1
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Wardman JF, Withers SG. Carbohydrate-active enzyme (CAZyme) discovery and engineering via (Ultra)high-throughput screening. RSC Chem Biol 2024; 5:595-616. [PMID: 38966674 PMCID: PMC11221537 DOI: 10.1039/d4cb00024b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/16/2024] [Indexed: 07/06/2024] Open
Abstract
Carbohydrate-active enzymes (CAZymes) constitute a diverse set of enzymes that catalyze the assembly, degradation, and modification of carbohydrates. These enzymes have been fashioned into potent, selective catalysts by millennia of evolution, and yet are also highly adaptable and readily evolved in the laboratory. To identify and engineer CAZymes for different purposes, (ultra)high-throughput screening campaigns have been frequently utilized with great success. This review provides an overview of the different approaches taken in screening for CAZymes and how mechanistic understandings of CAZymes can enable new approaches to screening. Within, we also cover how cutting-edge techniques such as microfluidics, advances in computational approaches and synthetic biology, as well as novel assay designs are leading the field towards more informative and effective screening approaches.
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Affiliation(s)
- Jacob F Wardman
- Department of Biochemistry and Molecular Biology, University of British Columbia Vancouver BC V6T 1Z3 Canada
- Michael Smith Laboratories, University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Stephen G Withers
- Department of Biochemistry and Molecular Biology, University of British Columbia Vancouver BC V6T 1Z3 Canada
- Michael Smith Laboratories, University of British Columbia Vancouver BC V6T 1Z4 Canada
- Department of Chemistry, University of British Columbia Vancouver BC V6T 1Z1 Canada
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2
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Yan W, Li X, Zhao D, Xie M, Li T, Qian L, Ye C, Shi T, Wu L, Wang Y. Advanced strategies in high-throughput droplet screening for enzyme engineering. Biosens Bioelectron 2024; 248:115972. [PMID: 38171222 DOI: 10.1016/j.bios.2023.115972] [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: 08/21/2023] [Revised: 11/05/2023] [Accepted: 12/23/2023] [Indexed: 01/05/2024]
Abstract
Enzymes, as biocatalysts, play a cumulatively important role in environmental purification and industrial production of chemicals and pharmaceuticals. However, natural enzymes are limited by their physiological properties in practice, which need to be modified driven by requirements. Screening and isolating certain enzyme variants or ideal industrial strains with high yielding of target product enzymes is one of the main directions of enzyme engineering research. Droplet-based high-throughput screening (DHTS) technology employs massive monodisperse emulsion droplets as microreactors to achieve single strain encapsulation, as well as continuous monitoring for the inside mutant library. It can effectively sort out strains or enzymes with desired characteristics, offering a throughput of 108 events per hour. Much of the early literature focused on screening various engineered strains or designing signalling sorting strategies based on DHTS technology. However, the field of enzyme engineering lacks a comprehensive overview of advanced methods for microfluidic droplets and their cutting-edge developments in generation and manipulation. This review emphasizes the advanced strategies and frontiers of microfluidic droplet generation and manipulation facilitating enzyme engineering development. We also introduce design for various screening signals that cooperate with DHTS and devote to enzyme engineering.
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Affiliation(s)
- Wenxin Yan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Xiang Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Danshan Zhao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Meng Xie
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Ting Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Lu Qian
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China; Ministry of Education Key Laboratory of NSLSCS, Nanjing Normal University, Nanjing 210046, China.
| | - Tianqiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China.
| | - Lina Wu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China; Food Laboratory of Zhongyuan, Luohe, 462300, Henan, China.
| | - Yuetong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China.
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3
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Liu Z, Chen S, Wu J. Advances in ultrahigh-throughput screening technologies for protein evolution. Trends Biotechnol 2023; 41:1168-1181. [PMID: 37088569 DOI: 10.1016/j.tibtech.2023.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/28/2023] [Accepted: 03/14/2023] [Indexed: 04/25/2023]
Abstract
Inspired by natural evolution, directed evolution randomly mutates the gene of interest through artificial evolution conditions with variants being screened for the required properties. Directed evolution is vital to the enhancement of protein properties and comprises the construction of libraries with considerable diversity as well as screening methods with sufficient efficiency as key steps. Owing to the various characteristics of proteins, specific methods are urgently needed for library screening, which is one of the main limiting factors in accelerating evolution. This review initially organizes the principles of ultrahigh-throughput screening from the perspective of protein properties. It then provides a comprehensive introduction to the latest progress and future trends in ultrahigh-throughput screening technologies for directed evolution.
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Affiliation(s)
- Zhanzhi Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China
| | - Sheng Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China.
