Food Science, Harbin University, Harbin, Heilongjiang, PR China
| | - Li Zou
- Department of Forest Conservation, College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, PR China
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32
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Kim J, Hoang Nguyen Tran P, Lee SM. Current Challenges and Opportunities in Non-native Chemical Production by Engineered Yeasts. Front Bioeng Biotechnol 2021; 8:594061. [PMID: 33381497 PMCID: PMC7767886 DOI: 10.3389/fbioe.2020.594061] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/24/2020] [Indexed: 11/13/2022] Open
Abstract
Yeasts are promising industrial hosts for sustainable production of fuels and chemicals. Apart from efficient bioethanol production, yeasts have recently demonstrated their potential for biodiesel production from renewable resources. The fuel-oriented product profiles of yeasts are now expanding to include non-native chemicals with the advances in synthetic biology. In this review, current challenges and opportunities in yeast engineering for sustainable production of non-native chemicals will be discussed, with a focus on the comparative evaluation of a bioethanol-producing Saccharomyces cerevisiae strain and a biodiesel-producing Yarrowia lipolytica strain. Synthetic pathways diverging from the distinctive cellular metabolism of these yeasts guide future directions for product-specific engineering strategies for the sustainable production of non-native chemicals on an industrial scale.
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Affiliation(s)
- Jiwon Kim
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, South Korea.,Department of Biotechnology, Korea University, Seoul, South Korea
| | - Phuong Hoang Nguyen Tran
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, South Korea.,Division of Energy and Environment Technology, University of Science and Technology (UST), Daejeon, South Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, South Korea.,Division of Energy and Environment Technology, University of Science and Technology (UST), Daejeon, South Korea.,Green School, Korea University, Seoul, South Korea
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33
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Daletos G, Stephanopoulos G. Protein engineering strategies for microbial production of isoprenoids. Metab Eng Commun 2020; 11:e00129. [PMID: 32612930 PMCID: PMC7322351 DOI: 10.1016/j.mec.2020.e00129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 04/06/2020] [Accepted: 04/24/2020] [Indexed: 01/16/2023] Open
Abstract
Isoprenoids comprise one of the most chemically diverse family of natural products with high commercial interest. The structural diversity of isoprenoids is mainly due to the modular activity of three distinct classes of enzymes, including prenyl diphosphate synthases, terpene synthases, and cytochrome P450s. The heterologous expression of these enzymes in microbial systems is suggested to be a promising sustainable way for the production of isoprenoids. Several limitations are associated with native enzymes, such as low stability, activity, and expression profiles. To address these challenges, protein engineering has been applied to improve the catalytic activity, selectivity, and substrate turnover of enzymes. In addition, the natural promiscuity and modular fashion of isoprenoid enzymes render them excellent targets for combinatorial studies and the production of new-to-nature metabolites. In this review, we discuss key individual and multienzyme level strategies for the successful implementation of enzyme engineering towards efficient microbial production of high-value isoprenoids. Challenges and future directions of protein engineering as a complementary strategy to metabolic engineering are likewise outlined.
