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Li DX, Guo Q, Yang YX, Jiang SJ, Ji XJ, Ye C, Wang YT, Shi TQ. Recent Advances and Multiple Strategies of Monoterpenoid Overproduction in Saccharomyces cerevisiae and Yarrowia lipolytica. ACS Synth Biol 2024; 13:1647-1662. [PMID: 38860708 DOI: 10.1021/acssynbio.4c00297] [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: 06/12/2024]
Abstract
Monoterpenoids are an important subclass of terpenoids that play important roles in the energy, cosmetics, pharmaceuticals, and fragrances fields. With the development of biotechnology, microbial synthesis of monoterpenoids has received great attention. Yeasts such Saccharomyces cerevisiae and Yarrowia lipolytica are emerging as potential hosts for monoterpenoids production because of unique advantages including rapid growth cycles, mature gene editing tools, and clear genetic background. Recently, advancements in metabolic engineering and fermentation engineering have significantly enhanced the accumulation of monoterpenoids in cell factories. First, this review introduces the biosynthetic pathway of monoterpenoids and comprehensively summarizes the latest production strategies, which encompass enhancing precursor flux, modulating the expression of rate-limited enzymes, suppressing competitive pathway flux, mitigating cytotoxicity, optimizing substrate utilization, and refining the fermentation process. Subsequently, this review introduces four representative monoterpenoids. Finally, we outline the future prospects for efficient construction cell factories tailored for the production of monoterpenoids and other terpenoids.
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Affiliation(s)
- Dong-Xun Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Qi Guo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Yu-Xin Yang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Shun-Jie Jiang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Xiao-Jun Ji
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Yue-Tong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
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Wang X, Zhao C, Lu X, Zong H, Zhuge B. Development of a co-culture system for green production of caffeic acid from sugarcane bagasse hydrolysate. Front Microbiol 2024; 15:1379688. [PMID: 38567071 PMCID: PMC10985150 DOI: 10.3389/fmicb.2024.1379688] [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: 01/31/2024] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
Caffeic acid (CA) is a phenolic acid compound widely used in pharmaceutical and food applications. However, the efficient synthesis of CA is usually limited by the resources of individual microbial platforms. Here, a cross-kingdom microbial consortium was developed to synthesize CA from sugarcane bagasse hydrolysate using Escherichia coli and Candida glycerinogenes as chassis. In the upstream E. coli module, shikimate accumulation was improved by intensifying the shikimate synthesis pathway and blocking shikimate metabolism to provide precursors for the downstream CA synthesis module. In the downstream C. glycerinogenes module, conversion of p-coumaric acid to CA was improved by increasing the supply of the cytoplasmic cofactor FAD(H2). Further, overexpression of ABC transporter-related genes promoted efflux of CA and enhanced strain resistance to CA, significantly increasing CA titer from 103.8 mg/L to 346.5 mg/L. Subsequently, optimization of the inoculation ratio of strains SA-Ec4 and CA-Cg27 in this cross-kingdom microbial consortium resulted in an increase in CA titer to 871.9 mg/L, which was 151.6% higher compared to the monoculture strain CA-Cg27. Ultimately, 2311.6 and 1943.2 mg/L of CA were obtained by optimization of the co-culture system in a 5 L bioreactor using mixed sugar and sugarcane bagasse hydrolysate, respectively, with 17.2-fold and 14.6-fold enhancement compared to the starting strain. The cross-kingdom microbial consortium developed in this study provides a reference for the production of other aromatic compounds from inexpensive raw materials.
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Affiliation(s)
- Xihui Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Cui Zhao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xinyao Lu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Hong Zong
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Bin Zhuge
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
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Emelianov G, Song DU, Jang N, Ko M, Kim SK, Rha E, Shin J, Kwon KK, Kim H, Lee DH, Lee H, Lee SG. Engineered Methylococcus capsulatus Bath for efficient methane conversion to isoprene. BIORESOURCE TECHNOLOGY 2024; 393:130098. [PMID: 38040299 DOI: 10.1016/j.biortech.2023.130098] [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: 10/20/2023] [Revised: 11/22/2023] [Accepted: 11/22/2023] [Indexed: 12/03/2023]
Abstract
Isoprene has numerous industrial applications, including rubber polymer and potential biofuel. Microbial methane-based isoprene production could be a cost-effective and environmentally benign process, owing to a reduced carbon footprint and economical utilization of methane. In this study, Methylococcus capsulatus Bath was engineered to produce isoprene from methane by introducing the exogenous mevalonate (MVA) pathway. Overexpression of MVA pathway enzymes and isoprene synthase from Populus trichocarpa under the control of a phenol-inducible promoter substantially improved isoprene production. M. capsulatus Bath was further engineered using a CRISPR-base editor to disrupt the expression of soluble methane monooxygenase (sMMO), which oxidizes isoprene to cause toxicity. Additionally, optimization of the metabolic flux in the MVA pathway and culture conditions increased isoprene production to 228.1 mg/L, the highest known titer for methanotroph-based isoprene production. The developed methanotroph could facilitate the efficient conversion of methane to isoprene, resulting in the sustainable production of value-added chemicals.
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Affiliation(s)
- Georgii Emelianov
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea.
| | - Dong-Uk Song
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Graduate School of Engineering Biology, Korea Advanced Institute of Science & Technology (KAIST), Daejeon 34141, Republic of Korea.
| | - Nulee Jang
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea.
| | - Minji Ko
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea.
| | - Seong Keun Kim
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea.
| | - Eugene Rha
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea.
| | - Jonghyeok Shin
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea.
| | - Kil Koang Kwon
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea.
| | - Haseong Kim
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea; Graduate School of Engineering Biology, Korea Advanced Institute of Science & Technology (KAIST), Daejeon 34141, Republic of Korea.
| | - Dae-Hee Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea; Graduate School of Engineering Biology, Korea Advanced Institute of Science & Technology (KAIST), Daejeon 34141, Republic of Korea; Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon-si, Gyeonggi-do 16419, Republic of Korea.
| | - Hyewon Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea.
| | - Seung-Goo Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea; Graduate School of Engineering Biology, Korea Advanced Institute of Science & Technology (KAIST), Daejeon 34141, Republic of Korea.
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Wefelmeier K, Schmitz S, Kösters BJ, Liebal UW, Blank LM. Methanol bioconversion into C3, C4, and C5 platform chemicals by the yeast Ogataea polymorpha. Microb Cell Fact 2024; 23:8. [PMID: 38172830 PMCID: PMC10763331 DOI: 10.1186/s12934-023-02283-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND One carbon (C1) molecules such as methanol have the potential to become sustainable feedstocks for biotechnological processes, as they can be derived from CO2 and green hydrogen, without the need for arable land. Therefore, we investigated the suitability of the methylotrophic yeast Ogataea polymorpha as a potential production organism for platform chemicals derived from methanol. We selected acetone, malate, and isoprene as industrially relevant products to demonstrate the production of compounds with 3, 4, or 5 carbon atoms, respectively. RESULTS We successfully engineered O. polymorpha for the production of all three molecules and demonstrated their production using methanol as carbon source. We showed that the metabolism of O. polymorpha is well suited to produce malate as a product and demonstrated that the introduction of an efficient malate transporter is essential for malate production from methanol. Through optimization of the cultivation conditions in shake flasks, which included pH regulation and constant substrate feeding, we were able to achieve a maximum titer of 13 g/L malate with a production rate of 3.3 g/L/d using methanol as carbon source. We further demonstrated the production of acetone and isoprene as additional heterologous products in O. polymorpha, with maximum titers of 13.6 mg/L and 4.4 mg/L, respectively. CONCLUSION These findings highlight how O. polymorpha has the potential to be applied as a versatile cell factory and contribute to the limited knowledge on how methylotrophic yeasts can be used for the production of low molecular weight biochemicals from methanol. Thus, this study can serve as a point of reference for future metabolic engineering in O. polymorpha and process optimization efforts to boost the production of platform chemicals from renewable C1 carbon sources.
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Affiliation(s)
- Katrin Wefelmeier
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074, Aachen, Germany
| | - Simone Schmitz
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074, Aachen, Germany
| | - Benjamin Jonas Kösters
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074, Aachen, Germany
| | - Ulf Winfried Liebal
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074, Aachen, Germany
| | - Lars Mathias Blank
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074, Aachen, Germany.
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Bureau JA, Oliva ME, Dong Y, Ignea C. Engineering yeast for the production of plant terpenoids using synthetic biology approaches. Nat Prod Rep 2023; 40:1822-1848. [PMID: 37523210 DOI: 10.1039/d3np00005b] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
Covering: 2011-2022The low amounts of terpenoids produced in plants and the difficulty in synthesizing these complex structures have stimulated the production of terpenoid compounds in microbial hosts by metabolic engineering and synthetic biology approaches. Advances in engineering yeast for terpenoid production will be covered in this review focusing on four directions: (1) manipulation of host metabolism, (2) rewiring and reconstructing metabolic pathways, (3) engineering the catalytic activity, substrate selectivity and product specificity of biosynthetic enzymes, and (4) localizing terpenoid production via enzymatic fusions and scaffolds, or subcellular compartmentalization.
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Affiliation(s)
| | | | - Yueming Dong
- Department of Bioengineering, McGill University, Montreal, QC, H3A 0C3, Canada.
| | - Codruta Ignea
- Department of Bioengineering, McGill University, Montreal, QC, H3A 0C3, Canada.
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Li Z, Deng Y, Yang GY. Growth-coupled high throughput selection for directed enzyme evolution. Biotechnol Adv 2023; 68:108238. [PMID: 37619825 DOI: 10.1016/j.biotechadv.2023.108238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/03/2023] [Accepted: 08/20/2023] [Indexed: 08/26/2023]
Abstract
Directed enzyme evolution has revolutionized the rapid development of enzymes with desired properties. However, the lack of a high-throughput method to identify the most suitable variants from a large pool of genetic diversity poses a major bottleneck. To overcome this challenge, growth-coupled in vivo high-throughput selection approaches (GCHTS) have emerged as a novel selection system for enzyme evolution. GCHTS links the survival of the host cell with the properties of the target protein, resulting in a screening system that is easily measurable and has a high throughput-scale limited only by transformation efficiency. This allows for the rapid identification of desired variants from a pool of >109 variants in each experiment. In recent years, GCHTS approaches have been extensively utilized in the directed evolution of multiple enzymes, demonstrating success in catalyzing non-native substrates, enhancing catalytic activity, and acquiring novel functions. This review introduces three main strategies employed to achieve GCHTS: the elimination of toxic compounds via desired variants, enabling host cells to thrive in hazardous conditions; the complementation of an auxotroph with desired variants, where essential genes for cell growth have been eliminated; and the control of the transcription or expression of a reporter gene related to host cell growth, regulated by the desired variants. Additionally, we highlighted the recent developments in the in vivo continuous evolution of enzyme technology, including phage-assisted continuous evolution (PACE) and orthogonal DNA Replication (OrthoRep). Furthermore, this review discusses the challenges and future prospects in the field of growth-coupled selection for protein engineering.