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4
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Gantz M, Neun S, Medcalf EJ, van Vliet LD, Hollfelder F. Ultrahigh-Throughput Enzyme Engineering and Discovery in In Vitro Compartments. Chem Rev 2023; 123:5571-5611. [PMID: 37126602 PMCID: PMC10176489 DOI: 10.1021/acs.chemrev.2c00910] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Novel and improved biocatalysts are increasingly sourced from libraries via experimental screening. The success of such campaigns is crucially dependent on the number of candidates tested. Water-in-oil emulsion droplets can replace the classical test tube, to provide in vitro compartments as an alternative screening format, containing genotype and phenotype and enabling a readout of function. The scale-down to micrometer droplet diameters and picoliter volumes brings about a >107-fold volume reduction compared to 96-well-plate screening. Droplets made in automated microfluidic devices can be integrated into modular workflows to set up multistep screening protocols involving various detection modes to sort >107 variants a day with kHz frequencies. The repertoire of assays available for droplet screening covers all seven enzyme commission (EC) number classes, setting the stage for widespread use of droplet microfluidics in everyday biochemical experiments. We review the practicalities of adapting droplet screening for enzyme discovery and for detailed kinetic characterization. These new ways of working will not just accelerate discovery experiments currently limited by screening capacity but profoundly change the paradigms we can probe. By interfacing the results of ultrahigh-throughput droplet screening with next-generation sequencing and deep learning, strategies for directed evolution can be implemented, examined, and evaluated.
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Affiliation(s)
- Maximilian Gantz
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Stefanie Neun
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Elliot J Medcalf
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Liisa D van Vliet
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
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5
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Vanella R, Kovacevic G, Doffini V, Fernández de Santaella J, Nash MA. High-throughput screening, next generation sequencing and machine learning: advanced methods in enzyme engineering. Chem Commun (Camb) 2022; 58:2455-2467. [PMID: 35107442 PMCID: PMC8851469 DOI: 10.1039/d1cc04635g] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 01/23/2022] [Indexed: 12/29/2022]
Abstract
Enzyme engineering is an important biotechnological process capable of generating tailored biocatalysts for applications in industrial chemical conversion and biopharma. Typical enhancements sought in enzyme engineering and in vitro evolution campaigns include improved folding stability, catalytic activity, and/or substrate specificity. Despite significant progress in recent years in the areas of high-throughput screening and DNA sequencing, our ability to explore the vast space of functional enzyme sequences remains severely limited. Here, we review the currently available suite of modern methods for enzyme engineering, with a focus on novel readout systems based on enzyme cascades, and new approaches to reaction compartmentalization including single-cell hydrogel encapsulation techniques to achieve a genotype-phenotype link. We further summarize systematic scanning mutagenesis approaches and their merger with deep mutational scanning and massively parallel next-generation DNA sequencing technologies to generate mutability landscapes. Finally, we discuss the implementation of machine learning models for computational prediction of enzyme phenotypic fitness from sequence. This broad overview of current state-of-the-art approaches for enzyme engineering and evolution will aid newcomers and experienced researchers alike in identifying the important challenges that should be addressed to move the field forward.
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Affiliation(s)
- Rosario Vanella
- Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.
| | - Gordana Kovacevic
- Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.
| | - Vanni Doffini
- Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.
| | - Jaime Fernández de Santaella
- Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.
| | - Michael A Nash
- Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.
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6
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Liu D, Sun M, Zhang J, Hu R, Fu W, Xuanyuan T, Liu W. Single-cell droplet microfluidics for biomedical applications. Analyst 2022; 147:2294-2316. [DOI: 10.1039/d1an02321g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review focuses on the recent advances in the fundamentals of single-cell droplet microfluidics and its applications in biomedicine, providing insights into design and establishment of single-cell microsystems and their further performance.
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Affiliation(s)
- Dan Liu
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Meilin Sun
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Jinwei Zhang
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Rui Hu
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Wenzhu Fu
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Tingting Xuanyuan
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Wenming Liu
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
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7
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Directed Evolution Methods for Enzyme Engineering. Molecules 2021; 26:molecules26185599. [PMID: 34577070 PMCID: PMC8470892 DOI: 10.3390/molecules26185599] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/17/2021] [Accepted: 08/17/2021] [Indexed: 11/22/2022] Open
Abstract
Enzymes underpin the processes required for most biotransformations. However, natural enzymes are often not optimal for biotechnological uses and must be engineered for improved activity, specificity and stability. A rich and growing variety of wet-lab methods have been developed by researchers over decades to accomplish this goal. In this review such methods and their specific attributes are examined.
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8
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Li M, Liu H, Zhuang S, Goda K. Droplet flow cytometry for single-cell analysis. RSC Adv 2021; 11:20944-20960. [PMID: 35479393 PMCID: PMC9034116 DOI: 10.1039/d1ra02636d] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 06/06/2021] [Indexed: 01/22/2023] Open
Abstract
The interrogation of single cells has revolutionised biology and medicine by providing crucial unparalleled insights into cell-to-cell heterogeneity. Flow cytometry (including fluorescence-activated cell sorting) is one of the most versatile and high-throughput approaches for single-cell analysis by detecting multiple fluorescence parameters of individual cells in aqueous suspension as they flow past through a focus of excitation lasers. However, this approach relies on the expression of cell surface and intracellular biomarkers, which inevitably lacks spatial and temporal phenotypes and activities of cells, such as secreted proteins, extracellular metabolite production, and proliferation. Droplet microfluidics has recently emerged as a powerful tool for the encapsulation and manipulation of thousands to millions of individual cells within pico-litre microdroplets. Integrating flow cytometry with microdroplet architectures surrounded by aqueous solutions (e.g., water-in-oil-in-water (W/O/W) double emulsion and hydrogel droplets) opens avenues for new cellular assays linking cell phenotypes to genotypes at the single-cell level. In this review, we discuss the capabilities and applications of droplet flow cytometry (DFC). This unique technique uses standard commercially available flow cytometry instruments to characterise or select individual microdroplets containing single cells of interest. We explore current challenges associated with DFC and present our visions for future development.