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Affiliation(s)
- Georgios Daletos
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
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34
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Muhammad A, Feng X, Rasool A, Sun W, Li C. Production of plant natural products through engineered Yarrowia lipolytica. Biotechnol Adv 2020; 43:107555. [DOI: 10.1016/j.biotechadv.2020.107555] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/13/2020] [Accepted: 05/12/2020] [Indexed: 12/18/2022]
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35
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Carpita NC, McCann MC. Redesigning plant cell walls for the biomass-based bioeconomy. J Biol Chem 2020; 295:15144-15157. [PMID: 32868456 PMCID: PMC7606688 DOI: 10.1074/jbc.rev120.014561] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/30/2020] [Indexed: 01/28/2023] Open
Abstract
Lignocellulosic biomass-the lignin, cellulose, and hemicellulose that comprise major components of the plant cell well-is a sustainable resource that could be utilized in the United States to displace oil consumption from heavy vehicles, planes, and marine-going vessels and commodity chemicals. Biomass-derived sugars can also be supplied for microbial fermentative processing to fuels and chemicals or chemically deoxygenated to hydrocarbons. However, the economic value of biomass might be amplified by diversifying the range of target products that are synthesized in living plants. Genetic engineering of lignocellulosic biomass has previously focused on changing lignin content or composition to overcome recalcitrance, the intrinsic resistance of cell walls to deconstruction. New capabilities to remove lignin catalytically without denaturing the carbohydrate moiety have enabled the concept of the "lignin-first" biorefinery that includes high-value aromatic products. The structural complexity of plant cell-wall components also provides substrates for polymeric and functionalized target products, such as thermosets, thermoplastics, composites, cellulose nanocrystals, and nanofibers. With recent advances in the design of synthetic pathways, lignocellulosic biomass can be regarded as a substrate at various length scales for liquid hydrocarbon fuels, chemicals, and materials. In this review, we describe the architectures of plant cell walls and recent progress in overcoming recalcitrance and illustrate the potential for natural or engineered biomass to be used in the emerging bioeconomy.
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Affiliation(s)
- Nicholas C Carpita
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA; Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Maureen C McCann
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA; Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA.
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36
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Bradley SA, Zhang J, Jensen MK. Deploying Microbial Synthesis for Halogenating and Diversifying Medicinal Alkaloid Scaffolds. Front Bioeng Biotechnol 2020; 8:594126. [PMID: 33195162 PMCID: PMC7644825 DOI: 10.3389/fbioe.2020.594126] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/02/2020] [Indexed: 11/13/2022] Open
Abstract
Plants produce some of the most potent therapeutics and have been used for thousands of years to treat human diseases. Today, many medicinal natural products are still extracted from source plants at scale as their complexity precludes total synthesis from bulk chemicals. However, extraction from plants can be an unreliable and low-yielding source for human therapeutics, making the supply chain for some of these life-saving medicines expensive and unstable. There has therefore been significant interest in refactoring these plant pathways in genetically tractable microbes, which grow more reliably and where the plant pathways can be more easily engineered to improve the titer, rate and yield of medicinal natural products. In addition, refactoring plant biosynthetic pathways in microbes also offers the possibility to explore new-to-nature chemistry more systematically, and thereby help expand the chemical space that can be probed for drugs as well as enable the study of pharmacological properties of such new-to-nature chemistry. This perspective will review the recent progress toward heterologous production of plant medicinal alkaloids in microbial systems. In particular, we focus on the refactoring of halogenated alkaloids in yeast, which has created an unprecedented opportunity for biosynthesis of previously inaccessible new-to-nature variants of the natural alkaloid scaffolds.
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Affiliation(s)
| | | | - Michael K. Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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37
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Pramastya H, Xue D, Abdallah II, Setroikromo R, Quax WJ. High level production of amorphadiene using Bacillus subtilis as an optimized terpenoid cell factory. N Biotechnol 2020; 60:159-167. [PMID: 33148534 DOI: 10.1016/j.nbt.2020.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/09/2023]
Abstract
The anti-malarial drug artemisinin, produced naturally in the plant Artemisia annua, experiences unstable and insufficient supply as its production relies heavily on the plant source. To meet the massive demand for this compound, metabolic engineering of microbes has been studied extensively. In this study, we focus on improving the production of amorphadiene, a crucial artemisinin precursor, in Bacillus subtilis. The expression level of the plant-derived amorphadiene synthase (ADS) was upregulated by fusion with green fluorescent protein (GFP). Furthermore, a co-expression system of ADS and a synthetic operon carrying the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway genes was established. Subsequently, farnesyl pyrophosphate synthase (FPPS), a key enzyme in formation of the sesquiterpene precursor farnesyl pyrophosphate (FPP), was expressed to supply sufficient substrate for ADS. The consecutive combination of these features yielded a B. subtilis strain expressing chromosomally integrated GFP-ADS followed by FPPS and a plasmid encoded synthetic operon showing a stepwise increased production of amorphadiene. An experimental design-aided systematic medium optimization was used to maximize the production level for the most promising engineered B. subtilis strain, resulting in an amorphadiene yield of 416 ± 15 mg/L, which is 20-fold higher than that previously reported in B. subtilis and more than double the production in Escherichia coli or Saccharomyces cerevisiae on a shake flask fermentation level.
