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Liu W, Deng Y, Li Y, Yang L, Zhu L, Jiang L. Coupling protein scaffold and biosilicification: A sustainable and recyclable approach for d-mannitol production via one-step purification and immobilization of multienzymes. Int J Biol Macromol 2024; 269:132196. [PMID: 38723818 DOI: 10.1016/j.ijbiomac.2024.132196] [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: 01/31/2024] [Revised: 04/22/2024] [Accepted: 05/06/2024] [Indexed: 05/12/2024]
Abstract
Enzymatic synthesis of biochemicals in vitro is vital in synthetic biology for its efficiency, minimal by-products, and easy product separation. However, challenges like enzyme preparation, stability, and reusability persist. Here, we introduced a protein scaffold and biosilicification coupled system, providing a singular process for the purification and immobilization of multiple enzymes. Using d-mannitol as a model, we initially constructed a self-assembling EE/KK protein scaffold for the co-immobilization of glucose dehydrogenase and mannitol dehydrogenase. Under an enzyme-to-scaffold ratio of 1:8, a d-mannitol yield of 0.692 mol/mol was achieved within 4 h, 2.16-fold higher than the free enzymes. The immobilized enzymes retained 70.9 % of the initial joint activity while the free ones diminished nearly to inactivity after 8 h. Furthermore, we incorporated the biosilicification peptide CotB into the EE/KK scaffold, inducing silica deposition, which enabled the one-step purification and immobilization process assisted by Spy/Snoop protein-peptide pairs. The coupled system demonstrated a comparable d-mannitol yield to that of EE/KK scaffold and 1.34-fold higher remaining activities after 36 h. Following 6 cycles of reaction, the immobilized system retained the capability to synthesize 56.4 % of the initial d-mannitol titer. The self-assembly co-immobilization platform offers an effective approach for enzymatic synthesis of d-mannitol and other biochemicals.
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Affiliation(s)
- Wei Liu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Yuanping Deng
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Ying Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Li Yang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Liying Zhu
- School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China.
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, Jiangsu 211816, China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China.
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2
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Hu H, Li J, Jiang W, Jiang Y, Wan Y, Wang Y, Xin F, Zhang W. Strategies for the biological synthesis of D-glucuronic acid and its derivatives. World J Microbiol Biotechnol 2024; 40:94. [PMID: 38349469 DOI: 10.1007/s11274-024-03900-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/17/2024] [Indexed: 02/15/2024]
Abstract
D-glucuronic acid is a kind of glucose derivative, which has excellent properties such as anti-oxidation, treatment of liver disease and hyperlipidemia, and has been widely used in medicine, cosmetics, food and other fields. The traditional production methods of D-glucuronic acid mainly include natural extraction and chemical synthesis, which can no longer meet the growing market demand. The production of D-glucuronic acid by biocatalysis has become a promising alternative method because of its high efficiency and environmental friendliness. This review describes different production methods of D-glucuronic acid, including single enzyme catalysis, multi-enzyme cascade, whole cell catalysis and co-culture, as well as the intervention of some special catalysts. In addition, some feasible enzyme engineering strategies are provided, including the application of enzyme immobilized scaffold, enzyme mutation and high-throughput screening, which provide good ideas for the research of D-glucuronic acid biocatalysis.
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Affiliation(s)
- Haibo Hu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Jiawen Li
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Wankui Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Yidong Wan
- Jiangsu Biochemical Chiral Engineering Technology Research Center, Changmao Biochemical Engineering Co., Ltd, Changzhou, 213034, People's Republic of China
| | - Yanxia Wang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211800, People's Republic of China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China.
- Jiangsu Biochemical Chiral Engineering Technology Research Center, Changmao Biochemical Engineering Co., Ltd, Changzhou, 213034, People's Republic of China.
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China.
- Jiangsu Biochemical Chiral Engineering Technology Research Center, Changmao Biochemical Engineering Co., Ltd, Changzhou, 213034, People's Republic of China.
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Yang L, Choi CHJ, Wang J, Xia J, Zhang L, Ngai T, Zi Y, Huang Z. Celebrating 60 Years of The Chinese University of Hong Kong: Research Highlights in Nanoscience and Nanotechnology. ACS NANO 2024; 18:4-13. [PMID: 38112319 DOI: 10.1021/acsnano.3c11732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Recent breakthroughs and advances in nanoscience and nanotechnology have profoundly impacted young-generation education, accelerated knowledge transfer to enhance the quality of life, and improved environmental and economic sustainability. The Chinese University of Hong Kong (CUHK), a globally recognized education and research institute, has played a crucial role in promoting major strategic research directions in nanoscience, including translational biomedicine and information and automation technology, as well as environment and sustainability. To celebrate the 60th Anniversary of CUHK, we present this Virtual Issue that showcases the cutting-edge research at CUHK published in ACS Nano.
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Affiliation(s)
- Lin Yang
- The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, People's Republic of China
| | - Chung Hang Jonathan Choi
- The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, People's Republic of China
| | - Jianfang Wang
- The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, People's Republic of China
| | - Jiang Xia
- The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, People's Republic of China
| | - Li Zhang
- The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, People's Republic of China
| | - To Ngai
- The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, People's Republic of China
| | - Yunlong Zi
- The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, People's Republic of China
| | - Zhifeng Huang
- The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, People's Republic of China
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4
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Zhang M, Luo M, Chen G, Guo H, Zhao J. Study on the properties of a dual-system-based protein scaffold for orthogonal self-assembly. Int J Biol Macromol 2024; 256:127946. [PMID: 37977451 DOI: 10.1016/j.ijbiomac.2023.127946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/06/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023]
Abstract
Protein scaffolds possessing the ability to efficiently organize enzymes to improve the catalytic performance, enzyme stability and provide an optimal micro-environment for biocatalysis. Here, SpyCatcher fused to the C-terminus of Treptavidin (a variant of streptavidin) to construct a chimeric tetramers protein scaffold (Tr-SC) with dual orthogonal conjugation moieties. The results showed that the expressed Tr-SC scaffold was an active tetramer with good stability under 80 °C and pH 6.5-8.5, which could bind 4 SpyTag-mCherry and 4 Biotin-EGFP. Tr-SC scaffold can bind 1-4 ligands alone under different conditions. The order in which protein scaffolds bind to proteins has little effect on the final complex structure. It is more difficult for SpyTag-mCherry than Biotin-EGFP to bind to Tr-SC, so incomplete conjugates of a hexameric complex composed of 2 SpyTag-mCherry and 4 Biotin-EGFP form when the molar ratio of scaffold and two ligands is 1:4:4. Therefore, it was suggest that the Tr-SC can first bind to excess SpyTag-protein and mixed with Biotin-protein to promote the formation of higher multimers. The results can be important reference for more extensive use of Tr-SC to construct heterologous protein polymers and assembly of heterologous enzyme molecular machine in vitro to carry on efficient cascade reaction in the future.
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Affiliation(s)
- Meng Zhang
- Department of Bioengineering and Biotechnology, Huaqiao University, Jimei Ave. 668, Xiamen 361021, China
| | - Mianxing Luo
- Department of Bioengineering and Biotechnology, Huaqiao University, Jimei Ave. 668, Xiamen 361021, China
| | - Guo Chen
- Department of Bioengineering and Biotechnology, Huaqiao University, Jimei Ave. 668, Xiamen 361021, China.
| | - Hongwei Guo
- Department of Bioengineering and Biotechnology, Huaqiao University, Jimei Ave. 668, Xiamen 361021, China
| | - Jun Zhao
- Department of Bioengineering and Biotechnology, Huaqiao University, Jimei Ave. 668, Xiamen 361021, China
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Chen Z, Wu T, Yu S, Li M, Fan X, Huo YX. Self-assembly systems to troubleshoot metabolic engineering challenges. Trends Biotechnol 2024; 42:43-60. [PMID: 37451946 DOI: 10.1016/j.tibtech.2023.06.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/18/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023]
Abstract
Enzyme self-assembly is a technology in which enzyme units can aggregate into ordered macromolecules, assisted by scaffolds. In metabolic engineering, self-assembly strategies have been explored for aggregating multiple enzymes in the same pathway to improve sequential catalytic efficiency, which in turn enables high-level production. The performance of the scaffolds is critical to the formation of an efficient and stable assembly system. This review comprehensively analyzes these scaffolds by exploring how they assemble, and it illustrates how to apply self-assembly strategies for different modules in metabolic engineering. Functional modifications to scaffolds will further promote efficient strategies for production.
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Affiliation(s)
- Zhenya Chen
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Tong Wu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Shengzhu Yu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Min Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Xuanhe Fan
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China.
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6
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Kim JE, Kang JH, Kwon WH, Lee I, Park SJ, Kim CH, Jeong WJ, Choi JS, Kim K. Self-assembling biomolecules for biosensor applications. Biomater Res 2023; 27:127. [PMID: 38053161 PMCID: PMC10696764 DOI: 10.1186/s40824-023-00466-8] [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: 10/01/2023] [Accepted: 11/22/2023] [Indexed: 12/07/2023] Open
Abstract
Molecular self-assembly has received considerable attention in biomedical fields as a simple and effective method for developing biomolecular nanostructures. Self-assembled nanostructures can exhibit high binding affinity and selectivity by displaying multiple ligands/receptors on their surface. In addition, the use of supramolecular structure change upon binding is an intriguing approach to generate binding signal. Therefore, many self-assembled nanostructure-based biosensors have been developed over the past decades, using various biomolecules (e.g., peptides, DNA, RNA, lipids) and their combinations with non-biological substances. In this review, we provide an overview of recent developments in the design and fabrication of self-assembling biomolecules for biosensing. Furthermore, we discuss representative electrochemical biosensing platforms which convert the biochemical reactions of those biomolecules into electrical signals (e.g., voltage, ampere, potential difference, impedance) to contribute to detect targets. This paper also highlights the successful outcomes of self-assembling biomolecules in biosensor applications and discusses the challenges that this promising technology needs to overcome for more widespread use.
