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Babinskas J, Sabotič J, Matijošytė I. Synthesis and application of a phenazine class substrate for high-throughput screening of laccase activity. Appl Microbiol Biotechnol 2024; 108:66. [PMID: 38194139 PMCID: PMC10776486 DOI: 10.1007/s00253-023-12958-7] [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: 08/23/2023] [Revised: 11/06/2023] [Accepted: 11/19/2023] [Indexed: 01/10/2024]
Abstract
Biocatalysis is one of the greatest tools for implementing the 12 principles of Green chemistry. Biocatalysts are bio-based, highly efficient and selective, operate at moderate conditions, and can be reused multiple times. However, the wider application of biocatalysts is plagued by a plethora of drawbacks, such as poor stability at operating conditions, inadequate efficiency of catalytic systems, a small number of commercially available biocatalysts, and a lack of substrates or methods for their discovery and development. In this work, we address the lack of suitable substrates for high-throughput screening of laccase by synthesising and investigating a newly developed phenazine-type substrate - Ferbamine. Investigation of Ferbamine pH and thermal stability indicated that its long-term stability in an aqueous medium is superior to that of commercially available substrates and does not require organic solvents. Ferbamine displayed convincing performance in detecting laccase activity on Ferbamine-agar plates in commercial laccase products and the collection of extracts from wild terrestrial fungi (42 species, 65 extracts), of which 26 species have not been described to have laccase activity prior to this work. Incubation of microorganisms on Ferbamine-agar plates showed its compatibility with live colonies. Ferbamine proved to be an easy-to-use substrate, which could be a great addition to the toolbox of methods for the functional analysis of laccases.
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Affiliation(s)
- Justinas Babinskas
- Life Sciences Center, Institute of Biotechnology, Sector of Applied Biocatalysis, Vilnius University, Saulėtekio ave. 7, Vilnius, LT-10257, Lithuania
| | - Jerica Sabotič
- Department of Biotechnology, Jožef Stefan Institute, Jamova cesta 39, Ljubljana, 1000, Slovenia
| | - Inga Matijošytė
- Life Sciences Center, Institute of Biotechnology, Sector of Applied Biocatalysis, Vilnius University, Saulėtekio ave. 7, Vilnius, LT-10257, Lithuania.
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2
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Sun X, Gao F, Fan C, Yang S, Zhao T, Tu T, Luo H, Yao B, Huang H, Su X. Sub-genomic RNAi-assisted strain evolution of filamentous fungi for enhanced protein production. Appl Environ Microbiol 2024; 90:e0208223. [PMID: 38899886 PMCID: PMC11267940 DOI: 10.1128/aem.02082-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Genetic engineering at the genomic scale provides a rapid means to evolve microbes for desirable traits. However, in many filamentous fungi, such trials are daunted by low transformation efficiency. Differentially expressed genes under certain conditions may contain important regulatory factors. Accordingly, although manipulating these subsets of genes only can largely reduce the time and labor, engineering at such a sub-genomic level may also be able to improve the microbial performance. Herein, first using the industrially important cellulase-producing filamentous fungus Trichoderma reesei as a model organism, we constructed suppression subtractive hybridization (SSH) libraries enriched with differentially expressed genes under cellulase induction (MM-Avicel) and cellulase repression conditions (MM-Glucose). The libraries, in combination with RNA interference, enabled sub-genomic engineering of T. reesei for enhanced cellulase production. The ability of T. reesei to produce endoglucanase was improved by 2.8~3.3-fold. In addition, novel regulatory genes (tre49304, tre120391, and tre123541) were identified to affect cellulase expression in T. reesei. Iterative manipulation using the same strategy further increased the yield of endoglucanase activity to 75.6 U/mL, which was seven times as high as that of the wild type (10.8 U/mL). Moreover, using Humicola insolens as an example, such a sub-genomic RNAi-assisted strain evolution proved to be also useful in other industrially important filamentous fungi. H. insolens is a filamentous fungus commonly used to produce catalase, albeit with similarly low transformation efficiency and scarce knowledge underlying the regulation of catalase expression. By combining SSH and RNAi, a strain of H. insolens producing 28,500 ± 288 U/mL of catalase was obtained, which was 1.9 times as high as that of the parent strain.IMPORTANCEGenetic engineering at the genomic scale provides an unparalleled advantage in microbial strain improvement, which has previously been limited only to the organisms with high transformation efficiency such as Saccharomyces cerevisiae and Escherichia coli. Herein, using the filamentous fungus Trichoderma reesei as a model organism, we demonstrated that the advantage of suppression subtractive hybridization (SSH) to enrich differentially expressed genes and the convenience of RNA interference to manipulate a multitude of genes could be combined to overcome the inadequate transformation efficiency. With this sub-genomic evolution strategy, T. reesei could be iteratively engineered for higher cellulase production. Intriguingly, Humicola insolens, a fungus with even little knowledge in gene expression regulation, was also improved for catalase production. The same strategy may also be expanded to engineering other microorganisms for enhanced production of proteins, organic acids, and secondary metabolites.
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Affiliation(s)
- Xianhua Sun
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fei Gao
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chao Fan
- Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, China
| | - Shuyan Yang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tong Zhao
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyun Su
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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3
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Vardar-Yel N, Tütüncü HE, Sürmeli Y. Lipases for targeted industrial applications, focusing on the development of biotechnologically significant aspects: A comprehensive review of recent trends in protein engineering. Int J Biol Macromol 2024; 273:132853. [PMID: 38838897 DOI: 10.1016/j.ijbiomac.2024.132853] [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: 04/15/2024] [Revised: 05/26/2024] [Accepted: 05/31/2024] [Indexed: 06/07/2024]
Abstract
Lipases are remarkable biocatalysts, adept at catalyzing the breakdown of diverse compounds into glycerol, fatty acids, and mono- and di-glycerides via hydrolysis. Beyond this, they facilitate esterification, transesterification, alcoholysis, acidolysis, and more, making them versatile in industrial applications. In industrial processes, lipases that exhibit high stability are favored as they can withstand harsh conditions. However, most native lipases are unable to endure adverse conditions, making them unsuitable for industrial use. Protein engineering proves to be a potent technology in the development of lipases that can function effectively under challenging conditions and fulfill criteria for various industrial processes. This review concentrated on new trends in protein engineering to enhance the diversity of lipase genes and employed in silico methods for predicting and comprehensively analyzing target mutations in lipases. Additionally, key molecular factors associated with industrial characteristics of lipases, including thermostability, solvent tolerance, catalytic activity, and substrate preference have been elucidated. The present review delved into how industrial traits can be enhanced through directed evolution (epPCR, gene shuffling), rational design (FRESCO, ASR), combined engineering strategies (i.e. CAST, ISM, and FRISM) as protein engineering methodologies in contexts of biodiesel production, food processing, and applications of detergent, pharmaceutics, and plastic degradation.