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Affiliation(s)
- Zhengqun Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuting Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guang-Yu Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Li M, Yang R, Guo J, Liu M, Yang J. Optimization of IspS ib stability through directed evolution to improve isoprene production. Appl Environ Microbiol 2023; 89:e0121823. [PMID: 37815338 PMCID: PMC10617563 DOI: 10.1128/aem.01218-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 08/11/2023] [Indexed: 10/11/2023] Open
Abstract
Enzyme stability is often a limiting factor in the microbial production of high-value-added chemicals and commercial enzymes. A previous study by our research group revealed that the unstable isoprene synthase from Ipomoea batatas (IspSib) critically limits isoprene production in engineered Escherichia coli. Directed evolution was, therefore, performed in the present study to improve the thermostability of IspSib. First, a tripartite protein folding system designated as lac'-IspSib-'lac, which could couple the stability of IspSib to antibiotic ampicillin resistance, was successfully constructed for the high-throughput screening of variants. Directed evolution of IspSib was then performed through two rounds of random mutation and site-saturation mutation, which produced three variants with higher stability: IspSibN397V A476V, IspSibN397V A476T, and IspSibN397V A476C. The subsequent in vitro thermostability test confirmed the increased protein stability. The melting temperatures of the screened variants IspSibN397V A476V, IspSibN397V A476T, and IspSibN397V A476C were 45.1 ± 0.9°C, 46.1 ± 0.7°C, and 47.2 ± 0.3°C, respectively, each of which was higher than the melting temperature of wild-type IspSib (41.5 ± 0.4°C). The production of isoprene at the shake-flask fermentation level was increased by 1.94-folds, to 1,335 mg/L, when using IspSibN397V A476T. These findings provide insights into the optimization of the thermostability of terpene synthases, which are key enzymes for isoprenoid production in engineered microorganisms. In addition, the present study would serve as a successful example of improving enzyme stability without requiring detailed structural information or catalytic reaction mechanisms.IMPORTANCEThe poor thermostability of IspSib critically limits isoprene production in engineered Escherichia coli. A tripartite protein folding system designated as lac'-IspSib-'lac, which could couple the stability of IspSib to antibiotic ampicillin resistance, was successfully constructed for the first time. In order to improve the enzyme stability of IspSib, the directed evolution of IspSib was performed through error-PCR, and high-throughput screening was realized using the lac'-IspSib-'lac system. Three positive variants with increased thermostability were obtained. The thermostability test and the melting temperature analysis confirmed the increased stability of the enzyme. The production of isoprene was increased by 1.94-folds, to 1,335 mg/L, using IspSibN397V A476T. The directed evolution process reported here is also applicable to other terpene synthases key to isoprenoid production.
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Affiliation(s)
- Meijie Li
- Energy-rich Compound Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Rumeng Yang
- Energy-rich Compound Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Jing Guo
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
| | - Min Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Jianming Yang
- Energy-rich Compound Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
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Wu Y, Deng J, Zheng Z, Chen N, Luo X, Tang H. Engineering an Efficient Expression Using Heterologous GAL Promoters and Transcriptional Activators in Saccharomyces cerevisiae. ACS Synth Biol 2023; 12:1859-1867. [PMID: 37224271 DOI: 10.1021/acssynbio.3c00243] [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: 05/26/2023]
Abstract
Galactose-inducible (GAL) promoters have been widely used in metabolic engineering in Saccharomyces cerevisiae for production of valuable products. Endogenous GAL promoters and GAL transcription factors have often been engineered to improve GAL promoter activities. Heterologous GAL promoters and GAL activator (Gal4p-like transcriptional activators), although existing in other yeasts or fungi, have not been well explored. In this study, we comprehensively characterized the activation effects of Gal4p activators from different yeasts or fungi on a variant of GAL promoters. Overexpressing endogenous Gal4p driven by PHHF1 increased the activities of native PGAL1 and heterologous PSkGAL2 by 131.20% and 72.45%, respectively. Furthermore, eight transcriptional activators from different organisms were characterized and most of them exhibited functions that were consistent with ScGal4p. Expression of KlLac9p from Kluyveromyces lactis further increased the activity of PScGAL1 and PSkGAL2 by 41.56% and 100.63%, respectively, compared to ScGal4p expression, and was able to evade Gal80p inhibition. This optimized GAL expression system can be used to increase the production of β-carotene by 9.02-fold in S. cerevisiae. Our study demonstrated that a combination of heterologous transcriptional activators and GAL promoters provided novel insights into the optimization of the GAL expression system.
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Affiliation(s)
- Yanling Wu
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jiliang Deng
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zhaohui Zheng
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Nanzhu Chen
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xiaozhou Luo
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Hongting Tang
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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9
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Bian Q, Jiao X, Chen Y, Yu H, Ye L. Hierarchical dynamic regulation of Saccharomyces cerevisiae for enhanced lutein biosynthesis. Biotechnol Bioeng 2023; 120:536-552. [PMID: 36369967 DOI: 10.1002/bit.28286] [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: 07/27/2022] [Revised: 10/26/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022]
Abstract
Lutein, as a carotenoid with strong antioxidant capacity and an important component of macular pigment in the retina, has wide applications in pharmaceutical, food, feed, and cosmetics industries. Besides extraction from plant and algae, microbial fermentation using engineered cell factories to produce lutein has emerged as a promising route. However, intra-pathway competition between the lycopene cyclases and the conflict between cell growth and production are two major challenges. In our previous study, de novo synthesis of lutein had been achieved in Saccharomyces cerevisiae by dividing the pathway into two stages (δ-carotene formation and conversion) using temperature as the input signal to realize sequential cyclation of lycopene. However, lutein production was limited to microgram level, which is still too low to meet industrial demand. In this study, a dual-signal hierarchical dynamic regulation system was developed and applied to divide lutein biosynthesis into three stages in response to glucose concentration and culture temperature. By placing the genes involved in δ-carotene formation under the glucose-responsive ADH2 promoter and genes involved in the conversion of δ-carotene to lutein under temperature-responsive GAL promoters, the growth-production conflict and intra-pathway competition were simultaneously resolved. Meanwhile, the rate-limiting lycopene ε-cyclation and carotene hydroxylation reactions were improved by screening for lycopene ε-cyclase with higher activity and fine tuning of the P450 enzymes and their redox partners. Finally, a lutein titer of 19.92 mg/L (4.53 mg/g DCW) was obtained in shake-flask cultures using the engineered yeast strain YLutein-3S-6, which is the highest lutein titer ever reported in heterologous production systems.
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Affiliation(s)
- Qi Bian
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
| | - Xue Jiao
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Ye Chen
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorders, Institute of Genetics, Zhejiang University, Hangzhou, China
| | - Hongwei Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Lidan Ye
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
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Xu M, Sun M, Meng X, Zhang W, Shen Y, Liu W. Engineering Pheromone-Mediated Quorum Sensing with Enhanced Response Output Increases Fucosyllactose Production in Saccharomyces cerevisiae. ACS Synth Biol 2023; 12:238-248. [PMID: 36520033 DOI: 10.1021/acssynbio.2c00507] [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] [Indexed: 12/23/2022]
Abstract
Engineering dynamic control of gene expression is desirable because many engineered functions interfere with endogenous cellular processes that have evolved to facilitate growth and survival. Minimizing conflict between growth and production phases can therefore improve product titers in microbial cell factories. We developed an autoinduced gene expression system by rewiring the Saccharomyces cerevisiae pheromone response pathway. To ameliorate growth reduction due to the early onset response at low population densities, α-pheromone of Kluyveromyces lactis (Kα) instead of S. cerevisiae (Sα) was expressed in mating type "a" yeast. Kα-induced expression of pathway genes was further enhanced by the transcriptional activator Gal4p expressed under the control of the pheromone-responsive FUS1 promoter (Pfus1). As a demonstration, the engineered circuit combined with the deletion of the endogenous galactose metabolic pathway genes was applied to the production of human milk oligosaccharides, 2'-fucosyllactose (2'-FL) and 3-fucosllactose (3-FL). The engineered strains produced 3.37 g/L 2'-FL and 2.36 g/L 3-FL on glucose with a volumetric productivity of 0.14 and 0.03 g/L·h-1 in batch flask cultivation, respectively. These represented 147 and 153% increases over the control strains on galactose wherein the respective pathway genes are expressed under GAL promoters only. Further fed-batch fermentation achieved titers of 32.05 and 20.91 g/L for 2' and 3-FL, respectively. The genetic program developed here thus represents a promising option for implementing dynamic regulation in yeast and could be used for the production of biochemicals that may place a heavy metabolic burden on cell growth.
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Affiliation(s)
- Mingyuan Xu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
| | - Mengtong Sun
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
| | - Xiangfeng Meng
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
| | - Weixin Zhang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
| | - Yu Shen
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
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11
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Volk MJ, Tran VG, Tan SI, Mishra S, Fatma Z, Boob A, Li H, Xue P, Martin TA, Zhao H. Metabolic Engineering: Methodologies and Applications. Chem Rev 2022; 123:5521-5570. [PMID: 36584306 DOI: 10.1021/acs.chemrev.2c00403] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Metabolic engineering aims to improve the production of economically valuable molecules through the genetic manipulation of microbial metabolism. While the discipline is a little over 30 years old, advancements in metabolic engineering have given way to industrial-level molecule production benefitting multiple industries such as chemical, agriculture, food, pharmaceutical, and energy industries. This review describes the design, build, test, and learn steps necessary for leading a successful metabolic engineering campaign. Moreover, we highlight major applications of metabolic engineering, including synthesizing chemicals and fuels, broadening substrate utilization, and improving host robustness with a focus on specific case studies. Finally, we conclude with a discussion on perspectives and future challenges related to metabolic engineering.
