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Sato R, Minamihata K, Wakabayashi R, Goto M, Kamiya N. Molecular crowding elicits the acceleration of enzymatic crosslinking of macromolecular substrates. Org Biomol Chem 2023; 21:306-314. [PMID: 36342388 DOI: 10.1039/d2ob01549h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Cytoplasm contains high concentrations of biomacromolecules. Protein behavior under such crowded conditions is reportedly different from that in an aqueous buffer solution, mainly owing to the effect of volume exclusion caused by the presence of macromolecules. Using a crosslinking reaction catalyzed by microbial transglutaminase (MTG) as a model, we herein systematically determined how the substrate size affects enzymatic activity in both dilute and crowded solutions of dextran. We first observed a threefold reduction in MTG-mediated crosslinking of a pair of small peptide substrates in 15 wt% dextran solution. In contrast, when proteinaceous substrates were involved, the crosslinking rates in 15 wt% dextran solutions accelerated markedly to levels comparable with the level in the absence of dextran. Our results provide new insights into the action of enzymes with regard to macromolecular substrates under crowded conditions, of which the potential utility was demonstrated by the formation of highly crosslinked protein polymers.
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Affiliation(s)
- Ryo Sato
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan.
| | - Kosuke Minamihata
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan.
| | - Rie Wakabayashi
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan.
| | - Masahiro Goto
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan. .,Division of Biotechnology, Center for Future Chemistry, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
| | - Noriho Kamiya
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan. .,Division of Biotechnology, Center for Future Chemistry, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
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2
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Pei X, Luo Z, Qiao L, Xiao Q, Zhang P, Wang A, Sheldon RA. Putting precision and elegance in enzyme immobilisation with bio-orthogonal chemistry. Chem Soc Rev 2022; 51:7281-7304. [PMID: 35920313 DOI: 10.1039/d1cs01004b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The covalent immobilisation of enzymes generally involves the use of highly reactive crosslinkers, such as glutaraldehyde, to couple enzyme molecules to each other or to carriers through, for example, the free amino groups of lysine residues, on the enzyme surface. Unfortunately, such methods suffer from a lack of precision. Random formation of covalent linkages with reactive functional groups in the enzyme leads to disruption of the three dimensional structure and accompanying activity losses. This review focuses on recent advances in the use of bio-orthogonal chemistry in conjunction with rec-DNA to affect highly precise immobilisation of enzymes. In this way, cost-effective combination of production, purification and immobilisation of an enzyme is achieved, in a single unit operation with a high degree of precision. Various bio-orthogonal techniques for putting this precision and elegance into enzyme immobilisation are elaborated. These include, for example, fusing (grafting) peptide or protein tags to the target enzyme that enable its immobilisation in cell lysate or incorporating non-standard amino acids that enable the application of bio-orthogonal chemistry.
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Affiliation(s)
- Xiaolin Pei
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Zhiyuan Luo
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Li Qiao
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Qinjie Xiao
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Pengfei Zhang
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Anming Wang
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Roger A Sheldon
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, PO Wits, 2050, Johannesburg, South Africa. .,Department of Biotechnology, Section BOC, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
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3
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Dong W, Sun H, Chen Q, Hou L, Chang Y, Luo H. SpyTag/Catcher chemistry induces the formation of active inclusion bodies in E. coli. Int J Biol Macromol 2022; 199:358-371. [PMID: 35031313 DOI: 10.1016/j.ijbiomac.2022.01.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 02/09/2023]
Abstract
SpyTag/Catcher chemistry is usually applied to engineer robust enzymes via head-to-tail cyclization using spontaneous intramolecular isopeptide bond formation. However, the SpyTag/Catcher induced intercellular protein assembly in vivo cannot be ignored. It was found that some active inclusion bodies had generated to different proportions in the expression of six SpyTag/Catcher labeled proteins (CatIBs-STCProtein). Some factors that may affect the formation of CatIBs-STCProtein were discussed, and the subunit quantities were found to be strongly positively related to the formation of protein aggregates. Approximately 85.44% of the activity of the octameric protein leucine dehydrogenase (LDH) was expressed in aggregates, while the activity of the monomeric protein green fluorescence protein (GFP) in aggregates was 12.51%. The results indicated that SpyTag/Catcher can be used to form protein aggregates in E. coli. To facilitate the advantages of CatIBs-STCProtein, we took the CatIBs-STCLDH as an example and further chemically cross-linked with glutaraldehyde to obtain novel cross-linked enzyme aggregates (CLEAs-CatIBs-STCLDH). CLEAs-CatIBs-STCLDH had good thermal stability and organic solvents stability, and its activity remained 51.03% after incubation at 60 °C for 100 mins. Moreover, the crosslinked CatIBs-STCLDH also showed superior stability over traditional CLEAs, and its activity remained 98.70% after 10 cycles of catalysis.