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Affiliation(s)
- Nurcan Vardar-Yel
- Department of Medical Laboratory Techniques, Altınbaş University, 34145 İstanbul, Turkey
| | - Havva Esra Tütüncü
- Department of Nutrition and Dietetics, Malatya Turgut Özal University, 44210 Malatya, Turkey
| | - Yusuf Sürmeli
- Department of Agricultural Biotechnology, Tekirdağ Namık Kemal University, 59030 Tekirdağ, Turkey.
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4
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O'Connell A, Barry A, Burke AJ, Hutton AE, Bell EL, Green AP, O'Reilly E. Biocatalysis: landmark discoveries and applications in chemical synthesis. Chem Soc Rev 2024; 53:2828-2850. [PMID: 38407834 DOI: 10.1039/d3cs00689a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Biocatalysis has become an important tool in chemical synthesis, allowing access to complex molecules with high levels of activity and selectivity and with low environmental impact. Key discoveries in protein engineering, bioinformatics, recombinant technology and DNA sequencing have contributed towards the rapid acceleration of the field. This tutorial review explores enzyme engineering strategies and high-throughput screening approaches that have been applied for the discovery and development of enzymes for synthetic application. Landmark developments in the field are discussed and have been carefully selected to highlight the diverse synthetic applications of enzymes within the pharmaceutical, agricultural, food and chemical industries. The design and development of artificial biocatalytic cascades is also examined. This tutorial review will give readers an insight into the landmark discoveries and milestones that have helped shape and grow this branch of catalysis since the discovery of the first enzyme.
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Affiliation(s)
- Adam O'Connell
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Amber Barry
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Ashleigh J Burke
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Amy E Hutton
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Elizabeth L Bell
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Anthony P Green
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Elaine O'Reilly
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland.
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5
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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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6
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Parida D, Katare K, Ganguly A, Chakraborty D, Konar O, Nogueira R, Bala K. Molecular docking and metagenomics assisted mitigation of microplastic pollution. CHEMOSPHERE 2024; 351:141271. [PMID: 38262490 DOI: 10.1016/j.chemosphere.2024.141271] [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: 09/29/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 01/25/2024]
Abstract
Microplastics, tiny, flimsy, and direct progenitors of principal and subsidiary plastics, cause environmental degradation in aquatic and terrestrial entities. Contamination concerns include irrevocable impacts, potential cytotoxicity, and negative health effects on mortals. The detection, recovery, and degradation strategies of these pollutants in various biota and ecosystems, as well as their impact on plants, animals, and humans, have been a topic of significant interest. But the natural environment is infested with several types of plastics, all having different chemical makeup, structure, shape, and origin. Plastic trash acts as a substrate for microbial growth, creating biofilms on the plastisphere surface. This colonizing microbial diversity can be glimpsed with meta-genomics, a culture-independent approach. Owing to its comprehensive description of microbial communities, genealogical evidence on unconventional biocatalysts or enzymes, genomic correlations, evolutionary profile, and function, it is being touted as one of the promising tools in identifying novel enzymes for the degradation of polymers. Additionally, computational tools such as molecular docking can predict the binding of these novel enzymes to the polymer substrate, which can be validated through in vitro conditions for its environmentally feasible applications. This review mainly deals with the exploration of metagenomics along with computational tools to provide a clearer perspective into the microbial potential in the biodegradation of microplastics. The computational tools due to their polymathic nature will be quintessential in identifying the enzyme structure, binding affinities of the prospective enzymes to the substrates, and foretelling of degradation pathways involved which can be quite instrumental in the furtherance of the plastic degradation studies.
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Affiliation(s)
- Dinesh Parida
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, 453552, India.
| | - Konica Katare
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, 453552, India.
| | - Atmaadeep Ganguly
- Department of Microbiology, Ramakrishna Mission Vivekananda Centenary College, West Bengal State University, Kolkata, 700118, India.
| | - Disha Chakraborty
- Department of Botany, Shri Shikshayatan College, University of Calcutta, Lord Sinha Road, Kolkata, 700071, India.
| | - Oisi Konar
- Department of Botany, Shri Shikshayatan College, University of Calcutta, Lord Sinha Road, Kolkata, 700071, India.
| | - Regina Nogueira
- Institute of Sanitary Engineering and Waste Management, Leibniz Universität, Hannover, Germany.
| | - Kiran Bala
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, 453552, India.
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7
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Sarangi PK, Srivastava RK, Sahoo UK, Singh AK, Parikh J, Bansod S, Parsai G, Luqman M, Shadangi KP, Diwan D, Lanterbecq D, Sharma M. Biotechnological innovations in nanocellulose production from waste biomass with a focus on pineapple waste. CHEMOSPHERE 2024; 349:140833. [PMID: 38043620 DOI: 10.1016/j.chemosphere.2023.140833] [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: 06/26/2023] [Revised: 11/17/2023] [Accepted: 11/26/2023] [Indexed: 12/05/2023]
Abstract
New materials' synthesis and utilization have shown many critical challenges in healthcare and other industrial sectors as most of these materials are directly or indirectly developed from fossil fuel resources. Environmental regulations and sustainability concepts have promoted the use of natural compounds with unique structures and properties that can be biodegradable, biocompatible, and eco-friendly. In this context, nanocellulose (NC) utility in different sectors and industries is reported due to their unique properties including biocompatibility and antimicrobial characteristics. The bacterial nanocellulose (BNC)-based materials have been synthesized by bacterial cells and extracted from plant waste materials including pineapple plant waste biomass. These materials have been utilized in the form of nanofibers and nanocrystals. These materials are found to have excellent surface properties, low density, and good transparency, and are rich in hydroxyl groups for their modifications to other useful products. These materials are well utilized in different sectors including biomedical or health care centres, nanocomposite materials, supercapacitors, and polymer matrix production. This review explores different approaches for NC production from pineapple waste residues using biotechnological interventions, approaches for their modification, and wider applications in different sectors. Recent technological developments in NC production by enzymatic treatment are critically discussed. The utilization of pineapple waste-derived NC from a bioeconomic perspective is summarized in the paper. The chemical composition and properties of nanocellulose extracted from pineapple waste may have unique characteristics compared to other sources. Pineapple waste for nanocellulose production aligns with the principles of sustainability, waste reduction, and innovation, making it a promising and novel approach in the field of nanocellulose materials.