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Affiliation(s)
- Ji-Eun Kim
- Department of Chemical & Biochemical Engineering, Dongguk University, Seoul, 04620, Republic of Korea
| | - Jeon Hyeong Kang
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
| | - Woo Hyun Kwon
- Laboratory of Tissue Engineering, Korea Institute of Radiological and Medical Sciences, Seoul, 01812, Republic of Korea
- Department of Materials Science and Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Inseo Lee
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
| | - Sang Jun Park
- Laboratory of Tissue Engineering, Korea Institute of Radiological and Medical Sciences, Seoul, 01812, Republic of Korea
| | - Chun-Ho Kim
- Laboratory of Tissue Engineering, Korea Institute of Radiological and Medical Sciences, Seoul, 01812, Republic of Korea
| | - Woo-Jin Jeong
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea.
- Department of Biological Engineering, Inha University, Incheon, 22212, Republic of Korea.
| | - Jun Shik Choi
- Laboratory of Tissue Engineering, Korea Institute of Radiological and Medical Sciences, Seoul, 01812, Republic of Korea.
| | - Kyobum Kim
- Department of Chemical & Biochemical Engineering, Dongguk University, Seoul, 04620, Republic of Korea.
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7
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Guo Y, Li Q, Ji D, Tian L, Meurer J, Chi W. A Ubiquitin-Based Module Directing Protein-Protein Interactions in Chloroplasts. Int J Mol Sci 2023; 24:16673. [PMID: 38068997 PMCID: PMC10706609 DOI: 10.3390/ijms242316673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/18/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
A promising approach for the genetic engineering of multiprotein complexes in living cells involves designing and reconstructing the interaction between two proteins that lack native affinity. Thylakoid-embedded multiprotein complexes execute the light reaction of plant photosynthesis, but their engineering remains challenging, likely due to difficulties in accurately targeting heterologous membrane-bound proteins to various sub-compartments of thylakoids. In this study, we developed a ubiquitin-based module (Nub-Cub) capable of directing interactions in vivo between two chloroplast proteins lacking native affinities. We applied this module to genetically modify thylakoid multiprotein complexes. We demonstrated the functionality of the Nub-Cub module in the model organism Arabidopsis thaliana. Employing this system, we successfully modified the Photosystem II (PSII) complex by ectopically attaching an extrinsic subunit of PSII, PsbTn1, to CP26-a component of the antenna system of PSII. Surprisingly, this mandatory interaction between CP26 and PsbTn1 in plants impairs the efficiency of electron transport in PSII and unexpectedly results in noticeable defects in leaf development. Our study not only offers a general strategy to modify multiprotein complexes embedded in thylakoid membranes but it also sheds light on the possible interplay between two proteins without native interaction.
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Affiliation(s)
- Yinjie Guo
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (Y.G.); (Q.L.); (D.J.); (L.T.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiuxin Li
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (Y.G.); (Q.L.); (D.J.); (L.T.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Daili Ji
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (Y.G.); (Q.L.); (D.J.); (L.T.)
| | - Lijin Tian
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (Y.G.); (Q.L.); (D.J.); (L.T.)
| | - Jörg Meurer
- Faculty of Biology, Plant Molecular Biology, Ludwig-Maximilians University, D-82152 Munich, Germany;
| | - Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (Y.G.); (Q.L.); (D.J.); (L.T.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
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8
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Liu M, Song Y, Zhang YHPJ, You C. Carrier-Free Immobilization of Multi-Enzyme Complex Facilitates In Vitro Synthetic Enzymatic Biosystem for Biomanufacturing. CHEMSUSCHEM 2023; 16:e202202153. [PMID: 36538347 DOI: 10.1002/cssc.202202153] [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: 11/17/2022] [Revised: 12/20/2022] [Indexed: 06/17/2023]
Abstract
A method is developed for carrier-free immobilization of multi-enzyme complexes with more than four enzymes by utilization of polypeptide interactions (SpyCatcher-SpyTag and dockerin-cohesin) and enzyme component self-oligomerization. Two pairs of scaffoldins with different arrangements of SpyCatcher-SpyTag and cohesins are prepared to recruit the four dockerin-containing cascade enzymes (i. e., alpha-glucan phosphorylase, phosphoglucomutase, inositol 1-phosphate synthase, and inositol 1-phosphatase) that can convert starch into inositol, forming multi-enzyme complexes. These self-assembled enzyme complexes show higher initial reaction rates than the four-enzyme cocktail. Moreover, water-insoluble self-assembled multi-enzyme complexes are observed, being the carrier-free immobilized multi-enzyme complex aggregates. These immobilized enzyme complexes can be recycled easily by simple centrifuging followed by resuspension for another round of reaction. Not only can these immobilized enzyme complexes be obtained by mixing the purified enzyme components, but also by the mixing of crude cell extracts. Therefore, the strategy for the carrier-free immobilization of enzyme complex sheds light on improving the catalytic capability of in vitro synthetic enzymatic biosystems.
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Affiliation(s)
- Miaomiao Liu
- Department of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230022, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
| | - Yunhong Song
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
| | - Yi-Heng P Job Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, People's Republic of China
| | - Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, People's Republic of China
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Liu M, Wang Y, Jiang H, Han Y, Xia J. Synthetic Multienzyme Assemblies for Natural Product Biosynthesis. Chembiochem 2023; 24:e202200518. [PMID: 36625563 DOI: 10.1002/cbic.202200518] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/11/2023]
Abstract
In nature, enzymes that catalyze sequential reactions are often assembled as clusters or complexes. The formation of multienzyme complexes, or metabolons, brings the enzyme active sites into proximity to promote intermediate transfer, decrease intermediate leakage, and streamline the metabolic flux towards the desired products. We and others have developed synthetic versions of metabolons through various strategies to enhance the catalytic rates for synthesizing valuable chemicals inside microbes. Synthetic multienzyme complexes range from static enzyme nanostructures to dynamic enzyme coacervates. Enzyme complexation optimizes the metabolic fluxes inside microbes, increases the product titer, and supplies the field with high-yield microbe strains that are amenable to large-scale fermentation. Enzyme complexes constructed inside microbial cells can be separated as independent entities and catalyze biosynthetic reactions ex vivo; such a feature gains these complexes another name, "synthetic organelles" - new subcellular entities with independent structures and functions. Still, the field is seeking new strategies to better balance dynamicity and confinement and to achieve finer control of local compartmentalization in the cells, as the natural multienzyme complexes do. Industrial applications of synthetic multienzyme complexes for the large-scale production of valuable chemicals are yet to be realized. This review focuses on synthetic multienzyme complexes that are constructed and function inside microbial cells.
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Affiliation(s)
- Min Liu
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yue Wang
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Hao Jiang
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yongxu Han
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Jiang Xia
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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10
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Huang S, Ba F, Liu WQ, Li J. Stapled NRPS enhances the production of valinomycin in Escherichia coli. Biotechnol Bioeng 2023; 120:793-802. [PMID: 36510694 DOI: 10.1002/bit.28303] [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: 10/14/2022] [Revised: 12/06/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022]
Abstract
Nonribosomal peptides (NRPs) are a large family of secondary metabolites with notable bioactivities, which distribute widely in natural resources across microbes and plants. To obtain these molecules, heterologous production of NRPs in robust surrogate hosts like Escherichia coli represent a feasible approach. However, reconstitution of the full biosynthetic pathway in a host often leads to low productivity, which is at least in part due to the low efficiency of enzyme interaction in vivo except for the well-known reasons of metabolic burden (e.g., expression of large NRP synthetases-NRPSs with molecular weights of >100 kDa) and cellular toxicity on host cells. To enhance the catalytic efficiency of large NRPSs in vivo, here we propose to staple NRPS enzymes by using short peptide/protein pairs (e.g., SpyTag/SpyCatcher) for enhanced NRP production. We achieve this goal by introducing a stapled NRPS system for the biosynthesis of the antibiotic NRP valinomycin in E. coli. The results indicate that stapled valinomycin synthetase (Vlm1 and Vlm2) enables higher product accumulation than those two free enzymes (e.g., the maximum improvement is nearly fourfold). After further optimization by strain and bioprocess engineering, the final valinomycin titer maximally reaches about 2800 µg/L, which is 73 times higher than the initial titer of 38 µg/L. We expect that stapling NRPS enzymes will be a promising catalytic strategy for high-level biosynthesis of NRP natural products.
