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Azevedo A, Teixeira-Santos R, Gomes LC, Duarte SOD, Monteiro GA, Mergulhão FJ. Engineering Escherichia coli Biofilms for Curcumin Production. Molecules 2025; 30:2031. [PMID: 40363836 PMCID: PMC12073880 DOI: 10.3390/molecules30092031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2025] [Revised: 03/21/2025] [Accepted: 04/28/2025] [Indexed: 05/15/2025] Open
Abstract
Biofilms are emerging platforms for the production of valuable compounds. The present study is the first to assess the capacity of Escherichia coli biofilms to produce curcumin through the expression of a biosynthetic pathway involving three genes: 4-coumarate-CoA ligase (4CL), diketide-CoA synthase (DCS), and curcumin synthase (CURS). The effects of chemical induction with isopropyl β-d-1-thiogalactopyranoside (IPTG) and ferulic acid (FA), and the incubation temperature on biofilm formation and curcumin production were evaluated. Biofilms were formed in 12-well microtiter plates over three days and then induced with 1 mM IPTG and FA at 2 or 8 mM. After induction, the samples were incubated for two days at 26 or 30 °C. Total and culturable planktonic and biofilm cells, as well as biofilm thickness and volumetric and specific curcumin production, were assessed on days 3, 4, and 5. The results demonstrated that biofilms produced up to 10-fold higher curcumin levels (0.9-2.2 fg·cell-1) than their planktonic counterparts (0.1-0.3 fg·cell-1). The highest specific curcumin production (2.2 fg·cell-1) was achieved using 8 mM FA. However, no significant differences in curcumin production were observed between the induced samples incubated at the tested temperatures. These results validated the potential of biofilm systems for expressing a complete exogenous biosynthetic pathway using metabolic engineering, particularly for curcumin production.
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Affiliation(s)
- Ana Azevedo
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (A.A.); (R.T.-S.); (L.C.G.)
- ALICE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Rita Teixeira-Santos
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (A.A.); (R.T.-S.); (L.C.G.)
- ALICE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Luciana C. Gomes
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (A.A.); (R.T.-S.); (L.C.G.)
- ALICE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Sofia O. D. Duarte
- iBB—Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisboa, Portugal; (S.O.D.D.); (G.A.M.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Gabriel A. Monteiro
- iBB—Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisboa, Portugal; (S.O.D.D.); (G.A.M.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Filipe J. Mergulhão
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (A.A.); (R.T.-S.); (L.C.G.)
- ALICE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
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2
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Qiu D, Ding H, Zhou C, Hou Z, Zhang G. Ferulic acid production in Escherichia coli by engineering caffeic acid O-methyltransferase. Int J Biol Macromol 2025; 306:141764. [PMID: 40049493 DOI: 10.1016/j.ijbiomac.2025.141764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2024] [Revised: 03/02/2025] [Accepted: 03/03/2025] [Indexed: 05/03/2025]
Abstract
Methylation is a key step for the structure diversification of natural products, however, the low activity and substrate promiscuity of methyltransferase remain challenges for efficient biosynthesis. In this study, taking the synthesis of ferulic acid as a case, we attempted to improve the catalytic efficiency of caffeic acid O-methyltransferase (AtCOMT) by engineering its binding pocket and interactions with substrate. Through reshaping the substrate binding pocket and increasing the hydrogen bond network, L125R/I317E mutant with highly catalytic efficiency and substrate specificity was obtained. Compared with the wild-type AtCOMT, the kcat/Km increased by 5.79-fold. Molecular dynamics simulation verified that the increased activity and specificity of AtCOMT were derived from the tighter substrate binding pocket and stronger enzyme-substrate interactions produced by the designed hydrogen bonds and salt bridges. Eventually, 1.273 g/L ferulic acid was obtained by fed-batch fermentation, which was 21.3-fold compared with the WT. This work provided the foundation for efficient synthesis of ferulic acid by AtCOMT, and also illustrated that rational design of substrate binding pocket and hydrogen bond network would be an effective strategy for improving the activity and substrate specificity of enzyme.
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Affiliation(s)
- Di Qiu
- School of Chemistry and Chemical Engineering/ State Key Laboratory Incubation Base for Green Processing of Chemical Engineering, Shihezi University, Shihezi 832003, PR China
| | - Haifeng Ding
- School of Chemistry and Chemical Engineering/ State Key Laboratory Incubation Base for Green Processing of Chemical Engineering, Shihezi University, Shihezi 832003, PR China
| | - Chao Zhou
- School of Chemistry and Chemical Engineering/ State Key Laboratory Incubation Base for Green Processing of Chemical Engineering, Shihezi University, Shihezi 832003, PR China
| | - Zhenling Hou
- School of Chemistry and Chemical Engineering/ State Key Laboratory Incubation Base for Green Processing of Chemical Engineering, Shihezi University, Shihezi 832003, PR China
| | - Genlin Zhang
- School of Chemistry and Chemical Engineering/ State Key Laboratory Incubation Base for Green Processing of Chemical Engineering, Shihezi University, Shihezi 832003, PR China.