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Affiliation(s)
- Prakash Kumar Sarangi
- College of Agriculture, Central Agricultural University, Imphal, 795004, Manipur, India
| | - Rajesh Kumar Srivastava
- Department of Biotechnology, GIT, Gandhi Institute of Technology and Management (GITAM), Visakhapatnam, 530045, India
| | | | - Akhilesh Kumar Singh
- Department of Biotechnology, Mahatma Gandhi Central University, Motihari, 845401, India
| | - Jigisha Parikh
- Department of Chemical Engineering, Sardar Vallabhbhai National Institute of Technology, Surat, 395007, Gujarat, India
| | - Shama Bansod
- Department of Chemical Engineering, Sardar Vallabhbhai National Institute of Technology, Surat, 395007, Gujarat, India
| | - Ganesh Parsai
- Department of Chemical Engineering, Sardar Vallabhbhai National Institute of Technology, Surat, 395007, Gujarat, India
| | - Mohammad Luqman
- Chemical Engineering Department, College of Engineering, Taibah University, Yanbu Al-Bahr-83, Al-Bandar District 41911, Kingdom of Saudi Arabia
| | - Krushna Prasad Shadangi
- Department of Chemical Engineering, Veer Surendra Sai University of Technology, Burla, Sambalpur, Odisha, 768018, India
| | - Deepti Diwan
- Washington University, School of Medicine, Saint Louis, MO, USA
| | - Deborah Lanterbecq
- Laboratoire de Biotechnologie et Biologie Appliquée, CARAH ASBL, Rue Paul Pastur, 11, Ath, 7800, Belgium
| | - Minaxi Sharma
- Laboratoire de Biotechnologie et Biologie Appliquée, CARAH ASBL, Rue Paul Pastur, 11, Ath, 7800, Belgium.
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8
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Hwang HG, Ye DY, Jung GY. Biosensor-guided discovery and engineering of metabolic enzymes. Biotechnol Adv 2023; 69:108251. [PMID: 37690614 DOI: 10.1016/j.biotechadv.2023.108251] [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: 05/08/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/12/2023]
Abstract
A variety of chemicals have been produced through metabolic engineering approaches, and enhancing biosynthesis performance can be achieved by using enzymes with high catalytic efficiency. Accordingly, a number of efforts have been made to discover enzymes in nature for various applications. In addition, enzyme engineering approaches have been attempted to suit specific industrial purposes. However, a significant challenge in enzyme discovery and engineering is the efficient screening of enzymes with the desired phenotype from extensive enzyme libraries. To overcome this bottleneck, genetically encoded biosensors have been developed to specifically detect target molecules produced by enzyme activity at the intracellular level. Especially, the biosensors facilitate high-throughput screening (HTS) of targeted enzymes, expanding enzyme discovery and engineering strategies with advances in systems and synthetic biology. This review examines biosensor-guided HTS systems and highlights studies that have utilized these tools to discover enzymes in diverse areas and engineer enzymes to enhance their properties, such as catalytic efficiency, specificity, and stability.
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Affiliation(s)
- Hyun Gyu Hwang
- Institute of Environmental and Energy Technology, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea.
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9
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Marshall LR, Bhattacharya S, Korendovych IV. Fishing for Catalysis: Experimental Approaches to Narrowing Search Space in Directed Evolution of Enzymes. JACS AU 2023; 3:2402-2412. [PMID: 37772192 PMCID: PMC10523367 DOI: 10.1021/jacsau.3c00315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 09/30/2023]
Abstract
Directed evolution has transformed protein engineering offering a path to rapid improvement of protein properties. Yet, in practice it is limited by the hyper-astronomic protein sequence search space, and approaches to identify mutagenic hot spots, i.e., locations where mutations are most likely to have a productive impact, are needed. In this perspective, we categorize and discuss recent progress in the experimental approaches (broadly defined as structural, bioinformatic, and dynamic) to hot spot identification. Recent successes in harnessing protein dynamics and machine learning approaches provide new opportunities for the field and will undoubtedly help directed evolution reach its full potential.
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Affiliation(s)
- Liam R. Marshall
- Department of Chemistry, Syracuse
University, 111 College Place, Syracuse, New York 13224, United States
| | - Sagar Bhattacharya
- Department of Chemistry, Syracuse
University, 111 College Place, Syracuse, New York 13224, United States
| | - Ivan V. Korendovych
- Department of Chemistry, Syracuse
University, 111 College Place, Syracuse, New York 13224, United States
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10
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Kyomuhimbo HD, Feleni U, Haneklaus NH, Brink H. Recent Advances in Applications of Oxidases and Peroxidases Polymer-Based Enzyme Biocatalysts in Sensing and Wastewater Treatment: A Review. Polymers (Basel) 2023; 15:3492. [PMID: 37631549 PMCID: PMC10460086 DOI: 10.3390/polym15163492] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/10/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Oxidase and peroxidase enzymes have attracted attention in various biotechnological industries due to their ease of synthesis, wide range of applications, and operation under mild conditions. Their applicability, however, is limited by their poor stability in harsher conditions and their non-reusability. As a result, several approaches such as enzyme engineering, medium engineering, and enzyme immobilization have been used to improve the enzyme properties. Several materials have been used as supports for these enzymes to increase their stability and reusability. This review focusses on the immobilization of oxidase and peroxidase enzymes on metal and metal oxide nanoparticle-polymer composite supports and the different methods used to achieve the immobilization. The application of the enzyme-metal/metal oxide-polymer biocatalysts in biosensing of hydrogen peroxide, glucose, pesticides, and herbicides as well as blood components such as cholesterol, urea, dopamine, and xanthine have been extensively reviewed. The application of the biocatalysts in wastewater treatment through degradation of dyes, pesticides, and other organic compounds has also been discussed.
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Affiliation(s)
- Hilda Dinah Kyomuhimbo
- Department of Chemical Engineering, University of Pretoria, Pretoria 0028, South Africa;
| | - Usisipho Feleni
- Institute for Nanotechnology and Water Sustainability (iNanoWS), College of Science, Engineering and Technology, University of South Africa, Florida Campus, Roodepoort, Johannesburg 1710, South Africa;
| | - Nils H. Haneklaus
- Transdisciplinarity Laboratory Sustainable Mineral Resources, University for Continuing Education Krems, 3500 Krems, Austria;
| | - Hendrik Brink
- Department of Chemical Engineering, University of Pretoria, Pretoria 0028, South Africa;
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11
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Kroll A, Ranjan S, Engqvist MKM, Lercher MJ. A general model to predict small molecule substrates of enzymes based on machine and deep learning. Nat Commun 2023; 14:2787. [PMID: 37188731 DOI: 10.1038/s41467-023-38347-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 04/21/2023] [Indexed: 05/17/2023] Open
Abstract
For most proteins annotated as enzymes, it is unknown which primary and/or secondary reactions they catalyze. Experimental characterizations of potential substrates are time-consuming and costly. Machine learning predictions could provide an efficient alternative, but are hampered by a lack of information regarding enzyme non-substrates, as available training data comprises mainly positive examples. Here, we present ESP, a general machine-learning model for the prediction of enzyme-substrate pairs with an accuracy of over 91% on independent and diverse test data. ESP can be applied successfully across widely different enzymes and a broad range of metabolites included in the training data, outperforming models designed for individual, well-studied enzyme families. ESP represents enzymes through a modified transformer model, and is trained on data augmented with randomly sampled small molecules assigned as non-substrates. By facilitating easy in silico testing of potential substrates, the ESP web server may support both basic and applied science.