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Affiliation(s)
- Shuhui Huang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Fang Ba
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Wan-Qiu Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
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11
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Chen R, Wan L, Zhu Y, Liu Y, Zhang W, Mu W. Spatial organization of pathway enzymes via self-assembly to improve 2'-fucosyllactose biosynthesis in engineered Escherichia coli. Biotechnol Bioeng 2023; 120:524-535. [PMID: 36326175 DOI: 10.1002/bit.28279] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 10/22/2022] [Accepted: 10/30/2022] [Indexed: 11/05/2022]
Abstract
As one of the most abundant components in human milk oligosaccharides, 2'-fucosyllactose (2'-FL) possesses versatile beneficial health effects. Although most studies focused on overexpressing or fine-tuning the expression of pathway enzymes and achieved a striking increase of 2'-FL production, directly facilitating the metabolic flux toward the key intermediate GDP-l-fucose seems to be ignored. Here, multienzyme complexes consisting of sequential pathway enzymes were constructed by using specific peptide interaction motifs in recombinant Escherichia coli to achieve a higher titer of 2'-FL. Specifically, we first fine-tuned the expression level of pathway enzymes and balanced the metabolic flux toward 2'-FL synthesis. Then, two key enzymes (GDP-mannose 4,6-dehydratase and GDP- l-fucose synthase) were self-assembled into enzyme complexes in vivo via a short peptide interaction pair RIAD-RIDD (RI anchoring disruptor-RI dimer D/D domains), resulting in noticeable improvement of 2'-FL production. Next, to further strengthen the metabolic flux toward 2'-FL, three pathway enzymes were further aggregated into multienzyme assemblies by using another orthogonal protein interaction motif (Spycatcher-SpyTag or PDZ-PDZlig). Intracellular multienzyme assemblies remarkably enlarged the flux toward 2'-FL biosynthesis and showed a 2.1-fold increase of 2'-FL production compared with a strain expressing free-floating and unassembled enzymes. The optimally engineered strain EZJ23 accumulated 4.8 g/L 2'-FL in shake flask fermentation and was capable of producing 25.1 g/L 2'-FL by fed-batch cultivation. This work provides novel approaches for further improvement and large-scale production of 2'-FL and demonstrates the effectiveness of spatial assembly of pathway enzymes to improve the production of valuable products in the engineered host strain.
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Affiliation(s)
- Roulin Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Li Wan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yuanlin Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
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12
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Construction of Bi-Enzyme Self-Assembly Clusters Based on SpyCatcher/SpyTag for the Efficient Biosynthesis of (R)-Ethyl 2-hydroxy-4-phenylbutyrate. Biomolecules 2023; 13:biom13010091. [PMID: 36671476 PMCID: PMC9855569 DOI: 10.3390/biom13010091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
Cascade reactions catalyzed by multi-enzyme systems are important in science and industry and can be used to synthesize drugs and nutrients. In this study, two types of macromolecules of bi-enzyme self-assembly clusters (BESCs) consisting of carbonyl reductase (CpCR) and glucose dehydrogenase (GDH) were examined. Stereoselective CpCR and GDH were successfully fused with SpyCatcher and SpyTag, respectively, to obtain four enzyme modules, namely: SpyCatcher-CpCR, SpyCatcher-GDH, SpyTag-CpCR, and SpyTag-GDH, which were covalently coupled in vitro to form two types of hydrogel-like BESCs: CpCR-SpyCatcher-SpyTag-GDH and GDH-SpyCatcher-SpyTag-CpCR. CpCR-SpyCatcher-SpyTag-GDH showed a better activity and efficiently converted ethyl 2-oxo-4-phenylbutyrate (OPBE) to ethyl(R)2-hydroxy-4-phenylbutanoate ((R)-HPBE), while regenerating NADPH. At 30 °C and pH 7, the conversion rate of OPBE with CpCR-SpyCatcher-SpyTag-GDH as a catalyst reached 99.9%, with the ee% of (R)-HPBE reaching above 99.9%. This conversion rate was 2.4 times higher than that obtained with the free bi-enzyme. The pH tolerance and temperature stability of the BESCs were also improved compared with those of the free enzymes. In conclusion, bi-enzyme assemblies were docked using SpyCatcher/SpyTag to produce BESCs with a special structure and excellent catalytic activity, improving the catalytic efficiency of the enzyme.
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13
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Chen Z, Yue Z, Yang K, Li S. Nanomaterials: small particles show huge possibilities for cancer immunotherapy. J Nanobiotechnology 2022; 20:484. [DOI: 10.1186/s12951-022-01692-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/27/2022] [Indexed: 11/17/2022] Open
Abstract
AbstractWith the economy's globalization and the population's aging, cancer has become the leading cause of death in most countries. While imposing a considerable burden on society, the high morbidity and mortality rates have continuously prompted researchers to develop new oncology treatment options. Anti-tumor regimens have evolved from early single surgical treatment to combined (or not) chemoradiotherapy and then to the current stage of tumor immunotherapy. Tumor immunotherapy has undoubtedly pulled some patients back from the death. However, this strategy of activating or boosting the body's immune system hardly benefits most patients. It is limited by low bioavailability, low response rate and severe side effects. Thankfully, the rapid development of nanotechnology has broken through the bottleneck problem of anti-tumor immunotherapy. Multifunctional nanomaterials can not only kill tumors by combining anti-tumor drugs but also can be designed to enhance the body's immunity and thus achieve a multi-treatment effect. It is worth noting that the variety of nanomaterials, their modifiability, and the diversity of combinations allow them to shine in antitumor immunotherapy. In this paper, several nanobiotics commonly used in tumor immunotherapy at this stage are discussed, and they activate or enhance the body's immunity with their unique advantages. In conclusion, we reviewed recent advances in tumor immunotherapy based on nanomaterials, such as biological cell membrane modification, self-assembly, mesoporous, metal and hydrogels, to explore new directions and strategies for tumor immunotherapy.
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14
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Li L, Chen G. Precise Assembly of Proteins and Carbohydrates for Next-Generation Biomaterials. J Am Chem Soc 2022; 144:16232-16251. [PMID: 36044681 DOI: 10.1021/jacs.2c04418] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The complexity and diversity of biomacromolecules make them a unique class of building blocks for generating precise assemblies. They are particularly available to a new generation of biomaterials integrated with living systems due to their intrinsic properties such as accurate recognition, self-organization, and adaptability. Therefore, many excellent approaches have been developed, leading to a variety of quite practical outcomes. Here, we review recent advances in the fabrication and application of artificially precise assemblies by employing proteins and carbohydrates as building blocks, followed by our perspectives on some of new challenges, goals, and opportunities for the future research directions in this field.
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Affiliation(s)
- Long Li
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, People's Republic of China
| | - Guosong Chen
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, People's Republic of China.,Multiscale Research Institute for Complex Systems, Fudan University, Shanghai 200433, People's Republic of China
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15
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Chen Y, Ming D, Zhu L, Huang H, Jiang L. Tailoring the Tag/Catcher System by Integrating Covalent Bonds and Noncovalent Interactions for Highly Efficient Protein Self-Assembly. Biomacromolecules 2022; 23:3936-3947. [PMID: 35998650 DOI: 10.1021/acs.biomac.2c00765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Covalent bonds and noncovalent interactions play crucial roles in enzyme self-assembly. Here, we designed a Tag/Catcher system named NGTag/NGCatcher in which the Catcher is a highly charged protein that can bind proteins with positively charged tails and rapidly form a stable isopeptide bond with NGTag. In this study, we present a multienzyme strategy based on covalent bonds and noncovalent interactions. In vitro, mCherry, YFP, and GFP can form protein-rich three-dimensional networks based on NGCatcher, NGTag, and RK (Arginine/Lysine) tails, respectively. Furthermore, this technology was applied to improve lycopene production in Escherichia coli. Three key enzymes were involved in lycopene production variants from Deinococcus wulumuqiensis R12 of NGCatcher_CrtE, NGTag_Idi, and RKIspARK, where the multienzyme complexes were clearly observed in vivo and in vitro, and the lycopene production in vivo was 17.8-fold higher than that in the control group. The NGTag/NGCatcher system will provide new opportunities for in vivo and in vitro multienzyme catalysis.
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Affiliation(s)
- Yao Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China.,College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Dengming Ming
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Liying Zhu
- School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - He Huang
- College of Pharmaceutical Science, Nanjing Tech University, Nanjing 211816, China.,School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Ling Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
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16
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Li Y, Wang J, Huang F, Zhang Y, Zheng M. DNA-directed coimmobilization of multiple enzymes on organic−inorganic hybrid DNA flowers. Front Bioeng Biotechnol 2022; 10:951394. [PMID: 36032715 PMCID: PMC9400012 DOI: 10.3389/fbioe.2022.951394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
The artificial multienzyme systems developed by mimicking nature has attracted much interest. However, precisely controlled compositions and ratios of multienzymatic co-immobilization systems are still limited by the indistinguishable nature of enzymes. Herein, a strategy for fabricating DNA-directed immobilization of horseradish peroxidase (HRP) and glucose oxidase (GOx) on hybrid DNA nanoflowers (GOx-HRP@hDFs) is presented. The preparation of micron-sized hybrid DNA flowers (hDFs) begins with the predetermined repeatable polymer-like DNA sequences which contained two strands. The hDFs structure is generated through one-pot rolling circle amplification (RCA) and self-assembly with magnesium pyrophosphate inorganic crystals. Based on the rigid-base pairing, GOx and HRP conjugated with sequences complementary to strands would be anchored to the predesigned locations, respectively. By adjusting the loading amount/ratio of enzymes properly, the maximal catalytic efficiency can be precisely regulated. The reaction activity of GOx-HRP@hDFs was 7.4 times higher than that of the free GOx-HRP under the optimal mole ratio (GOx/HRP 4:1). In addition, this multienzyme catalyst system exhibits excellent precision, specificity, reproducibility, and long-term storage stability when applied to real human blood samples. The preceding results validate that GOx-HRP@hDFs are promising candidates for personal diabetes detection.