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3
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Bozkurt EU, Ørsted EC, Volke DC, Nikel PI. Accelerating enzyme discovery and engineering with high-throughput screening. Nat Prod Rep 2024. [PMID: 39403004 DOI: 10.1039/d4np00031e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
Abstract
Covering: up to August 2024Enzymes play an essential role in synthesizing value-added chemicals with high specificity and selectivity. Since enzymes utilize substrates derived from renewable resources, biocatalysis offers a pathway to an efficient bioeconomy with reduced environmental footprint. However, enzymes have evolved over millions of years to meet the needs of their host organisms, which often do not align with industrial requirements. As a result, enzymes frequently need to be tailored for specific industrial applications. Combining enzyme engineering with high-throughput screening has emerged as a key approach for developing novel biocatalysts, but several challenges are yet to be addressed. In this review, we explore emergent strategies and methods for isolating, creating, and characterizing enzymes optimized for bioproduction. We discuss fundamental approaches to discovering and generating enzyme variants and identifying those best suited for specific applications. Additionally, we cover techniques for creating libraries using automated systems and highlight innovative high-throughput screening methods that have been successfully employed to develop novel biocatalysts for natural product synthesis.
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Affiliation(s)
- Eray U Bozkurt
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Emil C Ørsted
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
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4
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Rainha J, Rodrigues JL, Rodrigues LR. De Novo Biosynthesis of Curcumin in Saccharomyces cerevisiae. ACS Synth Biol 2024; 13:1727-1736. [PMID: 38787640 PMCID: PMC11197086 DOI: 10.1021/acssynbio.4c00059] [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: 01/29/2024] [Revised: 05/17/2024] [Accepted: 05/17/2024] [Indexed: 05/26/2024]
Abstract
Curcumin, a natural polyphenol derived from turmeric, has attracted immense interest due to its diverse pharmacological properties. Traditional extraction methods from Curcuma longa plants present limitations in meeting the growing demand for this bioactive compound, giving significance to its production by genetically modified microorganisms. Herein, we have developed an engineered Saccharomyces cerevisiae to produce curcumin from glucose. A pathway composed of the 4-hydroxyphenylacetate 3-monooxygenase oxygenase complex from Pseudomonas aeruginosa and Salmonella enterica, caffeic acid O-methyltransferase from Arabidopsis thaliana, feruloyl-CoA synthetase from Pseudomonas paucimobilis, and diketide-CoA synthase and curcumin synthase from C. longa was introduced in a p-coumaric acid overproducing S. cerevisiae strain. This strain produced 240.1 ± 15.1 μg/L of curcumin. Following optimization of phenylpropanoids conversion, a strain capable of producing 4.2 ± 0.6 mg/L was obtained. This study reports for the first time the successful de novo production of curcumin in S. cerevisiae.
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Affiliation(s)
- João Rainha
- Centre
of Biological Engineering, University of
Minho, Braga 4710-057, Portugal
| | - Joana L. Rodrigues
- Centre
of Biological Engineering, University of
Minho, Braga 4710-057, Portugal
- LABBELS—Associate
Laboratory, Braga 4710-057, Portugal
| | - Lígia R. Rodrigues
- Centre
of Biological Engineering, University of
Minho, Braga 4710-057, Portugal
- LABBELS—Associate
Laboratory, Braga 4710-057, Portugal
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5
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Beganovic S, Wittmann C. Medical properties, market potential, and microbial production of golden polyketide curcumin for food, biomedical, and cosmetic applications. Curr Opin Biotechnol 2024; 87:103112. [PMID: 38518404 DOI: 10.1016/j.copbio.2024.103112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 03/01/2024] [Accepted: 03/03/2024] [Indexed: 03/24/2024]
Abstract
Curcumin, a potent plant polyketide in turmeric, has gained recognition for its outstanding health benefits, including anti-inflammatory, antioxidant, and anticancer effects. Classical turmeric farming, which is widely used to produce curcumin, is linked to deforestation, soil degradation, excessive water use, and reduced biodiversity. In recent years, the microbial synthesis of curcumin has been achieved and optimized through novel strategies, offering increased safety, improved sustainability, and the potential to revolutionize production. Here, we discuss recent breakthroughs in microbial engineering and fermentation techniques, as well as their capacity to increase the yield, purity, and cost-effectiveness of curcumin production. The utilization of microbial systems not only addresses supply chain limitations but also helps meet the growing demand for curcumin in various industries, including pharmaceuticals, foods, and cosmetics.
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Affiliation(s)
- Selma Beganovic
- Institute of Systems Biotechnology, Saarland University, Germany
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6
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Utomo JC, Barrell HB, Kumar R, Smith J, Brant MS, De la Hoz Siegler H, Ro DK. Reconstructing curcumin biosynthesis in yeast reveals the implication of caffeoyl-shikimate esterase in phenylpropanoid metabolic flux. Metab Eng 2024; 82:286-296. [PMID: 38387678 DOI: 10.1016/j.ymben.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/31/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
Curcumin is a polyphenolic natural product from the roots of turmeric (Curcuma longa). It has been a popular coloring and flavoring agent in food industries with known health benefits. The conventional phenylpropanoid pathway is known to proceed from phenylalanine via p-coumaroyl-CoA intermediate. Although hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) plays a key catalysis in the biosynthesis of phenylpropanoid products at the downstream of p-coumaric acid, a recent discovery of caffeoyl-shikimate esterase (CSE) showed that an alternative pathway exists. Here, the biosynthetic efficiency of the conventional and the alternative pathway in producing feruloyl-CoA was examined using curcumin production in yeast. A novel modular multiplex genome-edit (MMG)-CRISPR platform was developed to facilitate rapid integrations of up to eight genes into the yeast genome in two steps. Using this MMG-CRISPR platform and metabolic engineering strategies, the alternative CSE phenylpropanoid pathway consistently showed higher titers (2-19 folds) of curcumin production than the conventional pathway in engineered yeast strains. In shake flask cultures using a synthetic minimal medium without phenylalanine, the curcumin production titer reached up to 1.5 mg/L, which is three orders of magnitude (∼4800-fold) improvement over non-engineered base strain. This is the first demonstration of de novo curcumin biosynthesis in yeast. Our work shows the critical role of CSE in improving the metabolic flux in yeast towards the phenylpropanoid biosynthetic pathway. In addition, we showcased the convenience and reliability of modular multiplex CRISPR/Cas9 genome editing in constructing complex synthetic pathways in yeast.