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Affiliation(s)
- Ming Li
- School of Engineering, Macquarie University Sydney NSW 2109 Australia
- Biomolecular Discovery Research Centre, Macquarie University Sydney NSW 2109 Australia
| | - Hangrui Liu
- Department of Physics and Astronomy, Macquarie University Sydney NSW 2109 Australia
| | - Siyuan Zhuang
- School of Engineering, Macquarie University Sydney NSW 2109 Australia
| | - Keisuke Goda
- Department of Chemistry, The University of Tokyo Tokyo 113-0033 Japan
- Institute of Technological Sciences, Wuhan University 430072 Hubei PR China
- Department of Bioengineering, University of California Los Angeles CA 90095 USA
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9
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Wang M, Nai MH, Huang RYJ, Leo HL, Lim CT, Chen CH. High-throughput functional profiling of single adherent cells via hydrogel drop-screen. LAB ON A CHIP 2021; 21:764-774. [PMID: 33506832 DOI: 10.1039/d0lc01294g] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Single-adherent-cell phenotyping on an extracellular matrix (ECM) is essential to determine cellular biological functions, such as morphological adaptations and biomolecule secretions, correlated to medical treatments and metastasis, yet there is no available platform for such high-throughput screening. Here, a novel hydrogel drop-screen device was developed to rapidly measure large-scale single-cell morphologies and multiple secretions on substrates for phenotype profiling. Single cells were first anchored to microfluidically fabricated gelatin particles providing mechanical stimulations similar to those from ECM in vivo. The cellular morphologies were then examined by quantifying the amount of cytoskeleton expressed on the particles. With droplet encapsulation, adherent single-cell multiplexed secretion analysis of a disintegrin and metalloproteinases (ADAMs) and matrix metalloproteinases (MMPs) was conducted at a throughput of ∼102 cells per second, revealing distinct functional heterogeneities associated with extracellular mechanical stimulations. The level of cell heterogeneity increased with increasing substrate stuffiness. Moreover, because of the promising screening capability, a database related to both nontumorigenic and tumorigenic breast cells (MCF10A, MCF-7, and MDA-MB-231) was constructed. The respective cell distributions and heterogeneities based on the morphologies and secreted bioindicators, such as MMP-2, MMP-3, MMP-9, and ADAM-8, were measured and found to correspond to the progress of tumor metastasis.
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Affiliation(s)
- Ming Wang
- NUS Graduate School for Integrative Sciences & Engineering, National University of Singapore, 21 Lower Kent Ridge Road, 119077 Singapore and Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 117583 Singapore and Institute for Health Innovation and Technology (iHealthtech), MD6, 14 Medical Drive 14-01, 117599 Singapore
| | - Mui Hoon Nai
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 117583 Singapore
| | - Ruby Yun-Ju Huang
- College of Medicine, National Taiwan University, No.1 Jen-Ai Road, Taipei, 10051, Taiwan and Graduate Institute of Oncology, College of Medicine, National Taiwan University, No. 1, Sec. 4, Roosevelt road, Taipei, 10617, Taiwan and Department of Biomedical Engineering, National Taiwan University, No.1, Sec.1, Jen-Ai Road, Taipei, 10051, Taiwan
| | - Hwa Liang Leo
- NUS Graduate School for Integrative Sciences & Engineering, National University of Singapore, 21 Lower Kent Ridge Road, 119077 Singapore and Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 117583 Singapore
| | - Chwee Teck Lim
- NUS Graduate School for Integrative Sciences & Engineering, National University of Singapore, 21 Lower Kent Ridge Road, 119077 Singapore and Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 117583 Singapore and Institute for Health Innovation and Technology (iHealthtech), MD6, 14 Medical Drive 14-01, 117599 Singapore and Mechanobiology Institute, National University of Singapore, 117411 Singapore
| | - Chia-Hung Chen
- Department of Biomedical Engineering, City University of Hong Kong, Y6700, 83 Tat Chee Avenue, Hong Kong SAR, China.
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10
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Affiliation(s)
- Zhongmin Tang
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics Chinese Academy of Sciences, Shanghai 200050, P. R. China
- Center for Nanomedicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Peiran Zhao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, P. R. China
| | - Han Wang
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics Chinese Academy of Sciences, Shanghai 200050, P. R. China
| | - Yanyan Liu
- Department of Materials Science, Fudan University, Shanghai 200433, P. R. China
| | - Wenbo Bu
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics Chinese Academy of Sciences, Shanghai 200050, P. R. China
- Department of Materials Science, Fudan University, Shanghai 200433, P. R. China
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11
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Herzog PL, Borghi E, Traxlmayr MW, Obinger C, Sikes HD, Peterbauer CK. Developing a cell-bound detection system for the screening of oxidase activity using the fluorescent peroxide sensor roGFP2-Orp1. Protein Eng Des Sel 2020; 33:gzaa019. [PMID: 32930800 PMCID: PMC7720637 DOI: 10.1093/protein/gzaa019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 06/02/2020] [Accepted: 07/08/2020] [Indexed: 11/14/2022] Open
Abstract
Accurate yet efficient high-throughput screenings have emerged as essential technology for enzyme engineering via directed evolution. Modern high-throughput screening platforms for oxidoreductases are commonly assisted by technologies such as surface display and rely on emulsification techniques to facilitate single-cell analysis via fluorescence-activated cell sorting. Empowered by the dramatically increased throughput, the screening of significantly larger sequence spaces in acceptable time frames is achieved but usually comes at the cost of restricted applicability. In this work, we tackle this problem by utilizing roGFP2-Orp1 as a fluorescent one-component detection system for enzymatic H2O2 formation. We determined the kinetic parameters of the roGFP2-Orp1 reaction with H2O2 and established an efficient immobilization technique for the sensor on Saccharomyces cerevisiae cells employing the lectin Concanavalin A. This allowed to realize a peroxide-sensing shell on enzyme-displaying cells, a system that was successfully employed to screen for H2O2 formation of enzyme variants in a whole-cell setting.