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Affiliation(s)
- Yali Li
- Insititute of Food & Nutrition Science and Technology, Shandong Academy of Agricultural Sciences, Jinan, China
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Key Laboratory of Oilseeds Processing, Ministry of Agriculture, Wuhan, China
| | - Jing Wang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Key Laboratory of Oilseeds Processing, Ministry of Agriculture, Wuhan, China
| | - Fenghong Huang
- Insititute of Food & Nutrition Science and Technology, Shandong Academy of Agricultural Sciences, Jinan, China
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Key Laboratory of Oilseeds Processing, Ministry of Agriculture, Wuhan, China
- *Correspondence: Fenghong Huang, ; Yufei Zhang, ; Mingming Zheng,
| | - Yufei Zhang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Key Laboratory of Oilseeds Processing, Ministry of Agriculture, Wuhan, China
- *Correspondence: Fenghong Huang, ; Yufei Zhang, ; Mingming Zheng,
| | - Mingming Zheng
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Key Laboratory of Oilseeds Processing, Ministry of Agriculture, Wuhan, China
- *Correspondence: Fenghong Huang, ; Yufei Zhang, ; Mingming Zheng,
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17
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Wang Y, Liu M, Wei Q, Wu W, He Y, Gao J, Zhou R, Jiang L, Qu J, Xia J. Phase-Separated Multienzyme Compartmentalization for Terpene Biosynthesis in a Prokaryote. Angew Chem Int Ed Engl 2022; 61:e202203909. [PMID: 35562330 DOI: 10.1002/anie.202203909] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Indexed: 01/18/2023]
Abstract
Liquid-liquid phase separation (LLPS) forms biomolecular condensates or coacervates in cells. Metabolic enzymes can form phase-separated subcellular compartments that enrich enzymes, cofactors, and substrates. Herein, we report the construction of synthetic multienzyme condensates that catalyze the biosynthesis of a terpene, α-farnesene, in the prokaryote E. coli. RGGRGG derived from LAF-1 was used as the scaffold protein to form the condensates by LLPS. Multienzyme condensates were then formed by assembling two enzymes Idi and IspA through an RIAD/RIDD interaction. Multienzyme condensates constructed inside E. coli cells compartmentalized the cytosolic space into regions of high and low enzyme density and led to a significant enhancement of α-farnesene production. This work demonstrates LLPS-driven compartmentalization of the cytosolic space of prokaryotic cells, condensation of a biosynthetic pathway, and enhancement of the biosynthesis of α-farnesene.
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Affiliation(s)
- Yue Wang
- Department of Chemistry and Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Min Liu
- Department of Chemistry and Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Qixin Wei
- Department of Chemistry and Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Wanjie Wu
- Departments of Electronic and Computer Engineering, Center of Systems Biology and Human Health, School of Science and Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Yanping He
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Jiayang Gao
- Center for Cell & Developmental Biology, School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Renjie Zhou
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Liwen Jiang
- Center for Cell & Developmental Biology, School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Jianan Qu
- Departments of Electronic and Computer Engineering, Center of Systems Biology and Human Health, School of Science and Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Jiang Xia
- Department of Chemistry and Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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18
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Lam NT, McCluskey JB, Glover DJ. Harnessing the Structural and Functional Diversity of Protein Filaments as Biomaterial Scaffolds. ACS APPLIED BIO MATERIALS 2022; 5:4668-4686. [PMID: 35766918 DOI: 10.1021/acsabm.2c00275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The natural ability of many proteins to polymerize into highly structured filaments has been harnessed as scaffolds to align functional molecules in a diverse range of biomaterials. Protein-engineering methodologies also enable the structural and physical properties of filaments to be tailored for specific biomaterial applications through genetic engineering or filaments built from the ground up using advances in the computational prediction of protein folding and assembly. Using these approaches, protein filament-based biomaterials have been engineered to accelerate enzymatic catalysis, provide routes for the biomineralization of inorganic materials, facilitate energy production and transfer, and provide support for mammalian cells for tissue engineering. In this review, we describe how the unique structural and functional diversity in natural and computationally designed protein filaments can be harnessed in biomaterials. In addition, we detail applications of these protein assemblies as material scaffolds with a particular emphasis on applications that exploit unique properties of specific filaments. Through the diversity of protein filaments, the biomaterial engineer's toolbox contains many modular protein filaments that will likely be incorporated as the main structural component of future biomaterials.
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Affiliation(s)
- Nga T Lam
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Joshua B McCluskey
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Dominic J Glover
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
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19
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Zeng R, Lv C, Zang J, Zhang T, Zhao G. Designing Stacked Assembly of Type III Rubisco for CO 2 Fixation with Higher Efficiency. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:7049-7057. [PMID: 35670363 DOI: 10.1021/acs.jafc.2c02521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The slow catalytic rate of the carboxylation enzyme d-ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is a major barrier to increasing the rate of carbon assimilation from the atmosphere into the biosphere. It is of great importance to establish a method to improve the carboxylation efficiency of Rubisco. Inspired by the assembly of Rubisco in carboxysomes, herein, we presented a rational protein engineering approach for the construction of one-dimensional (1D) protein arrays of type III Rubisco through designed π-π stacking interactions by using crystal structural information as a guide. In aqueous solutions, the dimensions of these 1D protein arrays collectively span nearly the entire nano- and micrometer scale (200 nm to 5.0 μm) by adjusting protein and NaCl concentrations. As a result, the stacked Rubisco assemblies increase by 40% in the carboxylase activity, while their turnover number (kcat) is around twofold larger than that of wild-type III Rubisco. Notably, upon heat treatment at temperature up to 75 °C for 30 min, most of the assembled nanostructures and the enzyme activity are retained. More importantly, the initial relative activity of stacked assemblies retained 91% after 10 cycles of reuse. This work provides a simple, effective solution for the improvement of the CO2 carboxylation efficiency of Rubisco.
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Affiliation(s)
- Ruiqi Zeng
- College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, China
| | - Chenyan Lv
- College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, China
| | - Jiachen Zang
- College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, China
| | - Tuo Zhang
- College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, China
| | - Guanghua Zhao
- College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, China
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20
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Shin CH, Park SC, Park IG, Kim H, An B, Lee C, Kim SH, Lee J, Lee JM, Oh SJ. Cytosolic microRNA-inducible nuclear translocation of Cas9 protein for disease-specific genome modification. Nucleic Acids Res 2022; 50:5919-5933. [PMID: 35640600 PMCID: PMC9177975 DOI: 10.1093/nar/gkac431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 05/03/2022] [Accepted: 05/10/2022] [Indexed: 11/13/2022] Open
Abstract
MicroRNA-dependent mRNA decay plays an important role in gene silencing by facilitating posttranscriptional and translational repression. Inspired by this intrinsic nature of microRNA-mediated mRNA cleavage, here, we describe a microRNA-targeting mRNA as a switch platform called mRNA bridge mimetics to regulate the translocation of proteins. We applied the mRNA bridge mimetics platform to Cas9 protein to confer it the ability to translocate into the nucleus via cleavage of the nuclear export signal. This system performed programmed gene editing in vitro and in vivo. Combinatorial treatment with cisplatin and miR-21-EZH2 axis-targeting CRISPR Self Check-In improved sensitivity to chemotherapeutic drugs in vivo. Using the endogenous microRNA-mediated mRNA decay mechanism, our platform is able to remodel a cell's natural biology to allow the entry of precise drugs into the nucleus, devoid of non-specific translocation. The mRNA bridge mimetics strategy is promising for applications in which the reaction must be controlled via intracellular stimuli and modulates Cas9 proteins to ensure safe genome modification in diseased conditions.
