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Wu R, Li D, Chen Q, Luo Z, Zhou J, Mao J. Optimization of vanillin biosynthesis in Escherichia coli K12 MG1655 through metabolic engineering. BIORESOURCE TECHNOLOGY 2024; 411:131189. [PMID: 39127360 DOI: 10.1016/j.biortech.2024.131189] [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: 05/05/2024] [Revised: 07/24/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024]
Abstract
Vanillin is an important flavouring agent applied in food, spices, pharmaceutical industries and other fields. Microbial biosynthesis of vanillin is considered a sustainable and economically feasible alternative to traditional chemical synthesis. In this study, Escherichia coli K12 MG1655 was used for the de novo synthesis of VAN by screening highly active carboxylic acid reductases and catechol O-methyltransferases, optimising the protocatechuic acid pathway, and regulating competitive metabolic pathways. Additionally, major alcohol by-products were identified and decreased by deleting three endogenous aldo-keto reductases and three alcohol dehydrogenases. Finally, a highest VAN titer was achieved to 481.2 mg/L in a 5 L fermenter from glucose. This work provides a valuable example of pathway engineering and screens several enzyme variants for the first time in E. coli.
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Affiliation(s)
- Renga Wu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Dong Li
- Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qihang Chen
- Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhengshan Luo
- Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jian Mao
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Jiangnan University (Shaoxing) Industrial Technology Research Institute, National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing, Zhejiang 312000, China.
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2
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Liu SC, Xin X, He ZJ, Xie ZH, Xie ZX, Liu ZH, Li BZ, Yuan YJ. Biological conversion of lignin-derived ferulic acid from wheat bran into vanillin. Int J Biol Macromol 2024; 281:136406. [PMID: 39389498 DOI: 10.1016/j.ijbiomac.2024.136406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 09/21/2024] [Accepted: 10/06/2024] [Indexed: 10/12/2024]
Abstract
Lignin is a promising feedstock for producing vanillin, one of the most extensively used flavor enhancers. However, the biotransformation performance of lignin derivatives into vanillin is still unsatisfactory. In this study, an efficient conversion strategy of lignin into vanillin was established by employing engineered Saccharomyces cerevisiae as a whole-cell biocatalyst. Optimization of cell culture media and whole-cell bioconversion improved the production efficiency of vanillin. The vanillin titer reached 15.3 mM with a molar yield of 71 % in fed-batch fermentation mode, while incorporating in-situ product separation, demonstrated a remarkable 2.6-fold increase. The whole-cell bioconversion, coupled with in-situ separation, successfully converted real lignin hydrolysate into a record vanillin titer of 21.1 mM, equivalent to 1.8 mg of vanillin per gram of wheat bran biomass. The whole-cell bioconversion process integrated in-situ product separation, represents a sustainable approach for vanillin production and offers a promising pathway for lignin valorization.
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Affiliation(s)
- Shi-Chang Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, China
| | - Xin Xin
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, China
| | - Zi-Jing He
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, China
| | - Zi-Han Xie
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, China
| | - Ze-Xiong Xie
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, China
| | - Zhi-Hua Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, China
| | - Bing-Zhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, China.
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, China
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3
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Dong P, Fan Y, Huo YX, Sun L, Guo S. Pathway-Adapted Biosensor for High-Throughput Screening of O-Methyltransferase and its Application in Vanillin Synthesis. ACS Synth Biol 2024; 13:2873-2886. [PMID: 39208264 DOI: 10.1021/acssynbio.4c00287] [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] [Indexed: 09/04/2024]
Abstract
Vanillin is a widely used flavoring compound in the food, pharmaceutical, and cosmetics area. However, the biosynthesis of vanillin from low-cost shikimic acid is significantly hindered by the low activity of the rate-limiting enzyme, caffeate O-methyltransferase (COMT). To screen COMT variants with improved conversion rates, we designed a biosensing system that is adaptable to the COMT-mediated vanillin synthetic pathway. Through the evolution of aldehyde transcriptional factor YqhC, we obtained a dual-responsive variant, MuYqhC, which positively responds to the product and negatively responds to the substrate, with no response to intermediates. Using the MuYqhC-based vanillin biosensor, we successfully identified a COMT variant, Mu176, that displayed a 7-fold increase in the conversion rate compared to the wild-type COMT. This variant produced 2.38 mM vanillin from 3 mM protocatechuic acid, achieving a conversion rate of 79.33%. The enhanced activity of Mu176 was attributed to an enlarged binding pocket and strengthened substrate interaction. Applying Mu176 to Bacillus subtilis increased the level of vanillin production from shikimic acid by 2.39-fold. Further optimization of the production chassis, increasing the S-adenosylmethionine supply and the precursor concentration, elevated the vanillin titer to 1 mM, marking the highest level of vanillin production from shikimic acid in Bacillus. Our work highlights the significance of the MuYqhC-based biosensing system and the Mu176 variant in vanillin production.
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Affiliation(s)
- Pengyu Dong
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, 100081 Beijing, China
| | - Yunjuan Fan
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, 100081 Beijing, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, 100081 Beijing, China
- Tangshan Research Institute, Beijing Institute of Technology, 063611 Tangshan, Hebei, China
| | - Lichao Sun
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, 100081 Beijing, China
- Tangshan Research Institute, Beijing Institute of Technology, 063611 Tangshan, Hebei, China
| | - Shuyuan Guo
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, 100081 Beijing, China
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4
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Shi Y, Lu S, Zhou X, Wang X, Zhang C, Wu N, Dong T, Xing S, Wang Y, Xiao W, Yao M. Systematic metabolic engineering enables highly efficient production of vitamin A in Saccharomyces cerevisiae. Synth Syst Biotechnol 2024; 10:58-67. [PMID: 39247801 PMCID: PMC11380465 DOI: 10.1016/j.synbio.2024.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 08/14/2024] [Accepted: 08/14/2024] [Indexed: 09/10/2024] Open
Abstract
Vitamin A is a micronutrient critical for versatile biological functions and has been widely used in the food, cosmetics, pharmaceutical, and nutraceutical industries. Synthetic biology and metabolic engineering enable microbes, especially the model organism Saccharomyces cerevisiae (generally recognised as safe) to possess great potential for the production of vitamin A. Herein, we first generated a vitamin A-producing strain by mining β-carotene 15,15'-mono(di)oxygenase from different sources and identified two isoenzymes Mbblh and Ssbco with comparable catalytic properties but different catalytic mechanisms. Combinational expression of isoenzymes increased the flux from β-carotene to vitamin A metabolism. To modulate the vitamin A components, retinol dehydrogenase 12 from Homo sapiens was introduced to achieve more than 90 % retinol purity using shake flask fermentation. Overexpressing POS5Δ17 enhanced the reduced nicotinamide adenine dinucleotide phosphate pool, and the titer of vitamin A was elevated by almost 46 %. Multi-copy integration of the key rate-limiting step gene Mbblh further improved the synthesis of vitamin A. Consequently, the titer of vitamin A in the strain harbouring the Ura3 marker was increased to 588 mg/L at the shake-flask level. Eventually, the highest reported titer of 5.21 g/L vitamin A in S. cerevisiae was achieved in a 1-L bioreactor. This study unlocked the potential of S. cerevisiae for synthesising vitamin A in a sustainable and economical way, laying the foundation for the commercial-scale production of bio-based vitamin A.
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Affiliation(s)
- Yi Shi
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, China
| | - Shuhuan Lu
- CABIO Bioengineering (Wuhan) Co., Ltd, Wuhan, 430075, China
| | - Xiao Zhou
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, China
| | - Xinhui Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, China
| | - Chenglong Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, China
| | - Nan Wu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, China
| | - Tianyu Dong
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, China
| | - Shilong Xing
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, China
| | - Ying Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, China
| | - Wenhai Xiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, China
- School of Life Sciences, Faculty of Medicine, Tianjin University, China
- Georgia Tech Shenzhen Institute, Tianjin University, Shenzhen, 518071, China
| | - Mingdong Yao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, China
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5
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Dickey RM, Gopal MR, Nain P, Kunjapur AM. Recent developments in enzymatic and microbial biosynthesis of flavor and fragrance molecules. J Biotechnol 2024; 389:43-60. [PMID: 38616038 DOI: 10.1016/j.jbiotec.2024.04.004] [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: 02/16/2024] [Revised: 04/08/2024] [Accepted: 04/08/2024] [Indexed: 04/16/2024]
Abstract
Flavors and fragrances are an important class of specialty chemicals for which interest in biomanufacturing has risen during recent years. These naturally occurring compounds are often amenable to biosynthesis using purified enzyme catalysts or metabolically engineered microbial cells in fermentation processes. In this review, we provide a brief overview of the categories of molecules that have received the greatest interest, both academically and industrially, by examining scholarly publications as well as patent literature. Overall, we seek to highlight innovations in the key reaction steps and microbial hosts used in flavor and fragrance manufacturing.
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Affiliation(s)
- Roman M Dickey
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711, USA
| | - Madan R Gopal
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711, USA
| | - Priyanka Nain
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711, USA
| | - Aditya M Kunjapur
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711, USA.
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6
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Ren Y, Qin Z, Li C, Yuan B, Yang Y, Qu G, Sun Z. Engineering the activity and thermostability of a carboxylic acid reductase in the conversion of vanillic acid to vanillin. J Biotechnol 2024; 386:19-27. [PMID: 38521166 DOI: 10.1016/j.jbiotec.2024.03.004] [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: 02/06/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 03/25/2024]
Abstract
Vanillin is a valuable natural product that can be used as a fragrance and additive. Recent research in the biosynthesis of vanillin has brought attention to a key enzyme, carboxylic acid reductase (CAR), which catalyzes the reduction of vanillic acid to vanillin. Nevertheless, the biosynthesis of vanillin is hampered by the low activity and stability of CAR. As such, a rational design campaign was conducted on a well-documented carboxylic acid reductase from Segniliparus rugosus (SrCAR), using vanillic acid as the model substrate. After combined active site saturation and iterative site-specific mutagenesis, the best quadruple mutant N292H/K524S/A627L/E1121W (M3) was successfully obtained. In comparison to the wildtype SrCAR, M3 demonstrated a 4.2-fold increase in catalytic efficiency (kcat/Km), and its half-life (t1/2) was enhanced by 3.8 times up to 385.08 minutes at 40 °C. In silico docking and molecular dynamics simulation provided insights into the improved activity and stability. In the subsequent preparative-scale reaction with 100 mM (16.8 g L-1) vanillic acid, the whole cell catalysis utilizing M3 produced 10.15 g·L-1 of vanillin and 1.11 g·L-1 of vanillyl alcohol, respectively. This work demonstrates a dual improvement in the activity and thermal stability of SrCAR, thereby potentially facilitating the application of carboxylic acid reductase in the biosynthesis of vanillin.