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Affiliation(s)
- Joseph Christian Utomo
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Hailey Brynn Barrell
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Rahul Kumar
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Jessica Smith
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Maximilian Simon Brant
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Hector De la Hoz Siegler
- Department of Chemical and Petroleum Engineering, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Dae-Kyun Ro
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada.
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7
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Chen J, Wang W, Wang L, Wang H, Hu M, Zhou J, Du G, Zeng W. Efficient De Novo Biosynthesis of Curcumin in Escherichia coli by Optimizing Pathway Modules and Increasing the Malonyl-CoA Supply. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:566-576. [PMID: 38154088 DOI: 10.1021/acs.jafc.3c07379] [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: 12/30/2023]
Abstract
Curcumin is a natural phenylpropanoid compound with various biological activities and is widely used in food and pharmaceuticals. A de novo curcumin biosynthetic pathway was constructed in Escherichia coli BL21(DE3). Optimization of the curcumin biosynthesis module achieved a curcumin titer of 26.8 ± 0.6 mg/L. Regulating the metabolic fluxes of the β-oxidation pathway and fatty acid elongation cycle and blocking the endogenous malonyl-CoA consumption pathway increased the titer to 113.6 ± 7.1 mg/L. Knockout of endogenous curcumin reductase (curA) and intermediate product detoxification by heterologous expression of the solvent-resistant pump (srpB) increased the titer to 137.5 ± 3.0 mg/L. A 5 L pilot-scale fermentation, using a three-stage pH alternation strategy, increased the titer to 696.2 ± 20.9 mg/L, 178.5-fold higher than the highest curcumin titer from de novo biosynthesis previously reported, thereby laying the foundation for efficient biosynthesis of curcumin and its derivatives.
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Affiliation(s)
- Jianbin Chen
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Weigao Wang
- Department of Chemical Engineering, Stanford University, 443 Via Ortega, Stanford, California 94305, United States
| | - Lian Wang
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Huijing Wang
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - MingLong Hu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Weizhu Zeng
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
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Barreto JVDO, Casanova LM, Junior AN, Reis-Mansur MCPP, Vermelho AB. Microbial Pigments: Major Groups and Industrial Applications. Microorganisms 2023; 11:2920. [PMID: 38138065 PMCID: PMC10745774 DOI: 10.3390/microorganisms11122920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Microbial pigments have many structures and functions with excellent characteristics, such as being biodegradable, non-toxic, and ecologically friendly, constituting an important source of pigments. Industrial production presents a bottleneck in production cost that restricts large-scale commercialization. However, microbial pigments are progressively gaining popularity because of their health advantages. The development of metabolic engineering and cost reduction of the bioprocess using industry by-products opened possibilities for cost and quality improvements in all production phases. We are thus addressing several points related to microbial pigments, including the major classes and structures found, the advantages of use, the biotechnological applications in different industrial sectors, their characteristics, and their impacts on the environment and society.
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Affiliation(s)
| | | | | | | | - Alane Beatriz Vermelho
- Bioinovar Laboratory, Institute of Microbiology Paulo de Goes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (J.V.d.O.B.); (L.M.C.); (A.N.J.); (M.C.P.P.R.-M.)
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9
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Effendi SSW, Ng IS. Challenges and opportunities for engineered Escherichia coli as a pivotal chassis toward versatile tyrosine-derived chemicals production. Biotechnol Adv 2023; 69:108270. [PMID: 37852421 DOI: 10.1016/j.biotechadv.2023.108270] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/30/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
Growing concerns over limited fossil resources and associated environmental problems are motivating the development of sustainable processes for the production of high-volume fuels and high-value-added compounds. The shikimate pathway, an imperative pathway in most microorganisms, is branched with tyrosine as the rate-limiting step precursor of valuable aromatic substances. Such occurrence suggests the shikimate pathway as a promising route in developing microbial cell factories with multiple applications in the nutraceutical, pharmaceutical, and chemical industries. Therefore, an increasing number of studies have focused on this pathway to enable the biotechnological manufacture of pivotal and versatile aromatic products. With advances in genome databases and synthetic biology tools, genetically programmed Escherichia coli strains are gaining immense interest in the sustainable synthesis of chemicals. Engineered E. coli is expected to be the next bio-successor of fossil fuels and plants in commercial aromatics synthesis. This review summarizes successful and applicable genetic and metabolic engineering strategies to generate new chassis and engineer the iterative pathway of the tyrosine route in E. coli, thus addressing the opportunities and current challenges toward the realization of sustainable tyrosine-derived aromatics.
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Affiliation(s)
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan.