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Affiliation(s)
- P L Herzog
- Food Biotechnology Laboratory, Department of Food Science and Technology, BOKU – University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
| | - E Borghi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 287, 41124 Modena, Italy
| | - M W Traxlmayr
- Institute of Biochemistry, Department of Chemistry, BOKU – University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - C Obinger
- Institute of Biochemistry, Department of Chemistry, BOKU – University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - H D Sikes
- Department of Chemical Engineering, MIT – Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge 02139, MA, USA
| | - C K Peterbauer
- Food Biotechnology Laboratory, Department of Food Science and Technology, BOKU – University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
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12
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Graham AJ, Dundas CM, Hillsley A, Kasprak DS, Rosales AM, Keitz BK. Genetic Control of Radical Cross-linking in a Semisynthetic Hydrogel. ACS Biomater Sci Eng 2020; 6:1375-1386. [PMID: 33313392 DOI: 10.1021/acsbiomaterials.9b01773] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Enhancing materials with the qualities of living systems, including sensing, computation, and adaptation, is an important challenge in designing next-generation technologies. Living materials address this challenge by incorporating live cells as actuating components that control material function. For abiotic materials, this requires new methods that couple genetic and metabolic processes to material properties. Toward this goal, we demonstrate that extracellular electron transfer (EET) from Shewanella oneidensis can be leveraged to control radical cross-linking of a methacrylate-functionalized hyaluronic acid hydrogel. Cross-linking rates and hydrogel mechanics, specifically storage modulus, were dependent on various chemical and biological factors, including S. oneidensis genotype. Bacteria remained viable and metabolically active in the networks for a least 1 week, while cell tracking revealed that EET genes also encode control over hydrogel microstructure. Moreover, construction of an inducible gene circuit allowed transcriptional control of storage modulus and cross-linking rate via the tailored expression of a key electron transfer protein, MtrC. Finally, we quantitatively modeled hydrogel stiffness as a function of steady-state mtrC expression and generalized this result by demonstrating the strong relationship between relative gene expression and material properties. This general mechanism for radical cross-linking provides a foundation for programming the form and function of synthetic materials through genetic control over extracellular electron transfer.
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Affiliation(s)
- Austin J Graham
- McKetta Department of Chemical Engineering and Center for Dynamics and Control of Materials, University of Texas at Austin, Austin, Texas 78712, United States
| | - Christopher M Dundas
- McKetta Department of Chemical Engineering and Center for Dynamics and Control of Materials, University of Texas at Austin, Austin, Texas 78712, United States
| | - Alexander Hillsley
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Dain S Kasprak
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Adrianne M Rosales
- McKetta Department of Chemical Engineering and Center for Dynamics and Control of Materials, University of Texas at Austin, Austin, Texas 78712, United States
| | - Benjamin K Keitz
- McKetta Department of Chemical Engineering and Center for Dynamics and Control of Materials, University of Texas at Austin, Austin, Texas 78712, United States
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13
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Markel U, Essani KD, Besirlioglu V, Schiffels J, Streit WR, Schwaneberg U. Advances in ultrahigh-throughput screening for directed enzyme evolution. Chem Soc Rev 2020; 49:233-262. [PMID: 31815263 DOI: 10.1039/c8cs00981c] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enzymes are versatile catalysts and their synthetic potential has been recognized for a long time. In order to exploit their full potential, enzymes often need to be re-engineered or optimized for a given application. (Semi-) rational design has emerged as a powerful means to engineer proteins, but requires detailed knowledge about structure function relationships. In turn, directed evolution methodologies, which consist of iterative rounds of diversity generation and screening, can improve an enzyme's properties with virtually no structural knowledge. Current diversity generation methods grant us access to a vast sequence space (libraries of >1012 enzyme variants) that may hide yet unexplored catalytic activities and selectivity. However, the time investment for conventional agar plate or microtiter plate-based screening assays represents a major bottleneck in directed evolution and limits the improvements that are obtainable in reasonable time. Ultrahigh-throughput screening (uHTS) methods dramatically increase the number of screening events per time, which is crucial to speed up biocatalyst design, and to widen our knowledge about sequence function relationships. In this review, we summarize recent advances in uHTS for directed enzyme evolution. We shed light on the importance of compartmentalization to preserve the essential link between genotype and phenotype and discuss how cells and biomimetic compartments can be applied to serve this function. Finally, we discuss how uHTS can inspire novel functional metagenomics approaches to identify natural biocatalysts for novel chemical transformations.