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Affiliation(s)
- Yaoyao Ren
- Tianjin University of Science and Technology, College of Biotechnology, Tianjin 300457, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Zongmin Qin
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Congcong Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Bo Yuan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China; Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yang Yang
- Tianjin University of Science and Technology, College of Biotechnology, Tianjin 300457, China
| | - Ge Qu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China; Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
| | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China; Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
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7
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Hilgendorf K, Wang Y, Miller MJ, Jin YS. Precision fermentation for improving the quality, flavor, safety, and sustainability of foods. Curr Opin Biotechnol 2024; 86:103084. [PMID: 38394936 DOI: 10.1016/j.copbio.2024.103084] [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: 12/12/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024]
Abstract
Precision fermentation involves the rewiring of metabolic pathways in generally recognized as safe microorganisms, fermentation scale-up, and downstream processing to produce food ingredients from abundant and inexpensive substrates. Using precise genome editing of food-fermenting microorganisms, precision fermentation can also produce fermented foods with more desirable properties. These genetic tools allow for the manipulation of flavors and nutritional content in fermented foods, the economic production of functional food ingredients, and the sustainable production of otherwise-costly macronutrients. By introducing the metabolic designs, genetic modifications, and resulting products of engineered microorganisms developed through academic and industrial research, this review aims to provide insights into the potentials and challenges of precision fermentation for the economic, safe, and sustainable production of foods.
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Affiliation(s)
- Karson Hilgendorf
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yirong Wang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Michael J Miller
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, IL, USA
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, IL, USA.
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Venkataraman S, Athilakshmi JK, Rajendran DS, Bharathi P, Kumar VV. A comprehensive review of eclectic approaches to the biological synthesis of vanillin and their application towards the food sector. Food Sci Biotechnol 2024; 33:1019-1036. [PMID: 38440686 PMCID: PMC10908958 DOI: 10.1007/s10068-023-01484-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/24/2023] [Accepted: 11/09/2023] [Indexed: 03/06/2024] Open
Abstract
Vanillin, a highly regarded flavor compound, has earned widespread recognition for its natural and aromatic qualities, piquing substantial interest in the scientific community. This comprehensive review delves deeply into the intricate world of vanillin synthesis, encompassing a wide spectrum of methodologies, including enzymatic, microbial, and immobilized systems. This investigation provides a thorough analysis of the precursors of vanillin and also offers a comprehensive overview of its transformation through these diverse processes, making it an invaluable resource for researchers and enthusiasts alike. The elucidation of different substrates such as ferulic acid, eugenol, veratraldehyde, vanillic acid, glucovanillin, and C6-C3 phenylpropanoids adds a layer of depth and insight to the understanding of vanillin synthesis. Moreover, this comprehensive review explores the multifaceted applications of vanillin within the food industry. While commonly known as a flavoring agent, vanillin transcends this role by finding extensive use in food preservation and food packaging. The review meticulously examines the remarkable preservative properties of vanillin, providing a profound understanding of its crucial role in the culinary and food science sectors, thus making it an indispensable reference for professionals and researchers in these domains. Graphical abstract
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Affiliation(s)
- Swethaa Venkataraman
- Integrated Bioprocessing Laboratory, Department of Biotechnology, School of Bioengineering, Faculty of Engineering and Technology, SRM Institute of Science and Technology (SRM IST), Kattankulathur, Chengalpattu, 603203 India
| | - Jothyswarupha Krishnakumar Athilakshmi
- Integrated Bioprocessing Laboratory, Department of Biotechnology, School of Bioengineering, Faculty of Engineering and Technology, SRM Institute of Science and Technology (SRM IST), Kattankulathur, Chengalpattu, 603203 India
| | - Devi Sri Rajendran
- Integrated Bioprocessing Laboratory, Department of Biotechnology, School of Bioengineering, Faculty of Engineering and Technology, SRM Institute of Science and Technology (SRM IST), Kattankulathur, Chengalpattu, 603203 India
| | - Priyadharshini Bharathi
- Integrated Bioprocessing Laboratory, Department of Biotechnology, School of Bioengineering, Faculty of Engineering and Technology, SRM Institute of Science and Technology (SRM IST), Kattankulathur, Chengalpattu, 603203 India
| | - Vaidyanathan Vinoth Kumar
- Integrated Bioprocessing Laboratory, Department of Biotechnology, School of Bioengineering, Faculty of Engineering and Technology, SRM Institute of Science and Technology (SRM IST), Kattankulathur, Chengalpattu, 603203 India
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9
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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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10
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Gu Y, Jiang Y, Li C, Zhu J, Lu X, Ge J, Hu M, Deng J, Ma J, Yang Z, Sun X, Xue F, Du G, Xu P, Huang H. High titer production of gastrodin enabled by systematic refactoring of yeast genome and an antisense-transcriptional regulation toolkit. Metab Eng 2024; 82:250-261. [PMID: 38428728 DOI: 10.1016/j.ymben.2024.02.016] [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: 12/02/2023] [Revised: 02/07/2024] [Accepted: 02/26/2024] [Indexed: 03/03/2024]
Abstract
Gastrodin, a phenolic glycoside, is a prominent component of Gastrodia elata, which is renowned for its sedative, hypnotic, anticonvulsant, and neuroprotective activities. Engineering heterologous production of plant natural products in microbial host represents a safe, cost-effective, and scalable alternative to plant extraction. Here, we present the construction of an engineered Yarrowia lipolytica yeast that achieves a high-titer production of gastrodin. We systematically refactored the yeast genome by enhancing the flux of the shikimate pathway and optimizing the glucosyl transfer system. We introduced more than five dozen of genetic modifications onto the yeast genome, including enzyme screening, alleviation of rate-limiting steps, promoter selection, genomic integration site optimization, downregulation of competing pathways, and elimination of gastrodin degradation. Meanwhile, we developed a Copper-induced Antisense-Transcriptional Regulation (CATR) tool. The developed CATR toolkit achieved dynamic repression and activation of violacein synthesis through the addition of copper in Y. lipolytica. This strategy was further used to dynamically regulate the pyruvate kinase node to effectively redirect glycolytic flux towards the shikimate pathway while maintaining cell growth at proper rate. Taken together, these efforts resulted in 9477.1 mg/L of gastrodin in shaking flaks and 13.4 g/L of gastrodin with a yield of 0.149 g/g glucose in a 5-L bioreactor, highlighting the potential for large-scale and sustainable production of gastrodin from microbial fermentation.
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Affiliation(s)
- Yang Gu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Yaru Jiang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Changfan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Jiang Zhu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Xueyao Lu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Jianyue Ge
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Mengchen Hu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jieying Deng
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jingbo Ma
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, Anhui, 237012, China
| | - Zhiliang Yang
- Zhejiang Key Laboratory of Antifungal Drugs, Zhejiang Hisun Pharmaceutical Co., Ltd, Taizhou, 318000, China
| | - Xiaoman Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Feng Xue
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China.
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Peng Xu
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology (GTIIT), Shantou, Guangdong, 515063, China.
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China.
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11
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Lv Y, Chang J, Zhang W, Dong H, Chen S, Wang X, Zhao A, Zhang S, Alam MA, Wang S, Du C, Xu J, Wang W, Xu P. Improving Microbial Cell Factory Performance by Engineering SAM Availability. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3846-3871. [PMID: 38372640 DOI: 10.1021/acs.jafc.3c09561] [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: 02/20/2024]
Abstract
Methylated natural products are widely spread in nature. S-Adenosyl-l-methionine (SAM) is the secondary abundant cofactor and the primary methyl donor, which confer natural products with structural and functional diversification. The increasing demand for SAM-dependent natural products (SdNPs) has motivated the development of microbial cell factories (MCFs) for sustainable and efficient SdNP production. Insufficient and unsustainable SAM availability hinders the improvement of SdNP MCF performance. From the perspective of developing MCF, this review summarized recent understanding of de novo SAM biosynthesis and its regulatory mechanism. SAM is just the methyl mediator but not the original methyl source. Effective and sustainable methyl source supply is critical for efficient SdNP production. We compared and discussed the innate and relatively less explored alternative methyl sources and identified the one involving cheap one-carbon compound as more promising. The SAM biosynthesis is synergistically regulated on multilevels and is tightly connected with ATP and NAD(P)H pools. We also covered the recent advancement of metabolic engineering in improving intracellular SAM availability and SdNP production. Dynamic regulation is a promising strategy to achieve accurate and dynamic fine-tuning of intracellular SAM pool size. Finally, we discussed the design and engineering constraints underlying construction of SAM-responsive genetic circuits and envisioned their future applications in developing SdNP MCFs.