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10
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Perez Rojo F, Pillow JJ, Kaur P. Bioprospecting microbes and enzymes for the production of pterocarpans and coumestans. Front Bioeng Biotechnol 2023; 11:1154779. [PMID: 37187887 PMCID: PMC10175578 DOI: 10.3389/fbioe.2023.1154779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
The isoflavonoid derivatives, pterocarpans and coumestans, are explored for multiple clinical applications as osteo-regenerative, neuroprotective and anti-cancer agents. The use of plant-based systems to produce isoflavonoid derivatives is limited due to cost, scalability, and sustainability constraints. Microbial cell factories overcome these limitations in which model organisms such as Saccharomyces cerevisiae offer an efficient platform to produce isoflavonoids. Bioprospecting microbes and enzymes can provide an array of tools to enhance the production of these molecules. Other microbes that naturally produce isoflavonoids present a novel alternative as production chassis and as a source of novel enzymes. Enzyme bioprospecting allows the complete identification of the pterocarpans and coumestans biosynthetic pathway, and the selection of the best enzymes based on activity and docking parameters. These enzymes consolidate an improved biosynthetic pathway for microbial-based production systems. In this review, we report the state-of-the-art for the production of key pterocarpans and coumestans, describing the enzymes already identified and the current gaps. We report available databases and tools for microbial bioprospecting to select the best production chassis. We propose the use of a holistic and multidisciplinary bioprospecting approach as the first step to identify the biosynthetic gaps, select the best microbial chassis, and increase productivity. We propose the use of microalgal species as microbial cell factories to produce pterocarpans and coumestans. The application of bioprospecting tools provides an exciting field to produce plant compounds such as isoflavonoid derivatives, efficiently and sustainably.
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Affiliation(s)
- Fernando Perez Rojo
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - J. Jane Pillow
- UWA School of Human Sciences, The University of Western Australia, Perth, WA, Australia
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
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11
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Du Y, Wang M, Chen Sun C, Yu H. Construction of an ultra-strong PtacM promoter via engineering the core-element spacer and 5' untranslated region for versatile applications in Corynebacterium glutamicum. BIOTECHNOLOGY NOTES (AMSTERDAM, NETHERLANDS) 2022; 3:88-96. [PMID: 39416452 PMCID: PMC11446368 DOI: 10.1016/j.biotno.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/13/2022] [Accepted: 11/18/2022] [Indexed: 10/19/2024]
Abstract
As one of the most important synthetic biology elements in transcriptional regulation, promoters play irreplaceable roles in metabolic engineering. For the industrial microorganism Corynebacterium glutamicum, both the construction of a promoter library with gradient strength and the creation of ultra-strong promoters are essential for the production of target enzymes and compounds. In this work, the spacer sequence (both length and base) between the -35 and -10 regions, and the 5'-terminal untranslated region (5'UTR) were particularly highlighted to investigate their contributions to promoter strength. We constructed a series of artificially induced promoters based on the classical tac promoter using C. glutamicum ATCC13032 as the host. Here, we explored the effect of sequence length between the -35 and -10 regions on the strength of the tac promoter, and found that the mutant with 15 nt spacer length (PtacL15) was transcriptionally stronger than the classic Ptac (16 nt); subsequently, based on PtacL15, we explored the effect of the nucleotide sequence in the spacer region on transcriptional strength, and screened the strongest PtacL15m-110 (GAACAGGCTTTATCT), and PtacL15m-87 (AGTCGCTAAGACTCA); finally, we investigated the effect of the length of the 5'-terminal untranslated region (5'UTR) and screened out the optimal PtacM4 mutant with a 5'UTR length of 32 nt. Based on our new findings on the optimal spacer length (15 nt), nucleotide sequence (AGTCGCTAAGACTCA), and 5'UTR (truncated 32 nt), an ultra-strong PtacM, whose transcriptional strength was about 3.25 times that of the original Ptac, was obtained. We anticipate that these promoters with gradient transcriptional strength and the ultra-strong PtacM will play an important role in the construction of recombinant strains and industrial production.
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Affiliation(s)
- Yan Du
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Beijing, 100084, China
| | - Miaomiao Wang
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Beijing, 100084, China
| | - Claudia Chen Sun
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Huimin Yu
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Beijing, 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
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12
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Liu C, Li S. Engineered biosynthesis of plant polyketides by type III polyketide synthases in microorganisms. Front Bioeng Biotechnol 2022; 10:1017190. [PMID: 36312548 PMCID: PMC9614166 DOI: 10.3389/fbioe.2022.1017190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/04/2022] [Indexed: 11/28/2022] Open
Abstract
Plant specialized metabolites occupy unique therapeutic niches in human medicine. A large family of plant specialized metabolites, namely plant polyketides, exhibit diverse and remarkable pharmaceutical properties and thereby great biomanufacturing potential. A growing body of studies has focused on plant polyketide synthesis using plant type III polyketide synthases (PKSs), such as flavonoids, stilbenes, benzalacetones, curcuminoids, chromones, acridones, xanthones, and pyrones. Microbial expression of plant type III PKSs and related biosynthetic pathways in workhorse microorganisms, such as Saccharomyces cerevisiae, Escherichia coli, and Yarrowia lipolytica, have led to the complete biosynthesis of multiple plant polyketides, such as flavonoids and stilbenes, from simple carbohydrates using different metabolic engineering approaches. Additionally, advanced biosynthesis techniques led to the biosynthesis of novel and complex plant polyketides synthesized by diversified type III PKSs. This review will summarize efforts in the past 10 years in type III PKS-catalyzed natural product biosynthesis in microorganisms, especially the complete biosynthesis strategies and achievements.