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Affiliation(s)
- Michael J Volk
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Vinh G Tran
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shih-I Tan
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - Shekhar Mishra
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Zia Fatma
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Aashutosh Boob
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Hongxiang Li
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pu Xue
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Teresa A Martin
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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12
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Zhang Y, Cao X, Wang J, Tang F. Enhancement of linalool production in Saccharomyces cerevisiae by utilizing isopentenol utilization pathway. Microb Cell Fact 2022; 21:212. [PMID: 36243714 PMCID: PMC9571491 DOI: 10.1186/s12934-022-01934-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/25/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Linalool is a monoterpenoid, also a vital silvichemical with commercial applications in cosmetics, flavoring ingredients, and medicines. Regulation of mevalonate (MVA) pathway metabolic flux is a common strategy to engineer Saccharomyces cerevisiae for efficient linalool production. However, metabolic regulation of the MVA pathway is complex and involves competition for central carbon metabolism, resulting in limited contents of target metabolites. RESULTS In this study, first, a truncated linalool synthase (t26AaLS1) from Actinidia arguta was selected for the production of linalool in S. cerevisiae. To simplify the complexity of the metabolic regulation of the MVA pathway and increase the flux of isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), we introduced the two-step isopentenyl utilization pathway (IUP) into S. cerevisiae, which could produce large amounts of IPP/DMAPP. Further, the S. cerevisiae IDI1 (ecoding isopentenyl diphosphate delta-isomerase) and ERG20F96W-N127W (encoding farnesyl diphosphate synthase) genes were integrated into the yeast genome, combined with the strategies of copy number variation of the t26AaLS1 and ERG20F96W-N127W genes to increase the metabolic flux of the downstream IPP, as well as optimization of isoprenol and prenol concentrations, resulting in a 4.8-fold increase in the linalool titer. Eventually, under the optimization of carbon sources and Mg2+ addition, a maximum linalool titer of 142.88 mg/L was obtained in the two-phase extractive shake flask fermentation. CONCLUSIONS The results show that the efficient synthesis of linalool in S. cerevisiae could be achieved through a two-step pathway, gene expression adjustment, and optimization of culture conditions. The study may provide a valuable reference for the other monoterpenoid production in S. cerevisiae.
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Affiliation(s)
- Yaoyao Zhang
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Centre for Bamboo and Rattan, No. 8 Futong Dongdajie, Wangjing, Beijing, 100102, Chaoyang District, China
| | - Xianshuang Cao
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Centre for Bamboo and Rattan, No. 8 Futong Dongdajie, Wangjing, Beijing, 100102, Chaoyang District, China
| | - Jin Wang
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Centre for Bamboo and Rattan, No. 8 Futong Dongdajie, Wangjing, Beijing, 100102, Chaoyang District, China
| | - Feng Tang
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Centre for Bamboo and Rattan, No. 8 Futong Dongdajie, Wangjing, Beijing, 100102, Chaoyang District, China.
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13
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Li W, Cui L, Mai J, Shi TQ, Lin L, Zhang ZG, Ledesma-Amaro R, Dong W, Ji XJ. Advances in Metabolic Engineering Paving the Way for the Efficient Biosynthesis of Terpenes in Yeasts. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:9246-9261. [PMID: 35854404 DOI: 10.1021/acs.jafc.2c03917] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Terpenes are a large class of secondary metabolites with diverse structures and functions that are commonly used as valuable raw materials in food, cosmetics, and medicine. With the development of metabolic engineering and emerging synthetic biology tools, these important terpene compounds can be sustainably produced using different microbial chassis. Currently, yeasts such as Saccharomyces cerevisiae and Yarrowia lipolytica have received extensive attention as potential hosts for the production of terpenes due to their clear genetic background and endogenous mevalonate pathway. In this review, we summarize the natural terpene biosynthesis pathways and various engineering strategies, including enzyme engineering, pathway engineering, and cellular engineering, to further improve the terpene productivity and strain stability in these two widely used yeasts. In addition, the future prospects of yeast-based terpene production are discussed in light of the current progress, challenges, and trends in this field. Finally, guidelines for future studies are also emphasized.
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Affiliation(s)
- Wenjuan Li
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Liuwei Cui
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Jie Mai
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 1 Wenyuan Road, Nanjing 210046, People's Republic of China
| | - Lu Lin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Zhi-Gang Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Xiao-Jun Ji
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
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14
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Zuo Y, Xiao F, Gao J, Ye C, Jiang L, Dong C, Lian J. Establishing Komagataella phaffii as a Cell Factory for Efficient Production of Sesquiterpenoid α-Santalene. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:8024-8031. [PMID: 35729733 DOI: 10.1021/acs.jafc.2c02353] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Santalene, a major component of the sandalwood essential oil, is a typical representative of sesquiterpenes and has important applications in medicine, food, flavors, and other fields. Due to the limited supply of natural sandalwood resources, there is a growing interest in engineering microbial cell factories for the mass production of santalene. In the present study, Komagataella phaffii (also known as Pichia pastoris) was established as a cell factory for high-level production of α-santalene for the first time. The metabolic fluxes were rewired toward α-santalene biosynthesis through the optimization of promoters to drive the expression of the α-santalene synthase (SAS) gene, overexpression of the key mevalonate pathway genes (i.e., tHMG1, IDI1, and ERG20), and multi-copy integration of the SAS expression cassette. In combination with medium optimization and bioprocess engineering, the optimal strain (STE-9) was able to produce α-santalene with a titer as high as 829.8 ± 70.6 mg/L, 4.4 ± 0.3 g/L, and 21.5 ± 1.6 g/L in a shake flask, batch fermenter, and fed-batch fermenter, respectively. These represented the highest production of α-santalene ever reported, highlighting the advantages of K. phaffii cell factories for the production of terpenoids and other natural products.
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Affiliation(s)
- Yimeng Zuo
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
| | - Feng Xiao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
| | - Jucan Gao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
| | - Cuifang Ye
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
| | - Lihong Jiang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Chang Dong
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
- Zhejiang Key Laboratory of Smart Biomaterials, Zhejiang University, Hangzhou 310027, China
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15
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Li H, Ma W, Lyv Y, Gao S, Zhou J. Glycosylation Modification Enhances (2 S)-Naringenin Production in Saccharomyces cerevisiae. ACS Synth Biol 2022; 11:2339-2347. [PMID: 35704764 DOI: 10.1021/acssynbio.2c00065] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
(2S)-Naringenin is an important flavonoid precursor, with multiple nutritional and pharmacological activities. Both (2S)-naringenin and other flavonoid production are hindered by poor water solubility and inhibited cell growth. To address this, we increased solubility and improved cell growth by partially glycosylating (2S)-naringenin to naringenin-7-O-glucoside, which facilitated increased extracellular secretion, by knocking out endogenous glycosyl hydrolase genes, EXG1 and SPR1, and expressing the glycosyltransferase gene (UGT733C6). Naringenin-7-O-glucoside synthesis was further improved by optimizing UDP-glucose and shikimate pathways. Then, hydrochloric acid was used to hydrolyze naringenin-7-O-glucoside to (2S)-naringenin outside the cell. Thus, our optimized Saccharomyces cerevisiae strain E32T19 produced 1184.1 mg/L (2S)-naringenin, a 7.9-fold increase on the starting strain. Therefore. we propose that glycosylation modification is a useful strategy for the efficient heterologous biosynthesis of (2S)-naringenin in S. cerevisiae.
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Affiliation(s)
- Hongbiao Li
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China.,Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China.,Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Wenjian Ma
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Yunbin Lyv
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Song Gao
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China.,Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China.,Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
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16
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Identification of the sesquiterpene synthase AcTPS1 and high production of (-)-germacrene D in metabolically engineered Saccharomyces cerevisiae. Microb Cell Fact 2022; 21:89. [PMID: 35585553 PMCID: PMC9115970 DOI: 10.1186/s12934-022-01814-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/03/2022] [Indexed: 12/04/2022] Open
Abstract
Background The sesquiterpene germacrene D is a highly promising product due to its wide variety of insecticidal activities and ability to serve as a precursor for many other sesquiterpenes. Biosynthesis of high value compounds through genome mining for synthases and metabolic engineering of microbial factories, especially Saccharomyces cerevisiae, has been proven to be an effective strategy. However, there have been no studies on the de novo synthesis of germacrene D from carbon sources in microbes. Hence, the construction of the S. cerevisiae cell factory to achieve high production of germacrene D is highly desirable. Results We identified five putative sesquiterpene synthases (AcTPS1 to AcTPS5) from Acremonium chrysogenum and the major product of AcTPS1 characterized by in vivo, in vitro reaction and NMR detection was revealed to be (–)-germacrene D. After systematically comparing twenty-one germacrene D synthases, AcTPS1 was found to generate the highest amount of (–)-germacrene D and was integrated into the terpene precursor-enhancing yeast strain, achieving 376.2 mg/L of (–)-germacrene D. Iterative engineering was performed to improve the production of (–)-germacrene D, including increasing the copy numbers of AcTPS1, tHMG1 and ERG20, and downregulating or knocking out other inhibitory factors (such as erg9, rox1, dpp1). Finally, the optimal strain LSc81 achieved 1.94 g/L (–)-germacrene D in shake-flask fermentation and 7.9 g/L (–)-germacrene D in a 5-L bioreactor, which is the highest reported (–)-germacrene D titer achieved to date. Conclusion We successfully achieved high production of (–)-germacrene D in S. cerevisiae through terpene synthase mining and metabolic engineering, providing an impressive example of microbial overproduction of high-value compounds. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01814-4.
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17
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Fordjour E, Mensah EO, Hao Y, Yang Y, Liu X, Li Y, Liu CL, Bai Z. Toward improved terpenoids biosynthesis: strategies to enhance the capabilities of cell factories. BIORESOUR BIOPROCESS 2022; 9:6. [PMID: 38647812 PMCID: PMC10992668 DOI: 10.1186/s40643-022-00493-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 01/04/2022] [Indexed: 02/22/2023] Open
Abstract
Terpenoids form the most diversified class of natural products, which have gained application in the pharmaceutical, food, transportation, and fine and bulk chemical industries. Extraction from naturally occurring sources does not meet industrial demands, whereas chemical synthesis is often associated with poor enantio-selectivity, harsh working conditions, and environmental pollutions. Microbial cell factories come as a suitable replacement. However, designing efficient microbial platforms for isoprenoid synthesis is often a challenging task. This has to do with the cytotoxic effects of pathway intermediates and some end products, instability of expressed pathways, as well as high enzyme promiscuity. Also, the low enzymatic activity of some terpene synthases and prenyltransferases, and the lack of an efficient throughput system to screen improved high-performing strains are bottlenecks in strain development. Metabolic engineering and synthetic biology seek to overcome these issues through the provision of effective synthetic tools. This review sought to provide an in-depth description of novel strategies for improving cell factory performance. We focused on improving transcriptional and translational efficiencies through static and dynamic regulatory elements, enzyme engineering and high-throughput screening strategies, cellular function enhancement through chromosomal integration, metabolite tolerance, and modularization of pathways.