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Affiliation(s)
- Yongkun Lv
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Jinmian Chang
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Weiping Zhang
- Bloomage Biotechnology Corporation Limited, 678 Tianchen Street, Jinan, Shandong 250101, China
| | - Hanyu Dong
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Song Chen
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Xian Wang
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Anqi Zhao
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, China
| | - Shen Zhang
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Md Asraful Alam
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Shilei Wang
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Chaojun Du
- Nanyang Research Institute of Zhengzhou University, Nanyang Institute of Technology, No. 80 Changjiang Road, Nanyang 473004, China
| | - Jingliang Xu
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
- National Key Laboratory of Biobased Transportation Fuel Technology, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Weigao Wang
- Department of Chemical Engineering, Stanford University, 443 Via Ortega, Palo Alto, California 94305, United States
| | - Peng Xu
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology (GTIIT), Shantou, Guangdong 515063, China
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12
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Li J, Fu J, Shang Y, Wei W, Zhang P, Wang X, Ye BC. Metabolic Engineering of Pseudomonas putida KT2440 for De Novo Biosynthesis of Vanillic Acid. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4217-4224. [PMID: 38356383 DOI: 10.1021/acs.jafc.3c07828] [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: 02/16/2024]
Abstract
Vanillic acid (VA), as a plant-derived phenolic acid compound, has widespread applications and good market prospects. However, the traditional production process cannot meet market demand. In this study, Pseudomonas putida KT2440 was used for de novo biosynthesis of VA. Multiple metabolic engineering strategies were applied to construct these P. putida-based cell factories, including the introduction of a Hs-OMTopt, engineering the cofactor S-adenosylmethionine supply pathway through the overexpression of metX and metH, reforming solubility of Hs-OMTopt, increasing a second copy of Hs-OMTopt, and the optimization of the fermentation medium. The resulting strain, XCS17, de novo biosynthesized 5.4 g/L VA from glucose in a fed-batch fermentation system; this is the highest VA production titer reported up to recently. This study showed that P. putida KT2440 is a robust platform for achieving the effective production of phenolic acids.
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Affiliation(s)
- Jin Li
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jianli Fu
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yanzhe Shang
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wenping Wei
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ping Zhang
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xue Wang
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
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13
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Hebra T, Smrčková H, Elkatmis B, Převorovský M, Pluskal T. POMBOX: A Fission Yeast Cloning Toolkit for Molecular and Synthetic Biology. ACS Synth Biol 2024; 13:558-567. [PMID: 37991801 PMCID: PMC10877588 DOI: 10.1021/acssynbio.3c00529] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 11/23/2023]
Abstract
The fission yeast Schizosaccharomyces pombe is a popular model organism in molecular biology and cell physiology. With its ease of genetic manipulation and growth, supported by in-depth functional annotations in the PomBase database and genome-wide metabolic models,S. pombe is an attractive option for synthetic biology applications. However,S. pombe currently lacks modular tools for generating genetic circuits with more than 1 transcriptional unit. We developed a toolkit to address this gap. Adapted from the MoClo-YTK plasmid kit for Saccharomyces cerevisiae and using the same modular cloning grammar, our POMBOX toolkit is designed to facilitate fast, efficient, and modular construction of genetic circuits inS. pombe. It allows for interoperability when working with DNA sequences that are functional in bothS. cerevisiae and S. pombe (e.g., protein tags, antibiotic resistance cassettes, and coding sequences). Moreover, POMBOX enables the modular assembly of multigene pathways and increases the possible pathway length from 6 to 12 transcriptional units. We also adapted the stable integration vector homology arms to Golden Gate assembly and tested the genomic integration success rates depending on different sequence sizes, from 4 to 24 kb. We included 14 S. pombe promoters that we characterized using two fluorescent proteins, in both minimally defined (EMM2─Edinburgh minimal media) and complex (YES─yeast extract with supplements) media. Then, we examined the efficacy of 6 S. cerevisiae and 6 synthetic terminators in S. pombe. Finally, we used the POMBOX kit for a synthetic biology application in metabolic engineering and expressed plant enzymes in S. pombe to produce specialized metabolite precursors, namely, methylxanthine, amorpha-4,11-diene, and cinnamic acid from the purine, mevalonate, and aromatic amino acid pathways.
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Affiliation(s)
- Téo Hebra
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague, Czech Republic
| | - Helena Smrčková
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague, Czech Republic
| | - Büsra Elkatmis
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague, Czech Republic
| | - Martin Převorovský
- Department
of Cell Biology, Faculty of Science, Charles
University, 128 00 Prague, Czech
Republic
| | - Tomáš Pluskal
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague, Czech Republic
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14
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Mo Q, Yuan J. Minimal aromatic aldehyde reduction (MARE) yeast platform for engineering vanillin production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:4. [PMID: 38184607 PMCID: PMC10771647 DOI: 10.1186/s13068-023-02454-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 12/19/2023] [Indexed: 01/08/2024]
Abstract
BACKGROUND Vanillin represents one of the most widely used flavoring agents in the world. However, microbial synthesis of vanillin is hindered by the host native metabolism that could rapidly degrade vanillin to the byproducts. RESULTS Here, we report that the industrial workhorse Saccharomyces cerevisiae was engineered by systematic deletion of oxidoreductases to improve the vanillin accumulation. Subsequently, we harnessed the minimal aromatic aldehyde reduction (MARE) yeast platform for de novo synthesis of vanillin from glucose. We investigated multiple coenzyme-A free pathways to improve vanillin production in yeast. The vanillin productivity in yeast was enhanced by multidimensional engineering to optimize the supply of cofactors (NADPH and S-adenosylmethionine) together with metabolic reconfiguration of yeast central metabolism. The final yeast strain with overall 24 genetic modifications produced 365.55 ± 7.42 mg l-1 vanillin in shake-flasks, which represents the best reported vanillin titer from glucose in yeast. CONCLUSIONS The success of vanillin overproduction in budding yeast showcases the great potential of synthetic biology for the creation of suitable biocatalysts to meet the requirement in industry. Our work lays a foundation for the future implementation of microbial production of aromatic aldehydes in budding yeast.
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Affiliation(s)
- Qiwen Mo
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, 361102, China
| | - Jifeng Yuan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, 361102, China.
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15
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Xu L, Liaqat F, Sun J, Khazi MI, Xie R, Zhu D. Advances in the vanillin synthesis and biotransformation: A review. RENEWABLE AND SUSTAINABLE ENERGY REVIEWS 2024; 189:113905. [DOI: 10.1016/j.rser.2023.113905] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
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16
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Bi Y, Wang J, Li J, Chou HH, Ren T, Li J, Zhang K. Engineering acetylation platform for the total biosynthesis of D-amino acids. Metab Eng 2023; 80:25-32. [PMID: 37689258 DOI: 10.1016/j.ymben.2023.09.001] [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: 07/18/2023] [Revised: 08/29/2023] [Accepted: 09/03/2023] [Indexed: 09/11/2023]
Abstract
Optically pure D-amino acids are key chemicals with various applications. Although the production of specific D-amino acids has been achieved by chemical synthesis or with in vitro enzyme catalysts, it is challenging to convert a simple carbon source into D-amino acids with high efficiency. Here, we design an artificial metabolic pathway by engineering bacteria to heterologously express racemase and N-acetyltransferase to produce N-acetyl-D-amino acids from L-amino acids. This new platform allows the cytotoxicity of D-amino acids to be avoided. The universal potential of this acetylation protection strategy for effectively synthesizing optically pure D-amino acids is demonstrated by testing sixteen amino acid targets. Furthermore, we combine pathway optimization and metabolic engineering in Escherichia coli and achieve practically useful efficiency with four specific examples, including N-acetyl-D-valine, N-acetyl-D-serine, N-acetyl-D-phenylalanine and N-acetyl-D-phenylglycine, with titers reaching 5.65 g/L, 5.25 g/L, 8.025 g/L and 130 mg/L, respectively. This work opens up opportunities for synthesizing D-amino acids directly from simple carbon sources, avoiding costly and unsustainable conventional approaches.
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Affiliation(s)
- Yanqi Bi
- Fudan University, 220 Handan Road, Shanghai, 201100, China; School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Jingyu Wang
- School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Jialong Li
- School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Hsiang-Hui Chou
- School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Tianhua Ren
- School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Jinlin Li
- School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Kechun Zhang
- School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China.
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17
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Chen L, Li K, Chen H, Li Z. Reviewing the Source, Physiological Characteristics, and Aroma Production Mechanisms of Aroma-Producing Yeasts. Foods 2023; 12:3501. [PMID: 37761210 PMCID: PMC10529235 DOI: 10.3390/foods12183501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Flavor is an essential element of food quality. Flavor can be improved by adding flavoring substances or via microbial fermentation to impart aroma. Aroma-producing yeasts are a group of microorganisms that can produce aroma compounds, providing a strong aroma to foods and thus playing a great role in the modern fermentation industry. The physiological characteristics of aroma-producing yeast, including alcohol tolerance, acid tolerance, and salt tolerance, are introduced in this article, beginning with their origins and biological properties. The main mechanism of aroma-producing yeast is then analyzed based on its physiological roles in the fermentation process. Functional enzymes such as proteases, lipases, and glycosidase are released by yeast during the fermentation process. Sugars, fats, and proteins in the environment can be degraded by these enzymes via pathways such as glycolysis, methoxylation, the Ehrlich pathway, and esterification, resulting in the production of various aromatic esters (such as ethyl acetate and ethyl caproate), alcohols (such as phenethyl alcohol), and terpenes (such as monoterpenes, sesquiterpenes, and squalene). Furthermore, yeast cells can serve as cell synthesis factories, wherein specific synthesis pathways can be introduced into cells using synthetic biology techniques to achieve high-throughput production. In addition, the applications of aroma yeast in the food, pharmaceutical, and cosmetic industries are summarized, and the future development trends of aroma yeasts are discussed to provide a theoretical basis for their application in the food fermentation industry.
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Affiliation(s)
- Li Chen
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China; (L.C.); (K.L.)
| | - Ke Li
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China; (L.C.); (K.L.)
| | - Huitai Chen
- Hunan Guoyuan Liquor Industry Co., Ltd., Yueyang 414000, China;
| | - Zongjun Li
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China; (L.C.); (K.L.)