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Affiliation(s)
| | - Sijin Li
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
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13
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Lyu X, Lyu Y, Yu H, Chen W, Ye L, Yang R. Biotechnological advances for improving natural pigment production: a state-of-the-art review. BIORESOUR BIOPROCESS 2022; 9:8. [PMID: 38647847 PMCID: PMC10992905 DOI: 10.1186/s40643-022-00497-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/17/2022] [Indexed: 12/14/2022] Open
Abstract
In current years, natural pigments are facing a fast-growing global market due to the increase of people's awareness of health and the discovery of novel pharmacological effects of various natural pigments, e.g., carotenoids, flavonoids, and curcuminoids. However, the traditional production approaches are source-dependent and generally subject to the low contents of target pigment compounds. In order to scale-up industrial production, many efforts have been devoted to increasing pigment production from natural producers, via development of both in vitro plant cell/tissue culture systems, as well as optimization of microbial cultivation approaches. Moreover, synthetic biology has opened the door for heterologous biosynthesis of pigments via design and re-construction of novel biological modules as well as biological systems in bio-platforms. In this review, the innovative methods and strategies for optimization and engineering of both native and heterologous producers of natural pigments are comprehensively summarized. Current progress in the production of several representative high-value natural pigments is also presented; and the remaining challenges and future perspectives are discussed.
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Affiliation(s)
- Xiaomei Lyu
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Yan Lyu
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Hongwei Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, People's Republic of China
| | - WeiNing Chen
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, Singapore, 637459, Singapore
| | - Lidan Ye
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, People's Republic of China.
| | - Ruijin Yang
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.
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14
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Rainha J, Rodrigues JL, Faria C, Rodrigues LR. Curcumin biosynthesis from ferulic acid by engineered Saccharomyces cerevisiae. Biotechnol J 2021; 17:e2100400. [PMID: 34882970 DOI: 10.1002/biot.202100400] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 12/07/2021] [Accepted: 12/07/2021] [Indexed: 01/01/2023]
Abstract
BACKGROUND AND GOAL Curcumin is a polyphenolic compound found in Curcuma longa. This bioactive molecule has several reported health-benefit effects, being the anticarcinogenic activity among the most promising ones. However, curcumin extraction from natural sources is hampered by impure products obtained from harsh chemicals and limited by plant seasonality and high prices. Therefore, curcumin heterologous production emerged as an interesting alternative. Escherichia coli has been explored as chassis but the implementation of the pathway in Saccharomyces cerevisiae can have several advantages, including its generally regarded as safe status. Hence, S. cerevisiae was engineered for the first time to produce curcumin from its precursor ferulic acid. METHODS AND RESULTS The enzymes 4-coumarate-CoA ligase (4CL1) from Arabidopsis thaliana or feruloyl-CoA synthetase (FerA) from Pseudomonas paucimobilis and type III polyketide synthases (PKSs) from Oryza sativa or C. longa were expressed in BY4741 strain. To avoid ferulic acid deviation, the gene FDC1 coding a ferulic acid decarboxylase was deleted. The maximum curcumin titer was obtained with FerA combined with C. longa PKSs (2.7 mg L-1 ). CONCLUSIONS AND IMPLICATIONS Up to our knowledge, this is the first work reporting the expression of a feruloyl-CoA synthase and also curcuminoid biosynthetic enzymes in S. cerevisiae, and consequently, curcumin production.
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Affiliation(s)
- João Rainha
- CEB-Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Joana L Rodrigues
- CEB-Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Cristiana Faria
- CEB-Centre of Biological Engineering, University of Minho, Braga, Portugal.,SilicoLife Lda., Braga, Portugal
| | - Lígia R Rodrigues
- CEB-Centre of Biological Engineering, University of Minho, Braga, Portugal
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15
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Heo KT, Park KW, Won J, Lee B, Jang JH, Ahn JO, Hwang BY, Hong YS. Construction of an Artificial Biosynthetic Pathway for Zingerone Production in Escherichia coli Using Benzalacetone Synthase from Piper methysticum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:14620-14629. [PMID: 34812612 DOI: 10.1021/acs.jafc.1c05534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Zingerone (vanillylacetone; 4-hydroxy-3-methoxyphenylethyl methyl ketone) is a key component responsible for the pungency of ginger (Zingiber officinale). In this study, it was confirmed that a type III polyketide synthase (PKS) gene (pmpks) from Piper methysticum exhibits feruloyl-CoA-preferred benzalacetone synthase (BAS) activity. Based on these results, we constructed an artificial biosynthetic pathway for zingerone production from supplemented ferulic acid with 4-coumarate CoA ligase (4CL), PmPKS, and benzalacetone reductase (BAR). Furthermore, a de novo pathway for the production of zingerone was assembled using six heterologous genes, encoding tyrosine ammonia-lyase (optal), cinnamate-4-hydroxlase (sam5), caffeic acid O-methyltransferase (com), 4CL (4cl2nt), BAS (pmpks), and BAR (rzs1), in Escherichia coli. Using the engineered l-tyrosine-overproducing E. coli ΔCOS4 strain as a host, a maximum yield of 24.03 ± 2.53 mg/L zingerone was achieved by complete de novo synthesis.