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Affiliation(s)
- Wenge Dong
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Hongxu Sun
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Qiwei Chen
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Liangyu Hou
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Yanhong Chang
- Department of Environmental Engineering, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China; Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, Beijing 100083, China.
| | - Hui Luo
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China.
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4
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Permana D, Putra HE, Djaenudin D. Designed protein multimerization and polymerization for functionalization of proteins. Biotechnol Lett 2022; 44:341-365. [PMID: 35083582 PMCID: PMC8791688 DOI: 10.1007/s10529-021-03217-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/04/2021] [Indexed: 12/15/2022]
Abstract
Abstract Multimeric and polymeric proteins are large biomacromolecules consisting of multiple protein molecules as their monomeric units, connected through covalent or non-covalent bonds. Genetic modification and post-translational modifications (PTMs) of proteins offer alternative strategies for designing and creating multimeric and polymeric proteins. Multimeric proteins are commonly prepared by genetic modification, whereas polymeric proteins are usually created through PTMs. There are two methods that can be applied to create polymeric proteins: self-assembly and crosslinking. Self-assembly offers a spontaneous reaction without a catalyst, while the crosslinking reaction offers some catalyst options, such as chemicals and enzymes. In addition, enzymes are excellent catalysts because they provide site-specificity, rapid reaction, mild reaction conditions, and activity and functionality maintenance of protein polymers. However, only a few enzymes are applicable for the preparation of protein polymers. Most of the other enzymes are effective only for protein conjugation or labeling. Here, we review novel and applicable strategies for the preparation of multimeric proteins through genetic modification and self-assembly. We then describe the formation of protein polymers through site-selective crosslinking reactions catalyzed by enzymes, crosslinking reactions of non-natural amino acids, and protein-peptide (SpyCatcher/SpyTag) interactions. Finally, we discuss the potential applications of these protein polymers. Graphical abstract ![]()
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Affiliation(s)
- Dani Permana
- Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan. .,Research Unit for Clean Technology, The National Research and Innovation Agency of Republic of Indonesia, Jl. Cisitu, Bandung, 40135, Indonesia.
| | - Herlian Eriska Putra
- Research Unit for Clean Technology, The National Research and Innovation Agency of Republic of Indonesia, Jl. Cisitu, Bandung, 40135, Indonesia
| | - Djaenudin Djaenudin
- Research Unit for Clean Technology, The National Research and Innovation Agency of Republic of Indonesia, Jl. Cisitu, Bandung, 40135, Indonesia
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Tang S, Liao D, Li X, Lin Y, Han S, Zheng S. Cell-Free Biosynthesis System: Methodology and Perspective of in Vitro Efficient Platform for Pyruvate Biosynthesis and Transformation. ACS Synth Biol 2021; 10:2417-2433. [PMID: 34529398 DOI: 10.1021/acssynbio.1c00252] [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] [Indexed: 11/30/2022]
Abstract
The modification of intracellular metabolic pathways by metabolic engineering has generated many engineered strains with relatively high yields of various target products in the past few decades. However, the unpredictable accumulation of toxic products, the cell membrane barrier, and competition between the carbon flux of cell growth and product synthesis have severely retarded progress toward the industrial-scale production of many essential chemicals. On the basis of an in-depth understanding of intracellular metabolic pathways, scientists intend to explore more sustainable methods and construct a cell-free biosynthesis system in vitro. In this review, the synthesis and application of pyruvate as a platform compound is used as an example to introduce cell-free biosynthesis systems. We systematically summarize a proposed methodology workflow of cell-free biosynthesis systems, including pathway design, enzyme mining, enzyme modification, multienzyme assembly, and pathway optimization. Some new methods, such as machine learning, are also mentioned in this review.