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18
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Pyne ME, Bagley JA, Narcross L, Kevvai K, Exley K, Davies M, Wang Q, Whiteway M, Martin VJJ. Screening non-conventional yeasts for acid tolerance and engineering Pichia occidentalis for production of muconic acid. Nat Commun 2023; 14:5294. [PMID: 37652930 PMCID: PMC10471774 DOI: 10.1038/s41467-023-41064-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/22/2023] [Indexed: 09/02/2023] Open
Abstract
Saccharomyces cerevisiae is a workhorse of industrial biotechnology owing to the organism's prominence in alcohol fermentation and the suite of sophisticated genetic tools available to manipulate its metabolism. However, S. cerevisiae is not suited to overproduce many bulk bioproducts, as toxicity constrains production at high titers. Here, we employ a high-throughput assay to screen 108 publicly accessible yeast strains for tolerance to 20 g L-1 adipic acid (AA), a nylon precursor. We identify 15 tolerant yeasts and select Pichia occidentalis for production of cis,cis-muconic acid (CCM), the precursor to AA. By developing a genome editing toolkit for P. occidentalis, we demonstrate fed-batch production of CCM with a maximum titer (38.8 g L-1), yield (0.134 g g-1 glucose) and productivity (0.511 g L-1 h-1) that surpasses all metrics achieved using S. cerevisiae. This work brings us closer to the industrial bioproduction of AA and underscores the importance of host selection in bioprocessing.
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Affiliation(s)
- Michael E Pyne
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Department of Biology, University of Western Ontario, Ontario, Canada
| | - James A Bagley
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
| | - Lauren Narcross
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Amyris, Inc., Emeryville, CA, USA
| | - Kaspar Kevvai
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Pivot Bio, Berkeley, CA, USA
| | - Kealan Exley
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Novo Nordisk Foundation Center for Biosustainability, Lyngby, Denmark
| | - Meghan Davies
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- BenchSci, Toronto, ON, Canada
| | | | - Malcolm Whiteway
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
| | - Vincent J J Martin
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada.
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada.
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19
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Biggs BW, Tyo KEJ. Aromatic natural products synthesis from aromatic lignin monomers using Acinetobacter baylyi ADP1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.24.554694. [PMID: 37662333 PMCID: PMC10473687 DOI: 10.1101/2023.08.24.554694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Achieving sustainable chemical synthesis and a circular economy will require process innovation to minimize or recover existing waste streams. Valorization of lignin biomass has the ability to advance this goal. While lignin has proved a recalcitrant feedstock for upgrading, biological approaches can leverage native microbial metabolism to simplify complex and heterogeneous feedstocks to tractable starting points for biochemical upgrading. Recently, we demonstrated that one microbe with lignin relevant metabolism, Acinetobacter baylyi ADP1, is both highly engineerable and capable of undergoing rapid design-build-test-learn cycles, making it an ideal candidate for these applications. Here, we utilize these genetic traits and ADP1's native β-ketoadipate metabolism to convert mock alkali pretreated liquor lignin (APL) to two valuable natural products, vanillin-glucoside and resveratrol. En route, we create strains with up to 22 genetic modifications, including up to 8 heterologously expressed enzymes. Our approach takes advantage of preexisting aromatic species in APL (vanillate, ferulate, and p-coumarate) to create shortened biochemical routes to end products. Together, this work demonstrates ADP1's potential as a platform for upgrading lignin waste streams and highlights the potential for biosynthetic methods to maximize the existing chemical potential of lignin aromatic monomers.
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Affiliation(s)
- Bradley W. Biggs
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Keith E. J. Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
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20
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Liu Y, Sun L, Huo YX, Guo S. Strategies for improving the production of bio-based vanillin. Microb Cell Fact 2023; 22:147. [PMID: 37543600 PMCID: PMC10403864 DOI: 10.1186/s12934-023-02144-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/10/2023] [Indexed: 08/07/2023] Open
Abstract
Vanillin (4-hydroxy-3-methoxybenzaldehyde) is one of the most popular flavors with wide applications in food, fragrance, and pharmaceutical industries. However, the high cost and limited yield of plant extraction failed to meet the vast market demand of natural vanillin. Vanillin biotechnology has emerged as a sustainable and cost-effective alternative to supply vanillin. In this review, we explored recent advances in vanillin biosynthesis and highlighted the potential of vanillin biotechnology. In particular, we addressed key challenges in using microorganisms and provided promising approaches for improving vanillin production with a special focus on chassis development, pathway construction and process optimization. Future directions of vanillin biosynthesis using inexpensive precursors are also thoroughly discussed.
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Affiliation(s)
- Ying Liu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Lichao Sun
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
- Beijing Institute of Technology (Tangshan) Translational Research Center, Hebei, 063611, China.
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
- Beijing Institute of Technology (Tangshan) Translational Research Center, Hebei, 063611, China
| | - Shuyuan Guo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
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21
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de Ruijter JC, Aisala H, Jokinen I, Krogerus K, Rischer H, Toivari M. Production and sensory analysis of grape flavoured beer by co-fermentation of an industrial and a genetically modified laboratory yeast strain. Eur Food Res Technol 2023; 249:1-10. [PMID: 37362347 PMCID: PMC10148978 DOI: 10.1007/s00217-023-04274-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/18/2023] [Accepted: 04/22/2023] [Indexed: 06/28/2023]
Abstract
The so-called "craft beer revolution" has increased the demand for new styles of beers, often with new ingredients like flavour extracts. In recent years, synthetic biology has realized the production of a plethora of plant secondary metabolites in microbial hosts, which could provide an alternative source for these compounds. In this study, we selected a in situ flavour production approach for grape flavour addition. We used an O-methyl anthranilate (OmANT) producing laboratory Saccharomyces cerevisiae strain in co-fermentations with an industrial beer yeast strain WLP644. The laboratory strain provided an ease of genetic manipulation and the desirable properties of the WLP644 strain were not modified in this approach. In shake flasks, a 10:90 ratio of the yeasts produced grape flavoured beer with the yeast produced flavour compound in a range normally used for flavoured beverages. Hopped and unhopped beers were analysed by VTT's trained sensory panel and with olfactory GC-MS. OmANT was successfully detected from the beers as a floral odour and flavour. Moreover, no off-flavours were detected and aroma profiles outside the grape flavour were rather similar. These results indicate that the co-fermentation principle is a suitable approach to change the flavour profiles of beers with a simple yeast strain drop-in approach. Supplementary Information The online version contains supplementary material available at 10.1007/s00217-023-04274-1.
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Affiliation(s)
- Jorg C. de Ruijter
- Sustainable Products and Materials, VTT Technical Research Centre of Finland Ltd, Espoo, Uusimaa Finland
| | - Heikki Aisala
- Sustainable Products and Materials, VTT Technical Research Centre of Finland Ltd, Espoo, Uusimaa Finland
| | - Iina Jokinen
- Sustainable Products and Materials, VTT Technical Research Centre of Finland Ltd, Espoo, Uusimaa Finland
| | - Kristoffer Krogerus
- Sustainable Products and Materials, VTT Technical Research Centre of Finland Ltd, Espoo, Uusimaa Finland
| | - Heiko Rischer
- Sustainable Products and Materials, VTT Technical Research Centre of Finland Ltd, Espoo, Uusimaa Finland
| | - Mervi Toivari
- Sustainable Products and Materials, VTT Technical Research Centre of Finland Ltd, Espoo, Uusimaa Finland
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22
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Butler ND, Anderson SR, Dickey RM, Nain P, Kunjapur AM. Combinatorial gene inactivation of aldehyde dehydrogenases mitigates aldehyde oxidation catalyzed by E. coli resting cells. Metab Eng 2023; 77:294-305. [PMID: 37100193 DOI: 10.1016/j.ymben.2023.04.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/11/2023] [Accepted: 04/23/2023] [Indexed: 04/28/2023]
Abstract
Aldehydes are attractive chemical targets both as end products in the flavors and fragrances industry and as intermediates due to their propensity for C-C bond formation. Here, we identify and address unexpected oxidation of a model collection of aromatic aldehydes, including many that originate from biomass degradation. When diverse aldehydes are supplemented to E. coli cells grown under aerobic conditions, as expected they are either reduced by the wild-type MG1655 strain or stabilized by a strain engineered for reduced aromatic aldehyde reduction (the E. coli RARE strain). Surprisingly, when these same aldehydes are supplemented to resting cell preparations of either E. coli strain, under many conditions we observe substantial oxidation. By performing combinatorial inactivation of six candidate aldehyde dehydrogenase genes in the E. coli genome using multiplexed automatable genome engineering (MAGE), we demonstrate that this oxidation can be substantially slowed, with greater than 50% retention of 6 out of 8 aldehydes when assayed 4 h after their addition. Given that our newly engineered strain exhibits reduced oxidation and reduction of aromatic aldehydes, we dubbed it the E. coli ROAR strain. We applied the new strain to resting cell biocatalysis for two kinds of reactions - the reduction of 2-furoic acid to furfural and the condensation of 3-hydroxy-benzaldehyde and glycine to form a beta hydroxylated non-standard amino acid. In each case, we observed substantial improvements in product titer 20 h after reaction initiation (9-fold and 10-fold, respectively). Moving forward, the use of this strain to generate resting cells should allow aldehyde product isolation, further enzymatic conversion, or chemical reactivity under cellular contexts that better accommodate aldehyde toxicity.
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Affiliation(s)
- Neil D Butler
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newar, DE, 19716, USA
| | - Shelby R Anderson
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newar, DE, 19716, USA
| | - Roman M Dickey
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newar, DE, 19716, USA
| | - Priyanka Nain
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newar, DE, 19716, USA
| | - Aditya M Kunjapur
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newar, DE, 19716, USA.
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23
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Abstract
Our current food system relies on unsustainable practices, which often fail to provide healthy diets to a growing population. Therefore, there is an urgent demand for new sustainable nutrition sources and processes. Microorganisms have gained attention as a new food source solution, due to their low carbon footprint, low reliance on land, water and seasonal variations coupled with a favourable nutritional profile. Furthermore, with the emergence and use of new tools, specifically in synthetic biology, the uses of microorganisms have expanded showing great potential to fulfil many of our dietary needs. In this review, we look at the different applications of microorganisms in food, and examine the history, state-of-the-art and potential to disrupt current foods systems. We cover both the use of microbes to produce whole foods out of their biomass and as cell factories to make highly functional and nutritional ingredients. The technical, economical, and societal limitations are also discussed together with the current and future perspectives.
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Affiliation(s)
- Alicia E Graham
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.