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Affiliation(s)
- Ulrich Markel
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany.
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14
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Ma C, Tan ZL, Lin Y, Han S, Xing X, Zhang C. Gel microdroplet–based high-throughput screening for directed evolution of xylanase-producing Pichia pastoris. J Biosci Bioeng 2019; 128:662-668. [DOI: 10.1016/j.jbiosc.2019.05.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 05/11/2019] [Accepted: 05/13/2019] [Indexed: 01/24/2023]
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15
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Zou Z, Gau E, El-Awaad I, Jakob F, Pich A, Schwaneberg U. Selective Functionalization of Microgels with Enzymes by Sortagging. Bioconjug Chem 2019; 30:2859-2869. [DOI: 10.1021/acs.bioconjchem.9b00568] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Zhi Zou
- DWI − Leibniz-Institute for Interactive Materials, Forckenbeckstraβe 50, 52074 Aachen, Germany
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Elisabeth Gau
- DWI − Leibniz-Institute for Interactive Materials, Forckenbeckstraβe 50, 52074 Aachen, Germany
- Functional and Interactive Polymers, Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
| | - Islam El-Awaad
- DWI − Leibniz-Institute for Interactive Materials, Forckenbeckstraβe 50, 52074 Aachen, Germany
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Felix Jakob
- DWI − Leibniz-Institute for Interactive Materials, Forckenbeckstraβe 50, 52074 Aachen, Germany
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Andrij Pich
- DWI − Leibniz-Institute for Interactive Materials, Forckenbeckstraβe 50, 52074 Aachen, Germany
- Functional and Interactive Polymers, Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
- Aachen Maastricht Institute for Biobased Materials (AMIBM), Maastricht University, Brightlands Chemelot Campus, Urmonderbaan22, 6167 RD Geleen, The Netherlands
| | - Ulrich Schwaneberg
- DWI − Leibniz-Institute for Interactive Materials, Forckenbeckstraβe 50, 52074 Aachen, Germany
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
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16
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Chiu FWY, Stavrakis S. High-throughput droplet-based microfluidics for directed evolution of enzymes. Electrophoresis 2019; 40:2860-2872. [PMID: 31433062 PMCID: PMC6899980 DOI: 10.1002/elps.201900222] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/10/2019] [Accepted: 08/12/2019] [Indexed: 01/12/2023]
Abstract
Natural enzymes have evolved over millions of years to allow for their effective operation within specific environments. However, it is significant to note that despite their wide structural and chemical diversity, relatively few natural enzymes have been successfully applied to industrial processes. To address this limitation, directed evolution (DE) (a method that mimics the process of natural selection to evolve proteins toward a user‐defined goal) coupled with droplet‐based microfluidics allows the detailed analysis of millions of enzyme variants on ultra‐short timescales, and thus the design of novel enzymes with bespoke properties. In this review, we aim at presenting the development of DE over the last years and highlighting the most important advancements in droplet‐based microfluidics, made in this context towards the high‐throughput demands of enzyme optimization. Specifically, an overview of the range of microfluidic unit operations available for the construction of DE platforms is provided, focusing on their suitability and benefits for cell‐based assays, as in the case of directed evolution experimentations.
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Affiliation(s)
- Flora W Y Chiu
- Institute for Chemical and Bioengineering, ETH Zürich, Zürich, Switzerland
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, ETH Zürich, Zürich, Switzerland
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17
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Reyhani A, McKenzie TG, Fu Q, Qiao GG. Fenton‐Chemistry‐Mediated Radical Polymerization. Macromol Rapid Commun 2019; 40:e1900220. [DOI: 10.1002/marc.201900220] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/11/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Amin Reyhani
- Polymer Science Group, Department of Chemical EngineeringThe University of Melbourne Parkville VIC 3010 Australia
| | - Thomas G. McKenzie
- Polymer Science Group, Department of Chemical EngineeringThe University of Melbourne Parkville VIC 3010 Australia
| | - Qiang Fu
- Polymer Science Group, Department of Chemical EngineeringThe University of Melbourne Parkville VIC 3010 Australia
| | - Greg G. Qiao
- Polymer Science Group, Department of Chemical EngineeringThe University of Melbourne Parkville VIC 3010 Australia
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18
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Vanella R, Ta DT, Nash MA. Enzyme‐mediated hydrogel encapsulation of single cells for high‐throughput screening and directed evolution of oxidoreductases. Biotechnol Bioeng 2019; 116:1878-1886. [DOI: 10.1002/bit.27002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/09/2019] [Accepted: 04/25/2019] [Indexed: 01/10/2023]
Affiliation(s)
- Rosario Vanella
- Department of ChemistryUniversity of BaselBasel Switzerland
- Department of Biosystems Science and EngineeringETH ZurichBasel Switzerland
| | - Duy Tien Ta
- Department of ChemistryUniversity of BaselBasel Switzerland
- Department of Biosystems Science and EngineeringETH ZurichBasel Switzerland
| | - Michael A. Nash
- Department of ChemistryUniversity of BaselBasel Switzerland
- Department of Biosystems Science and EngineeringETH ZurichBasel Switzerland
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19
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Apitius L, Rübsam K, Jakesch C, Jakob F, Schwaneberg U. Ultrahigh‐throughput screening system for directed polymer binding peptide evolution. Biotechnol Bioeng 2019; 116:1856-1867. [DOI: 10.1002/bit.26990] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 03/28/2019] [Accepted: 04/11/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Lina Apitius