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Affiliation(s)
- Eric Fordjour
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Emmanuel Osei Mensah
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Yunpeng Hao
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Yankun Yang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Xiuxia Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Ye Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Chun-Li Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China.
| | - Zhonghu Bai
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China.
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18
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Liu HR, Ahmad N, Lv B, Li C. Advances in production and structural derivatization of the promising molecule ursolic acid. Biotechnol J 2021; 16:e2000657. [PMID: 34096160 DOI: 10.1002/biot.202000657] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 05/16/2021] [Accepted: 05/18/2021] [Indexed: 02/05/2023]
Abstract
Ursolic acid (UA) is a ursane-type pentacyclic triterpenoid compound, naturally produced in plants via specialized metabolism and exhibits vast range of remarkable physiological activities and pharmacological manifestations. Owing to significant safety and efficacy in different medical conditions, UA may serve as a backbone to produce its derivatives with novel therapeutic functions. This review aims to provide ideas for exploring more diverse structures to improve UA pharmacological activity and increasing its biological yield to meet the industrial requirements by systematically reviewing the current research progress of UA. We first provides an overview of the pharmacological activities, acquisition methods and structural modifications of UA. Among them, we focused on the synthetic modifications of UA to yield valuable derivatives with enhanced therapeutic potential. Furthermore, harnessing the essential advances for green synthesis of UA and its derivatives by advent of metabolic engineering and synthetic biology are of great concern. In this regard, all pivotal advances for enhancing the production of UA have been discussed. In combination with the advantages of UA biosynthesis and transformation strategy, large-scale microbial production of UA is a promising platform for further exploration.
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Affiliation(s)
- Hao-Ran Liu
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Nadeem Ahmad
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Bo Lv
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, P. R. China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China
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19
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Lin J, Yao Z, Lyu X, Ye L, Yu H. Development of a dual temperature control system for isoprene biosynthesis in Saccharomyces cerevisiae. Front Chem Sci Eng 2021. [DOI: 10.1007/s11705-021-2088-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Deng J, Wu Y, Zheng Z, Chen N, Luo X, Tang H, Keasling JD. A synthetic promoter system for well-controlled protein expression with different carbon sources in Saccharomyces cerevisiae. Microb Cell Fact 2021; 20:202. [PMID: 34663323 PMCID: PMC8522093 DOI: 10.1186/s12934-021-01691-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/27/2021] [Indexed: 11/24/2022] Open
Abstract
Background Saccharomyces cerevisiae is an important synthetic biology chassis for microbial production of valuable molecules. Promoter engineering has been frequently applied to generate more synthetic promoters with a variety of defined characteristics in order to achieve a well-regulated genetic network for high production efficiency. Galactose-inducible (GAL) expression systems, composed of GAL promoters and multiple GAL regulators, have been widely used for protein overexpression and pathway construction in S. cerevisiae. However, the function of each element in synthetic promoters and how they interact with GAL regulators are not well known. Results Here, a library of synthetic GAL promoters demonstrate that upstream activating sequences (UASs) and core promoters have a synergistic relationship that determines the performance of each promoter under different carbon sources. We found that the strengths of synthetic GAL promoters could be fine-tuned by manipulating the sequence, number, and substitution of UASs. Core promoter replacement generated synthetic promoters with a twofold strength improvement compared with the GAL1 promoter under multiple different carbon sources in a strain with GAL1 and GAL80 engineering. These results represent an expansion of the classic GAL expression system with an increased dynamic range and a good tolerance of different carbon sources. Conclusions In this study, the effect of each element on synthetic GAL promoters has been evaluated and a series of well-controlled synthetic promoters are constructed. By studying the interaction of synthetic promoters and GAL regulators, synthetic promoters with an increased dynamic range under different carbon sources are created. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01691-3.
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Affiliation(s)
- Jiliang Deng
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute for Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.,State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yanling Wu
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute for Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Zhaohui Zheng
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute for Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Nanzhu Chen
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute for Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Xiaozhou Luo
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute for Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Hongting Tang
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute for Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Jay D Keasling
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute for Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.,Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Chemical and Biomolecular Engineering & Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
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21
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Shaikh KM, Odaneth AA. Metabolic engineering of Yarrowia lipolytica for the production of isoprene. Biotechnol Prog 2021; 37:e3201. [PMID: 34369095 DOI: 10.1002/btpr.3201] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/24/2021] [Accepted: 08/05/2021] [Indexed: 12/27/2022]
Abstract
Yarrowia lipolytica has recently emerged as a prominent microbial host for production of terpenoids. Its robust metabolism and growth in wide range of substrates offer several advantages at industrial scale. In the present study, we investigate the metabolic potential of Y. lipolytica to produce isoprene. Sustainable production of isoprene has been attempted through engineering several microbial hosts; however, the engineering studies performed so far are challenged with low titers. Engineering of Y. lipolytica, which have inherent high acetyl-CoA flux could fuel precursors into the biosynthesis of isoprene and thus is an approach that would offer sustainable production opportunities. The present work, therefore, explores this opportunity wherein a codon-optimized IspS gene (single copy) of Pueraria montana was integrated into the Y. lipolytica genome. With no detectable isoprene level during the growth or stationary phase of modified strain, attempts were made to overexpress enzymes from MVA pathway. GC-FID analyses of gas collected during stationary phase revealed that engineered strains were able to produce detectable isoprene only after overexpressing HMGR (or tHMGR). The significant role of HMGR (tHMGR) in diverting the pathway flux toward DMAPP is thus highlighted in our study. Nevertheless, the final recombinant strains overexpressing HMGR (tHMGR) along with Erg13 and IDI showed isoprene titers of ~500 μg/L and yields of ~80 μg/g. Further characterization of the recombinant strains revealed high lipid and squalene content compared to the unmodified strain. Overall, the preliminary results of our laboratory-scale studies represent Y. lipolytica as a promising host for fermentative production of isoprene.
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Affiliation(s)
- Kurshedaktar M Shaikh
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology (formerly UDCT), Mumbai, India
| | - Annamma A Odaneth
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology (formerly UDCT), Mumbai, India
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22
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Wang J, Zhu L, Li Y, Xu S, Jiang W, Liang C, Fang Y, Chu A, Zhang L, Ding Z, Shi G. Enhancing Geranylgeraniol Production by Metabolic Engineering and Utilization of Isoprenol as a Substrate in Saccharomyces cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:4480-4489. [PMID: 33823596 DOI: 10.1021/acs.jafc.1c00508] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The amount of geranylgeranyl diphosphate (GGPP) is vital for microbial production of geranylgeraniol (GGOH) in Saccharomyces cerevisiae. In this study, a GGPP synthase with stronger catalytic ability was used to increase the supply of GGPP, and an engineered strain producing 374.02 mg/L GGOH at the shake flask level was constructed. Then, by increasing the metabolic flux of the mevalonate (MVA) pathway and the supply of isopentenyl pyrophosphate (IPP), the titer was further increased to 772.98 mg/L at the shake flask level, and we achieved the highest GGOH titer to date of 5.07 g/L in a 5 L bioreactor. This is the first report on the utilization of isoprenol for increasing the amount of IPP and enhancing GGOH production in S. cerevisiae. In the future, these strategies and engineered strains can be used to enhance the production of other terpenoids in S. cerevisiae.
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Affiliation(s)
- Junhua Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Linghuan Zhu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Youran Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Sha Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Wei Jiang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, People's Republic of China
| | - Chaojuan Liang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Yakun Fang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Alex Chu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Liang Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Zhongyang Ding
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Guiyang Shi
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
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23
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Wang J, Jiang W, Liang C, Zhu L, Li Y, Mo Q, Xu S, Chu A, Zhang L, Ding Z, Shi G. Overproduction of α-Farnesene in Saccharomyces cerevisiae by Farnesene Synthase Screening and Metabolic Engineering. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:3103-3113. [PMID: 33683134 DOI: 10.1021/acs.jafc.1c00008] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Maximizing the flux of farnesyl diphosphate (FPP) to farnesene biosynthesis is the main challenge of farnesene overproduction in Saccharomyces cerevisiae. In this study, we screened α-farnesene synthase from soybean (Fsso) with a higher catalytic ability. Combining the overexpression of the mevalonate (MVA) pathway with the expression of Fsso, an engineered yeast strain producing 190.5 mg/L α-farnesene was screened with poor growth. By decreasing the copies of 3-hydroxy-3-methylglutaryl-coenzyme (HMGR) overexpressed, the titer was increased to 417.8 mg/L. Then, the coexpression of Fsso and HMGR under the control of the GAL promoter and inactivation of lipid phosphate phosphatase encoded by DPP1 promoted the titer to 1163.7 mg/L. The titer was further increased to 1477.2 mg/L at the shake flask level with better growth by the construction of a prototrophic strain. Finally, the highest α-farnesene production of 10.4 g/L in S. cerevisiae was obtained by fed-batch fermentation in a 5 L bioreactor.
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Affiliation(s)
- Junhua Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Wei Jiang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai 201106, People's Republic of China
| | - Chaojuan Liang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Linghuan Zhu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Youran Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Qin Mo
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai 201106, People's Republic of China
| | - Sha Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Alex Chu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Liang Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Zhongyang Ding
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Guiyang Shi
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
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24
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Baptista SL, Costa CE, Cunha JT, Soares PO, Domingues L. Metabolic engineering of Saccharomyces cerevisiae for the production of top value chemicals from biorefinery carbohydrates. Biotechnol Adv 2021; 47:107697. [PMID: 33508428 DOI: 10.1016/j.biotechadv.2021.107697] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 12/16/2022]
Abstract
The implementation of biorefineries for a cost-effective and sustainable production of energy and chemicals from renewable carbon sources plays a fundamental role in the transition to a circular economy. The US Department of Energy identified a group of key target compounds that can be produced from biorefinery carbohydrates. In 2010, this list was revised and included organic acids (lactic, succinic, levulinic and 3-hydroxypropionic acids), sugar alcohols (xylitol and sorbitol), furans and derivatives (hydroxymethylfurfural, furfural and furandicarboxylic acid), biohydrocarbons (isoprene), and glycerol and its derivatives. The use of substrates like lignocellulosic biomass that impose harsh culture conditions drives the quest for the selection of suitable robust microorganisms. The yeast Saccharomyces cerevisiae, widely utilized in industrial processes, has been extensively engineered to produce high-value chemicals. For its robustness, ease of handling, genetic toolbox and fitness in an industrial context, S. cerevisiae is an ideal platform for the founding of sustainable bioprocesses. Taking these into account, this review focuses on metabolic engineering strategies that have been applied to S. cerevisiae for converting renewable resources into the previously identified chemical targets. The heterogeneity of each chemical and its manufacturing process leads to inevitable differences between the development stages of each process. Currently, 8 of 11 of these top value chemicals have been already reported to be produced by recombinant S. cerevisiae. While some of them are still in an early proof-of-concept stage, others, like xylitol or lactic acid, are already being produced from lignocellulosic biomass. Furthermore, the constant advances in genome-editing tools, e.g. CRISPR/Cas9, coupled with the application of innovative process concepts such as consolidated bioprocessing, will contribute for the establishment of S. cerevisiae-based biorefineries.