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Affiliation(s)
- Alexander Kroll
- Institute for Computer Science and Department of Biology, Heinrich Heine University, D-40225, Düsseldorf, Germany
| | - Sahasra Ranjan
- Department of Computer Science and Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Martin K M Engqvist
- Department of Biology and Bioengineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- EnginZyme AB, Tomtebodevägen 6, 17165, Stockholm, Sweden
| | - Martin J Lercher
- Institute for Computer Science and Department of Biology, Heinrich Heine University, D-40225, Düsseldorf, Germany.
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12
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Vasina M, Kovar D, Damborsky J, Ding Y, Yang T, deMello A, Mazurenko S, Stavrakis S, Prokop Z. In-depth analysis of biocatalysts by microfluidics: An emerging source of data for machine learning. Biotechnol Adv 2023; 66:108171. [PMID: 37150331 DOI: 10.1016/j.biotechadv.2023.108171] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 05/09/2023]
Abstract
Nowadays, the vastly increasing demand for novel biotechnological products is supported by the continuous development of biocatalytic applications which provide sustainable green alternatives to chemical processes. The success of a biocatalytic application is critically dependent on how quickly we can identify and characterize enzyme variants fitting the conditions of industrial processes. While miniaturization and parallelization have dramatically increased the throughput of next-generation sequencing systems, the subsequent characterization of the obtained candidates is still a limiting process in identifying the desired biocatalysts. Only a few commercial microfluidic systems for enzyme analysis are currently available, and the transformation of numerous published prototypes into commercial platforms is still to be streamlined. This review presents the state-of-the-art, recent trends, and perspectives in applying microfluidic tools in the functional and structural analysis of biocatalysts. We discuss the advantages and disadvantages of available technologies, their reproducibility and robustness, and readiness for routine laboratory use. We also highlight the unexplored potential of microfluidics to leverage the power of machine learning for biocatalyst development.
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Affiliation(s)
- Michal Vasina
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic
| | - David Kovar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic
| | - Yun Ding
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Tianjin Yang
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland; Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Andrew deMello
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Stanislav Mazurenko
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic.
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland.
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic.
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13
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Baskaran B, Gill TM, Furst AL. An Improved Spectrophotometric Method for Toluene-4-Monooxygenase Activity. Chemistry 2023; 29:e202203322. [PMID: 36593585 PMCID: PMC10423644 DOI: 10.1002/chem.202203322] [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: 10/26/2022] [Revised: 12/28/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023]
Abstract
Monooxygenases, an important class of enzymes, have been the subject of enzyme engineering due to their high activity and versatile substrate scope. Reactions performed by these biocatalysts have long been monitored by a colorimetric method involving the coupling of a dye precursor to naphthalene hydroxylation products generated by the enzyme. Despite the popularity of this method, we found the dye product to be unstable, preventing quantitative readout. By incorporating an extraction step to solubilize the dye produced, we have improved this assay to the point where quantitation of enzyme activity is possible. Further, by incorporating spectral deconvolution, we have, for the first time, enabled independent quantification of the two possible regioisomeric products: 1-naphthol and 2-naphthol. Previously, such analysis was only possible with chromatographic separation, increasing the cost and complexity of analysis. The efficacy of our improved workflow was evaluated by monitoring the activity of a toluene-4-monooxygenase enzyme from Pseudomonas mendocina KR-1. Our colorimetric regioisomer quantification was found to be consistent with chromatographic analysis by HPLC. The development and validation of a quantitative colorimetric assay for monooxygenase activity that enables regioisomeric distinction and quantification represents a significant advance in analytical methods to monitor enzyme activity. By maintaining facile, low-cost, high-throughput readout while incorporating quantification, this assay represents an important alternative to more expensive chromatographic quantification techniques.
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Affiliation(s)
- Barathkumar Baskaran
- Deparment of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Thomas M. Gill
- Deparment of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Ariel L. Furst
- Deparment of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
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14
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Nielsen JR, Weusthuis RA, Huang WE. Growth-coupled enzyme engineering through manipulation of redox cofactor regeneration. Biotechnol Adv 2023; 63:108102. [PMID: 36681133 DOI: 10.1016/j.biotechadv.2023.108102] [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: 09/01/2022] [Revised: 01/11/2023] [Accepted: 01/15/2023] [Indexed: 01/20/2023]
Abstract
Enzymes need to be efficient, robust, and highly specific for their effective use in commercial bioproduction. These properties can be introduced using various enzyme engineering techniques, with random mutagenesis and directed evolution (DE) often being chosen when there is a lack of structural information -or mechanistic understanding- of the enzyme. The screening or selection step of DE is the limiting part of this process, since it must ideally be (ultra)-high throughput, specifically target the catalytic activity of the enzyme and have an accurately quantifiable metric for said activity. Growth-coupling selection strategies involve coupling a desired enzyme activity to cellular metabolism and therefore growth, where growth (rate) becomes the output metric. Redox cofactors (NAD+/NADH and NADP+/NADPH) have recently been identified as promising target molecules for growth coupling, owing to their essentiality for cellular metabolism and ubiquitous nature. Redox cofactor oxidation or reduction can be disrupted through metabolic engineering and the use of specific culturing conditions, rendering the cell inviable unless a 'rescue' reaction complements the imposed metabolic deficiency. Using this principle, enzyme variants displaying improved cofactor oxidation or reduction rates can be selected for through an increased growth rate of the cell. In recent years, several E. coli strains have been developed that are deficient in the oxidation or reduction of NAD+/NADH and NADP+/NADPH pairs, and of non-canonical redox cofactor pairs NMN+/NMNH and NCD+/NCDH, which provides researchers with a versatile toolbox of enzyme engineering platforms. A range of redox cofactor dependent enzymes have since been engineered using a variety of these strains, demonstrating the power of using this growth-coupling technique for enzyme engineering. This review aims to summarize the metabolic engineering involved in creating strains auxotrophic for the reduced or oxidized state of redox cofactors, and the resulting successes in using them for enzyme engineering. Perspectives on the unique features and potential future applications of this technique are also presented.
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Affiliation(s)
- Jochem R Nielsen
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, United Kingdom.
| | - Ruud A Weusthuis
- Department of Bioprocess Engineering, Wageningen University & Research, Wageningen 6700AA, the Netherlands.
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, United Kingdom.