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24
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Basri RS, Rahman RNZRA, Kamarudin NHA, Ali MSM. Carboxylic acid reductases: Structure, catalytic requirements, and applications in biotechnology. Int J Biol Macromol 2023; 240:124526. [PMID: 37080403 DOI: 10.1016/j.ijbiomac.2023.124526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/07/2023] [Accepted: 04/16/2023] [Indexed: 04/22/2023]
Abstract
Biocatalysts have been gaining extra attention in recent decades due to their industrial-relevance properties, which may hasten the transition to a cleaner environment. Carboxylic acid reductases (CARs) are large, multi-domain proteins that can catalyze the reduction of carboxylic acids to corresponding aldehydes, with the presence of adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide phosphate (NADPH). This biocatalytic reaction is of great interest due to the abundance of carboxylic acids in nature and the ability of CAR to convert carboxylic acids to a wide range of aldehydes essentially needed as end products such as vanillin or reaction intermediates for several compounds production such as alcohols, alkanes, and amines. This modular enzyme, found in bacteria and fungi, demands an activation via post-translational modification by the phosphopantetheinyl transferase (PPTase). Recent advances in the characterization and structural studies of CARs revealed valuable information about the enzymes' dynamics, mechanisms, and unique features. In this comprehensive review, we summarize the previous findings on the phylogeny, structural and mechanistic insight of the domains, post-translational modification requirement, strategies for the cofactors regeneration, the extensively broad aldehyde-related industrial application properties of CARs, as well as their recent immobilization approaches.
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Affiliation(s)
- Rose Syuhada Basri
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Nor Hafizah Ahmad Kamarudin
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Centre of Foundation Studies for Agricultural Science, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
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25
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Ren J, Barton CD, Zhan J. Engineered production of bioactive polyphenolic O-glycosides. Biotechnol Adv 2023; 65:108146. [PMID: 37028465 DOI: 10.1016/j.biotechadv.2023.108146] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 03/04/2023] [Accepted: 04/02/2023] [Indexed: 04/09/2023]
Abstract
Polyphenolic compounds (such as quercetin and resveratrol) possess potential medicinal values due to their various bioactivities, but poor water solubility hinders their health benefits to humankind. Glycosylation is a well-known post-modification method to biosynthesize natural product glycosides with improved hydrophilicity. Glycosylation has profound effects on decreasing toxicity, increasing bioavailability and stability, together with changing bioactivity of polyphenolic compounds. Therefore, polyphenolic glycosides can be used as food additives, therapeutics, and nutraceuticals. Engineered biosynthesis provides an environmentally friendly and cost-effective approach to generate polyphenolic glycosides through the use of various glycosyltransferases (GTs) and sugar biosynthetic enzymes. GTs transfer the sugar moieties from nucleotide-activated diphosphate sugar (NDP-sugar) donors to sugar acceptors such as polyphenolic compounds. In this review, we systematically review and summarize the representative polyphenolic O-glycosides with various bioactivities and their engineered biosynthesis in microbes with different biotechnological strategies. We also review the major routes towards NDP-sugar formation in microbes, which is significant for producing unusual or novel glycosides. Finally, we discuss the trends in NDP-sugar based glycosylation research to promote the development of prodrugs that positively impact human health and wellness.
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Affiliation(s)
- Jie Ren
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT 84322-4105, USA
| | - Caleb Don Barton
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT 84322-4105, USA
| | - Jixun Zhan
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT 84322-4105, USA.
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26
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Bennis NX, Kostanjšek M, van den Broek M, Daran JMG. Improving CRISPR-Cas9 mediated genome integration in interspecific hybrid yeasts. N Biotechnol 2023; 76:49-62. [PMID: 37028644 DOI: 10.1016/j.nbt.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/03/2023] [Accepted: 04/04/2023] [Indexed: 04/08/2023]
Abstract
Saccharomyces pastorianus is not a classical taxon, it is an interspecific hybrid resulting from the cross of Saccharomyces cerevisiae and Saccharomyces eubayanus. Exhibiting heterosis for phenotypic traits such as wort α-oligosaccharide consumption and fermentation at low temperature, it has been domesticated to become the main workhorse of the brewing industry. Although CRISPR-Cas9 has been shown to be functional in S. pastorianus, repair of CRISPR- induced double strand break is unpredictable and preferentially uses the homoeologous chromosome as template, preventing targeted introduction of the desired repair construct. Here, we demonstrate that lager hybrids can be edited with near 100% efficiency at carefully selected landing sites on the chimeric SeScCHRIII. The landing sites were systematically selected and evaluated for (i) absence of loss of heterozygosity upon CRISPR-editing, (ii) efficiency of the gRNA, and (iii) absence of effect on strain physiology. Successful examples of highly efficient single and double gene integration illustrated that genome editing can be applied in interspecies hybrids, paving the way to a new impulse to lager yeast strain development. DATA AVAILABILITY: Data underlying graphs and figures found in this manuscript are deposited at the 4TU research dat center (https://data.4tu.nl/info/en/) and available through the doi: 10.4121/21648329.
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27
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Muratovska N, Carlquist M. Recombinant yeast for production of the pain receptor modulator nonivamide from vanillin. FRONTIERS IN CHEMICAL ENGINEERING 2023. [DOI: 10.3389/fceng.2022.1097215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
We report on the development of a method based on recombinant yeast Saccharomyces cerevisiae to produce nonivamide, a capsaicinoid and potent agonist of the pain receptor TRPV1. Nonivamide was produced in a two-step batch process where yeast was i) grown aerobically on glucose and ii) used to produce nonivamide from vanillin and non-anoic acid by bioconversion. The yeast was engineered to express multiple copies of an amine transaminase from Chromobacterium violaceum (CvTA), along with an NADH-dependent alanine dehydrogenase from Bacillus subtilis (BsAlaDH) to enable efficient reductive amination of vanillin. Oxygen-limited conditions and the use of ethanol as a co-substrate to regenerate NADH were identified to favour amination over the formation of the by-products vanillic alcohol and vanillic acid. The native alcohol dehydrogenase ADH6 was deleted to further reduce the formation of vanillic alcohol. A two-enzyme system consisting of an N-acyltransferase from Capsicum annuum (CaAT), and a CoA ligase from Sphingomonas sp. Ibu-2 (IpfF) was co-expressed to produce the amide. This study provides proof of concept for yeast-based production of non-ivamide by combined transamination and amidation of vanillin.
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28
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Systems metabolic engineering upgrades Corynebacterium glutamicum to high-efficiency cis, cis-muconic acid production from lignin-based aromatics. Metab Eng 2023; 75:153-169. [PMID: 36563956 DOI: 10.1016/j.ymben.2022.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/14/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
Lignin displays a highly challenging renewable. To date, massive amounts of lignin, generated in lignocellulosic processing facilities, are for the most part merely burned due to lacking value-added alternatives. Aromatic lignin monomers of recognized relevance are in particular vanillin, and to a lesser extent vanillate, because they are accessible at high yield from softwood-lignin using industrially operated alkaline oxidative depolymerization. Here, we metabolically engineered C. glutamicum towards cis, cis-muconate (MA) production from these key aromatics. Starting from the previously created catechol-based producer C. glutamicum MA-2, systems metabolic engineering first discovered an unspecific aromatic aldehyde reductase that formed aromatic alcohols from vanillin, protocatechualdehyde, and p- hydroxybenzaldehyde, and was responsible for the conversion up to 57% of vanillin into vanillyl alcohol. The alcohol was not re-consumed by the microbe later, posing a strong drawback on the producer. The identification and subsequent elimination of the encoding fudC gene completely abolished vanillyl alcohol formation. Second, the initially weak flux through the native vanillin and vanillate metabolism was enhanced up to 2.9-fold by implementing synthetic pathway modules. Third, the most efficient protocatechuate decarboxylase AroY for conversion of the midstream pathway intermediate protocatechuate into catechol was identified out of several variants in native and codon optimized form and expressed together with the respective helper proteins. Fourth, the streamlined modules were all genomically combined which yielded the final strain MA-9. MA-9 produced bio-based MA from vanillin, vanillate, and seven structurally related aromatics at maximum selectivity. In addition, MA production from softwood-based vanillin, obtained through alkaline depolymerization, was demonstrated.
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29
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Sieow BFL, De Sotto R, Seet ZRD, Hwang IY, Chang MW. Synthetic Biology Meets Machine Learning. Methods Mol Biol 2023; 2553:21-39. [PMID: 36227537 DOI: 10.1007/978-1-0716-2617-7_2] [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] [Indexed: 06/16/2023]
Abstract
This chapter outlines the myriad applications of machine learning (ML) in synthetic biology, specifically in engineering cell and protein activity, and metabolic pathways. Though by no means comprehensive, the chapter highlights several prominent computational tools applied in the field and their potential use cases. The examples detailed reinforce how ML algorithms can enhance synthetic biology research by providing data-driven insights into the behavior of living systems, even without detailed knowledge of their underlying mechanisms. By doing so, ML promises to increase the efficiency of research projects by modeling hypotheses in silico that can then be tested through experiments. While challenges related to training dataset generation and computational costs remain, ongoing improvements in ML tools are paving the way for smarter and more streamlined synthetic biology workflows that can be readily employed to address grand challenges across manufacturing, medicine, engineering, agriculture, and beyond.
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Affiliation(s)
- Brendan Fu-Long Sieow
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Graduate School for Integrative Sciences and Engineering Programme, National University of Singapore, Singapore, Singapore
| | - Ryan De Sotto
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Zhi Ren Darren Seet
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - In Young Hwang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Matthew Wook Chang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore.