- DWI – Leibniz‐Institute for Interactive MaterialsAachen Germany
- RWTH Aachen UniversityAachen Germany
| | - Kristin Rübsam
- DWI – Leibniz‐Institute for Interactive MaterialsAachen Germany
| | | | - Felix Jakob
- DWI – Leibniz‐Institute for Interactive MaterialsAachen Germany
- RWTH Aachen UniversityAachen Germany
| | - Ulrich Schwaneberg
- DWI – Leibniz‐Institute for Interactive MaterialsAachen Germany
- RWTH Aachen UniversityAachen Germany
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20
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Sanagavarapu K, Nüske E, Nasir I, Meisl G, Immink JN, Sormanni P, Vendruscolo M, Knowles TPJ, Malmendal A, Cabaleiro-Lago C, Linse S. A method of predicting the in vitro fibril formation propensity of Aβ40 mutants based on their inclusion body levels in E. coli. Sci Rep 2019; 9:3680. [PMID: 30842594 PMCID: PMC6403284 DOI: 10.1038/s41598-019-39216-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 12/12/2018] [Indexed: 12/12/2022] Open
Abstract
Overexpression of recombinant proteins in bacteria may lead to their aggregation and deposition in inclusion bodies. Since the conformational properties of proteins in inclusion bodies exhibit many of the characteristics typical of amyloid fibrils. Based on these findings, we hypothesize that the rate at which proteins form amyloid fibrils may be predicted from their propensity to form inclusion bodies. To establish a method based on this concept, we first measured by SDS-PAGE and confocal microscopy the level of inclusion bodies in E. coli cells overexpressing the 40-residue amyloid-beta peptide, Aβ40, wild-type and 24 charge mutants. We then compared these results with a number of existing computational aggregation propensity predictors as well as the rates of aggregation measured in vitro for selected mutants. Our results show a strong correlation between the level of inclusion body formation and aggregation propensity, thus demonstrating the power of this approach and its value in identifying factors modulating aggregation kinetics.
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Affiliation(s)
- Kalyani Sanagavarapu
- Lund University, Biochemistry and Structural Biology, Chemical Center, Lund, Sweden.
| | | | - Irem Nasir
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 N, Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Georg Meisl
- University of Cambridge, Chemistry Department, Lensfield Road, Cambridge, UK
| | - Jasper N Immink
- Lund University, Physical Chemistry, Chemical Center, Lund, Sweden
| | - Pietro Sormanni
- University of Cambridge, Chemistry Department, Lensfield Road, Cambridge, UK
| | - Michele Vendruscolo
- University of Cambridge, Chemistry Department, Lensfield Road, Cambridge, UK
| | - Tuomas P J Knowles
- University of Cambridge, Chemistry Department, Lensfield Road, Cambridge, UK.,Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, UK
| | - Anders Malmendal
- Lund University, Biochemistry and Structural Biology, Chemical Center, Lund, Sweden
| | - Celia Cabaleiro-Lago
- Lund University, Biochemistry and Structural Biology, Chemical Center, Lund, Sweden.,Faculty of natural sciences, Kristianstad University, Kristianstad, Sweden
| | - Sara Linse
- Lund University, Biochemistry and Structural Biology, Chemical Center, Lund, Sweden.
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21
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Development of GFP-based high-throughput screening system for directed evolution of glucose oxidase. J Biosci Bioeng 2019; 127:30-37. [DOI: 10.1016/j.jbiosc.2018.07.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 06/26/2018] [Accepted: 07/01/2018] [Indexed: 01/15/2023]
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22
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Integrating enzyme immobilization and protein engineering: An alternative path for the development of novel and improved industrial biocatalysts. Biotechnol Adv 2018; 36:1470-1480. [DOI: 10.1016/j.biotechadv.2018.06.002] [Citation(s) in RCA: 168] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 05/02/2018] [Accepted: 06/04/2018] [Indexed: 12/15/2022]
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23
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Qu J, Zhao X, Ma PX, Guo B. Injectable antibacterial conductive hydrogels with dual response to an electric field and pH for localized "smart" drug release. Acta Biomater 2018; 72:55-69. [PMID: 29555459 DOI: 10.1016/j.actbio.2018.03.018] [Citation(s) in RCA: 239] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 02/25/2018] [Accepted: 03/07/2018] [Indexed: 12/28/2022]
Abstract
Injectable hydrogels with multistimuli responsiveness to electrical field and pH as a drug delivery system have been rarely reported. Herein, we developed a series of injectable conductive hydrogels as "smart" drug carrier with the properties of electro-responsiveness, pH-sensitivity, and inherent antibacterial activity. The hydrogels were prepared by mixing chitosan-graft-polyaniline (CP) copolymer and oxidized dextran (OD) as a cross-linker. The chemical structures, morphologies, electrochemical property, swelling ratio, conductivity, rheological property, in vitro and in vivo biodegradation, and gelation time of hydrogels were characterized. The pH-responsive behavior was verified by drug release from hydrogels in PBS solutions with different pH values (pH = 7.4 or 5.5) in an in vitro model. As drug carriers with electric-driven release, the release rate of the model drugs amoxicillin and ibuprofen loaded within CP/OD hydrogels dramatically increased when an increase in voltage was applied. Both chitosan and polyaniline with inherent antibacterial properties endowed the hydrogels with excellent antibacterial properties. Furthermore, cytotoxicity tests of the hydrogels using L929 cells confirmed their good cytocompatibility. The in vivo biocompatibility of the hydrogels was verified by H&E staining. Together, all these results suggest that these injectable