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15
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Zhang J, Li Q, Wang Q, Zhao J, Zhu Y, Su T, Qi Q, Wang Q. Heme biosensor-guided in vivo pathway optimization and directed evolution for efficient biosynthesis of heme. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:33. [PMID: 36859288 PMCID: PMC9979517 DOI: 10.1186/s13068-023-02285-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 02/18/2023] [Indexed: 03/03/2023]
Abstract
BACKGROUND Heme has attracted much attention because of its wide applications in medicine and food. The products of genes hemBCDEFY convert 5-aminolevulinic acid to protoporphyrin IX (PPIX; the immediate precursor of heme); protoporphyrin ferrochelatase (FECH) inserts Fe2+ into PPIX to generate heme. Biosynthesis of heme is limited by the need for optimized expression levels of multiple genes, complex regulatory mechanisms, and low enzymatic activity; these problems need to be overcome in metabolic engineering to improve heme synthesis. RESULTS We report a heme biosensor-guided screening strategy using the heme-responsive protein HrtR to regulate tcR expression in Escherichia coli, providing a quantifiable link between the intracellular heme concentration and cell survival in selective conditions (i.e., the presence of tetracycline). This system was used for rapid enrichment screening of heme-producing strains from a library with random ribosome binding site (RBS) variants and from a FECH mutant library. Through up to four rounds of iterative evolution, strains with optimal RBS intensities for the combination of hemBCDEFY were screened; we obtained a PPIX titer of 160.8 mg/L, the highest yield yet reported in shaken-flask fermentation. A high-activity FECH variant was obtained from the saturation mutagenesis library. Fed-batch fermentation of strain SH20C, harboring the optimized hemBCDEFY and the FECH mutant, produced 127.6 mg/L of heme. CONCLUSION We sequentially improved the multigene biosynthesis pathway of PPIX and performed in vivo directed evolution of FECH, based on a heme biosensor, which demonstrated the effectiveness of the heme biosensor-based pathway optimization strategy and broadens our understanding of the mechanism of heme synthesis.
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Affiliation(s)
- Jian Zhang
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Qingbin Li
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Qi Wang
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Jingyu Zhao
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Yuan Zhu
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Tianyuan Su
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Qingsheng Qi
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China ,grid.9227.e0000000119573309CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
| | - Qian Wang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China. .,CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, People's Republic of China.
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16
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Sürmeli Y, Şanlı-Mohamed G. Engineering of xylanases for the development of biotechnologically important characteristics. Biotechnol Bioeng 2023; 120:1171-1188. [PMID: 36715367 DOI: 10.1002/bit.28339] [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: 10/22/2022] [Revised: 12/19/2022] [Accepted: 01/26/2023] [Indexed: 01/31/2023]
Abstract
Xylanases are the main biocatalysts used for the reduction of the xylan backbone from hemicellulose, randomly splitting off β-1,4-glycosidic linkages between xylopyranosyl residues. Xylanase market has been annually estimated at 500 million US Dollars and they are potentially used in broad industrial process ranges such as paper pulp biobleaching, xylo-oligosaccharide production, and biofuel manufacture from lignocellulose. The highly stable xylanases are preferred in the downstream procedure of industrial processes because they can tolerate severe conditions. Almost all native xylanases can not endure adverse conditions thus they are industrially not proper to be utilized. Protein engineering is a powerful technology for developing xylanases, which can effectively work in adverse conditions and can meet requirements for industrial processes. This study considered state-of-the-art strategies of protein engineering for creating the xylanase gene diversity, high-throughput screening systems toward upgraded traits of the xylanases, and the prediction and comprehensive analysis of the target mutations in xylanases by in silico methods. Also, key molecular factors have been elucidated for industrial characteristics (alkaliphilic enhancement, thermal stability, and catalytic performance) of GH11 family xylanases. The present review explores industrial characteristics improved by directed evolution, rational design, and semi-rational design as protein engineering approaches for pulp bleaching process, xylooligosaccharides production, and biorefinery & bioenergy production.
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Affiliation(s)
- Yusuf Sürmeli
- Department of Agricultural Biotechnology, Tekirdağ Namık Kemal University, Tekirdağ, Turkey
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17
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Zhang F, Fan X, Xu K, Wang S, Shi S, Yi L, Zhang G. Development of a Bacterial FhuD-Lysozyme-SsrA Mediated Autolytic (FLSA) System for Effective Release of Intracellular Products. ACS Synth Biol 2023; 12:196-202. [PMID: 36580286 DOI: 10.1021/acssynbio.2c00466] [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: 12/30/2022]
Abstract
Developing effective bacterial autolytic systems for fast release of intracellular bioproducts could simplify purification procedures and help with the high throughput screening of mutant libraries in protein engineering. Here, we developed a fast and tightly regulated E. coli autolytic system, named the FhuD-lysozyme-SsrA mediated autolytic (FLSA) system, by integrating the secretion signal peptide, T7 lysozyme, and E. coli ClpX/P-SsrA protein degradation machinery. To decrease the cytotoxicity of leaky T7 lysozymes, the SsrA tag was fused to the C-terminus of T7 lysozyme to confer a tight regulation of its production. Using sfGFP as a reporter, we demonstrated that anchoring the Sec-Tat dual pathway signal peptide FhuD to the N-terminus of T7 lysozyme-SsrA could give the highest cell lysing efficiency. The optimization of the FLSA system indicated that weak alkaline conditions (pH 8.0) and 0.5% Triton X-100 could further increase the lysing efficiency by about 24%. The FLSA system was validated by efficient production of sfGFP and human growth hormone 1 (hGH1) in a shake flask, with a cell lytic efficiency of approximately 82% and 80%, respectively. Besides, the FLSA system was applied for large-scale fermentation, in which approximately 90% sGFP was released with a cell density OD600 of 110. Moreover, the FLSA system was also tested for α-amylase mutant library screening in microplates, and the results showed that intracellular α-amylase can be efficiently released out of cells for activity quantitation. In all, the FLSA system can facilitate the release of intracellular recombinant proteins into the cell culture medium, which has the potential to serve as an integrated system for large-scale production of recombinant targets and high throughput enzyme engineering in synthetic biology.
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Affiliation(s)
- Faying Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.,School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Xian Fan
- School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Ke Xu
- School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Shihui Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Shuobo Shi
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Li Yi
- School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Guimin Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.,School of Life Sciences, Hubei University, Wuhan 430062, China
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18
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Takekana M, Yoshida T, Yoshida E, Ono S, Horie S, Vavricka CJ, Hiratani M, Tsuge K, Ishii J, Hayakawa Y, Kondo A, Hasunuma T. Online SFE-SFC-MS/MS colony screening: A high-throughput approach for optimizing (-)-limonene production. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1215:123588. [PMID: 36587464 DOI: 10.1016/j.jchromb.2022.123588] [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: 09/11/2022] [Revised: 10/22/2022] [Accepted: 12/24/2022] [Indexed: 12/29/2022]
Abstract
Conventional analysis of microbial bioproducers requires the extraction of metabolites from liquid cultures, where the culturing steps are time consuming and greatly limit throughput. To break through this barrier, the current study aims to directly evaluate microbial bioproduction colonies by way of supercritical fluid extraction-supercritical fluid chromatography-triple quadrupole mass spectrometry (SFE-SFC-MS/MS). The online SFE-SFC-MS/MS system offers great potential for high-throughput analysis due to automated metabolite extraction without any need for pretreatment. This is the first report of SFE-SFC-MS/MS as a method for direct colony screening, as demonstrated in the high-throughput screening of (-)-limonene bioproducers. Compared with conventional analysis, the SFE-SFC-MS/MS system enables faster and more convenient screening of highly productive strains.