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Affiliation(s)
- Shiming Tang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Daocheng Liao
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Xuewen Li
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Shuangyan Han
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Suiping Zheng
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
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Minamihata K, Tanaka Y, Santoso P, Goto M, Kozome D, Taira T, Kamiya N. Orthogonal Enzymatic Conjugation Reactions Create Chitin Binding Domain Grafted Chitinase Polymers with Enhanced Antifungal Activity. Bioconjug Chem 2021; 32:1688-1698. [PMID: 34251809 DOI: 10.1021/acs.bioconjchem.1c00235] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enzymatic reaction offers site-specific conjugation of protein units to form protein conjugates or protein polymers with intrinsic functions. Herein, we report horseradish peroxidase (HRP)- and microbial transglutaminase (MTG)-catalyzed orthogonal conjugation reactions to create antifungal protein polymers composed of Pteris ryukyuensis chitinase-A (ChiA) and its two domains, catalytic domain, CatD, and chitin-binding domain, LysM2. We engineered the ChiA and CatD by introducing a peptide tag containing tyrosine (Y-tag) at N-termini and a peptide tag containing lysine and tyrosine (KY-tag) at C-termini to construct Y-ChiA-KY and Y-CatD-KY. Also, LysM2 with Y-tag and KY-tag (Y-LysM2-KY) or with a glutamine-containing peptide tag (Q-tag) (LysM2-Q) were constructed. The proteins with Y-tag and KY-tag were efficiently polymerized by HRP reaction through the formation of dityrosine bonds at the tyrosine residues in the peptide tags. The Y-CatD-KY polymer was further treated by MTG to orthogonally graft LysM2-Q to the KY-tag via isopeptide formation between the side chains of the glutamine and lysine residues in the peptide tags to form LysM2-grafted CatD polymer. The LysM2-grafted CatD polymer exhibited significantly higher antifungal activity than the homopolymer of Y-ChiA-KY and the random copolymer of Y-CatD-KY and Y-LysM2-KY, demonstrating that the structural differences of artificial chitinase polymers have a significant impact on the antifungal activity. This strategy of polymerization and grafting reaction of protein can contribute to the further research and development of functional protein polymers for specific applications in various fields in biotechnology.
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Affiliation(s)
- Kosuke Minamihata
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yusuke Tanaka
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Pugoh Santoso
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Masahiro Goto
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,Division of Biotechnology, Center for Future Chemistry, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Dan Kozome
- Department of Bioscience and Biotechnology, Faculty of Agriculture, University of the Ryukyus, 1 Senbaru, Nishihara-cho, Okinawa 903-0213, Japan
| | - Toki Taira
- Department of Bioscience and Biotechnology, Faculty of Agriculture, University of the Ryukyus, 1 Senbaru, Nishihara-cho, Okinawa 903-0213, Japan
| | - Noriho Kamiya
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,Division of Biotechnology, Center for Future Chemistry, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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7
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Permana D, Minamihata K, Goto M, Kamiya N. Strategies for Making Multimeric and Polymeric Bifunctional Protein Conjugates and Their Applications as Bioanalytical Tools. ANAL SCI 2021; 37:425-437. [PMID: 33455962 DOI: 10.2116/analsci.20scr07] [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] [Indexed: 11/23/2022]
Abstract
Enzymes play a central role in the detection of target molecules in biotechnological fields. Most probes used in detection are bifunctional proteins comprising enzymes and binding proteins conjugated by chemical reactions. To create a highly sensitive detection probe, it is essential to increase the enzyme-to-binding protein ratio in the probe. However, if the chemical reactions required to prepare the probe are insufficiently site-specific, the detection probe may lose functionality. Genetic modifications and enzyme-mediated post-translational modifications (PTMs) can ensure the site-specific conjugation of proteins. They are therefore promising strategies for the production of detection probes with high enzyme contents, i.e., polymeric bifunctional proteins. Herein, we review recent advances in the preparation of bifunctional protein conjugates and polymeric bifunctional protein conjugates for detection. We have summarized research on genetically fused proteins and enzymatically prepared polymeric bifunctional proteins, and will discuss the potential use of protein polymers in various detection applications.
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Affiliation(s)
- Dani Permana
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University.,Research Unit for Clean Technology, Indonesian Institute of Sciences (LIPI), Kampus LIPI Bandung
| | - Kosuke Minamihata
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University
| | - Masahiro Goto
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University.,Division of Biotechnology, Center for Future Chemistry, Kyushu University
| | - Noriho Kamiya
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University.,Division of Biotechnology, Center for Future Chemistry, Kyushu University
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Pasternack R, Hils M. Editorial for the special issue on transglutaminases in translation - Novel tools and methods impacting on diagnostics and therapeutics. Anal Biochem 2020; 607:113889. [PMID: 32745540 DOI: 10.1016/j.ab.2020.113889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
| | - Martin Hils
- Zedira GmbH, Roesslerstraße 83, 64293, Darmstadt, Germany.
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