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Affiliation(s)
- Hegar Pramastya
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, the Netherlands; Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, 40132, Bandung, Indonesia
| | - Dan Xue
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, the Netherlands
| | - Ingy I Abdallah
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, the Netherlands; Department of Pharmacognosy, Faculty of Pharmacy, Alexandria University, Egypt
| | - Rita Setroikromo
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, the Netherlands
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, the Netherlands.
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38
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Malico AA, Calzini MA, Gayen AK, Williams GJ. Synthetic biology, combinatorial biosynthesis, and chemo‑enzymatic synthesis of isoprenoids. J Ind Microbiol Biotechnol 2020; 47:675-702. [PMID: 32880770 PMCID: PMC7666032 DOI: 10.1007/s10295-020-02306-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 08/27/2020] [Indexed: 12/12/2022]
Abstract
Isoprenoids are a large class of natural products with myriad applications as bioactive and commercial compounds. Their diverse structures are derived from the biosynthetic assembly and tailoring of their scaffolds, ultimately constructed from two C5 hemiterpene building blocks. The modular logic of these platforms can be harnessed to improve titers of valuable isoprenoids in diverse hosts and to produce new-to-nature compounds. Often, this process is facilitated by the substrate or product promiscuity of the component enzymes, which can be leveraged to produce novel isoprenoids. To complement rational enhancements and even re-programming of isoprenoid biosynthesis, high-throughput approaches that rely on searching through large enzymatic libraries are being developed. This review summarizes recent advances and strategies related to isoprenoid synthetic biology, combinatorial biosynthesis, and chemo-enzymatic synthesis, focusing on the past 5 years. Emerging applications of cell-free biosynthesis and high-throughput tools are included that culminate in a discussion of the future outlook and perspective of isoprenoid biosynthetic engineering.
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Affiliation(s)
| | - Miles A Calzini
- Department of Chemistry, NC State University, Raleigh, NC, 27695, USA
| | - Anuran K Gayen
- Department of Chemistry, NC State University, Raleigh, NC, 27695, USA
| | - Gavin J Williams
- Department of Chemistry, NC State University, Raleigh, NC, 27695, USA.
- Comparative Medicine Institute, NC State University, Raleigh, NC, 27695, USA.
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39
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Engineering a Carotenoid-Overproducing Strain of Azospirillum brasilense for Heterologous Production of Geraniol and Amorphadiene. Appl Environ Microbiol 2020; 86:AEM.00414-20. [PMID: 32591387 DOI: 10.1128/aem.00414-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 06/22/2020] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli and Saccharomyces cerevisiae have been used extensively for heterologous production of a variety of secondary metabolites. Neither has an endogenous high-flux isoprenoid pathway, required for the production of terpenoids. Azospirillum brasilense, a nonphotosynthetic GRAS (generally recognized as safe) bacterium, produces carotenoids in the presence of light. The carotenoid production increases multifold upon inactivating a gene encoding an anti-sigma factor (ChrR1). We used this A. brasilense mutant (Car-1) as a host for the heterologous production of two high-value phytochemicals, geraniol and amorphadiene. Cloned genes (crtE1 and crtE2) of A. brasilense encoding native geranylgeranyl pyrophosphate synthases (GGPPS), when overexpressed and purified, did not produce geranyl pyrophosphate (GPP) in vitro Therefore, we cloned codon-optimized copies of the Catharanthus roseus genes encoding GPP synthase (GPPS) and geraniol synthase (GES) to show the endogenous intermediates of the carotenoid biosynthetic pathway in the Car-1 strain were utilized for the heterologous production of geraniol in A. brasilense Similarly, cloning and expression of a codon-optimized copy of the amorphadiene synthase (ads) gene from Artemisia annua also led to the heterologous production of amorphadiene in Car-1. Geraniol or amorphadiene content was estimated using gas chromatography-mass spectrometry (GC-MS) and GC. These results demonstrate that Car-1 is a promising host for metabolic engineering, as the naturally available endogenous pool of the intermediates of the carotenoid biosynthetic pathway of A. brasilense can be effectively utilized for the heterologous production of high-value phytochemicals.IMPORTANCE To date, the major host organisms used for the heterologous production of terpenoids, i.e., E. coli and S. cerevisiae, do not have high-flux isoprenoid pathways and involve tedious metabolic engineering to increase the precursor pool. Since carotenoid-producing bacteria carry endogenous high-flux isoprenoid pathways, we used a carotenoid-producing mutant of A. brasilense as a host to show its suitability for the heterologous production of geraniol and amorphadiene as a proof-of-concept. The advantages of using A. brasilense as a model system include (i) dispensability of carotenoids and (ii) the possibility of overproducing carotenoids through a single mutation to exploit high carbon flux for terpenoid production.