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Affiliation(s)
- Musashi Takekana
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Takanobu Yoshida
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Erika Yoshida
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan; Research Institute for Bioscience Products & Fine Chemicals. Ajinomoto Co., Inc. Kanagawa, Japan
| | - Sumika Ono
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | | | - Christopher J Vavricka
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Moe Hiratani
- Research Institute for Bioscience Products & Fine Chemicals. Ajinomoto Co., Inc. Kanagawa, Japan
| | - Kenji Tsuge
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Jun Ishii
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan; Engineering Biology Research Center, Kobe University, Kobe, Japan
| | | | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan; Engineering Biology Research Center, Kobe University, Kobe, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan; Engineering Biology Research Center, Kobe University, Kobe, Japan.
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19
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Lai J, Huang H, Lin M, Xu Y, Li X, Sun B. Enzyme catalyzes ester bond synthesis and hydrolysis: The key step for sustainable usage of plastics. Front Microbiol 2023; 13:1113705. [PMID: 36713200 PMCID: PMC9878459 DOI: 10.3389/fmicb.2022.1113705] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 12/29/2022] [Indexed: 01/15/2023] Open
Abstract
Petro-plastic wastes cause serious environmental contamination that require effective solutions. Developing alternatives to petro-plastics and exploring feasible degrading methods are two solving routes. Bio-plastics like polyhydroxyalkanoates (PHAs), polylactic acid (PLA), polycaprolactone (PCL), poly (butylene succinate) (PBS), poly (ethylene furanoate) s (PEFs) and poly (ethylene succinate) (PES) have emerged as promising alternatives. Meanwhile, biodegradation plays important roles in recycling plastics (e.g., bio-plastics PHAs, PLA, PCL, PBS, PEFs and PES) and petro-plastics poly (ethylene terephthalate) (PET) and plasticizers in plastics (e.g., phthalate esters, PAEs). All these bio- and petro-materials show structure similarity by connecting monomers through ester bond. Thus, this review focused on bio-plastics and summarized the sequences and structures of the microbial enzymes catalyzing ester-bond synthesis. Most of these synthetic enzymes belonged to α/β-hydrolases with conserved serine catalytic active site and catalyzed the polymerization of monomers by forming ester bond. For enzymatic plastic degradation, enzymes about PHAs, PBS, PCL, PEFs, PES and PET were discussed, and most of the enzymes also belonged to the α/β hydrolases with a catalytic active residue serine, and nucleophilically attacked the ester bond of substrate to generate the cleavage of plastic backbone. Enzymes hydrolysis of the representative plasticizer PAEs were divided into three types (I, II, and III). Type I enzymes hydrolyzed only one ester-bond of PAEs, type II enzymes catalyzed the ester-bond of mono-ester phthalates, and type III enzymes hydrolyzed di-ester bonds of PAEs. Divergences of catalytic mechanisms among these enzymes were still unclear. This review provided references for producing bio-plastics, and degrading or recycling of bio- and petro-plastics from an enzymatic point of view.
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Affiliation(s)
- Jinghui Lai
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commence, Beijing Technology and Business University, Beijing, China
| | - Huiqin Huang
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commence, Beijing Technology and Business University, Beijing, China
| | - Mengwei Lin
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commence, Beijing Technology and Business University, Beijing, China
| | - Youqiang Xu
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commence, Beijing Technology and Business University, Beijing, China,*Correspondence: Youqiang Xu, ✉
| | - Xiuting Li
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commence, Beijing Technology and Business University, Beijing, China,Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing, China
| | - Baoguo Sun
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commence, Beijing Technology and Business University, Beijing, China,Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing, China
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20
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Fan J, Yao Z, Yan C, Hao M, Dai J, Zou W, Ni M, Li T, Li L, Li S, Liu J, Huang Q, Zhou R. Discovery of a highly efficient TylF methyltransferase via random mutagenesis for improving tylosin production. Comput Struct Biotechnol J 2023; 21:2759-2766. [PMID: 37181661 PMCID: PMC10172623 DOI: 10.1016/j.csbj.2023.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/11/2023] [Accepted: 04/11/2023] [Indexed: 05/16/2023] Open
Abstract
Macrolides are currently a class of extensively used antibiotics in human and animal medicine. Tylosin is not only one of the most important veterinary macrolides but also an indispensable material for the bio- and chemo-synthesis of new generations of macrolide antibiotics. Thus, improving its production yield is of great value. As the key rate-limiting enzyme catalyzing the terminal step of tylosin biosynthesis in Streptomyces fradiae (S. fradiae), TylF methyltransferase's catalytic activity directly affects tylosin yield. In this study, a tylF mutant library of S. fradiae SF-3 was constructed based on error-prone PCR technology. After two steps of screening in 24-well plates and conical flask fermentation and enzyme activity assay, a mutant strain was identified with higher TylF activity and tylosin yield. The mutation of tyrosine to phenylalanine is localized at the 139th amino acid residue on TylF (TylFY139F), and protein structure simulations demonstrated that this mutation changed the protein structure of TylF. Compared with wild-type protein TylF, TylFY139F exhibited higher enzymatic activity and thermostability. More importantly, the Y139 residue in TylF is a previously unidentified position required for TylF activity and tylosin production in S. fradiae, indicating the further potential to engineer the enzyme. These findings provide helpful information for the directed molecular evolution of this important enzyme and the genetic modification of tylosin-producing bacteria.