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Affiliation(s)
- Cheol-Hee Shin
- Center for Biomaterials, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Su Chan Park
- Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Il-Geun Park
- Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hyerim Kim
- Program in Nanoscience and Technology, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
| | - Byoungha An
- Center for Biomaterials, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.,Division of Bio-Medical Science & Technology, Korea University of Science and Technology (UST), Seoul, Republic of Korea
| | - Choongil Lee
- Center for Biomaterials, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Sang-Heon Kim
- Center for Biomaterials, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.,Division of Bio-Medical Science & Technology, Korea University of Science and Technology (UST), Seoul, Republic of Korea
| | - Juyong Lee
- Department of Chemistry, College of Natural Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Ji Min Lee
- Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Seung Ja Oh
- Center for Biomaterials, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.,Division of Bio-Medical Science & Technology, Korea University of Science and Technology (UST), Seoul, Republic of Korea
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21
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Wang Y, Liu M, Wei Q, Wu W, He Y, Gao J, Zhou R, Jiang L, Qu J, Xia J. Phase‐Separated Multienzyme Compartmentalization for Terpene Biosynthesis in a Prokaryote. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yue Wang
- Chinese University of Hong Kong Shaw College: The Chinese University of Hong Kong Chemistry HONG KONG
| | - Min Liu
- The Chinese University of Hong Kong Chemistry HONG KONG
| | - Qixin Wei
- The Chinese University of Hong Kong Chemistry HONG KONG
| | - Wanjie Wu
- Hong Kong University of Science and Technology School of Engineering Engineering HONG KONG
| | - Yanping He
- The Chinese University of Hong Kong Department of Biomedical Engineering HONG KONG
| | - Jiayang Gao
- The Chinese University of Hong Kong School of Life Sciences HONG KONG
| | - Renjie Zhou
- The Chinese University of Hong Kong Department of Biomedical Engineering HONG KONG
| | - Liwen Jiang
- The Chinese University of Hong Kong School of Life Sciences HONG KONG
| | - Jianan Qu
- Hong Kong University of Science and Technology School of Engineering Engineering HONG KONG
| | - Jiang Xia
- The Chinese University of Hong Kong Department of Chemistry SC G59, Department of ChemistryThe Chinese University of Hong Kong 00000 Shatin HONG KONG
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22
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Chen Z, Gao XD, Li Z. Recent Advances Regarding the Physiological Functions and Biosynthesis of D-Allulose. Front Microbiol 2022; 13:881037. [PMID: 35495640 PMCID: PMC9048046 DOI: 10.3389/fmicb.2022.881037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/11/2022] [Indexed: 01/11/2023] Open
Abstract
D-Allulose, a generally regarded as safe (GRAS) sugar, is rare in nature. It is among the most promising sweeteners for future use due to its low caloric content, sucrose-like taste, and unique functions. D-Allulose has many physiological effects, such as antiobesity, antihyperglycemia, antidiabetes, anti-inflammatory, antioxidant, and neuroprotective effects. Therefore, D-allulose has important application value in the food, pharmaceutical, and healthcare industries. However, the high cost of D-allulose production limits its large-scale application. Currently, biotransformation is very attractive for D-allulose synthesis, with the two main methods of biosynthesis being the Izumoring strategy and the DHAP-dependent aldolase strategy. This article reviews recent advances regarding the physiological functions and biosynthesis of D-allulose. In addition, future perspectives on the production of D-allulose are presented.
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Affiliation(s)
- Zhou Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zijie Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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23
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Caparco AA, Dautel DR, Champion JA. Protein Mediated Enzyme Immobilization. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2106425. [PMID: 35182030 DOI: 10.1002/smll.202106425] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/22/2021] [Indexed: 06/14/2023]
Abstract
Enzyme immobilization is an essential technology for commercializing biocatalysis. It imparts stability, recoverability, and other valuable features that improve the effectiveness of biocatalysts. While many avenues to join an enzyme to solid phases exist, protein-mediated immobilization is rapidly developing and has many advantages. Protein-mediated immobilization allows for the binding interaction to be genetically coded, can be used to create artificial multienzyme cascades, and enables modular designs that expand the variety of enzymes immobilized. By designing around binding interactions between protein domains, they can be integrated into functional materials for protein immobilization. These materials are framed within the context of biocatalytic performance, immobilization efficiency, and stability of the materials. In this review, supports composed entirely of protein are discussed first, with systems such as cellulosomes and protein cages being discussed alongside newer technologies like spore-based biocatalysts and forizymes. Protein-composite materials such as polymersomes and protein-inorganic supraparticles are then discussed to demonstrate how protein-mediated strategies are applied to many classes of solid materials. Critical analysis and future directions of protein-based immobilization are then discussed, with a particular focus on both computational and design strategies to advance this area of research and make it more broadly applicable to many classes of enzymes.
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Affiliation(s)
- Adam A Caparco
- Department of Nanoengineering, University of California, San Diego, MC 0448, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Dylan R Dautel
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 950 Atlantic Drive NW, Atlanta, GA, 30332, USA
| | - Julie A Champion
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 950 Atlantic Drive NW, Atlanta, GA, 30332, USA
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24
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Liu Y, Ba F, Liu WQ, Wu C, Li J. Plug-and-Play Functionalization of Protein–Polymer Conjugates for Tunable Catalysis Enabled by Genetically Encoded “Click” Chemistry. ACS Catal 2022. [DOI: 10.1021/acscatal.2c00846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yushi Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Fang Ba
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wan-Qiu Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Changzhu Wu
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
- Danish Institute for Advanced Study (DIAS), University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
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25
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Huang J, Ding Y, Yao J, Zhang M, Zhang Y, Xie Z, Zuo J. Nasal Nanovaccines for SARS-CoV-2 to Address COVID-19. Vaccines (Basel) 2022; 10:vaccines10030405. [PMID: 35335037 PMCID: PMC8952855 DOI: 10.3390/vaccines10030405] [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: 11/02/2021] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 02/06/2023] Open
Abstract
COVID-19 is still prevalent around the globe. Although some SARS-CoV-2 vaccines have been distributed to the population, the shortcomings of vaccines and the continuous emergence of SARS-CoV-2 mutant virus strains are a cause for concern. Thus, it is vital to continue to improve vaccines and vaccine delivery methods. One option is nasal vaccination, which is more convenient than injections and does not require a syringe. Additionally, stronger mucosal immunity is produced under nasal vaccination. The easy accessibility of the intranasal route is more advantageous than injection in the context of the COVID-19 pandemic. Nanoparticles have been proven to be suitable delivery vehicles and adjuvants, and different NPs have different advantages. The shortcomings of the SARS-CoV-2 vaccine may be compensated by selecting or modifying different nanoparticles. It travels along the digestive tract to the intestine, where it is presented by GALT, tissue-resident immune cells, and gastrointestinal lymph nodes. Nasal nanovaccines are easy to use, safe, multifunctional, and can be distributed quickly, demonstrating strong prospects as a vaccination method for SARS-CoV-2, SARS-CoV-2 variants, or SARS-CoV-n.
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Affiliation(s)
- Jialu Huang
- The Laboratory of Translational Medicine, Hengyang Medical School, University of South China, Hengyang 421001, China; (J.H.); (M.Z.); (Y.Z.); (Z.X.)
| | - Yubo Ding
- Nanhua Hospital Affiliated to University of South China, Hengyang Medical School, University of South China, Hengyang 421002, China; (Y.D.); (J.Y.)
| | - Jingwei Yao
- Nanhua Hospital Affiliated to University of South China, Hengyang Medical School, University of South China, Hengyang 421002, China; (Y.D.); (J.Y.)
| | - Minghui Zhang
- The Laboratory of Translational Medicine, Hengyang Medical School, University of South China, Hengyang 421001, China; (J.H.); (M.Z.); (Y.Z.); (Z.X.)
| | - Yu Zhang
- The Laboratory of Translational Medicine, Hengyang Medical School, University of South China, Hengyang 421001, China; (J.H.); (M.Z.); (Y.Z.); (Z.X.)
| | - Zhuoyi Xie
- The Laboratory of Translational Medicine, Hengyang Medical School, University of South China, Hengyang 421001, China; (J.H.); (M.Z.); (Y.Z.); (Z.X.)
| | - Jianhong Zuo
- The Laboratory of Translational Medicine, Hengyang Medical School, University of South China, Hengyang 421001, China; (J.H.); (M.Z.); (Y.Z.); (Z.X.)
- Nanhua Hospital Affiliated to University of South China, Hengyang Medical School, University of South China, Hengyang 421002, China; (Y.D.); (J.Y.)
- The Third Affiliated Hospital of University of South China, Hengyang Medical School, University of South China, Hengyang 421900, China
- Correspondence: ; Tel.: +86-7345-675219
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26
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Sun Q, Heater BS, Li TL, Ye W, Guo Z, Chan MK. Cry3Aa*SpyCatcher Fusion Crystals Produced in Bacteria as Scaffolds for Multienzyme Coimmobilization. Bioconjug Chem 2022; 33:386-396. [PMID: 35100510 DOI: 10.1021/acs.bioconjchem.2c00003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The production of Cry3Aa enzyme fusion crystals in Bacillus thuringiensis provides a direct method to immobilize individual enzymes and thereby improve their stability and recyclability. Nevertheless, many reactions require multiple enzymes to produce a desired product; thus a general strategy was developed to extend our Cry3Aa technology to multienzyme coimmobilization. Here, we report the direct production of particles comprising a modified Cry3Aa (Cry3Aa*) fused to SpyCatcher002 (Cry3Aa*SpyCat2) for coimmobilization of model enzymes MenF, MenD, and MenH associated with the biosynthesis of menaquinone. The resultant coimmobilized particles showed improved reaction rates compared to free enzymes presumably due to the higher local enzyme substrate concentrations and enhanced enzyme coupling made possible by colocalization. Furthermore, coimmobilization of these enzymes on Cry3Aa*SpyCat2 led to increased thermal stability and recyclability of the overall multienzyme system. These characteristics together with its overall simplicity of production highlight the benefits of Cry3Aa*SpyCat2 crystals as a platform for enzyme coimmobilization.
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Affiliation(s)
- Qian Sun
- School of Life Sciences and Center of Novel Biomaterials, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Bradley S Heater
- School of Life Sciences and Center of Novel Biomaterials, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Tin Lok Li
- Hong Kong Branch of Guangdong Southern Marine Science and Engineering Laboratory (Guangzhou), Shenzhen Research Institute and Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Weijian Ye
- Hong Kong Branch of Guangdong Southern Marine Science and Engineering Laboratory (Guangzhou), Shenzhen Research Institute and Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Zhihong Guo
- Hong Kong Branch of Guangdong Southern Marine Science and Engineering Laboratory (Guangzhou), Shenzhen Research Institute and Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Michael K Chan
- School of Life Sciences and Center of Novel Biomaterials, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
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27
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Zhou C, Feng J, Wang J, Hao N, Wang X, Chen K. Design of an in vitro multienzyme cascade system for the biosynthesis of nicotinamide mononucleotide. Catal Sci Technol 2022. [DOI: 10.1039/d1cy01798e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Design the adenosine phosphate hydrolysis (APH) pathway multienzyme cascade system for the biosynthesis of nicotinamide mononucleotide (NMN) in vitro.