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40
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Liu X, Zhu X, Wang H, Liu T, Cheng J, Jiang H. Discovery and modification of cytochrome P450 for plant natural products biosynthesis. Synth Syst Biotechnol 2020; 5:187-199. [PMID: 32637672 PMCID: PMC7332504 DOI: 10.1016/j.synbio.2020.06.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/21/2020] [Accepted: 06/22/2020] [Indexed: 11/28/2022] Open
Abstract
Cytochrome P450s are widespread in nature and play key roles in the diversification and functional modification of plant natural products. Over the last few years, there has been remarkable progress in plant P450s identification with the rapid development of sequencing technology, "omics" analysis and synthetic biology. However, challenges still persist in respect of crystal structure, heterologous expression and enzyme engineering. Here, we reviewed several research hotspots of P450 enzymes involved in the biosynthesis of plant natural products, including P450 databases, gene mining, heterologous expression and protein engineering.
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Affiliation(s)
- Xiaonan Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxi Zhu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Wang
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Tian Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Jian Cheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Huifeng Jiang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
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41
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Yang D, Park SY, Park YS, Eun H, Lee SY. Metabolic Engineering of Escherichia coli for Natural Product Biosynthesis. Trends Biotechnol 2020; 38:745-765. [DOI: 10.1016/j.tibtech.2019.11.007] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/16/2019] [Accepted: 11/18/2019] [Indexed: 12/27/2022]
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42
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Huang L, Ho CT, Wang Y. Biosynthetic pathways and metabolic engineering of spice flavors. Crit Rev Food Sci Nutr 2020; 61:2047-2060. [PMID: 32462891 DOI: 10.1080/10408398.2020.1769547] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Historically, spices have played an important economic role, due to their large applications and unique flavor. The supply and cost of spice materials and their corresponding natural products are often affected by environmental, geopolitical and climatic conditions. Secondary metabolite composition, including certain flavor compounds in spice plants, is recognized and considered closely related to plant classification. Both genes and enzymes involved in the biosynthesis of spice flavors are constantly identified, which provides insight into metabolic engineering of flavor compounds (i.e. aroma and pungent compounds) from spice plants. In this review, a systematic meta-analysis was carried out based on a comprehensive literature survey of the flavor profiles of 36 spice plants from nine families. We also reviewed typical biosynthetic pathways and metabolic engineering of most representative aroma and pungent compounds that may assist in the future study of spice plants as biosynthetic factories facing a new challenge in creating spice products.