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Affiliation(s)
- Sara L Baptista
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar, Braga, Portugal
| | - Carlos E Costa
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar, Braga, Portugal
| | - Joana T Cunha
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar, Braga, Portugal
| | - Pedro O Soares
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar, Braga, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar, Braga, Portugal.
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25
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Zha WL, Zi JC. Advances in biotechnological production of santalenes and santalols. CHINESE HERBAL MEDICINES 2021; 13:90-97. [PMID: 36117763 PMCID: PMC9476758 DOI: 10.1016/j.chmed.2020.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/17/2020] [Accepted: 07/27/2020] [Indexed: 11/30/2022] Open
Abstract
Sandalwood essential oil has been widely used not only as natural medicines but also in perfumery and food industries, with sesquiterpenoids as its major components including (Z)- α-santalol and (Z)-β-santalol and so on. The mature heartwoods of Santalum album, Santalum austrocaledonicum and Santalum spicatum are the major plant resources for extracting sandalwood essential oil, which have been overexploited. Synthetic biology approaches have been successfully applied to produce natural products on large scale. In this review, we summarize biosynthetic enzymes of santalenes and santalols, including various santalene synthases (STSs) and cytochrome P450 monooxygenases (CYPs), and then highlight the advances of biotechnological production of santalenes and santalols in heterologous hosts, especially metabolic engineering strategies for constructing santalene- and santalol-producing Saccharomyces cerevisiae.
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Affiliation(s)
- Wen-long Zha
- Biotechnological Institute of Chinese Materia Medica, Jinan University, Guangzhou 510632, China
- College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Jia-chen Zi
- Biotechnological Institute of Chinese Materia Medica, Jinan University, Guangzhou 510632, China
- College of Pharmacy, Jinan University, Guangzhou 510632, China
- Corresponding author.
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26
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Metabolic Engineering and Synthetic Biology of Cyanobacteria for Carbon Capture and Utilization. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-019-0447-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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27
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Zhou P, Xu N, Yang Z, Du Y, Yue C, Xu N, Ye L. Directed evolution of the transcription factor Gal4 for development of an improved transcriptional regulation system in Saccharomyces cerevisiae. Enzyme Microb Technol 2020; 142:109675. [PMID: 33220863 DOI: 10.1016/j.enzmictec.2020.109675] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 08/27/2020] [Accepted: 09/19/2020] [Indexed: 01/17/2023]
Abstract
As a well-characterized eukaryotic DNA binding transcription factor, Gal4 has been extensively employed to construct controllable gene expression systems in Saccharomyces cerevisiae. The problem of insufficient inducibility arises in the constructs with multiples genes under control of GAL promoters due to the low expression level and activity of the native Gal4. In order to obtain improved transcriptional regulation systems for multi-gene pathways, Gal4 mutants with improved activity were created by directed evolution. During the preliminary screening, five positive Gal4 variants were isolated based on the lycopene-indicated high-throughput screening method. Analysis of the mutation sites revealed that the majority of positive mutations are localized in the middle homology region with unspecified function, suggesting an important role of this domain in transactivation of Gal4. Through combinatorial site-directed mutagenesis, the best variant Gal4T406A/V413A was obtained, which successfully increased the transcription of PGAL-driven lycopene pathway genes and led to 48 % higher lycopene accumulation relative to the wild-type Gal4. This study demonstrates the viability of modifying Gal4 activity by directed evolution for elevated expression of PGAL-driven genes and therefore enhanced production of the target metabolite.
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Affiliation(s)
- Pingping Zhou
- Joint International Research Laboratory of Agriculture and Agri-Product Safety/Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, The Ministry of Education of China, Yangzhou University, Yangzhou, 225009, PR China; College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, PR China.
| | - Nannan Xu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety/Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, The Ministry of Education of China, Yangzhou University, Yangzhou, 225009, PR China; College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, PR China
| | - Zhengfei Yang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety/Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, The Ministry of Education of China, Yangzhou University, Yangzhou, 225009, PR China; School of Food Science and Engineering, Yangzhou University, Yangzhou, 225009, PR China
| | - Yi Du
- Joint International Research Laboratory of Agriculture and Agri-Product Safety/Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, The Ministry of Education of China, Yangzhou University, Yangzhou, 225009, PR China; College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, PR China
| | - Chunlei Yue
- Joint International Research Laboratory of Agriculture and Agri-Product Safety/Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, The Ministry of Education of China, Yangzhou University, Yangzhou, 225009, PR China; College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, PR China
| | - Nan Xu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, PR China
| | - Lidan Ye
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, PR China.
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28
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Improved linalool production in Saccharomyces cerevisiae by combining directed evolution of linalool synthase and overexpression of the complete mevalonate pathway. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107655] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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29
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Tang H, Wu Y, Deng J, Chen N, Zheng Z, Wei Y, Luo X, Keasling JD. Promoter Architecture and Promoter Engineering in Saccharomyces cerevisiae. Metabolites 2020; 10:metabo10080320. [PMID: 32781665 PMCID: PMC7466126 DOI: 10.3390/metabo10080320] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/30/2020] [Accepted: 08/04/2020] [Indexed: 12/23/2022] Open
Abstract
Promoters play an essential role in the regulation of gene expression for fine-tuning genetic circuits and metabolic pathways in Saccharomyces cerevisiae (S. cerevisiae). However, native promoters in S. cerevisiae have several limitations which hinder their applications in metabolic engineering. These limitations include an inadequate number of well-characterized promoters, poor dynamic range, and insufficient orthogonality to endogenous regulations. Therefore, it is necessary to perform promoter engineering to create synthetic promoters with better properties. Here, we review recent advances related to promoter architecture, promoter engineering and synthetic promoter applications in S. cerevisiae. We also provide a perspective of future directions in this field with an emphasis on the recent advances of machine learning based promoter designs.
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Affiliation(s)
- Hongting Tang
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Chinese Academy of Sciences, Shenzhen 518055, China; (H.T.); (Y.W.); (J.D.); (N.C.); (Z.Z.)
| | - Yanling Wu
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Chinese Academy of Sciences, Shenzhen 518055, China; (H.T.); (Y.W.); (J.D.); (N.C.); (Z.Z.)
| | - Jiliang Deng
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Chinese Academy of Sciences, Shenzhen 518055, China; (H.T.); (Y.W.); (J.D.); (N.C.); (Z.Z.)
| | - Nanzhu Chen
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Chinese Academy of Sciences, Shenzhen 518055, China; (H.T.); (Y.W.); (J.D.); (N.C.); (Z.Z.)
| | - Zhaohui Zheng
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Chinese Academy of Sciences, Shenzhen 518055, China; (H.T.); (Y.W.); (J.D.); (N.C.); (Z.Z.)
| | - Yongjun Wei
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China;
| | - Xiaozhou Luo
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Chinese Academy of Sciences, Shenzhen 518055, China; (H.T.); (Y.W.); (J.D.); (N.C.); (Z.Z.)
- Correspondence: (X.L.); (J.D.K.)
| | - Jay D. Keasling
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Chinese Academy of Sciences, Shenzhen 518055, China; (H.T.); (Y.W.); (J.D.); (N.C.); (Z.Z.)
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Chemical and Biomolecular Engineering & Department of Bioengineering, University of California, Berkeley, CA 94720, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
- Correspondence: (X.L.); (J.D.K.)
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Bai C, Liu Y, Chen X, Qian Z, Liu H, Zhou X, Zhang Y, Cai M. Fungal statin pump protein improves monacolin J efflux and regulates its production in Komagataella phaffii. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-00321-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Monacolin J (MJ) is a key intermediate for the synthesis of cholesterol-lowering drug simvastatin. Current industrial production of MJ involves complicated chemical hydrolysis of microbial fermented lovastatin. Recently, heterologous production of MJ has been achieved in yeast and bacteria, but the resulting metabolic stress and excessive accumulation of the compound adversely affect cell activity.
Results
Five genes, tapA, stapA, slovI, smokI and smlcE, coding for fungal statin pump proteins were expressed in an MJ producing yeast strain, Komagataella phaffii J#9. Overexpression of these genes facilitated MJ production. Among them, tapA from Aspergillus terreus highly improved MJ production and led to a titer increase of 108%. Exogenous MJ feeding study on an MJ non-producing strain GS-PGAP-TapA was then performed, and the results illustrated tough entry of MJ into cells and possible efflux action of TapA. Further, intracellular and extracellular MJ levels of J#9 and J#9-TapA were analyzed. The extracellular MJ level of J#9-TapA increased faster, but its intracellular MJ percentage kept lower as compared to J#9. The results proved that TapA effectively excreted MJ from cells. Then functions of TapA were evaluated in a high-production bioreactor fermentation. Differently, TapA expression caused a low MJ titer but high intracellular MJ accumulation in J#9-TapA compared with J#9.
Conclusions
Statin pump proteins improved MJ production in K. phaffii in a shake flask. Exogenous MJ feeding and endogenous MJ producing experiments demonstrated the efflux function of TapA. TapA improved MJ production at low MJ levels in a shake flask, but decreased it at high MJ levels in a bioreactor. This finding is useful for statin pump improvement and metabolic engineering for statin bioproduction.