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Affiliation(s)
- Jingyan Fan
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhiming Yao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Chaoyue Yan
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Meilin Hao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Jun Dai
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Provincial Bioengineering Technology Research Center for Animal Health Products, Yingcheng 432400, China
- The HZAU-HVSEN Research Institute, Wuhan 430042, China
| | - Wenjin Zou
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Minghui Ni
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingting Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Lu Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease (Ministry of Science and Technology of China), Wuhan 430070, China
- Cooperative Innovation Center of Sustainable Pig Production, Wuhan 430070, China
| | - Shuo Li
- Hubei Provincial Bioengineering Technology Research Center for Animal Health Products, Yingcheng 432400, China
- The HZAU-HVSEN Research Institute, Wuhan 430042, China
| | - Jie Liu
- Hubei Provincial Bioengineering Technology Research Center for Animal Health Products, Yingcheng 432400, China
- The HZAU-HVSEN Research Institute, Wuhan 430042, China
| | - Qi Huang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease (Ministry of Science and Technology of China), Wuhan 430070, China
- Cooperative Innovation Center of Sustainable Pig Production, Wuhan 430070, China
- Correspondence to: College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
| | - Rui Zhou
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease (Ministry of Science and Technology of China), Wuhan 430070, China
- Cooperative Innovation Center of Sustainable Pig Production, Wuhan 430070, China
- The HZAU-HVSEN Research Institute, Wuhan 430042, China
- Correspondence to: College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
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21
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Shao F, Lee PW, Li H, Hsieh K, Wang TH. Emerging platforms for high-throughput enzymatic bioassays. Trends Biotechnol 2023; 41:120-133. [PMID: 35863950 PMCID: PMC9789168 DOI: 10.1016/j.tibtech.2022.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 05/19/2022] [Accepted: 06/14/2022] [Indexed: 12/27/2022]
Abstract
Enzymes have essential roles in catalyzing biological reactions and maintaining metabolic systems. Many in vitro enzymatic bioassays have been developed for use in industrial and research fields, such as cell biology, enzyme engineering, drug screening, and biofuel production. Of note, many of these require the use of high-throughput platforms. Although the microtiter plate remains the standard for high-throughput enzymatic bioassays, microfluidic arrays and droplet microfluidics represent emerging methods. Each has seen significant advances and offers distinct advantages; however, drawbacks in key performance metrics, including reagent consumption, reaction manipulation, reaction recovery, real-time measurement, concentration gradient range, and multiplexity, remain. Herein, we compare recent high-throughput platforms using the aforementioned metrics as criteria and provide insights into remaining challenges and future research trends.
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Affiliation(s)
- Fangchi Shao
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Pei-Wei Lee
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Hui Li
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA; Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA.
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22
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Tan Z, Chen G, Zhao Y, Shi H, Wang S, Bilal M, Li D, Li X. Digging and identification of novel microorganisms from the soil environments with high methanol-tolerant lipase production for biodiesel preparation. ENVIRONMENTAL RESEARCH 2022; 212:113570. [PMID: 35671798 DOI: 10.1016/j.envres.2022.113570] [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] [Received: 03/28/2022] [Revised: 05/21/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Converting renewable biomass into carbon-neutral biofuels is one of the most effective strategies to achieve zero carbon emissions and contribute to environmental protection. Microorganisms from the soil were primarily screened on the rhodamine B-plate for highly-active lipase producing strains and re-screened on a tributyrin-methanol plate using crude lipases produced from the initially screened-out strains. The lipase-producing strains with higher methanol-tolerant lipase were identified based on morphological characteristics and 16S rDNA sequencing. The crude lipases with much higher methanol-tolerance from screened top-4 strains, Stenotrophomonas maltophilia D18, Lysinibacillus fusiformis B23, Acinetobacter junii C69, and A. pittii C95 showed temperature optima of 25 °C, 35 °C, 30 °C, and 30 °C at pH 7.0, respectively, while their pH optima were 8.0, 7.0, 7.5, and 7.5 at each optimum temperature, respectively. After 24-h incubation, they retained more than 85% of their original activities in 25%, 15%, 20%, and 20% of methanol, respectively. They catalyzed the conversion of soybean oil into biodiesel by yields of 63.1%, 35.4%, 74.6%, and 78.5% after 24-h reactions, respectively. In conclusion, the as-isolated microorganisms producing high methanol-tolerant lipase are considered promising to provide robust biocatalyst for efficient biodiesel preparation and other industrial applications.
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Affiliation(s)
- Zhongbiao Tan
- Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, PR China.
| | - Gang Chen
- Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, PR China
| | - Yipin Zhao
- Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, PR China
| | - Hao Shi
- Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, PR China.
| | - Shiyan Wang
- Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, PR China
| | - Muhammad Bilal
- Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, PR China
| | - Dong Li
- Key Laboratory of Regional Resource Exploitation and Medicinal Research, School of Chemical Engineering, Huaiyin Institute of Technology, Huai'an, 223003, PR China
| | - Xiangqian Li
- Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, PR China
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23
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Hunt for α-amylase from metagenome and strategies to improve its thermostability: a systematic review. World J Microbiol Biotechnol 2022; 38:203. [PMID: 35999473 DOI: 10.1007/s11274-022-03396-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/18/2022] [Indexed: 10/15/2022]
Abstract
With the advent of green chemistry, the use of enzymes in industrial processes serves as an alternative to the conventional chemical catalysts. A high demand for sustainable processes for catalysis has brought a significant attention to hunt for novel enzymes. Among various hydrolases, the α-amylase has a gamut of biotechnological applications owing to its pivotal role in starch-hydrolysis. Industrial demand requires enzymes with thermostability and to ameliorate this crucial property, various methods such as protein engineering, directed evolution and enzyme immobilisation strategies are devised. Besides the traditional culture-dependent approach, metagenome from uncultured bacteria serves as a bountiful resource for novel genes/biocatalysts. Exploring the extreme-niches metagenome, advancements in protein engineering and biotechnology tools encourage the mining of novel α-amylase and its stable variants to tap its robust biotechnological and industrial potential. This review outlines α-amylase and its genetics, its catalytic domain architecture and mechanism of action, and various molecular methods to ameliorate its production. It aims to impart understanding on mechanisms involved in thermostability of α-amylase, cover strategies to screen novel genes from futile habitats and some molecular methods to ameliorate its properties.
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24
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Miwa H, Dimatteo R, de Rutte J, Ghosh R, Di Carlo D. Single-cell sorting based on secreted products for functionally defined cell therapies. MICROSYSTEMS & NANOENGINEERING 2022; 8:84. [PMID: 35874174 PMCID: PMC9303846 DOI: 10.1038/s41378-022-00422-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 05/18/2022] [Accepted: 06/13/2022] [Indexed: 05/13/2023]
Abstract
Cell therapies have emerged as a promising new class of "living" therapeutics over the last decade and have been particularly successful for treating hematological malignancies. Increasingly, cellular therapeutics are being developed with the aim of treating almost any disease, from solid tumors and autoimmune disorders to fibrosis, neurodegenerative disorders and even aging itself. However, their therapeutic potential has remained limited due to the fundamental differences in how molecular and cellular therapies function. While the structure of a molecular therapeutic is directly linked to biological function, cells with the same genetic blueprint can have vastly different functional properties (e.g., secretion, proliferation, cell killing, migration). Although there exists a vast array of analytical and preparative separation approaches for molecules, the functional differences among cells are exacerbated by a lack of functional potency-based sorting approaches. In this context, we describe the need for next-generation single-cell profiling microtechnologies that allow the direct evaluation and sorting of single cells based on functional properties, with a focus on secreted molecules, which are critical for the in vivo efficacy of current cell therapies. We first define three critical processes for single-cell secretion-based profiling technology: (1) partitioning individual cells into uniform compartments; (2) accumulating secretions and labeling via reporter molecules; and (3) measuring the signal associated with the reporter and, if sorting, triggering a sorting event based on these reporter signals. We summarize recent academic and commercial technologies for functional single-cell analysis in addition to sorting and industrial applications of these technologies. These approaches fall into three categories: microchamber, microfluidic droplet, and lab-on-a-particle technologies. Finally, we outline a number of unmet needs in terms of the discovery, design and manufacturing of cellular therapeutics and how the next generation of single-cell functional screening technologies could allow the realization of robust cellular therapeutics for all patients.