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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30
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De novo biosynthesis of vanillin in engineered Saccharomyces cerevisiae. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2022.118049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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31
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Coculture engineering for efficient production of vanillyl alcohol in Escherichia coli. ABIOTECH 2022; 3:292-300. [PMID: 36533265 PMCID: PMC9755795 DOI: 10.1007/s42994-022-00079-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/22/2022] [Indexed: 10/14/2022]
Abstract
Vanillyl alcohol is a precursor of vanillin, which is one of the most widely used flavor compounds. Currently, vanillyl alcohol biosynthesis still encounters the problem of low efficiency. In this study, coculture engineering was adopted to improve production efficiency of vanillyl alcohol in E. coli. First, two pathways were compared for biosynthesis of the immediate precursor 3, 4-dihydroxybenzyl alcohol in monocultures, and the 3-dehydroshikimate-derived pathway showed higher efficiency than the 4-hydroxybenzoate-derived pathway. To enhance the efficiency of the last methylation step, two strategies were used, and strengthening S-adenosylmethionine (SAM) regeneration showed positive effect while strengthening SAM biosynthesis showed negative effect. Then, the optimized pathway was assembled in a single cell. However, the biosynthetic efficiency was still low, and was not significantly improved by modular optimization of pathway genes. Thus, coculturing engineering strategy was adopted. At the optimal inoculation ratio, the titer reached 328.9 mg/L. Further, gene aroE was knocked out to reduce cell growth and improve 3,4-DHBA biosynthesis of the upstream strain. As a result, the titer was improved to 559.4 mg/L in shake flasks and to 3.89 g/L in fed-batch fermentation. These are the highest reported titers of vanillyl alcohol so far. This work provides an effective strategy for sustainable production of vanillyl alcohol.
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32
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Wang X, Yang B, Zhao W, Cao W, Shen Y, Li Z, Bao X. Capture Hi-C reveals the influence on dynamic three-dimensional chromosome organization perturbed by genetic variation or vanillin stress in Saccharomyces cerevisiae. Front Microbiol 2022; 13:1012377. [DOI: 10.3389/fmicb.2022.1012377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/20/2022] [Indexed: 11/18/2022] Open
Abstract
Studying the mechanisms of resistance to vanillin in microorganisms, which is derived from lignin and blocks a major pathway of DNA double-strand break repair in yeast, will benefit the design of robust cell factories that produce biofuels and chemicals using lignocellulosic materials. A high vanillin-tolerant Saccharomyces cerevisiae strain EMV-8 carrying site mutations compared to its parent strain NAN-27 was selected for the analyses. The dynamics of the chromatin structure of eukaryotic cells play a critical role in transcription and the regulation of gene expression and thus the phenotype. Consequently, Hi-C and transcriptome analyses were conducted in EMV-8 and NAN-27 in the log phase with or without vanillin stress to determine the effects of mutations and vanillin disturbance on the dynamics of three-dimensional chromosome organization and the influence of the organization on the transcriptome. The outcomes indicated that the chromosome interaction pattern disturbed by vanillin stress or genetic mutations in the log phase was similar to that in mouse cells. The short chromosomes contact the short chromosomes, and the long chromosomes contact the long chromosomes. In response to vanillin stress, the boundaries of the topologically associating domain (TAD) in the vanillin-tolerant strain EMV-8 were more stable than those in its parent strain NAN-27. The motifs of SFL1, STB3, and NHP6A/B were enriched at TAD boundaries in both EMV-8 and NAN-27 with or without vanillin, indicating that these four genes were probably related to TAD formation. The Indel mutation of YRR1, whose absence was confirmed to benefit vanillin tolerance in EMV-8, caused two new interaction sites that contained three genes, WTM2, PUP1, and ALE1, whose overexpression did not affect vanillin resistance in yeast. Overall, our results revealed that in the log phase, genetic mutations and vanillin disturbance have a negligible effect on three-dimensional chromosome organization, and the reformation or disappearance of TAD boundaries did not show an association with gene expression, which provides an example for studying yeast chromatin structure during stress tolerance using Hi-C technology.
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33
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Karlova R, Busscher J, Schempp FM, Buchhaupt M, van Dijk ADJ, Beekwilder J. Detoxification of monoterpenes by a family of plant glycosyltransferases. PHYTOCHEMISTRY 2022; 203:113371. [PMID: 36037906 DOI: 10.1016/j.phytochem.2022.113371] [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: 03/24/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Plant monoterpenes are challenging compounds, since they often act as solvents, and thus have both phytotoxic and antimicrobial properties. In this study an approach is developed to identify and characterize enzymes that can detoxify monoterpenoids, and thus would protect both plants and microbial production systems from these compounds. Plants respond to the presence of monoterpenes by expressing glycosyltransferases (UGTs), which conjugate the monoterpenoids into glycosides. By identifying these enzymes in a transcriptomics approach using Mentha × piperita, a family of UGTs was identified which is active on cyclic monoterpenoids such as menthol, and on acyclic monoterpenoids such as geranic acid. Other members of this family, from tomato, were also shown to be active on these monoterpenoids. In vitro and in vivo activity of different UGTs were tested with different substrates. We found that some glycosyltransferases significantly affect the toxicity of selected monoterpenoids in Escherichia coli, suggesting that glycosyltransferases can protect cells from monoterpenoid toxicity.
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Affiliation(s)
- Rumyana Karlova
- Laboratory of Plant Physiology, Droevendaalsesteeg 1, 6708 PB Wageningen University, the Netherlands
| | - Jeroen Busscher
- Laboratory of Plant Physiology, Droevendaalsesteeg 1, 6708 PB Wageningen University, the Netherlands
| | - Florence M Schempp
- DECHEMA Research Institute, Microbial Biotechnology, Frankfurt am Main, Germany
| | - Markus Buchhaupt
- DECHEMA Research Institute, Microbial Biotechnology, Frankfurt am Main, Germany
| | - Aalt D J van Dijk
- Laboratory of Bioinformatics, Wageningen University, Wageningen, the Netherlands
| | - Jules Beekwilder
- Laboratory of Plant Physiology, Droevendaalsesteeg 1, 6708 PB Wageningen University, the Netherlands; Wageningen Plant Research, PO Box 16, 6700 AA, Wageningen, the Netherlands.
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Llorente B, Williams TC, Goold HD, Pretorius IS, Paulsen IT. Harnessing bioengineered microbes as a versatile platform for space nutrition. Nat Commun 2022; 13:6177. [PMID: 36261466 PMCID: PMC9582011 DOI: 10.1038/s41467-022-33974-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 10/10/2022] [Indexed: 12/24/2022] Open
Abstract
Human enterprises through the solar system will entail long-duration voyages and habitation creating challenges in maintaining healthy diets. We discuss consolidating multiple sensory and nutritional attributes into microorganisms to develop customizable food production systems with minimal inputs, physical footprint, and waste. We envisage that a yeast collection bioengineered for one-carbon metabolism, optimal nutrition, and diverse textures, tastes, aromas, and colors could serve as a flexible food-production platform. Beyond its potential for supporting humans in space, bioengineered microbial-based food could lead to a new paradigm for Earth's food manufacturing that provides greater self-sufficiency and removes pressure from natural ecosystems.
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Affiliation(s)
- Briardo Llorente
- ARC Center of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, 2109, Australia.
- School of Natural Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
| | - Thomas C Williams
- ARC Center of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, 2109, Australia
- School of Natural Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Hugh D Goold
- ARC Center of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, 2109, Australia
- School of Natural Sciences, Macquarie University, Sydney, NSW, 2109, Australia
- New South Wales Department of Primary Industries, Orange, NSW, 2800, Australia
| | - Isak S Pretorius
- ARC Center of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, 2109, Australia
| | - Ian T Paulsen
- ARC Center of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, 2109, Australia
- School of Natural Sciences, Macquarie University, Sydney, NSW, 2109, Australia
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35
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Vasilev N. Medicinal Plants: Guests and Hosts in the Heterologous Expression of High-Value Products. PLANTA MEDICA 2022; 88:1175-1189. [PMID: 34521134 DOI: 10.1055/a-1576-4148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Medicinal plants play an important dual role in the context of the heterologous expression of high-value pharmaceutical products. On the one hand, the classical biochemical and modern omics approaches allowed for the discovery of various genes encoding biosynthetic pathways in medicinal plants. Recombinant DNA technology enabled introducing these genes and regulatory elements into host organisms and enhancing the heterologous production of the corresponding secondary metabolites. On the other hand, the transient expression of foreign DNA in plants facilitated the production of numerous proteins of pharmaceutical importance. This review summarizes several success stories of the engineering of plant metabolic pathways in heterologous hosts. Likewise, a few examples of recombinant protein expression in plants for therapeutic purposes are also highlighted. Therefore, the importance of medicinal plants has grown immensely as sources for valuable products of low and high molecular weight. The next step ahead for bioengineering is to achieve more success stories of industrial-scale production of secondary plant metabolites in microbial systems and to fully exploit plant cell factories' commercial potential for recombinant proteins.
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Affiliation(s)
- Nikolay Vasilev
- TU Dortmund University, Biochemical and Chemical Engineering, Technical Biochemistry, Dortmund, Germany
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36
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Skaliter O, Livneh Y, Agron S, Shafir S, Vainstein A. A whiff of the future: functions of phenylalanine-derived aroma compounds and advances in their industrial production. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1651-1669. [PMID: 35638340 PMCID: PMC9398379 DOI: 10.1111/pbi.13863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 05/15/2022] [Accepted: 05/25/2022] [Indexed: 05/19/2023]
Abstract
Plants produce myriad aroma compounds-odorous molecules that are key factors in countless aspects of the plant's life cycle, including pollinator attraction and communication within and between plants. For humans, aroma compounds convey accurate information on food type, and are vital for assessing the environment. The phenylpropanoid pathway is the origin of notable aroma compounds, such as raspberry ketone and vanillin. In the last decade, great strides have been made in elucidating this pathway with the identification of numerous aroma-related biosynthetic enzymes and factors regulating metabolic shunts. These scientific achievements, together with public acknowledgment of aroma compounds' medicinal benefits and growing consumer demand for natural products, are driving the development of novel biological sources for wide-scale, eco-friendly, and inexpensive production. Microbes and plants that are readily amenable to metabolic engineering are garnering attention as suitable platforms for achieving this goal. In this review, we discuss the importance of aroma compounds from the perspectives of humans, pollinators and plant-plant interactions. Focusing on vanillin and raspberry ketone, which are of high interest to the industry, we present key knowledge on the biosynthesis and regulation of phenylalanine-derived aroma compounds, describe advances in the adoption of microbes and plants as platforms for their production, and propose routes for improvement.