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Zhu Y, Zhou C, Wang Y, Li C. Transporter Engineering for Microbial Manufacturing. Biotechnol J 2020; 15:e1900494. [PMID: 32298528 DOI: 10.1002/biot.201900494] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 03/30/2020] [Indexed: 01/08/2023]
Abstract
Microbes play an important role in biotransformation and biosynthesis of biofuels, natural products, and polymers. Therefore, microbial manufacturing has been widely used in medicine, industry, and agriculture. However, common strategies including enzyme engineering, pathway optimization, and host engineering are generally inadequate to obtain an efficient microbial production system. Transporter engineering provides an alternative strategy to promote the transmembrane transfer of substrates, intermediates, and final products in microbial cells and thus enhances production by alleviating feedback inhibition and cytotoxicity caused by final products. According to the current studies in transport engineering, native transporters usually have low expression and poor transportation ability, resulting in inefficient transport processes and microbial production. In this review, current approaches for transporter mining, characterization, and verification are comprehensively summarized. Practical approaches to enhance the transport system in engineered cells, such as balancing transporter overexpression and cell growth, and evolution of native transporters are discussed. Furthermore, the applications of transporter engineering in microbial manufacturing, including enhancement of substrate utilization, concentration of metabolic flux to the target pathway, and acceleration of efflux and recovery of products, demonstrate its outstanding advantages and promising prospects.
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Affiliation(s)
- Ying Zhu
- Department of Biochemical Engineering, Institute for Synthetic Biosystem, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Chen Zhou
- Department of Biochemical Engineering, Institute for Synthetic Biosystem, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Ying Wang
- Department of Biochemical Engineering, Institute for Synthetic Biosystem, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Chun Li
- Department of Biochemical Engineering, Institute for Synthetic Biosystem, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
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An T, Zha W, Zi J. Biotechnological production of betulinic acid and derivatives and their applications. Appl Microbiol Biotechnol 2020; 104:3339-3348. [DOI: 10.1007/s00253-020-10495-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/14/2020] [Accepted: 02/20/2020] [Indexed: 11/25/2022]
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Zha W, An T, Li T, Zhu J, Gao K, Sun Z, Xu W, Lin P, Zi J. Reconstruction of the Biosynthetic Pathway of Santalols under Control of the GAL Regulatory System in Yeast. ACS Synth Biol 2020; 9:449-456. [PMID: 31940436 DOI: 10.1021/acssynbio.9b00479] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Sandalwood oil has been widely used in perfumery industries and aromatherapy. Santalols are its major components. Herein, we attempted to construct santalol-producing yeasts. To alter flux from predominant triterpenoid/steroid biosynthesis to sesquiterpenoid production, expression of ERG9 (encoding yeast squalene synthase) was depressed by replacing its innate promotor with PHXT1 and fermenting the resulting strains in galactose-rich media. And the genes related to santalol biosynthesis were overexpressed under control of GAL promotors, which linked santalol biosynthesis to GAL regulatory system. GAL4 (a transcriptional activator of GAL promotors) and PGM2 (a yeast phosphoglucomutase) were overexpressed to overall promote this artificial santalol biosynthetic pathway and enhance galactose uptake. 1.3 g/L santalols and 1.2 g/L Z-α-santalol were achieved in the strain WL17 expressing SaSS (α-santalene synthase from Santalum album) and WL19 expressing SanSyn (α-santalene synthase from Clausena lansium) by fed-batch fermentation, respectively. This study constructed the microbial santalol-producing platform for the first time.
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Affiliation(s)
- Wenlong Zha
- Biotechnological Institute of Chinese Materia Medic, Jinan University, Guangzhou 510632, China
- College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Tianyue An
- Biotechnological Institute of Chinese Materia Medic, Jinan University, Guangzhou 510632, China
- College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Ting Li
- Biotechnological Institute of Chinese Materia Medic, Jinan University, Guangzhou 510632, China
| | - Jianxun Zhu
- Biotechnological Institute of Chinese Materia Medic, Jinan University, Guangzhou 510632, China
| | - Ke Gao
- Biotechnological Institute of Chinese Materia Medic, Jinan University, Guangzhou 510632, China
| | - Zhenjiao Sun
- Guangdong Qingyunshan Pharmaceutical Co., Ltd., Shaoguan 512600, China
| | - Wendong Xu
- National Engineering Research Center for Modernization of Extraction and Separation Process of TCM/Guangzhou Hanfang Pharmaceutical Co., Ltd., Guangzhou 510240, China
| | - Pengcheng Lin
- College of Pharmacy, Qinghai Nationalities University, Xining 810007, China
| | - Jiachen Zi
- Biotechnological Institute of Chinese Materia Medic, Jinan University, Guangzhou 510632, China
- College of Pharmacy, Jinan University, Guangzhou 510632, China
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Meng X, Liu H, Xu W, Zhang W, Wang Z, Liu W. Metabolic engineering Saccharomyces cerevisiae for de novo production of the sesquiterpenoid (+)-nootkatone. Microb Cell Fact 2020; 19:21. [PMID: 32013959 PMCID: PMC6998195 DOI: 10.1186/s12934-020-1295-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 01/27/2020] [Indexed: 11/10/2022] Open
Abstract
Background (+)-Nootkatone is a highly valued sesquiterpenoid compound, exhibiting a typical grapefruit aroma and various desired biological activities for use as aromatics and pharmaceuticals. The high commercial demand of (+)-nootkatone is predominately met by chemical synthesis, which entails the use of environmentally harmful reagents. Efficient synthesis of (+)-nootkatone via biotechnological approaches is thus urgently needed to satisfy its industrial demand. However, there are only a limited number of studies that report the de novo synthesis of (+)-nootkatone from simple carbon sources in microbial cell factories, and with relatively low yield. Results As the direct precursor of (+)-nootkatone biosynthesis, (+)-valencene was first produced in large quantities in Saccharomyces cerevisiae by overexpressing (+)-valencene synthase CnVS of Callitropsis nootkatensis in combination with various mevalonate pathway (MVA) engineering strategies, including the expression of CnVS and farnesyl diphosphate synthase (ERG20) as a fused protein, overexpression of a truncated form of the rate-limiting enzyme 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) reductase (tHMG1), and downregulating the squalene synthase enzyme (ERG9). These approaches altogether brought the production of (+)-valencene to 217.95 mg/L. Secondly, we addressed the (+)-valencene oxidation by overexpressing the Hyoscyamus muticus premnaspirodiene oxygenase (HPO) variant (V482I/A484I) and cytochrome P450 reductase (ATR1) from Arabidopsis thaliana. However, (+)-valencene was predominantly oxidized to β-nootkatol and only minor amounts of (+)-nootkatone (9.66 mg/L) were produced. We further tackled the oxidation of β-nootkatol to (+)-nootkatone by screening various dehydrogenases. Our results showed that the short-chain dehydrogenase/reductase (SDR) superfamily dehydrogenases ZSD1 of Zingiber zerumbet and ABA2 of Citrus sinensis were capable of effectively catalyzing β-nootkatol oxidation to (+)-nootkatone. The yield of (+)-nootkatone increased to 59.78 mg/L and 53.48 mg/L by additional overexpression of ZSD1 and ABA2, respectively. Conclusion We successfully constructed the (+)-nootaktone biosynthesis pathway in S. cerevisiae by overexpressing the (+)-valencene synthase CnVS, cytochrome P450 monooxygenase HPO, and SDR family dehydrogenases combined with the MVA pathway engineering, providing a solid basis for the whole-cell production of (+)-nootkatone. The two effective SDR family dehydrogenases tested in this study will serve as valuable enzymatic tools in further optimizing (+)-nootkatone production.
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Affiliation(s)
- Xiangfeng Meng
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Hui Liu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Wenqiang Xu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Weixin Zhang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Zheng Wang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China.
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Zeng W, Guo L, Xu S, Chen J, Zhou J. High-Throughput Screening Technology in Industrial Biotechnology. Trends Biotechnol 2020; 38:888-906. [PMID: 32005372 DOI: 10.1016/j.tibtech.2020.01.001] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 01/01/2020] [Accepted: 01/03/2020] [Indexed: 12/14/2022]
Abstract
Based on the development of automatic devices and rapid assay methods, various high-throughput screening (HTS) strategies have been established for improving the performance of industrial microorganisms. We discuss the most significant factors that can improve HTS efficiency, including the construction of screening libraries with high diversity and the use of new detection methods to expand the search range and highlight target compounds. We also summarize applications of HTS for enhancing the performance of industrial microorganisms. Current challenges and potential improvements to HTS in industrial biotechnology are discussed in the context of rapid developments in synthetic biology, nanotechnology, and artificial intelligence. Rational integration will be an important driving force for constructing more efficient industrial microorganisms with wider applications in biotechnology.
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Affiliation(s)
- Weizhu Zeng
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Likun Guo
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Sha Xu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jian Chen
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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Ko YS, Kim JW, Lee JA, Han T, Kim GB, Park JE, Lee SY. Tools and strategies of systems metabolic engineering for the development of microbial cell factories for chemical production. Chem Soc Rev 2020; 49:4615-4636. [DOI: 10.1039/d0cs00155d] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This tutorial review covers tools, strategies, and procedures of systems metabolic engineering facilitating the development of microbial cell factories efficiently producing chemicals and materials.