pH-sensitive conductive hydrogels with antibacterial activity could be ideal candidates as smart drug delivery vehicles for precise doses of medicine to meet practical demand. STATEMENT OF SIGNIFICANCE Stimuli-responsive or "smart" hydrogels have attracted great attention in the field of biotechnology and biomedicine, especially on designing novel drug delivery systems. Compared with traditional implantable electronic delivery devices, the injectable hydrogels with electrical stimuli not only are easy to generate and control electrical field but also could avoid frequent invasive surgeries that offer a new avenue for chronic diseases. In addition, designing a drug carrier with pH-sensitive property could release drug efficiently in targeted acid environment, and it could reinforce the precise doses of medicine. Furthermore, caused by opportunistic microorganisms and rapid spread of antibiotic-resistant microbes, infection is still a serious threat for many clinical utilities. To overcome these barriers, we designed a series of injectable antibacterial conductive hydrogels based on chitosan-graft-polyaniline (CP) copolymer and oxidized dextran (OD), and we demonstrated their potential as "smart" delivery vehicles with electro-responsiveness and pH-responsive properties for triggered and localized release of drugs.
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24
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Zou Z, Mate DM, Rübsam K, Jakob F, Schwaneberg U. Sortase-Mediated High-Throughput Screening Platform for Directed Enzyme Evolution. ACS COMBINATORIAL SCIENCE 2018; 20:203-211. [PMID: 29363945 DOI: 10.1021/acscombsci.7b00153] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Sortase-catalyzed ligations have emerged as powerful tools for the site-specific ligation of peptides and proteins in material science and biocatalysis. In this work, a directed sortase evolution strategy (SortEvolve) has been developed as a general high-throughput screening (HTS) platform to improve activity of sortase A (application 1) and to perform directed laccase evolution through a semipurification process in 96-well microtiter plate (MTP) (application 2). A semipurification process in polypropylene MTP (PP-MTP) is achieved through the anchor peptide LCI, which acts as adhesion promoter. To validate the SortEvolve screening platform for both applications, three site-saturation mutagenesis (SSM) libraries of sortase A (Sa-SrtA) from Staphylococcus aureus (application 1) and two SSM libraries of the copper efflux oxidase (CueO laccase) from Escherichia coli (application 2) were generated at literature reported positions. After screening and rescreening, an array of Sa-SrtA variants (including the previously reported P94S, D160N, and D165A) and CueO variants (including the previously reported D439A and P444A) were identified. Further recombinant Sa-SrtA variant P94T/D160L/D165Q and CueO variant D439V/P444V were characterized with 22-fold and 103-fold improvements in catalytic efficiency compared with corresponding wild-types, respectively. An important advantage of the SortEvolve screening platform in comparison to many MTP-based screening systems is that the background noise was minimized (decreased 20-fold; application 2) due to the employed semipurification process. In essence, SortEvolve provides a universal surface-functionalized screening platform for sortases and enzymes in which especially background activity can be minimized to enable successful directed evolution campaigns.
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Affiliation(s)
- Zhi Zou
- DWI—Leibniz-Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Diana M. Mate
- DWI—Leibniz-Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany
| | - Kristin Rübsam
- DWI—Leibniz-Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany
| | - Felix Jakob
- DWI—Leibniz-Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany
| | - Ulrich Schwaneberg
- DWI—Leibniz-Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
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25
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Wang J, Ma X, Wei L, Zhu X, Zhu Y, Wang G, Mei T, Li J, Wang X. Construction of high-strength p(HEMA-co-AA) fluorescent hydrogels based on modified carbon dots as chemically crosslinkers. Colloid Polym Sci 2018. [DOI: 10.1007/s00396-018-4287-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Evolution of enzymes with new specificity by high-throughput screening using DmpR-based genetic circuits and multiple flow cytometry rounds. Sci Rep 2018; 8:2659. [PMID: 29422524 PMCID: PMC5805759 DOI: 10.1038/s41598-018-20943-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/26/2018] [Indexed: 11/12/2022] Open
Abstract
Genetic circuit-based biosensors are useful in detecting target metabolites or in vivo enzymes using transcription factors (Tx) as a molecular switch to express reporter signals, such as cellular fluorescence and antibiotic resistance. Herein, a phenol-detecting Tx (DmpR) was employed as a critical tool for enzyme engineering, specifically for the rapid analysis of numerous mutants with multiple mutations at the active site of tryptophan-indole lyase (TIL, EC 4.1.99.1). Cellular fluorescence was monitored cell-by-cell using flow cytometry to detect the creation of phenolic compounds by a new tyrosine-phenol-lyase (TPL, EC 4.1.99.2). In the TIL scaffold, target amino acids near the indole ring (Asp137, Phe304, Val394, Ile396 and His463) were mutated randomly to construct a large diversity of specificity variations. Collection of candidate positives by cell sorting using flow cytometry and subsequent shuffling of beneficial mutations identified a critical hit with four mutations (D137P, F304D, V394L, and I396R) in the TIL sequence. The variant displayed one-thirteenth the level of TPL activity, compared with native TPLs, and completely lost the original TIL activity. The findings demonstrate that hypersensitive, Tx-based biosensors could be useful critically to generate new activity from a related template, which would alleviate the current burden to high-throughput screening.