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Affiliation(s)
- Linhua Huang
- Citrus Research Institute, Southwest University, Xiema, Beibei, Chongqing, China.,Citrus Research and Education Center, University of Florida, Florida, USA
| | - Chi-Tang Ho
- Department of Food Science, Rutgers University, New Brunswick, NJ, USA
| | - Yu Wang
- Citrus Research and Education Center, University of Florida, Florida, USA
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43
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Xu X, Zhong H, Liu W, Tao Y. Extension of Genetic Marker List Using Unnatural Amino Acid System: An Efficient Genomic Modification Strategy in Escherichia coli. Front Bioeng Biotechnol 2020; 8:145. [PMID: 32411679 PMCID: PMC7198746 DOI: 10.3389/fbioe.2020.00145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/12/2020] [Indexed: 11/24/2022] Open
Abstract
Genetic manipulations including chromosome engineering are essential techniques used to restructure cell metabolism. Lambda/Red (λ/Red)-mediated recombination is the most commonly applied approach for chromosomal modulation in Escherichia coli. However, the efficiency of this method is significantly hampered by the laborious removal of the selectable markers. To overcome the problem, the integration helper plasmid was constructed, pSBC1a-CtR, which contains Red recombinase, Cre recombinase, and exogenous orthogonal aminoacyl-transfer RNA (tRNA) synthetase/tRNA pairs, allows an unnatural amino acid (UAA) to be genetically encoded at the defined site of the antibiotic resistance gene-encoded protein. When UAAs are not in the culture medium, there was no expression in the antibiotic resistance gene-encoded protein. Accordingly, the next procedure of antibiotic gene excising is not needed. To verify this method, poxB gene was knocked out successfully. Furthermore, sequential deletion of three target genes (galR, ptsG, and pgi) was able to generate neurosporene-producing strain marked by high growth rate. Thus, the site-specific incorporation UAA mutagenesis system were used to control and expand the use of conditional selectable marker, and the technique is used to facilitate a rapid continuous genome editing in Escherichia coli.
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Affiliation(s)
- Xinyi Xu
- Engineering Research Center of Molecular and & Neuroimaging, Ministry of Education, School of Life Sciences and Technology, Xidian University, Xi'an, China.,Chinese Academy of Sciences Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | | | - Weifeng Liu
- Chinese Academy of Sciences Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yong Tao
- Chinese Academy of Sciences Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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44
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Frey M. Traps and Pitfalls-Unspecific Reactions in Metabolic Engineering of Sesquiterpenoid Pathways. Molecules 2020; 25:E1935. [PMID: 32331245 PMCID: PMC7221646 DOI: 10.3390/molecules25081935] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/19/2020] [Accepted: 04/21/2020] [Indexed: 02/06/2023] Open
Abstract
The characterization of plant enzymes by expression in prokaryotic and eukaryotic (yeast and plants) heterologous hosts has widely been used in recent decades to elucidate metabolic pathways in plant secondary metabolism. Yeast and plant systems provide the cellular environment of a eukaryotic cell and the subcellular compartmentalization necessary to facilitate enzyme function. The expression of candidate genes in these cell systems and the identification of the resulting products guide the way for the identification of enzymes with new functions. However, in many cases, the detected compounds are not the direct enzyme products but are caused by unspecific subsequent reactions. Even if the mechanisms for these unspecific reactions are in many cases widely reported, there is a lack of overview of potential reactions that may occur to provide a guideline for researchers working on the characterization of new enzymes. Here, an across-the-board summary of rearrangement reactions of sesquiterpenes in metabolic pathway engineering is presented. The different kinds of unspecific reactions as well as their chemical and cellular background are explained and strategies how to spot and how to avoid these unspecific reactions are given. Also, a systematic approach of classification of unspecific reactions is introduced. It is hoped that this mini-review will stimulate a discussion on how to systematically classify unspecific reactions in metabolic engineering and to expand this approach to other classes of plant secondary metabolites.