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Affiliation(s)
- Cailian Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, People's Republic of China
| | - Jiao Feng
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, People's Republic of China
| | - Jing Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, People's Republic of China
| | - Ning Hao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, People's Republic of China
| | - Xin Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, People's Republic of China
| | - Kequan Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, People's Republic of China
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28
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Wen X, Lin H, Ren Y, Li C, Zhang C, Lin J, Lin J. Allitol bioproduction by recombinant Escherichia coli with NADH regeneration system co-expressing ribitol dehydrogenase (RDH) and formate dehydrogenase (FDH) in individual or in fusion. ELECTRON J BIOTECHN 2022. [DOI: 10.1016/j.ejbt.2021.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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29
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Enzyme self-aggregation in supramolecular self-assembly of glucose oxidase and catalase: Insight from molecular dynamics simulation based on coarse-grained method. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2021.111366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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30
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Artificial protein assemblies with well-defined supramolecular protein nanostructures. Biochem Soc Trans 2021; 49:2821-2830. [PMID: 34812854 DOI: 10.1042/bst20210808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/28/2021] [Accepted: 11/02/2021] [Indexed: 12/13/2022]
Abstract
Nature uses a wide range of well-defined biomolecular assemblies in diverse cellular processes, where proteins are major building blocks for these supramolecular assemblies. Inspired by their natural counterparts, artificial protein-based assemblies have attracted strong interest as new bio-nanostructures, and strategies to construct ordered protein assemblies have been rapidly expanding. In this review, we provide an overview of very recent studies in the field of artificial protein assemblies, with the particular aim of introducing major assembly methods and unique features of these assemblies. Computational de novo designs were used to build various assemblies with artificial protein building blocks, which are unrelated to natural proteins. Small chemical ligands and metal ions have also been extensively used for strong and bio-orthogonal protein linking. Here, in addition to protein assemblies with well-defined sizes, protein oligomeric and array structures with rather undefined sizes (but with definite repeat protein assembly units) also will be discussed in the context of well-defined protein nanostructures. Lastly, we will introduce multiple examples showing how protein assemblies can be effectively used in various fields such as therapeutics and vaccine development. We believe that structures and functions of artificial protein assemblies will be continuously evolved, particularly according to specific application goals.
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31
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Cox N, Charlier C, Vijayaraj R, De La Mare M, Barbe S, André I, Lippens G, Montanier CY. The covalent complex of Jo-In results from a long-lived, non-covalent intermediate state with near-native structure. Biochem Biophys Res Commun 2021; 589:223-228. [PMID: 34929445 DOI: 10.1016/j.bbrc.2021.12.028] [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: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 11/30/2022]
Abstract
Covalent protein complexes have been used to assemble enzymes in large scaffolds for biotechnology purposes. Although the catalytic mechanism of the covalent linking of such proteins is well known, the recognition and overall structural mechanisms driving the association are far less understood but could help further functional engineering of these complexes. Here, we study the Jo-In complex by NMR spectroscopy and molecular modelling. We characterize a transient non-covalent complex, with structural elements close to those in the final covalent complex. Using site specific mutagenesis, we further show that this non-covalent association is essential for the covalent complex to form.
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Affiliation(s)
- Neil Cox
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France
| | - Cyril Charlier
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France
| | - Ramadoss Vijayaraj
- Toulouse White Biotechnology, UMS INRA 1337, UMS CNRS 3582, Institut National des Sciences Appliquées de Toulouse, 31077, Toulouse, France
| | - Marion De La Mare
- Toulouse White Biotechnology, UMS INRA 1337, UMS CNRS 3582, Institut National des Sciences Appliquées de Toulouse, 31077, Toulouse, France
| | - Sophie Barbe
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France
| | - Isabelle André
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France
| | - Guy Lippens
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France.
| | - Cédric Y Montanier
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France.
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32
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Gad S, Ayakar S. Protein scaffolds: A tool for multi-enzyme assembly. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 32:e00670. [PMID: 34824995 PMCID: PMC8605239 DOI: 10.1016/j.btre.2021.e00670] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/13/2021] [Accepted: 09/03/2021] [Indexed: 12/31/2022]
Abstract
The synthesis of complex molecules using multiple enzymes simultaneously in one reaction vessel has rapidly emerged as a new frontier in the field of bioprocess technology. However, operating different enzymes together in a single vessel limits their operational performance which needs to be addressed. With this respect, scaffolding proteins play an immense role in bringing different enzymes together in a specific manner. The scaffolding improves the catalytic performance, enzyme stability and provides an optimal micro-environment for biochemical reactions. This review describes the components of protein scaffolds, different ways of constructing a protein scaffold-based multi-enzyme complex, and their effects on enzyme kinetics. Moreover, different conjugation strategies viz; dockerin-cohesin interaction, SpyTag-SpyCatcher system, peptide linker-based ligation, affibody, and sortase-mediated ligation are discussed in detail. Various analytical and characterization tools that have enabled the development of these scaffolding strategies are also reviewed. Such mega-enzyme complexes promise wider applications in the field of biotechnology and bioengineering.
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Affiliation(s)
- Shubhada Gad
- Department of Biotechnology, Institute of Chemical Technology - IndianOil Odisha Campus Bhubaneswar, Odisha 751013, India
| | - Sonal Ayakar
- Department of Biotechnology, Institute of Chemical Technology - IndianOil Odisha Campus Bhubaneswar, Odisha 751013, India
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33
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Zeng R, Lv C, Wang C, Zhao G. Bionanomaterials based on protein self-assembly: Design and applications in biotechnology. Biotechnol Adv 2021; 52:107835. [PMID: 34520791 DOI: 10.1016/j.biotechadv.2021.107835] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/06/2021] [Accepted: 09/08/2021] [Indexed: 01/13/2023]
Abstract
Elegant protein assembly to generate new biomaterials undergoes extremely rapid development for wide extension of biotechnology applications, which can be a powerful tool not only for creating nanomaterials but also for advancing understanding of the structure of life. Unique biological properties of proteins bestow these artificial biomaterials diverse functions that can permit them to be applied in encapsulation, bioimaging, biocatalysis, biosensors, photosynthetic apparatus, electron transport, magnetogenetic applications, vaccine development and antibodies design. This review gives a perspective view of the latest advances in the construction of protein-based nanomaterials. We initially start with distinguishable, specific interactions to construct sundry nanomaterials through protein self-assembly and concisely expound the assembly mechanism from the design strategy. And then, the design and construction of 0D, 1D, 2D, 3D protein assembled nanomaterials are especially highlighted. Furthermore, the potential applications have been discussed in detail. Overall, this review will illustrate how to fabricate highly sophisticated nanomaterials oriented toward applications in biotechnology based on the rules of supramolecular chemistry.
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Affiliation(s)
- Ruiqi Zeng
- College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, China
| | - Chenyan Lv
- College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, China
| | - Chengtao Wang
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University, No. 11 Fucheng Road, Haidian District, Beijing 100048, China
| | - Guanghua Zhao
- College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, China.
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34
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Li J, Zhu M, Wang S, Tao Z, Liu X, Huang X. Construction of coacervates in proteinosome hybrid microcompartments with enhanced cascade enzymatic reactions. Chem Commun (Camb) 2021; 57:11713-11716. [PMID: 34695173 DOI: 10.1039/d1cc05098b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A spatially segregative coacervate-in-proteinosome hybrid microcompartment is constructed by co-encapsulation of either positively or negatively charged polyelectrolytes within proteinosomes with enhanced cascade enzymatic reactions, providing a step towards the development of artificial eukaryotic cell like microcompartments.
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Affiliation(s)
- Junbo Li
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China.
| | - Mei Zhu
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China.
| | - Shengliang Wang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China.
| | - Zhengyu Tao
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China.
| | - Xiaoman Liu
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China.
| | - Xin Huang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China.