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27
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High-throughput strategies for the discovery and engineering of enzymes for biocatalysis. Bioprocess Biosyst Eng 2016; 40:161-180. [DOI: 10.1007/s00449-016-1690-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 10/05/2016] [Indexed: 12/16/2022]
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28
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Cell size selection in Chlamydomonas reinhardtii gametes using fluorescence activated cell sorting. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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29
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Malinowska KH, Nash MA. Enzyme- and affinity biomolecule-mediated polymerization systems for biological signal amplification and cell screening. Curr Opin Biotechnol 2016; 39:68-75. [DOI: 10.1016/j.copbio.2016.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 01/23/2016] [Indexed: 11/28/2022]
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30
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Körfer G, Pitzler C, Vojcic L, Martinez R, Schwaneberg U. In vitro flow cytometry-based screening platform for cellulase engineering. Sci Rep 2016; 6:26128. [PMID: 27184298 PMCID: PMC4869107 DOI: 10.1038/srep26128] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 04/15/2016] [Indexed: 01/08/2023] Open
Abstract
Ultrahigh throughput screening (uHTS) plays an essential role in directed evolution for tailoring biocatalysts for industrial applications. Flow cytometry-based uHTS provides an efficient coverage of the generated protein sequence space by analysis of up to 107 events per hour. Cell-free enzyme production overcomes the challenge of diversity loss during the transformation of mutant libraries into expression hosts, enables directed evolution of toxic enzymes, and holds the promise to efficiently design enzymes of human or animal origin. The developed uHTS cell-free compartmentalization platform (InVitroFlow) is the first report in which a flow cytometry-based screened system has been combined with compartmentalized cell-free expression for directed cellulase enzyme evolution. InVitroFlow was validated by screening of a random cellulase mutant library employing a novel screening system (based on the substrate fluorescein-di-β-D-cellobioside), and yielded significantly improved cellulase variants (e.g. CelA2-H288F-M1 (N273D/H288F/N468S) with 13.3-fold increased specific activity (220.60 U/mg) compared to CelA2 wildtype: 16.57 U/mg).
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Affiliation(s)
| | | | - Ljubica Vojcic
- RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany
| | - Ronny Martinez
- RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany
| | - Ulrich Schwaneberg
- RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany.,DWI an der RWTH Aachen e.V, Forckenbeckstraße 50, 52056 Aachen, Germany
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31
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High-Throughput Screening in Protein Engineering: Recent Advances and Future Perspectives. Int J Mol Sci 2015; 16:24918-45. [PMID: 26492240 PMCID: PMC4632782 DOI: 10.3390/ijms161024918] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 10/13/2015] [Accepted: 10/13/2015] [Indexed: 11/17/2022] Open
Abstract
Over the last three decades, protein engineering has established itself as an important tool for the development of enzymes and (therapeutic) proteins with improved characteristics. New mutagenesis techniques and computational design tools have greatly aided in the advancement of protein engineering. Yet, one of the pivotal components to further advance protein engineering strategies is the high-throughput screening of variants. Compartmentalization is one of the key features allowing miniaturization and acceleration of screening. This review focuses on novel screening technologies applied in protein engineering, highlighting flow cytometry- and microfluidics-based platforms.
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32
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Malinowska KH, Rind T, Verdorfer T, Gaub HE, Nash MA. Quantifying Synergy, Thermostability, and Targeting of Cellulolytic Enzymes and Cellulosomes with Polymerization-Based Amplification. Anal Chem 2015; 87:7133-40. [DOI: 10.1021/acs.analchem.5b00936] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Klara H. Malinowska
- Lehrstuhl für Angewandte
Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Thomas Rind
- Lehrstuhl für Angewandte
Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Tobias Verdorfer
- Lehrstuhl für Angewandte
Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Hermann E. Gaub
- Lehrstuhl für Angewandte
Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Michael A. Nash
- Lehrstuhl für Angewandte
Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
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33
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Lülsdorf N, Pitzler C, Biggel M, Martinez R, Vojcic L, Schwaneberg U. A flow cytometer-based whole cell screening toolbox for directed hydrolase evolution through fluorescent hydrogels. Chem Commun (Camb) 2015; 51:8679-82. [DOI: 10.1039/c5cc01791b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A high-throughput whole cell flow cytometer screening toolbox for hydrolases was validated by identification of improved esterase, lipase and cellulase variants.
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Affiliation(s)
- Nina Lülsdorf
- DWI-Leibniz Institut für Interaktive Materialien
- 52056 Aachen
- Germany
| | - Christian Pitzler
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Michael Biggel
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- 52074 Aachen
- Germany
| | | | - Ljubica Vojcic
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Ulrich Schwaneberg
- DWI-Leibniz Institut für Interaktive Materialien
- 52056 Aachen
- Germany
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
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