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Affiliation(s)
- Maximilian Frey
- Institute of Biology, Dept. of Biochemistry of Plant Secondary Metabolism (190b), University of Hohenheim, Garbenstraße 30, 70593 Stuttgart, Germany
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45
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Bacteria as genetically programmable producers of bioactive natural products. Nat Rev Chem 2020; 4:172-193. [PMID: 37128046 DOI: 10.1038/s41570-020-0176-1] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2020] [Indexed: 12/17/2022]
Abstract
Next to plants, bacteria account for most of the biomass on Earth. They are found everywhere, although certain species thrive only in specific ecological niches. These microorganisms biosynthesize a plethora of both primary and secondary metabolites, defined, respectively, as those required for the growth and maintenance of cellular functions and those not required for survival but offering a selective advantage for the producer under certain conditions. As a result, bacterial fermentation has long been used to manufacture valuable natural products of nutritional, agrochemical and pharmaceutical interest. The interactions of secondary metabolites with their biological targets have been optimized by millions of years of evolution and they are, thus, considered to be privileged chemical structures, not only for drug discovery. During the last two decades, functional genomics has allowed for an in-depth understanding of the underlying biosynthetic logic of secondary metabolites. This has, in turn, paved the way for the unprecedented use of bacteria as programmable biochemical workhorses. In this Review, we discuss the multifaceted use of bacteria as biological factories in diverse applications and highlight recent advances in targeted genetic engineering of bacteria for the production of valuable bioactive compounds. Emphasis is on current advances to access nature's abundance of natural products.
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46
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Lu Y, Yang Q, Lin Z, Yang X. A modular pathway engineering strategy for the high-level production of β-ionone in Yarrowia lipolytica. Microb Cell Fact 2020; 19:49. [PMID: 32103761 PMCID: PMC7045511 DOI: 10.1186/s12934-020-01309-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/17/2020] [Indexed: 12/21/2022] Open
Abstract
Background The GRAS and oleaginous yeast Yarrowia lipolytica (Y. lipolytica) is an attractive cell factory for the production of chemicals and biofuels. The production of many natural products of commercial interest have been investigated in this cell factory by introducing heterologous biosynthetic pathways and by modifying the endogenous pathways. However, since natural products anabolism involves long pathways and complex regulation, re-channelling carbon into the product of target compounds is still a cumbersome work, and often resulting in low production performance. Results In this work, the carotenogenic genes contained carB and bi-functional carRP from Mucor circinelloides and carotenoid cleavage dioxygenase 1 (CCD1) from Petunia hybrida were introduced to Y. lipolytica and led to the low production of β-ionone of 3.5 mg/L. To further improve the β-ionone synthesis, we implemented a modular engineering strategy for the construction and optimization of a biosynthetic pathway for the overproduction of β-ionone in Y. lipolytica. The strategy involved the enhancement of the cytosolic acetyl-CoA supply and the increase of MVA pathway flux, yielding a β-ionone titer of 358 mg/L in shake-flask fermentation and approximately 1 g/L (~ 280-fold higher than the baseline strain) in fed-batch fermentation. Conclusions An efficient β-ionone producing GRAS Y. lipolytica platform was constructed by combining integrated overexpressed of heterologous and native genes. A modular engineering strategy involved the optimization pathway and fermentation condition was investigated in the engineered strain and the highest β-ionone titer reported to date by a cell factory was achieved. This effective strategy can be adapted to enhance the biosynthesis of other terpenoids in Y. lipolytica.
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Affiliation(s)
- Yanping Lu
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou, 510006, China
| | - Qingyu Yang
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou, 510006, China
| | - Zhanglin Lin
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou, 510006, China.
| | - Xiaofeng Yang
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou, 510006, China.
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47
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Li M, Hou F, Wu T, Jiang X, Li F, Liu H, Xian M, Zhang H. Recent advances of metabolic engineering strategies in natural isoprenoid production using cell factories. Nat Prod Rep 2020; 37:80-99. [DOI: 10.1039/c9np00016j] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
This review covers the strategies mostly developed in the last three years for microbial production of isoprenoid, classified according to the engineering targets.