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35
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Keeble AH, Yadav VK, Ferla MP, Bauer CC, Chuntharpursat-Bon E, Huang J, Bon RS, Howarth M. DogCatcher allows loop-friendly protein-protein ligation. Cell Chem Biol 2021; 29:339-350.e10. [PMID: 34324879 PMCID: PMC8878318 DOI: 10.1016/j.chembiol.2021.07.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/09/2021] [Accepted: 07/02/2021] [Indexed: 12/14/2022]
Abstract
There are many efficient ways to connect proteins at termini. However, connecting at a loop is difficult because of lower flexibility and variable environment. Here, we have developed DogCatcher, a protein that forms a spontaneous isopeptide bond with DogTag peptide. DogTag/DogCatcher was generated initially by splitting a Streptococcus pneumoniae adhesin. We optimized DogTag/DogCatcher through rational design and evolution, increasing reaction rate by 250-fold and establishing millimolar solubility of DogCatcher. When fused to a protein terminus, DogTag/DogCatcher reacts slower than SpyTag003/SpyCatcher003. However, inserted in loops of a fluorescent protein or enzyme, DogTag reacts much faster than SpyTag003. Like many membrane proteins, the ion channel TRPC5 has no surface-exposed termini. DogTag in a TRPC5 extracellular loop allowed normal calcium flux and specific covalent labeling on cells in 1 min. DogTag/DogCatcher reacts under diverse conditions, at nanomolar concentrations, and to 98% conversion. Loop-friendly ligation should expand the toolbox for creating protein architectures. Spontaneous transamidation at internal sites harnessing a DogTag/DogCatcher pair DogCatcher is designed and bred for high solubility and rapid reaction Within protein loops DogTag can clamp on its partner faster than SpyTag003 Fast and faithful fluorescent labeling of an ion channel at the cell surface via DogTag
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Affiliation(s)
- Anthony H Keeble
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Vikash K Yadav
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Matteo P Ferla
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Claudia C Bauer
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Eulashini Chuntharpursat-Bon
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Jin Huang
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Robin S Bon
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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36
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Sequential co-immobilization of multienzyme nanodevices based on SpyCatcher and SpyTag for robust biocatalysis. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111673] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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37
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Wu J, Wang X, Xiao L, Wang F, Zhang Y, Li X. Synthetic Protein Scaffolds for Improving R-(-)-Linalool Production in Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:5663-5670. [PMID: 33983023 DOI: 10.1021/acs.jafc.1c01101] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
R-(-)-Linalool is widely used in the pharmaceutical, agrochemical, and fragrance industries; however, its applications are limited owing to low yield and high cost of production. To improve the production efficiency of R-(-)-linalool in Escherichia coli, three enzymes [E. coli-derived isopentenyl diphosphate isomerase, Abies grandis-derived geranyl diphosphate synthase, and Streptomyces clavuligerus-derived (3R)-linalool synthases] were physically colocalized to synthetic complexes using synthetic protein scaffolds of GTPase-binding domain, Src homology 3, and PSD95/DlgA/Zo-1. R-(-)-Linalool was produced at the highest concentration in the strain IGL114 containing a scaffold ratio of 1:1:4. By further optimizing the inducer, temperature, and glycerol concentration, the production titer of R-(-)-linalool in the shake flask was increased by approximately 10 times compared with that of the scaffold-free control and was 2.78 times the previously reported yield. The production in the fermenter was about 1.5 times the previous highest production. In general, the final strain accumulated 277.8 and 1523.2 mg/L R-(-)-linalool under the conditions of shake-flask and fed-batch fermentation, respectively. This study provides a foundation for the assembly of bacterial intracellular protein scaffolds.
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Affiliation(s)
- Jing Wu
- Jiangsu Provincial Key Laboratory for the Chemistry and Utilization of Agro-Forest Biomass, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Key Laboratory of Biomass-Based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
- International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing 210037, China
| | - Xun Wang
- Jiangsu Provincial Key Laboratory for the Chemistry and Utilization of Agro-Forest Biomass, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Key Laboratory of Biomass-Based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
- International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing 210037, China
| | - Longjie Xiao
- Jiangsu Provincial Key Laboratory for the Chemistry and Utilization of Agro-Forest Biomass, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Key Laboratory of Biomass-Based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
- International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing 210037, China
| | - Fei Wang
- Jiangsu Provincial Key Laboratory for the Chemistry and Utilization of Agro-Forest Biomass, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Key Laboratory of Biomass-Based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
- International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing 210037, China
| | - Yu Zhang
- Jiangsu Provincial Key Laboratory for the Chemistry and Utilization of Agro-Forest Biomass, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Key Laboratory of Biomass-Based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
- International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing 210037, China
| | - Xun Li
- Jiangsu Provincial Key Laboratory for the Chemistry and Utilization of Agro-Forest Biomass, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Key Laboratory of Biomass-Based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
- International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing 210037, China
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38
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Ali MY, Chang Q, Su Y, Wu J, Yan Q, Yin L, Zhang Y, Feng Y. Ordered Coimmobilization of Multimeric Enzyme Arrays with Enhanced Biocatalytic Cascade Performance. ACS APPLIED BIO MATERIALS 2021; 4:3027-3034. [DOI: 10.1021/acsabm.0c01148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mohamed Yassin Ali
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
- Biochemistry Department, Faculty of Agriculture, Fayoum University, 63514 Fayoum, Egypt
| | - Qing Chang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yuerong Su
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jinhong Wu
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Quande Yan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Liang Yin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yong Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
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Xu L, Wang LC, Su BM, Xu XQ, Lin J. Efficient biosynthesis of (2S, 3R)-4-methylsulfonylphenylserine by artificial self-assembly of enzyme complex combined with an intensified acetaldehyde elimination system. Bioorg Chem 2021; 110:104766. [PMID: 33662895 DOI: 10.1016/j.bioorg.2021.104766] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/17/2021] [Accepted: 02/20/2021] [Indexed: 01/13/2023]
Abstract
(2S, 3R)-4-methylsulfonylphenylserine [(2S, 3R)-MPS], a key chiral precursor for antibiotics florfenicol and thiamphenicol, could be asymmetrically synthesized by l-threonine transaldolase (LTTA) coupled with an acetaldehyde elimination system. The low efficiency of acetaldehyde elimination system blocked further accumulation of (2S, 3R)-MPS. To address this issue, strengthening acetaldehyde elimination system and enzyme self-assembly strategy were combined to accelerate biosynthesis of (2S, 3R)-MPS. The new multi-enzyme cascade with intensified acetaldehyde elimination system BL21 (PsLTTAD2/ScADH/BtGDH) could produce (2S, 3R)-MPS with a titer of 157.6 mM, 1.7-folds than that produced by the original system BL21 (PsLTTAD2/ApADH/CbFDH). Moreover, self-assembly of PsLTTAD2 and ScADH by respective fusion of SpyTag and SpyCatcher were carried out to develop a self-assembled multi-enzyme cascade BL21 (ST-PsLTTAD2/SC-ScADH/BtGDH). As a result, the yield of (2S, 3R)-MPS was up to 248.1 mM with 95% de. As far as we knew, that represented the highest yield of (2S, 3R)-MPS by enzymatic synthesis, and therefore was a promising and green route for industrial production of this valuable compound.
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Affiliation(s)
- Lian Xu
- College of Chemical Engineering, Fuzhou University, Fuzhou 350116, China
| | - Li-Chao Wang
- College of Chemical Engineering, Fuzhou University, Fuzhou 350116, China
| | - Bing-Mei Su
- College of Chemical Engineering, Fuzhou University, Fuzhou 350116, China
| | - Xin-Qi Xu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350116, China
| | - Juan Lin
- College of Chemical Engineering, Fuzhou University, Fuzhou 350116, China; College of Biological Science and Engineering, Fuzhou University, Fuzhou 350116, China.
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40
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Yan Y, Qiao Z, Hai X, Song W, Bi S. Versatile electrochemical biosensor based on bi-enzyme cascade biocatalysis spatially regulated by DNA architecture. Biosens Bioelectron 2021; 174:112827. [DOI: 10.1016/j.bios.2020.112827] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/10/2020] [Accepted: 11/16/2020] [Indexed: 12/29/2022]
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41
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Co-immobilization of multiple enzymes by self-assembly and chemical crosslinking for cofactor regeneration and robust biocatalysis. Int J Biol Macromol 2020; 162:445-453. [DOI: 10.1016/j.ijbiomac.2020.06.141] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/14/2020] [Accepted: 06/15/2020] [Indexed: 12/16/2022]
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Zhang W, Mo S, Liu M, Liu L, Yu L, Wang C. Rationally Designed Protein Building Blocks for Programmable Hierarchical Architectures. Front Chem 2020; 8:587975. [PMID: 33195088 PMCID: PMC7658299 DOI: 10.3389/fchem.2020.587975] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/05/2020] [Indexed: 01/23/2023] Open
Abstract
Diverse natural/artificial proteins have been used as building blocks to construct a variety of well-ordered nanoscale structures over the past couple of decades. Sophisticated protein self-assemblies have attracted great scientific interests due to their potential applications in disease diagnosis, illness treatment, biomechanics, bio-optics and bio-electronics, etc. This review outlines recent efforts directed to the creation of structurally defined protein assemblies including one-dimensional (1D) strings/rings/tubules, two-dimensional (2D) planar sheets and three-dimensional (3D) polyhedral scaffolds. We elucidate various innovative strategies for manipulating proteins to self-assemble into desired architectures. The emergent applications of protein assemblies as versatile platforms in medicine and material science with improved performances have also been discussed.