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Affiliation(s)
- Oded Skaliter
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovotIsrael
| | - Yarin Livneh
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovotIsrael
| | - Shani Agron
- Department of NeurobiologyThe Weizmann Institute of ScienceRehovotIsrael
| | - Sharoni Shafir
- B. Triwaks Bee Research Center, Department of Entomology, Institute of Environmental Sciences, Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovotIsrael
| | - Alexander Vainstein
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovotIsrael
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Unlocking the access to oxidized coenzyme A via a single-step green membrane-based purification. Sci Rep 2022; 12:12991. [PMID: 35906370 PMCID: PMC9338019 DOI: 10.1038/s41598-022-17250-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/22/2022] [Indexed: 11/30/2022] Open
Abstract
A new membrane-based strategy to purify oxidized coenzyme A ((CoAS)2) from adenosine triphosphate (ATP), adenosine diphosphate (ADP) and adenosine monophosphate (AMP) has been developed. Commercially available membranes were screened and studied (permeate flux and overall compounds retention) which allowed the identification of one efficient membrane (GK from Suez Water Technologies & Solutions). Different total compounds concentrations solutions were used in the system in order to find the following working conditions: 4 bars with a total compounds solution of 5.19 g L−1. Applying these conditions to a dia-filtration set-up allowed us to reach 68% pure (CoAS)2 in 4.8 diafiltration volumes (DV) and a 95% (CoAS)2 purity can be predicted in 8.5 DV. A comparative study of green metrics—i.e. process mass index (PMI)—of the classic chromatography vs the membrane-based one demonstrated the great advantages of the latter in terms of sustainability. This strategy unlocks the access to the essential and central cofactor that is coenzyme A.
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38
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Shmonova EA, Savrasova EA, Fedorova EN, Doroshenko VG. Comparative Analysis of Catabolic and Anabolic Dehydroshikimate Dehydratases for 3,4-DHBA Production in Escherichia coli. Microorganisms 2022; 10:microorganisms10071357. [PMID: 35889076 PMCID: PMC9324987 DOI: 10.3390/microorganisms10071357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/01/2022] [Accepted: 07/01/2022] [Indexed: 02/04/2023] Open
Abstract
The production of 3,4-dihydroxybenzoic acid (3,4-DHBA or protocatechuate) is a relevant task owing to 3,4-DHBA’s pharmaceutical properties and its use as a precursor for subsequent synthesis of high value-added chemicals. The microbial production of 3,4-DHBA using dehydroshikimate dehydratase (DSD) (EC: 4.2.1.118) has been demonstrated previously. DSDs from soil-dwelling organisms (where DSD is involved in quinate/shikimate degradation) and from Bacillus spp. (synthesizing the 3,4-DHBA-containing siderophore) were compared in terms of the kinetic properties and their ability to produce 3,4-DHBA. Catabolic DSDs from Corynebacterium glutamicum (QsuB) and Neurospora crassa (Qa-4) had higher Km (1 and 0.6 mM, respectively) and kcat (61 and 220 s−1, respectively) than biosynthetic AsbF from Bacillus thuringiensis (Km~0.04 mM, kcat~1 s−1). Product inhibition was found to be a crucial factor when choosing DSD for strain development. AsbF was more inhibited by 3,4-DHBA (IC50~0.08 mM), and Escherichia coli MG1655 ΔaroE PlacUV5-asbFattφ80 strain provided only 0.2 g/L 3,4-DHBA in test-tube fermentation. Isogenic strains MG1655 ΔaroE PlacUV5-qsuBattφ80 and MG1655 ΔaroE PlacUV5-qa-4attφ80 expressing QsuB and Qa-4 with IC50 ~0.35 mM and ~0.64 mM, respectively, accumulated 2.7 g/L 3,4-DHBA under the same conditions.
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Guo D, Wu S, Fu X, Pan H. De Novo Biosynthesis of Methyl Cinnamate in Engineered Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:7736-7741. [PMID: 35709502 DOI: 10.1021/acs.jafc.2c02638] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Methyl cinnamate with a fruity balsamic odor is an important fragrance ingredient in perfumes and cosmetics. Chemical processes are currently the only means of producing methyl cinnamate. But consumers prefer natural flavors. Therefore, it is necessary to design and develop microbial cell factories for the production of methyl cinnamate. In this study, we established for the first time a biosynthetic pathway in engineered Escherichia coli for production of methyl cinnamate from glucose. We further increased the methyl cinnamate production to 302 mg/L by increasing the availability of the metabolic precursors. Finally, the titer was increased to 458 mg/L in a two-phase culture system.
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Affiliation(s)
- Daoyi Guo
- Key Laboratory of Organo-Pharmaceutical Chemistry, Jiangxi Province, Gannan Normal University, Ganzhou 341000, China
| | - Shaoting Wu
- Key Laboratory of Organo-Pharmaceutical Chemistry, Jiangxi Province, Gannan Normal University, Ganzhou 341000, China
| | - Xiao Fu
- Key Laboratory of Organo-Pharmaceutical Chemistry, Jiangxi Province, Gannan Normal University, Ganzhou 341000, China
| | - Hong Pan
- Key Laboratory of Organo-Pharmaceutical Chemistry, Jiangxi Province, Gannan Normal University, Ganzhou 341000, China
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40
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Winkler M, Ling JG. Biocatalytic carboxylate reduction – recent advances and new enzymes. ChemCatChem 2022. [DOI: 10.1002/cctc.202200441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Margit Winkler
- Technische Universitat Graz Austrian Centre of Industrial Biotechnology Petersgasse 14 8010 Graz AUSTRIA
| | - Jonathan Guyang Ling
- Universiti Kebangsaan Malaysia Fakulti Sains dan Teknologi Department of Biological Sciences and Biotechnology 43600 Bangi MALAYSIA
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41
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Muratovska N, Silva P, Pozdniakova T, Pereira H, Grey C, Johansson B, Carlquist M. Towards engineered yeast as production platform for capsaicinoids. Biotechnol Adv 2022; 59:107989. [PMID: 35623491 DOI: 10.1016/j.biotechadv.2022.107989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 12/23/2022]
Abstract
Capsaicinoids are bioactive alkaloids produced by the chili pepper fruit and are known to be the most potent agonists of the human pain receptor TRPV1 (Transient Receptor Potential Cation Channel Subfamily V Member 1). They are currently produced by extraction from chili pepper fruit or by chemical synthesis. Transfer of the biosynthetic route to a microbial host could enable more efficient capsaicinoid production by fermentation and may also enable the use of synthetic biology to create a diversity of new compounds with potentially improved properties. This review summarises the current state of the art on the biosynthesis of capsaicinoid precursors in baker's yeast, Saccharomyces cerevisiae, and discusses bioengineering strategies for achieving total synthesis from sugar.
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Affiliation(s)
- Nina Muratovska
- Division of Applied Microbiology, Lund University, Box 124, 221 00 Lund, Sweden
| | - Paulo Silva
- CBMA - Center of Molecular and Environmental Biology Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - Tatiana Pozdniakova
- CBMA - Center of Molecular and Environmental Biology Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - Humberto Pereira
- CBMA - Center of Molecular and Environmental Biology Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - Carl Grey
- Division of Biotechnology, Lund University, Box 118, SE-221 00 Lund, Sweden
| | - Björn Johansson
- CBMA - Center of Molecular and Environmental Biology Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal.
| | - Magnus Carlquist
- Division of Applied Microbiology, Lund University, Box 124, 221 00 Lund, Sweden.
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Kim HS, Choi JA, Kim BY, Ferrer L, Choi JM, Wendisch VF, Lee JH. Engineered Corynebacterium glutamicum as the Platform for the Production of Aromatic Aldehydes. Front Bioeng Biotechnol 2022; 10:880277. [PMID: 35646884 PMCID: PMC9133326 DOI: 10.3389/fbioe.2022.880277] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/30/2022] [Indexed: 11/22/2022] Open
Abstract
Aromatic aldehydes, including 4-hydroxybenzaldehyde (4-HB aldehyde), protocatechuic (PC) aldehyde, and vanillin, are used as important flavors, fragrances, and pharmaceutical precursors and have several biological and therapeutic effects. Production of aromatic aldehydes in microbial hosts poses a challenge due to its rapid and endogenous reduction to alcohols. To address this hurdle, prospecting of the genome of Corynebacterium glutamicum yielded 27 candidate proteins that were used in comprehensive screening with a 4-hydroxybenzyl (4-HB) alcohol–producing strain. We identified that NCgl0324 has aromatic aldehyde reductase activity and contributed to 4-HB aldehyde reduction in vivo since the NCgl0324 deletion strain HB-Δ0324 produced 1.36 g/L of 4-HB aldehyde, that is, about 188% more than its parental strain. To demonstrate that NCgl0324 knockout can also improve production of PC aldehyde and vanillin, first, a basal MA303 strain that produces protocatechuate was engineered from 4-hydroxybenzoate-synthesizing C. glutamicum APS963, followed by deletion of NCgl0324 to generate PV-Δ0324. The PC aldehyde/alcohol or vanillin/vanillyl alcohol biosynthetic pathways, respectively, were able to be expanded from protocatechuate upon introduction of carboxylic acid reductase (CAR) and catechol O-methyltransferase encoded by a mutated comtm gene. In shake flask culture, the resulting NCgl0324 deletion strains PV-IΔ0324 and PV-IYΔ0324 were shown to produce 1.18 g/L PC aldehyde and 0.31 g/L vanillin, respectively. Thus, modulation of the identified NCgl0324 gene was shown to have the potential to boost production of valuable aromatic aldehydes and alcohols.