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Affiliation(s)
- Kyung Taek Heo
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Ochang-eup, CheongJu-si, Chungbuk 28116, Republic of Korea
- Department of Bio-Molecular Science, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon 34141, Republic of Korea
| | - Kyung Won Park
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Ochang-eup, CheongJu-si, Chungbuk 28116, Republic of Korea
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea
| | - Juhee Won
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Ochang-eup, CheongJu-si, Chungbuk 28116, Republic of Korea
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea
| | - Byeongsan Lee
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Ochang-eup, CheongJu-si, Chungbuk 28116, Republic of Korea
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea
| | - Jae-Hyuk Jang
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Ochang-eup, CheongJu-si, Chungbuk 28116, Republic of Korea
- Department of Bio-Molecular Science, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon 34141, Republic of Korea
| | - Jung-Oh Ahn
- Department of Bio-Molecular Science, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon 34141, Republic of Korea
- Biotechnology Process Engineering Center, KRIBB, 30 Yeongudanji-ro, Ochang-eup, CheongJu-si, Chungbuk 28116, Republic of Korea
| | - Bang Yeon Hwang
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea
| | - Young-Soo Hong
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Ochang-eup, CheongJu-si, Chungbuk 28116, Republic of Korea
- Department of Bio-Molecular Science, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon 34141, Republic of Korea
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16
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Yixuan L, Qaria MA, Sivasamy S, Jianzhong S, Daochen Z. Curcumin production and bioavailability: A comprehensive review of curcumin extraction, synthesis, biotransformation and delivery systems. INDUSTRIAL CROPS AND PRODUCTS 2021; 172:114050. [DOI: 10.1016/j.indcrop.2021.114050] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
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17
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Heo KT, Lee B, Jang JH, Ahn JO, Hong YS. Construction of an Artificial Biosynthetic Pathway for the Styrylpyrone Compound 11-Methoxy-Bisnoryangonin Produced in Engineered Escherichia coli. Front Microbiol 2021; 12:714335. [PMID: 34456894 PMCID: PMC8388576 DOI: 10.3389/fmicb.2021.714335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/15/2021] [Indexed: 12/04/2022] Open
Abstract
A cDNA clone (named pnpks), which shows high homology to the known chalcone synthase (CHS)-like type III PKS, was obtained from the leaves of Piper nigrum. The PnPKS protein with ferulic acid catalyzed lactonization instead of chalcone or stilbene formation. The new product was characterized as a styrylpyrone, 11-methoxy-bisnoryangonin, which is the lactonization compound of a linear triketide formed as the reaction product of PnPKS protein with ferulic acid. These results show that pnpks encodes a styrylpyrone synthase (SPS)-like PKS that catalyzes two-chain elongation with feruloyl CoA-linked starter substrates. Although these styrylpyrone compounds are promising for use in human healthcare, they are mainly obtained by extraction from raw plant or mushroom sources. For de novo synthesis of 11-methoxy-bisnoryangonin in the heterologous host Escherichia coli from a simple sugar as a starter, the artificial biosynthetic pathway contained five genes: optal, sam5, com, and 4cl2nt, along with the pnpks gene. The engineered L-tyrosine overproducing E. coli ∆COS1 strain, in which five biosynthetic genes were cloned into two vectors, pET-opT5M and pET22-4P, was cultured for 24 h in a minimal glucose medium containing ampicillin and kanamycin. As a result, 11-methoxy-bisnoryangonin production of up to 52.8 mg/L was achieved, which is approximately 8.5-fold higher than that in the parental E. coli strain harboring a plasmid for 11-methoxy-bisnoryangonin biosynthesis. As a potential styrylpyrone compound, 11-methoxy-bisnoryangonin, was successfully produced in E. coli from a simple glucose medium, and its production titer was also increased using engineered strains. This study provides a useful reference for establishing the biological manufacture of styrylpyrone compounds.
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Affiliation(s)
- Kyung Taek Heo
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju-si, South Korea.,Department of Bio-Molecular Science, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South Korea
| | - Byeongsan Lee
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju-si, South Korea
| | - Jae-Hyuk Jang
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju-si, South Korea.,Department of Bio-Molecular Science, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South Korea
| | - Jung-Oh Ahn
- Department of Bio-Molecular Science, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South Korea.,Biotechnology Process Engineering Center, KRIBB, Cheongju-si, South Korea
| | - Young-Soo Hong
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju-si, South Korea.,Department of Bio-Molecular Science, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South Korea
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18
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Singh S, Pandey P, Akhtar MQ, Negi AS, Banerjee S. A new synthetic biology approach for the production of curcumin and its glucoside in Atropa belladonna hairy roots. J Biotechnol 2021; 328:23-33. [PMID: 33422568 DOI: 10.1016/j.jbiotec.2020.12.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/27/2020] [Accepted: 12/30/2020] [Indexed: 10/22/2022]
Abstract
Curcumin has ignited global interest as an elite drugable molecule, owing to its time-honoured pharmacological activities against diverse human ailments. Limited natural accessibility and poor oral bioavailability caused major hurdles in the curcumin-based drug development process. We report the first successful testimony of curcumin and its glucoside synthesis in Atropa belladonna hairy roots (HR) through metabolic engineering. Re-routing the inherent biosynthetic precursors of the phenylpropanoid pathway of A. belladonna by heterologous expression of key curcumin biosynthetic pathway genes (i.e., Diketide-CoA synthase-DCS and Curcumin synthase-CURS3) and glucosyltransferase gene (CaUGT2) resulted in the production of curcumin and its glucoside in HR clones. Under shake-flask cultivation, the PGD2-HR1clone bearing DCS/ CURS3 genes showed the maximum curcumin yield (180.62 ± 4.7 μg/g DW), while the highest content of curcumin monoglucoside (32.63 ± 2.27 μg/g DW) along with curcumin (67.89 ± 2.56 μg/g DW) were noted in the PGD3-HR3 clone co-expressing DCS/CURS3 and CaUGT2 genes. Bioreactor up-scaling showed yield improvements in the PGD2-HR1 (2.3 fold curcumin) and the PGD3-HR3 clone (0.9 and 1.65 folds of curcumin-monoglucoside and curcumin respectively). These findings proved the advantageous use of HR cultures as the production source for curcumin and its glucoside, which remained unexplored so far.