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Affiliation(s)
- Wenbo Zhang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shanshan Mo
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mingwei Liu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lei Liu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Lanlan Yu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chenxuan Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Lang M, Pröschel M, Brüggen N, Sonnewald U. Tagging and catching: rapid isolation and efficient labeling of organelles using the covalent Spy-System in planta. PLANT METHODS 2020; 16:122. [PMID: 32905125 PMCID: PMC7465787 DOI: 10.1186/s13007-020-00663-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 08/24/2020] [Indexed: 05/12/2023]
Abstract
BACKGROUND Up-to-now, several biochemical methods have been developed to allow specific organelle isolation from plant tissues. These procedures are often time consuming, require substantial amounts of plant material, have low yield or do not result in pure organelle fractions. Moreover, barely a protocol allows rapid and flexible isolation of different subcellular compartments. The recently published SpySystem enables the in vitro and in vivo covalent linkage between proteins and protein complexes. Here we describe the use of this system to tag and purify plant organelles. RESULTS We developed a simple and specific method to in vivo tag and visualize, as well as isolate organelles of interest from crude plant extracts. This was achieved by expressing the covalent split-isopeptide interaction system, consisting of SpyTag and SpyCatcher, in Nicotiana benthamiana leaves. The functionality of the SpySystem in planta, combined with downstream applications, was proven. Using organelle-specific membrane anchor sequences to program the sub-cellular localization of the SpyTag peptide, we could tag the outer envelope of chloroplasts and mitochondria. By co-expression of a cytosolic, soluble eGFP-SpyCatcher fusion protein, we could demonstrate intermolecular isopeptide formation in planta and proper organelle targeting of the SpyTag peptides to the respective organelles. For one-step organelle purification, recombinantly expressed SpyCatcher protein was immobilized on magnetic microbeads via covalent thiol-etherification. To isolate tagged organelles, crude plant filtrates were mixed with SpyCatcher-coated beads which allowed isolation of SpyTag-labelled chloroplasts and mitochondria. The isolated organelles were intact, showed high yield and hardly contaminants and can be subsequently used for further molecular or biochemical analysis. CONCLUSION The SpySystem can be used to in planta label subcellular structures, which enables the one-step purification of organelles from crude plant extracts. The beauty of the system is that it works as a covalent toolbox. Labeling of different organelles with individual tags under control of cell-specific and/or inducible promoter sequences will allow the rapid organelle and cell-type specific purification. Simultaneous labeling of different organelles with specific Tag/Catcher combinations will enable simultaneous isolation of different organelles from one plant extract in future experiments.
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Affiliation(s)
- Martina Lang
- Division of Biochemistry, Department of Biology, Friedrich-Alexander-University Erlangen-Nuremberg, Staudtstrasse 5, 91058 Erlangen, Germany
| | - Marlene Pröschel
- Division of Biochemistry, Department of Biology, Friedrich-Alexander-University Erlangen-Nuremberg, Staudtstrasse 5, 91058 Erlangen, Germany
| | - Nico Brüggen
- Division of Biochemistry, Department of Biology, Friedrich-Alexander-University Erlangen-Nuremberg, Staudtstrasse 5, 91058 Erlangen, Germany
| | - Uwe Sonnewald
- Division of Biochemistry, Department of Biology, Friedrich-Alexander-University Erlangen-Nuremberg, Staudtstrasse 5, 91058 Erlangen, Germany
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Keeble AH, Howarth M. Power to the protein: enhancing and combining activities using the Spy toolbox. Chem Sci 2020; 11:7281-7291. [PMID: 33552459 PMCID: PMC7844731 DOI: 10.1039/d0sc01878c] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/30/2020] [Indexed: 12/27/2022] Open
Abstract
Proteins span an extraordinary range of shapes, sizes and functionalities. Therefore generic approaches are needed to overcome this diversity and stream-line protein analysis or application. Here we review SpyTag technology, now used in hundreds of publications or patents, and its potential for detecting and controlling protein behaviour. SpyTag forms a spontaneous and irreversible isopeptide bond upon binding its protein partner SpyCatcher, where both parts are genetically-encoded. New variants of this pair allow reaction at a rate approaching the diffusion limit, while reversible versions allow purification of SpyTagged proteins or tuned dynamic interaction inside cells. Anchoring of SpyTag-linked proteins has been established to diverse nanoparticles or surfaces, including gold, graphene and the air/water interface. SpyTag/SpyCatcher is mechanically stable, so is widely used for investigating protein folding and force sensitivity. A toolbox of scaffolds allows SpyTag-fusions to be assembled into defined multimers, from dimers to 180-mers, or unlimited 1D, 2D or 3D networks. Icosahedral multimers are being evaluated for vaccination against malaria, HIV and cancer. For enzymes, Spy technology has increased resilience, promoted substrate channelling, and assembled hydrogels for continuous flow biocatalysis. Combinatorial increase in functionality has been achieved through modular derivatisation of antibodies, light-emitting diodes or viral vectors. In living cells, SpyTag allowed imaging of protein trafficking, retargeting of CAR-T cell killing, investigation of heart contraction, and control of nucleosome position. The simple genetic encoding and rapid irreversible reaction provide diverse opportunities to enhance protein function. We describe limitations as well as future directions.
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Affiliation(s)
- Anthony H Keeble
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford , OX1 3QU , UK . ; Tel: +44 (0)1865 613200
| | - Mark Howarth
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford , OX1 3QU , UK . ; Tel: +44 (0)1865 613200
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Eibinger M, Ganner T, Plank H, Nidetzky B. A Biological Nanomachine at Work: Watching the Cellulosome Degrade Crystalline Cellulose. ACS CENTRAL SCIENCE 2020; 6:739-746. [PMID: 32490190 PMCID: PMC7256933 DOI: 10.1021/acscentsci.0c00050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Indexed: 05/14/2023]
Abstract
The cellulosome is a supramolecular multienzymatic protein complex that functions as a biological nanomachine of cellulosic biomass degradation. How the megadalton-size cellulosome adapts to a solid substrate is central to its mechanism of action and is also key for its efficient use in bioconversion applications. We report time-lapse visualization of crystalline cellulose degradation by individual cellulosomes from Clostridium thermocellum by atomic force microscopy. Upon binding to cellulose, the cellulosomes switch to elongated, even filamentous shapes and morph these dynamically at below 1 min time scale according to requirements of the substrate surface under attack. Compared with noncomplexed cellulases that peel off material while sliding along crystalline cellulose surfaces, the cellulosomes remain bound locally for minutes and remove the material lying underneath. The consequent roughening up of the surface leads to an efficient deconstruction of cellulose nanocrystals both from the ends and through fissions within. Distinct modes of cellulose nanocrystal deconstruction by nature's major cellulase systems are thus revealed.
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Affiliation(s)
- Manuel Eibinger
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Thomas Ganner
- Institute
for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
| | - Harald Plank
- Institute
for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
- Graz
Centre of Electron Microscopy, Steyrergasse 17, A-8010 Graz, Austria
| | - Bernd Nidetzky
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
- Austrian
Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
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46
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Zhang F, Zhang W. Encrypting Chemical Reactivity in Protein Sequences toward
Information‐Coded
Reactions
†. CHINESE J CHEM 2020. [DOI: 10.1002/cjoc.202000083] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Fan Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 China
| | - Wen‐Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 China
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Affiliation(s)
- Fei Sun
- Department of Chemical and Biological EngineeringThe Hong Kong University of Science and Technology, Clear Water Bay Kowloon Hong Kong SAR China
| | - Wen‐Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of EducationCenter for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 China
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Abstract
Proteins are versatile macromolecules with diverse structure, charge, and function. They are ideal building blocks for biomaterials for drug delivery, biosensing, or tissue engineering applications. Simultaneously, the need to develop green alternatives to chemical processes has led to renewed interest in multienzyme biocatalytic routes to fine, specialty, and commodity chemicals. Therefore, a method to reliably assemble protein complexes using protein-protein interactions would facilitate the rapid production of new materials. Here we show a method for modular assembly of protein materials using a supercharged protein as a scaffolding "hub" onto which target proteins bearing oppositely charged domains have been self-assembled. The physical properties of the material can be tuned through blending and heating and disassembly triggered using changes in pH or salt concentration. The system can be extended to the synthesis of living materials. Our modular method can be used to reliably direct the self-assembly of proteins using small charged tag domains that can be easily encoded in a fusion protein.
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Affiliation(s)
- James A. J. Arpino
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Karen Marie Polizzi
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
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49
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Abstract
Liquid-liquid phase separation forms condensates that feature a highly concentrated liquid phase, a defined yet dynamic boundary, and dynamic exchange at and across the boundary. Phase transition drives the formation of dynamic multienzyme complexes in cells, for example, the purinosome, which forms subcellular macrobodies responsible for de novo purine biosynthesis. Here, we construct synthetic versions of multienzyme biosynthetic systems by assembling enzymes in protein condensates. A synthetic protein phase separation system using component proteins from postsynaptic density in neuronal synapses, GKAP, Shank, and Homer provides the scaffold for assembly. Three sets of guest proteins: a pair of fluorescent proteins (CFP and YFP), three sequential enzymes in menaquinone biosynthesis pathway (MenF, MenD, and MenH), and two enzymes in terpene biosynthesis pathway (Idi and IspA) are assembled via peptide-peptide interactions in the condensate. First, we discover that coassembly of CFP and YFP exhibited a broad distribution of the FRET signal within the condensate. Second, a spontaneous enrichment of the rate-limiting enzyme MenD in the condensate is sufficient to increase the 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate production rate by 70%. Third, coassembly of both Idi and IspA in the protein condensate increases the farnesyl pyrophosphate production rate by more than 50%. Altogether, we show here that phase separation significantly accelerates the efficiency of multienzyme biocatalysis.
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Affiliation(s)
- Miao Liu
- Department of Chemistry, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Sicong He
- Department of Electronic and Computer Engineering, Center of Systems Biology and Human Health, School of Science and Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Lixin Cheng
- Department of Critical Care Medicine, Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518000, China
| | - Jianan Qu
- Department of Electronic and Computer Engineering, Center of Systems Biology and Human Health, School of Science and Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Jiang Xia
- Department of Chemistry, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Center for Cell & Developmental Biology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 02522, China
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50
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Vázquez-González M, Wang C, Willner I. Biocatalytic cascades operating on macromolecular scaffolds and in confined environments. Nat Catal 2020. [DOI: 10.1038/s41929-020-0433-1] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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