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Affiliation(s)
- Hyun-Song Kim
- Department of Food Science and Biotechnology, Kyungsung University, Busan, South Korea
| | - Jung-A Choi
- Department of Food Science and Biotechnology, Kyungsung University, Busan, South Korea
| | - Bu-Yeon Kim
- Department of Food Science and Biotechnology, Kyungsung University, Busan, South Korea
| | - Lenny Ferrer
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Jung-Min Choi
- Department of Food Science and Biotechnology, Kyungsung University, Busan, South Korea
| | - Volker F. Wendisch
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Jin-Ho Lee
- Department of Food Science and Biotechnology, Kyungsung University, Busan, South Korea
- *Correspondence: Jin-Ho Lee,
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Biotechnological production of specialty aromatic and aromatic-derivative compounds. World J Microbiol Biotechnol 2022; 38:80. [PMID: 35338395 DOI: 10.1007/s11274-022-03263-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/05/2022] [Indexed: 10/18/2022]
Abstract
Aromatic compounds are an important class of chemicals with different industrial applications. They are usually produced by chemical synthesis from petroleum-derived feedstocks, such as toluene, xylene and benzene. However, we are now facing threats from the excessive use of fossil fuels causing environmental problems such as global warming. Furthermore, fossil resources are not infinite, and will ultimately be depleted. To cope with these problems, the sustainable production of aromatic chemicals from renewable non-food biomass is urgent. With this in mind, the search for alternative methodologies to produce aromatic compounds using low-cost and environmentally friendly processes is becoming more and more important. Microorganisms are able to produce aromatic and aromatic-derivative compounds from sugar-based carbon sources. Metabolic engineering strategies as well as bioprocess optimization enable the development of microbial cell factories capable of efficiently producing aromatic compounds. This review presents current breakthroughs in microbial production of specialty aromatic and aromatic-derivative products, providing an overview on the general strategies and methodologies applied to build microbial cell factories for the production of these compounds. We present and describe some of the current challenges and gaps that must be overcome in order to render the biotechnological production of specialty aromatic and aromatic-derivative attractive and economically feasible at industrial scale.
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UGT72, a Major Glycosyltransferase Family for Flavonoid and Monolignol Homeostasis in Plants. BIOLOGY 2022; 11:biology11030441. [PMID: 35336815 PMCID: PMC8945231 DOI: 10.3390/biology11030441] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/07/2022] [Accepted: 03/11/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Phenylpropanoids are specialized metabolites playing crucial roles in plant developmental processes and in plant defense towards pathogens. The attachment of sugar moieties to these small hydrophobic molecules renders them more hydrophilic and increases their solubility. The UDP-glycosyltransferase 72 family (UGT72) of plants has been shown to glycosylate mainly two classes of phenylpropanoids, (i) the monolignols that are the building blocks of lignin, the second most abundant polymer after cellulose, and (ii) the flavonoids, which play determinant roles in plant interactions with other organisms and in response to stress. The purpose of this review is to bring an overview of the current knowledge of the UGT72 family and to highlight its role in the homeostasis of these molecules. Potential applications in pharmacology and in wood, paper pulp, and bioethanol production are given within the perspectives. Abstract Plants have developed the capacity to produce a diversified range of specialized metabolites. The glycosylation of those metabolites potentially decreases their toxicity while increasing their stability and their solubility, modifying their transport and their storage. The UGT, forming the largest glycosyltransferase superfamily in plants, combine enzymes that glycosylate mainly hormones and phenylpropanoids by using UDP-sugar as a sugar donor. Particularly, members of the UGT72 family have been shown to glycosylate the monolignols and the flavonoids, thereby being involved in their homeostasis. First, we explore primitive UGTs in algae and liverworts that are related to the angiosperm UGT72 family and their role in flavonoid homeostasis. Second, we describe the role of several UGT72s glycosylating monolignols, some of which have been associated with lignification. In addition, the role of other UGT72 members that glycosylate flavonoids and are involved in the development and/or stress response is depicted. Finally, the importance to explore the subcellular localization of UGTs to study their roles in planta is discussed.
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Zhou H, Xu Z, Cai C, Li J, Jin M. Deciphering the metabolic distribution of vanillin in Rhodococcus opacus during lignin valorization. BIORESOURCE TECHNOLOGY 2022; 347:126348. [PMID: 34798253 DOI: 10.1016/j.biortech.2021.126348] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
Vanillin bioconversion is important for the biological lignin valorization. In this study, the obscure vanillin metabolic distribution in Rhodoccous opacus PD630 was deciphered by combining the strategies of intermediate detection, putative gene prediction, and target gene verification. The results suggest that approximately 10% (mol/mol) of consumed vanillin is converted to vanillic acid for further metabolism, and a large amount is converted to dead-end vanillyl alcohol in R. opacus PD630. Subsequently, five vanillin reductases were identified in R. opacus PD630, among which Pd630_LPD03722 product exhibited the greatest activity. With the detected metabolic distributions of vanillin, the conversion of vanillin to muconic acid was facilitated by deleting domestic vanillin reductase genes and introducing vanillin dehydrogenase from Sphingobium sp. SYK-6. Ultimately, the muconic acid yield from vanillin increased to 97.83% (mol/mol) from the initial 10% (mol/mol). Moreover, this study demonstrated the existence of vanillin reductases in Escherichia coli, Bacillus subtilis, and Corynebacterium glutamicum.
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Affiliation(s)
- Huarong Zhou
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, PR China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, PR China
| | - Zhaoxian Xu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, PR China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, PR China
| | - Chenggu Cai
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, PR China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, PR China
| | - Jie Li
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, PR China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, PR China
| | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, PR China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, PR China.
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47
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Ma Q, Liu L, Zhao S, Huang Z, Li C, Jiang S, Li Q, Gu P. Biosynthesis of vanillin by different microorganisms: a review. World J Microbiol Biotechnol 2022; 38:40. [PMID: 35018518 DOI: 10.1007/s11274-022-03228-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/02/2022] [Indexed: 02/06/2023]
Abstract
Vanillin is a popular flavoring agent widely used around the world. Vanillin is generated by natural extraction, chemical synthesis, or tissue culture technology, but these production methods no longer meet the increasing worldwide demand for vanillin. Accordingly, a biotechnological approach may provide an effective replacement route to obtaining vanillin. Processes for environmentally friendly production of vanillin in microorganisms from different carbon sources, such as eugenol, isoeugenol, lignin, ferulic acid, sugars, and waste residues, with high productivity and yield have been developed. However, challenges remain for optimizing the vanillin biosynthesis process and further improving production titer and yield. In this review, successful and applicable strategies for increasing vanillin titer and yield in different microorganisms are summarized. Additionally, perspectives for further optimizing the production of vanillin are discussed.
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Affiliation(s)
- Qianqian Ma
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Liwen Liu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Shuo Zhao
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Zhaosong Huang
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Changtao Li
- RZBC GROUP CO., LTD., Rizhao, 276800, Shandong, People's Republic of China
| | - Shuixing Jiang
- RZBC GROUP CO., LTD., Rizhao, 276800, Shandong, People's Republic of China
| | - Qiang Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Pengfei Gu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China.
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48
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Seo SO, Jin YS. Next-Generation Genetic and Fermentation Technologies for Safe and Sustainable Production of Food Ingredients: Colors and Flavorings. Annu Rev Food Sci Technol 2022; 13:463-488. [DOI: 10.1146/annurev-food-052720-012228] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A growing human population is a significant issue in food security owing to the limited land and resources available for agricultural food production. To solve these problems, sustainable food manufacturing processes and the development of alternative foods and ingredients are needed. Metabolic engineering and synthetic biology can help solve the food security issue and satisfy the demand for alternative food production. Bioproduction of food ingredients by microbial fermentation is a promising method to replace current manufacturing processes, such as extraction from natural materials and chemical synthesis, with more ecofriendly and sustainable operations. This review highlights successful examples of bioproduction for food additives by engineered microorganisms, with an emphasis on colorants and flavors that are extensively used in the food industry. Recent strain engineering developments and fermentation strategies for producing selected food colorants and flavors are introduced with discussions on the current status and future perspectives. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Seung-Oh Seo
- Department of Food Science and Nutrition, Catholic University of Korea, Bucheon, Republic of Korea
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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49
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Mudziwapasi R, Mufandaedza J, Jomane FN, Songwe F, Ndudzo A, Nyamusamba RP, Takombwa AR, Mahla MG, Pullen J, Mlambo SS, Mahuni C, Mufandaedza E, Shoko R. Unlocking the potential of synthetic biology for improving livelihoods in sub-Saharan Africa. ALL LIFE 2022. [DOI: 10.1080/26895293.2021.2014986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Reagan Mudziwapasi
- Department of Crop and Soil Sciences, Faculty of Agricultural Sciences, Lupane State University, Lupane, Zimbabwe
| | | | - Fortune N. Jomane
- Department of Animal Science and Rangeland Management, Faculty of Agricultural Sciences, Lupane State University, Lupane, Zimbabwe
| | - Fanuel Songwe
- Department of Biosciences and Biotechnology, Faculty of Science and Technology, Midlands State University, Gweru, Zimbabwe
| | - Abigarl Ndudzo
- Department of Crop and Soil Sciences, Faculty of Agricultural Sciences, Lupane State University, Lupane, Zimbabwe
| | - Rutendo P. Nyamusamba
- Department of Crop and Soil Sciences, Faculty of Agricultural Sciences, Lupane State University, Lupane, Zimbabwe
| | | | - Melinda G. Mahla
- Department of Crop and Soil Sciences, Faculty of Agricultural Sciences, Lupane State University, Lupane, Zimbabwe
| | - Jessica Pullen
- Department of Crop and Soil Sciences, Faculty of Agricultural Sciences, Lupane State University, Lupane, Zimbabwe
| | - Sibonani S. Mlambo
- Department of Biotechnology, Faculty of Agriculture, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | | | - Edward Mufandaedza
- Department of Environmental Sciences, Faculty of Agricultural Sciences, Lupane State University, Lupane, Zimbabwe
| | - Ryman Shoko
- Department of Biology, Faculty of Agriculture, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
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50
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Wilde AS, Strucko T, Veje CR, Mortensen UH, Duedahl-Olesen L. Authentication of vanillin ex glucose – A first study on the influence of the glucose-source on the δ13C and δ2H value. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108389] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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