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Affiliation(s)
- Sailendra Singh
- Plant Biotechnology Department, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Pallavi Pandey
- Plant Biotechnology Department, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Md Qussen Akhtar
- Plant Biotechnology Department, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, Uttar Pradesh, India; School of Agriculture Sciences, K.K. University, Bihar Sharif, Nalanda, Bihar, India
| | - Arvind Singh Negi
- Medicinal Chemistry Department, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, Uttar Pradesh, India
| | - Suchitra Banerjee
- Plant Biotechnology Department, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, Uttar Pradesh, India.
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19
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Yang B, Feng X, Li C. Microbial Cell Factory for Efficiently Synthesizing Plant Natural Products via Optimizing the Location and Adaptation of Pathway on Genome Scale. Front Bioeng Biotechnol 2020; 8:969. [PMID: 32923436 PMCID: PMC7457125 DOI: 10.3389/fbioe.2020.00969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/27/2020] [Indexed: 01/03/2023] Open
Abstract
Plant natural products (PNPs) possess important pharmacological activities and are widely used in cosmetics, health care products, and as food additives. Currently, most PNPs are mainly extracted from cultivated plants, and the yield is limited by the long growth cycle, climate change and complex processing steps, which makes the process unsustainable. However, the complex structure of PNPs significantly reduces the efficiency of chemical synthesis. With the development of metabolic engineering and synthetic biology, heterologous biosynthesis of PNPs in microbial cell factories offers an attractive alternative. Based on the in-depth mining and analysis of genome and transcriptome data, the biosynthetic pathways of a number of natural products have been successfully elucidated, which lays the crucial foundation for heterologous production. However, there are several problems in the microbial synthesis of PNPs, including toxicity of intermediates, low enzyme activity, multiple auxotrophic dependence, and uncontrollable metabolic network. Although various metabolic engineering strategies have been developed to solve these problems, optimizing the location and adaptation of pathways on the whole-genome scale is an important strategy in microorganisms. From this perspective, this review introduces the application of CRISPR/Cas9 in editing PNPs biosynthesis pathways in model microorganisms, the influences of pathway location, and the approaches for optimizing the adaptation between metabolic pathways and chassis hosts for facilitating PNPs biosynthesis.
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Affiliation(s)
- Bo Yang
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Xudong Feng
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Chun Li
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China.,Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
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20
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Shen YP, Niu FX, Yan ZB, Fong LS, Huang YB, Liu JZ. Recent Advances in Metabolically Engineered Microorganisms for the Production of Aromatic Chemicals Derived From Aromatic Amino Acids. Front Bioeng Biotechnol 2020; 8:407. [PMID: 32432104 PMCID: PMC7214760 DOI: 10.3389/fbioe.2020.00407] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 04/14/2020] [Indexed: 12/16/2022] Open
Abstract
Aromatic compounds derived from aromatic amino acids are an important class of diverse chemicals with a wide range of industrial and commercial applications. They are currently produced via petrochemical processes, which are not sustainable and eco-friendly. In the past decades, significant progress has been made in the construction of microbial cell factories capable of effectively converting renewable carbon sources into value-added aromatics. Here, we systematically and comprehensively review the recent advancements in metabolic engineering and synthetic biology in the microbial production of aromatic amino acid derivatives, stilbenes, and benzylisoquinoline alkaloids. The future outlook concerning the engineering of microbial cell factories for the production of aromatic compounds is also discussed.