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Affiliation(s)
- Yoo-Sung Ko
- Metabolic and Biomolecular Engineering National Research Laboratory
- Systems Metabolic Engineering and Systems Healthcare (SMESH) Cross-Generation Collaborative Laboratory
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program)
- Institute for the BioCentury
- Korea Advanced Institute of Science and Technology (KAIST)
| | - Je Woong Kim
- Metabolic and Biomolecular Engineering National Research Laboratory
- Systems Metabolic Engineering and Systems Healthcare (SMESH) Cross-Generation Collaborative Laboratory
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program)
- Institute for the BioCentury
- Korea Advanced Institute of Science and Technology (KAIST)
| | - Jong An Lee
- Metabolic and Biomolecular Engineering National Research Laboratory
- Systems Metabolic Engineering and Systems Healthcare (SMESH) Cross-Generation Collaborative Laboratory
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program)
- Institute for the BioCentury
- Korea Advanced Institute of Science and Technology (KAIST)
| | - Taehee Han
- Metabolic and Biomolecular Engineering National Research Laboratory
- Systems Metabolic Engineering and Systems Healthcare (SMESH) Cross-Generation Collaborative Laboratory
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program)
- Institute for the BioCentury
- Korea Advanced Institute of Science and Technology (KAIST)
| | - Gi Bae Kim
- Metabolic and Biomolecular Engineering National Research Laboratory
- Systems Metabolic Engineering and Systems Healthcare (SMESH) Cross-Generation Collaborative Laboratory
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program)
- Institute for the BioCentury
- Korea Advanced Institute of Science and Technology (KAIST)
| | - Jeong Eum Park
- Metabolic and Biomolecular Engineering National Research Laboratory
- Systems Metabolic Engineering and Systems Healthcare (SMESH) Cross-Generation Collaborative Laboratory
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program)
- Institute for the BioCentury
- Korea Advanced Institute of Science and Technology (KAIST)
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory
- Systems Metabolic Engineering and Systems Healthcare (SMESH) Cross-Generation Collaborative Laboratory
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program)
- Institute for the BioCentury
- Korea Advanced Institute of Science and Technology (KAIST)
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Bu X, Lin JY, Cheng J, Yang D, Duan CQ, Koffas M, Yan GL. Engineering endogenous ABC transporter with improving ATP supply and membrane flexibility enhances the secretion of β-carotene in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:168. [PMID: 33062054 PMCID: PMC7548044 DOI: 10.1186/s13068-020-01809-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 10/05/2020] [Indexed: 05/17/2023]
Abstract
BACKGROUND Product toxicity is one of the bottlenecks for microbial production of biofuels, and transporter-mediated biofuel secretion offers a promising strategy to solve this problem. As a robust microbial host for industrial-scale production of biofuels, Saccharomyces cerevisiae contains a powerful transport system to export a wide range of toxic compounds to sustain survival. The aim of this study is to improve the secretion and production of the hydrophobic product (β-carotene) by harnessing endogenous ABC transporters combined with physiological engineering in S. cerevisiae. RESULTS Substrate inducibility is a prominent characteristic of most endogenous transporters. Through comparative proteomic analysis and transcriptional confirmation, we identified five potential ABC transporters (Pdr5p, Pdr10p, Snq2p, Yor1p, and Yol075cp) for β-carotene efflux. The accumulation of β-carotene also affects cell physiology in various aspects, including energy metabolism, mitochondrial translation, lipid metabolism, ergosterol biosynthetic process, and cell wall synthesis. Here, we adopted an inducible GAL promoter to overexpress candidate transporters and enhanced the secretion and intracellular production of β-carotene, in which Snq2p showed the best performance (a 4.04-fold and a 1.33-fold increase compared with its parental strain YBX-01, respectively). To further promote efflux capacity, two strategies of increasing ATP supply and improving membrane fluidity were following adopted. A 5.80-fold increase of β-carotene secretion and a 1.71-fold increase of the intracellular β-carotene production were consequently achieved in the engineered strain YBX-20 compared with the parental strain YBX-01. CONCLUSIONS Overall, our results showcase that engineering endogenous plasma membrane ABC transporters is a promising approach for hydrophobic product efflux in S. cerevisiae. We also highlight the importance of improving cell physiology to enhance the efficiency of ABC transporters, especially energy status and cell membrane properties.
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Affiliation(s)
- Xiao Bu
- Centre for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, 17 East Tsinghua Rd, Beijing, 100083 China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, 100083 China
| | - Jing-Yuan Lin
- Centre for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, 17 East Tsinghua Rd, Beijing, 100083 China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, 100083 China
| | - Jing Cheng
- Centre for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, 17 East Tsinghua Rd, Beijing, 100083 China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, 100083 China
| | - Dong Yang
- Beijing Key Laboratory of Functional Food From Plant Resources, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083 China
| | - Chang-Qing Duan
- Centre for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, 17 East Tsinghua Rd, Beijing, 100083 China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, 100083 China
| | - Mattheos Koffas
- Center for Biotechnology and Interdisciplinary Studies and Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180 USA
| | - Guo-Liang Yan
- Centre for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, 17 East Tsinghua Rd, Beijing, 100083 China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, 100083 China
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Gionfriddo M, De Gara L, Loreto F. Directed Evolution of Plant Processes: Towards a Green (r)Evolution? TRENDS IN PLANT SCIENCE 2019; 24:999-1007. [PMID: 31604600 DOI: 10.1016/j.tplants.2019.08.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/11/2019] [Accepted: 08/13/2019] [Indexed: 05/13/2023]
Abstract
Directed evolution (DE) is a powerful approach for generating proteins with new chemical and physical properties. It mimics the principles of Darwinian evolution by imposing selective pressure on a large population of molecules harboring random genetic variation in DNA, such that sequences with specific desirable properties are generated and selected. We propose that combining DE and genome-editing (DE-GE) technologies represents a powerful tool to discover and integrate new traits into plants for agronomic and biotechnological gain. DE-GE has the potential to deliver a new green (r)evolution research platform that can provide novel solutions to major trait delivery aspirations for sustainable agriculture, climate-resilient crops, and improved food security and nutritional quality.
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Affiliation(s)
- Matteo Gionfriddo
- Unit of Food Science and Human Nutrition, Campus Bio-Medico, University of Rome, Via Álvaro del Portillo 21, 00128 Rome, Italy; Department of Biology, Agriculture, and Food Sciences, National Research Council of Italy (CNR-DISBA), Piazzale Aldo Moro 7, 00185 Rome, Italy
| | - Laura De Gara
- Unit of Food Science and Human Nutrition, Campus Bio-Medico, University of Rome, Via Álvaro del Portillo 21, 00128 Rome, Italy.
| | - Francesco Loreto
- Department of Biology, Agriculture, and Food Sciences, National Research Council of Italy (CNR-DISBA), Piazzale Aldo Moro 7, 00185 Rome, Italy; Department of Biology, University Federico II, Via Cinthia, 80126 Naples, Italy.
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Ma B, Liu M, Li ZH, Tao X, Wei DZ, Wang FQ. Significantly Enhanced Production of Patchoulol in Metabolically Engineered Saccharomyces cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:8590-8598. [PMID: 31287301 DOI: 10.1021/acs.jafc.9b03456] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Patchoulol, a natural sesquiterpene compound, is widely used in perfumes and cosmetics. Several strategies were adopted to enhance patchoulol production in Saccharomyces cerevisiae: (i) farnesyl pyrophosphate (FPP) synthase and patchoulol synthase were fused to increase the utilization of FPP precursor; (ii) expression of the limiting genes of the mevalonate pathway was enhanced; (iii) squalene synthase was weakened by a glucose-inducible promoter of HXT1 (promoter for hexose transporter) to reduce metabolic flux from FPP to ergosterol; and (iv) farnesol biosynthesis was inhibited to decrease the consumption of FPP. Glucose was used to balance the trade-off between the competitive squalene and patchoulol pathways. The patchoulol production was 59.2 ± 0.7 mg/L in a shaken flask with a final production of 466.8 ± 12.3 mg/L (20.5 ± 0.5 mg/g dry cell weight) combined with fermentation optimization, which was 7.8-fold higher than the reported maximum production. The work significantly promoted the industrialization process of patchoulol production using biobased microbial platforms.
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Affiliation(s)
- Bin Ma
- State key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology , East China University of Science and Technology , Shanghai 200237 , China
| | - Min Liu
- State key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology , East China University of Science and Technology , Shanghai 200237 , China
| | - Zhen-Hai Li
- State key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology , East China University of Science and Technology , Shanghai 200237 , China
| | - Xinyi Tao
- State key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology , East China University of Science and Technology , Shanghai 200237 , China
| | - Dong-Zhi Wei
- State key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology , East China University of Science and Technology , Shanghai 200237 , China
| | - Feng-Qing Wang
- State key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology , East China University of Science and Technology , Shanghai 200237 , China
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Li M, Chen H, Liu C, Guo J, Xu X, Zhang H, Nian R, Xian M. Improvement of isoprene production in Escherichia coli by rational optimization of RBSs and key enzymes screening. Microb Cell Fact 2019; 18:4. [PMID: 30626394 PMCID: PMC6327615 DOI: 10.1186/s12934-018-1051-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 12/26/2018] [Indexed: 01/13/2023] Open
Abstract
Background As an essential platform chemical mostly used for rubber synthesis, isoprene is produced in industry through chemical methods, derived from petroleum. As an alternative, bio-production of isoprene has attracted much attention in recent years. Previous researches were mostly focused on key enzymes to improve isoprene production. In this research, besides screening of key enzymes, we also paid attention to expression intensity of non-key enzymes. Results Firstly, screening of key enzymes, IDI, MK and IspS, from other organisms and then RBS optimization of the key enzymes were carried out. The strain utilized IDIsa was firstly detected to produce more isoprene than other IDIs. IDIsa expression was improved after RBS modification, leading to 1610-fold increase of isoprene production. Secondly, RBS sequence optimization was performed to reduce translation initiation rate value of non-key enzymes, ERG19 and MvaE. Decreased ERG19 and MvaE expression and increased isoprene production were detected. The final strain showed 2.6-fold increase in isoprene production relative to the original strain. Furthermore, for the first time, increased key enzyme expression and decreased non-key enzyme expression after RBS sequence optimization were obviously detected through SDS-PAGE analysis. Conclusions This study prove that desired enzyme expression and increased isoprene production were obtained after RBS sequence optimization. RBS optimization of genes could be a powerful strategy for metabolic engineering of strain. Moreover, to increase the production of engineered strain, attention should not only be focused on the key enzymes, but also on the non-key enzymes. Electronic supplementary material The online version of this article (10.1186/s12934-018-1051-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Meijie Li
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.135 Songlin Road, Qingdao, 266101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Hailin Chen
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.135 Songlin Road, Qingdao, 266101, People's Republic of China
| | - Changqing Liu
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.135 Songlin Road, Qingdao, 266101, People's Republic of China
| | - Jing Guo
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.135 Songlin Road, Qingdao, 266101, People's Republic of China
| | - Xin Xu
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.135 Songlin Road, Qingdao, 266101, People's Republic of China
| | - Haibo Zhang
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.135 Songlin Road, Qingdao, 266101, People's Republic of China.
| | - Rui Nian
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.135 Songlin Road, Qingdao, 266101, People's Republic of China.
| | - Mo Xian
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.135 Songlin Road, Qingdao, 266101, People's Republic of China.
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42
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Ko SC, Lee HJ, Choi SY, Choi JI, Woo HM. Bio-solar cell factories for photosynthetic isoprenoids production. PLANTA 2019; 249:181-193. [PMID: 30078076 DOI: 10.1007/s00425-018-2969-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 08/01/2018] [Indexed: 05/08/2023]
Abstract
Photosynthetic production of isoprenoids in cyanobacteria is considered in terms of metabolic engineering and biological importance. Metabolic engineering of photosynthetic bacteria (cyanobacteria) has been performed to construct bio-solar cell factories that convert carbon dioxide to various value-added chemicals. Isoprenoids, which are found in nature and range from essential cell components to defensive molecules, have great value in cosmetics, pharmaceutics, and biofuels. In this review, we summarize the recent engineering of cyanobacteria for photosynthetic isoprenoids production as well as carbon molar basis comparisons with heterotrophic isoprenoids production in engineered Escherichia coli.