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Affiliation(s)
- Meijie Li
- Key Laboratory of Biobased Materials
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- P. R. China
| | - Feifei Hou
- Key Laboratory of Biobased Materials
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- P. R. China
| | - Tong Wu
- Key Laboratory of Biobased Materials
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- P. R. China
| | - Xinglin Jiang
- The Novo Nordisk Foundation Center for Biosustainability
- Technical University of Denmark
- Lyngby
- Denmark
| | - Fuli Li
- Key Laboratory of Biobased Materials
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- P. R. China
| | - Haobao Liu
- Ministry of Agriculture Key Laboratory for Tobacco Biology and Processing
- Tobacco Research Institute
- Chinese Academy of Agricultural Sciences
- Qingdao
- P. R. China
| | - Mo Xian
- Key Laboratory of Biobased Materials
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- P. R. China
| | - Haibo Zhang
- Key Laboratory of Biobased Materials
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- P. R. China
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48
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Helfrich EJN, Lin GM, Voigt CA, Clardy J. Bacterial terpene biosynthesis: challenges and opportunities for pathway engineering. Beilstein J Org Chem 2019; 15:2889-2906. [PMID: 31839835 PMCID: PMC6902898 DOI: 10.3762/bjoc.15.283] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/01/2019] [Indexed: 12/27/2022] Open
Abstract
Terpenoids are the largest and structurally most diverse class of natural products. They possess potent and specific biological activity in multiple assays and against diseases, including cancer and malaria as notable examples. Although the number of characterized terpenoid molecules is huge, our knowledge of how they are biosynthesized is limited, particularly when compared to the well-studied thiotemplate assembly lines. Bacteria have only recently been recognized as having the genetic potential to biosynthesize a large number of complex terpenoids, but our current ability to associate genetic potential with molecular structure is severely restricted. The canonical terpene biosynthetic pathway uses a single enzyme to form a cyclized hydrocarbon backbone followed by modifications with a suite of tailoring enzymes that can generate dozens of different products from a single backbone. This functional promiscuity of terpene biosynthetic pathways renders terpene biosynthesis susceptible to rational pathway engineering using the latest developments in the field of synthetic biology. These engineered pathways will not only facilitate the rational creation of both known and novel terpenoids, their development will deepen our understanding of a significant branch of biosynthesis. The biosynthetic insights gained will likely empower a greater degree of engineering proficiency for non-natural terpene biosynthetic pathways and pave the way towards the biotechnological production of high value terpenoids.
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Affiliation(s)
- Eric J N Helfrich
- Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, Boston, United States
| | - Geng-Min Lin
- Massachusetts Institute of Technology, Department of Biological Engineering, Cambridge, United States
| | - Christopher A Voigt
- Massachusetts Institute of Technology, Department of Biological Engineering, Cambridge, United States
| | - Jon Clardy
- Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, Boston, United States
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49
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Zhao TT, Feng GH, Chen W, Song YF, Dong X, Li GH, Zhang HJ, Wei W. Artificial bioconversion of carbon dioxide. CHINESE JOURNAL OF CATALYSIS 2019. [DOI: 10.1016/s1872-2067(19)63408-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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50
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Huang AC, Osbourn A. Plant terpenes that mediate below-ground interactions: prospects for bioengineering terpenoids for plant protection. PEST MANAGEMENT SCIENCE 2019; 75:2368-2377. [PMID: 30884099 PMCID: PMC6690754 DOI: 10.1002/ps.5410] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/05/2019] [Accepted: 03/13/2019] [Indexed: 05/03/2023]
Abstract
Plants are sessile organisms that have evolved various mechanisms to adapt to complex and changing environments. One important feature of plant adaption is the production of specialised metabolites. Terpenes are the largest class of specialised metabolites, with over 80 000 structures reported so far, and they have important ecological functions in plant adaptation. Here, we review the current knowledge on plant terpenes that mediate below-ground interactions between plants and other organisms, including microbes, herbivores and other plants. The discovery, functions and biosynthesis of these terpenes are discussed, and prospects for bioengineering terpenoids for plant protection are considered. © 2019 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Ancheng C Huang
- Department of Metabolic Biology, John Innes CentreNorwich Research ParkNorwichUK
| | - Anne Osbourn
- Department of Metabolic Biology, John Innes CentreNorwich Research ParkNorwichUK
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