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Affiliation(s)
- Yu-Ping Shen
- Guangdong Province Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals, Biomedical Center, School of Life Sciences, Institute of Synthetic Biology, Sun Yat-sen University, Guangzhou, China
| | - Fu-Xing Niu
- Guangdong Province Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals, Biomedical Center, School of Life Sciences, Institute of Synthetic Biology, Sun Yat-sen University, Guangzhou, China
| | - Zhi-Bo Yan
- Guangdong Province Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals, Biomedical Center, School of Life Sciences, Institute of Synthetic Biology, Sun Yat-sen University, Guangzhou, China
| | - Lai San Fong
- Guangdong Province Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals, Biomedical Center, School of Life Sciences, Institute of Synthetic Biology, Sun Yat-sen University, Guangzhou, China
| | - Yuan-Bin Huang
- Guangdong Province Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals, Biomedical Center, School of Life Sciences, Institute of Synthetic Biology, Sun Yat-sen University, Guangzhou, China
| | - Jian-Zhong Liu
- Guangdong Province Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals, Biomedical Center, School of Life Sciences, Institute of Synthetic Biology, Sun Yat-sen University, Guangzhou, China
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21
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Lautié E, Russo O, Ducrot P, Boutin JA. Unraveling Plant Natural Chemical Diversity for Drug Discovery Purposes. Front Pharmacol 2020; 11:397. [PMID: 32317969 PMCID: PMC7154113 DOI: 10.3389/fphar.2020.00397] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 03/16/2020] [Indexed: 12/11/2022] Open
Abstract
The screening and testing of extracts against a variety of pharmacological targets in order to benefit from the immense natural chemical diversity is a concern in many laboratories worldwide. And several successes have been recorded in finding new actives in natural products, some of which have become new drugs or new sources of inspiration for drugs. But in view of the vast amount of research on the subject, it is surprising that not more drug candidates were found. In our view, it is fundamental to reflect upon the approaches of such drug discovery programs and the technical processes that are used, along with their inherent difficulties and biases. Based on an extensive survey of recent publications, we discuss the origin and the variety of natural chemical diversity as well as the strategies to having the potential to embrace this diversity. It seemed to us that some of the difficulties of the area could be related with the technical approaches that are used, so the present review begins with synthetizing some of the more used discovery strategies, exemplifying some key points, in order to address some of their limitations. It appears that one of the challenges of natural product-based drug discovery programs should be an easier access to renewable sources of plant-derived products. Maximizing the use of the data together with the exploration of chemical diversity while working on reasonable supply of natural product-based entities could be a way to answer this challenge. We suggested alternative ways to access and explore part of this chemical diversity with in vitro cultures. We also reinforced how important it was organizing and making available this worldwide knowledge in an "inventory" of natural products and their sources. And finally, we focused on strategies based on synthetic biology and syntheses that allow reaching industrial scale supply. Approaches based on the opportunities lying in untapped natural plant chemical diversity are also considered.
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Affiliation(s)
- Emmanuelle Lautié
- Centro de Valorização de Compostos Bioativos da Amazônia (CVACBA)-Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Olivier Russo
- Institut de Recherches Internationales SERVIER, Suresnes, France
| | - Pierre Ducrot
- Molecular Modelling Department, 'PEX Biotechnologie, Chimie & Biologie, Institut de Recherches SERVIER, Croissy-sur-Seine, France
| | - Jean A Boutin
- Institut de Recherches Internationales SERVIER, Suresnes, France
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22
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Rodrigues JL, Gomes D, Rodrigues LR. A Combinatorial Approach to Optimize the Production of Curcuminoids From Tyrosine in Escherichia coli. Front Bioeng Biotechnol 2020; 8:59. [PMID: 32117938 PMCID: PMC7019186 DOI: 10.3389/fbioe.2020.00059] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/23/2020] [Indexed: 12/14/2022] Open
Abstract
Curcuminoids are well-known for their therapeutic properties. However, their extraction from natural sources is environmentally unfriendly, expensive and limited by seasonal variability, highlighting the need for alternative production processes. We propose an optimized artificial biosynthetic pathway to produce curcuminoids, including curcumin, in Escherichia coli. This pathway involves six enzymes, tyrosine ammonia lyase (TAL), 4-coumarate 3-hydroxylase (C3H), caffeic acid O-methyltransferase (COMT), 4-coumarate-CoA ligase (4CL), diketide-CoA synthase (DCS), and curcumin synthase (CURS1). Curcuminoids pathway was divided in two modules, the first module included TAL, C3H and COMT and the second one 4CL, DCS and CURS1. Optimizing the first module of the pathway, from tyrosine to ferulic acid, enabled obtaining the highest ferulic acid titer reported so far (1325.1 μM). Afterward, ferulic acid was used as substrate to optimize the second module of the pathway. We achieved the highest concentration of curcumin ever reported (1529.5 μM), corresponding to a 59.4% increase. Subsequently, curcumin and other curcuminoids were produced from tyrosine (using the whole pathway) in mono-culture. The production increased comparing to a previously reported pathway that used a caffeoyl-CoA O-methyltransferase enzyme (to convert caffeoyl-CoA to feruloyl-CoA) instead of COMT (to convert caffeic to ferulic acid). Additionally, the potential of a co-culture approach was evaluated to further improve curcuminoids production by reducing cells metabolic burden. We used one E. coli strain able to convert tyrosine to ferulic acid and another able to convert the hydroxycinnamic acids produced by the first one to curcuminoids. The co-culture strategies tested led to 6.6 times increase of total curcuminoids (125.8 μM) when compared to the mono-culture system. The curcuminoids production achieved in this study corresponds to a 6817% improvement. In addition, by using an inoculation ratio of 2:1, although total curcuminoids production decreased, curcumin production was enhanced and reached 43.2 μM, corresponding to an improvement of 160% comparing to mono-culture system. To our knowledge, these values correspond to the highest titers of curcuminoids obtained to date. These results demonstrate the enormous potential of modular co-culture engineering to produce curcumin, and other curcuminoids, from tyrosine.
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Affiliation(s)
- Joana L Rodrigues
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Daniela Gomes
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Lígia R Rodrigues
- Centre of Biological Engineering, University of Minho, Braga, Portugal
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23
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Pseudomonas putida in the quest of programmable chemistry. Curr Opin Biotechnol 2019; 59:111-121. [DOI: 10.1016/j.copbio.2019.03.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/15/2019] [Accepted: 03/12/2019] [Indexed: 11/19/2022]
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