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Affiliation(s)
- Sung Cheon Ko
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
| | - Hyun Jeong Lee
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
| | - Sun Young Choi
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
| | - Jong-Il Choi
- Department of Biotechnology and Bioengineering, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 61186, Republic of Korea
| | - Han Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea.
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43
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Zhao YJ, Li C. Biosynthesis of Plant Triterpenoid Saponins in Microbial Cell Factories. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:12155-12165. [PMID: 30387353 DOI: 10.1021/acs.jafc.8b04657] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Triterpenoid saponins are triterpenoid glycoside compounds which have been widely used in pharmaceutical, agricultural, and food industries. Traditionally, they are extracted from plants, which is time-consuming and environmentally unfriendly. Recently, de novo synthesis of triterpenoid saponins in microbial cell factories was realized, which provides a promising and green approach to alter the traditional supply way. However, the complex biosynthetic pathway and the poor suitability between the endogenous and heterogeneous pathways tremendously limit the yield of triterpenoid saponins. We introduce the biosynthetic pathways of triterpenoid saponins first, and we then summarize the microbial cell factories developed to produce these compounds. Further, we discuss the strategies applied to enhance the production. This paper systematically illustrates the biosynthesis of plant triterpenoid saponins in microbial cell factories.
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Affiliation(s)
- Yu-Jia Zhao
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , China
| | - Chun Li
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , China
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44
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Lian J, Mishra S, Zhao H. Recent advances in metabolic engineering of Saccharomyces cerevisiae: New tools and their applications. Metab Eng 2018; 50:85-108. [DOI: 10.1016/j.ymben.2018.04.011] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/09/2018] [Accepted: 04/13/2018] [Indexed: 10/17/2022]
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45
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Yao Z, Zhou P, Su B, Su S, Ye L, Yu H. Enhanced Isoprene Production by Reconstruction of Metabolic Balance between Strengthened Precursor Supply and Improved Isoprene Synthase in Saccharomyces cerevisiae. ACS Synth Biol 2018; 7:2308-2316. [PMID: 30145882 DOI: 10.1021/acssynbio.8b00289] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Isoprene, as a versatile bulk chemical, has wide industrial applications. Here, we attempted to improve isoprene biosynthesis in Saccharomyces cerevisiae by simultaneous strengthening of precursor supply and conversion via a combination of pathway compartmentation and protein engineering. At first, a superior isoprene synthase mutant ISPSLN was created by saturation mutagenesis, leading to almost 4-fold improvement in isoprene production. Subsequent introduction of ISPSLN to strains with strengthened precursor supply in either cytoplasm or mitochondria implied an imperfect match between the synthesis and conversion of the isopentenyl pyrophosphate (IPP)/dimethylallyl diphosphate (DMAPP) pool. To reconstruct metabolic balance between the upstream and downstream flux, additional copies of diphosphomevalonate decarboxylase gene ( MVD1) and isopentenyl-diphosphate delta-isomerase gene ( IDI1) were introduced into the cytoplasmic and mitochondrial engineered strains. Finally, the diploid strain created by mating the above haploid strains produced 11.9 g/L of isoprene, the highest ever reported in eukaryotic cells.
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Affiliation(s)
- Zhen Yao
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, PR China
| | - Pingping Zhou
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, PR China
| | - Bingmei Su
- Fujian Key Laboratory of Marine Enzyme Engineering, College of Biological Science and Engineering, Fuzhou University, Fuzhou 350116, PR China
| | - Sisi Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Lidan Ye
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, PR China
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Zhejiang University, Hangzhou 310027, PR China
| | - Hongwei Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, PR China
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Zhejiang University, Hangzhou 310027, PR China
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Zou H, Zhang T, Li L, Huang J, Zhang N, Shi M, Hao H, Xian M. Systematic Engineering for Improved Carbon Economy in the Biosynthesis of Polyhydroxyalkanoates and Isoprenoids. MATERIALS (BASEL, SWITZERLAND) 2018; 11:E1271. [PMID: 30042344 PMCID: PMC6117667 DOI: 10.3390/ma11081271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/10/2018] [Accepted: 07/19/2018] [Indexed: 11/23/2022]
Abstract
With the rapid development of synthetic biology and metabolic engineering, a broad range of biochemicals can be biosynthesized, which include polyhydroxyalkanoates and isoprenoids. However, some of the bio-approaches in chemical synthesis have just started to be applied outside of laboratory settings, and many require considerable efforts to achieve economies of scale. One of the often-seen barriers is the low yield and productivity, which leads to higher unit cost and unit capital investment for the bioconversion process. In general, higher carbon economy (less carbon wastes during conversion process from biomass to objective bio-based chemicals) will result in higher bioconversion yield, which results in less waste being generated during the process. To achieve this goal, diversified strategies have been applied; matured strategies include pathway engineering to block competitive pathways, enzyme engineering to enhance the activities of enzymes, and process optimization to improve biomass/carbon yield. In this review, we analyze the impact of carbon sources from different types of biomass on the yield of bio-based chemicals (especially for polyhydroxyalkanoates and isoprenoids). Moreover, we summarize the traditional strategies for improving carbon economy during the bioconversion process and introduce the updated techniques in building up non-natural carbon pathways, which demonstrate higher carbon economies than their natural counterparts.
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Affiliation(s)
- Huibin Zou
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.
| | - Tongtong Zhang
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Lei Li
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Jingling Huang
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Nan Zhang
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Mengxun Shi
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - He Hao
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Mo Xian
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.
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47
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Li M, Nian R, Xian M, Zhang H. Metabolic engineering for the production of isoprene and isopentenol by Escherichia coli. Appl Microbiol Biotechnol 2018; 102:7725-7738. [PMID: 30006784 PMCID: PMC6132537 DOI: 10.1007/s00253-018-9200-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 06/23/2018] [Accepted: 06/25/2018] [Indexed: 12/12/2022]
Abstract
The biotechnological production of isoprene and isopentenol has recently been studied. Isoprene, which is currently made mainly from petroleum, is an important platform chemical for synthesizing pesticides, medicines, oil additives, fragrances, and more and is especially important in the rubber production industry. Isopentenols, which have better combustion properties than well-known biofuels (ethanol), have recently received more attention. Supplies of petroleum, the conventional source of isoprene and isopentenols, are unsustainable, and chemical synthesis processes could cause serious environmental problems. As an alternative, the biosynthesis of isoprene and isopentenols in cell factories is more sustainable and environmentally friendly. With a number of advantages over other microorganisms, Escherichia coli is considered to be a powerful workhorse organism for producing these compounds. This review will highlight the recent advances in metabolic engineering for isoprene and isopentenol production, especially using E. coli cell factories.
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Affiliation(s)
- Meijie Li
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 135 Songling Road, Qingdao, 266101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Rui Nian
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 135 Songling Road, Qingdao, 266101, People's Republic of China
| | - Mo Xian
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 135 Songling Road, Qingdao, 266101, People's Republic of China.
| | - Haibo Zhang
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 135 Songling Road, Qingdao, 266101, People's Republic of China.
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48
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Liu Y, Bai C, Xu Q, Yu J, Zhou X, Zhang Y, Cai M. Improved methanol-derived lovastatin production through enhancement of the biosynthetic pathway and intracellular lovastatin efflux in methylotrophic yeast. BIORESOUR BIOPROCESS 2018. [DOI: 10.1186/s40643-018-0202-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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49
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Chaves JE, Melis A. Engineering isoprene synthesis in cyanobacteria. FEBS Lett 2018; 592:2059-2069. [PMID: 29689603 DOI: 10.1002/1873-3468.13052] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 03/21/2018] [Accepted: 04/05/2018] [Indexed: 11/05/2022]
Abstract
The renewable production of isoprene (Isp) hydrocarbons, to serve as fuel and synthetic chemistry feedstock, has attracted interest in the field recently. Isp (C5 H8 ) is naturally produced from sunlight, CO2 and H2 O photosynthetically in terrestrial plant chloroplasts via the terpenoid biosynthetic pathway and emitted in the atmosphere as a response to heat stress. Efforts to institute a high capacity continuous and renewable process have included heterologous expression of the Isp synthesis pathway in photosynthetic microorganisms. This review examines the premise and promise emanating from this relatively new research effort. Also examined are the metabolic engineering approaches applied in the quest of renewable Isp hydrocarbons production, the progress achieved so far, and barriers encountered along the way.
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Affiliation(s)
- Julie E Chaves
- Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Anastasios Melis
- Plant and Microbial Biology, University of California, Berkeley, CA, USA
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50
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Wang X, He Q, Yang Y, Wang J, Haning K, Hu Y, Wu B, He M, Zhang Y, Bao J, Contreras LM, Yang S. Advances and prospects in metabolic engineering of Zymomonas mobilis. Metab Eng 2018; 50:57-73. [PMID: 29627506 DOI: 10.1016/j.ymben.2018.04.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/31/2018] [Accepted: 04/01/2018] [Indexed: 12/22/2022]
Abstract
Biorefinery of biomass-based biofuels and biochemicals by microorganisms is a competitive alternative of traditional petroleum refineries. Zymomonas mobilis is a natural ethanologen with many desirable characteristics, which makes it an ideal industrial microbial biocatalyst for commercial production of desirable bioproducts through metabolic engineering. In this review, we summarize the metabolic engineering progress achieved in Z. mobilis to expand its substrate and product ranges as well as to enhance its robustness against stressful conditions such as inhibitory compounds within the lignocellulosic hydrolysates and slurries. We also discuss a few metabolic engineering strategies that can be applied in Z. mobilis to further develop it as a robust workhorse for economic lignocellulosic bioproducts. In addition, we briefly review the progress of metabolic engineering in Z. mobilis related to the classical synthetic biology cycle of "Design-Build-Test-Learn", as well as the progress and potential to develop Z. mobilis as a model chassis for biorefinery practices in the synthetic biology era.
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Affiliation(s)
- Xia Wang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Qiaoning He
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Yongfu Yang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Jingwen Wang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Katie Haning
- Institute for Cellular and Molecular Biology, Department of Chemical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, United States.
| | - Yun Hu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Bo Wu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, South Renmin Road, Chengdu 610041, China.
| | - Mingxiong He
- Key Laboratory of Development and Application of Rural Renewable Energy, Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, South Renmin Road, Chengdu 610041, China.
| | - Yaoping Zhang
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI, United States.
| | - Jie Bao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.
| | - Lydia M Contreras
- Institute for Cellular and Molecular Biology, Department of Chemical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, United States.
| | - Shihui Yang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
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