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Affiliation(s)
- Hiromi Miwa
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA 90095 USA
| | - Robert Dimatteo
- Department of Chemical and Biomolecular Engineering, University of California - Los Angeles, Los Angeles, CA 90095 USA
| | - Joseph de Rutte
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA 90095 USA
- Partillion Bioscience, Los Angeles, CA 90095 USA
| | - Rajesh Ghosh
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA 90095 USA
| | - Dino Di Carlo
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA 90095 USA
- Department of Mechanical and Aerospace Engineering, University of California - Los Angeles, Los Angeles, CA 90095 USA
- California NanoSystems Institute (CNSI), University of California - Los Angeles, Los Angeles, CA 90095 USA
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25
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Karamitros CS, Murray K, Winemiller B, Lamb C, Stone EM, D'Arcy S, Johnson KA, Georgiou G. Leveraging intrinsic flexibility to engineer enhanced enzyme catalytic activity. Proc Natl Acad Sci U S A 2022; 119:e2118979119. [PMID: 35658075 PMCID: PMC9191678 DOI: 10.1073/pnas.2118979119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 03/01/2022] [Indexed: 11/18/2022] Open
Abstract
Dynamic motions of enzymes occurring on a broad range of timescales play a pivotal role in all steps of the reaction pathway, including substrate binding, catalysis, and product release. However, it is unknown whether structural information related to conformational flexibility can be exploited for the directed evolution of enzymes with higher catalytic activity. Here, we show that mutagenesis of residues exclusively located at flexible regions distal to the active site of Homo sapiens kynureninase (HsKYNase) resulted in the isolation of a variant (BF-HsKYNase) in which the rate of the chemical step toward kynurenine was increased by 45-fold. Mechanistic pre–steady-state kinetic analysis of the wild type and the evolved enzyme shed light on the underlying effects of distal mutations (>10 Å from the active site) on the rate-limiting step of the catalytic cycle. Hydrogen-deuterium exchange coupled to mass spectrometry and molecular dynamics simulations revealed that the amino acid substitutions in BF-HsKYNase allosterically affect the flexibility of the pyridoxal-5′-phosphate (PLP) binding pocket, thereby impacting the rate of chemistry, presumably by altering the conformational ensemble and sampling states more favorable to the catalyzed reaction.
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Affiliation(s)
| | - Kyle Murray
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX 75080
| | - Brent Winemiller
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712
| | - Candice Lamb
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712
| | - Everett M. Stone
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
- Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, TX 78712
- LiveSTRONG Cancer Institutes, Dell Medical School, University of Texas at Austin, Austin, TX 78712
| | - Sheena D'Arcy
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX 75080
| | - Kenneth A. Johnson
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
- Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, TX 78712
- LiveSTRONG Cancer Institutes, Dell Medical School, University of Texas at Austin, Austin, TX 78712
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712
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26
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Gomes M, Rondelez Y, Leibler L. Lessons from Biomass Valorization for Improving Plastic-Recycling Enzymes. Annu Rev Chem Biomol Eng 2022; 13:457-479. [PMID: 35378043 DOI: 10.1146/annurev-chembioeng-092120-091054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Synthetic polymers such as plastics exhibit numerous advantageous properties that have made them essential components of our daily lives, with plastic production doubling every 15 years. The relatively low cost of petroleum-based polymers encourages their single use and overconsumption. Synthetic plastics are recalcitrant to biodegradation, and mismanagement of plastic waste leads to their accumulation in the ecosystem, resulting in a disastrous environmental footprint. Enzymes capable of depolymerizing plastics have been reported recently that may provide a starting point for eco-friendly plastic recycling routes. However, some questions remain about the mechanisms by which enzymes can digest insoluble solid substrates. We review the characterization and engineering of plastic-eating enzymes and provide some comparisons with the field of lignocellulosic biomass valorization. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering, Volume 13 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Margarida Gomes
- Laboratoire Gulliver (UMR 7083), CNRS, ESPCI Paris, PSL Research University, Paris, France; ;
| | - Yannick Rondelez
- Laboratoire Gulliver (UMR 7083), CNRS, ESPCI Paris, PSL Research University, Paris, France; ;
| | - Ludwik Leibler
- Laboratoire Gulliver (UMR 7083), CNRS, ESPCI Paris, PSL Research University, Paris, France; ;
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27
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Boock JT, Taw M, King BC, Conrado RJ, Gibson DM, DeLisa MP. Two-Tiered Selection and Screening Strategy to Increase Functional Enzyme Production in E. coli. Methods Mol Biol 2022; 2406:169-187. [PMID: 35089557 DOI: 10.1007/978-1-0716-1859-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Development of recombinant enzymes as industrial biocatalysts or metabolic pathway elements requires soluble expression of active protein. Here we present a two-step strategy, combining a directed evolution selection with an enzyme activity screen, to increase the soluble production of enzymes in the cytoplasm of E. coli. The directed evolution component relies on the innate quality control of the twin-arginine translocation pathway coupled with antibiotic selection to isolate point mutations that promote intracellular solubility. A secondary screen is applied to ensure the solubility enhancement has not compromised enzyme activity. This strategy has been successfully applied to increase the soluble production of a fungal endocellulase by 30-fold in E. coli without change in enzyme specific activity through two rounds of directed evolution.
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Affiliation(s)
- Jason T Boock
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA.
- Department of Chemical, Paper and Biomedical Engineering, Miami University (OH), Oxford, OH, USA.
| | - May Taw
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | - Brian C King
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, USA
| | - Robert J Conrado
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Donna M Gibson
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, USA
- USDA Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA
| | - Matthew P DeLisa
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
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28
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Kardashliev T, Weingartner A, Romero E, Schwaneberg U, Fraaije M, Panke S, Held M. Whole-cell screening of oxidative enzymes using genetically encoded sensors. Chem Sci 2021; 12:14766-14772. [PMID: 34820092 PMCID: PMC8597865 DOI: 10.1039/d1sc02578c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/20/2021] [Indexed: 11/23/2022] Open
Abstract
Biocatalysis is increasingly used for synthetic purposes in the chemical and especially the pharmaceutical industry. Enzyme discovery and optimization which is frequently needed to improve biocatalytic performance rely on high-throughput methods for activity determination. These methods should ideally be generic and applicable to entire enzyme families. Hydrogen peroxide (H2O2) is a product of several biocatalytic oxidations and its formation can serve as a proxy for oxidative activity. We designed a genetically encoded sensor for activity measurement of oxidative biocatalysts via the amount of intracellularly-formed H2O2. A key component of the sensor is an H2O2-sensitive transcriptional regulator, OxyR, which is used to control the expression levels of fluorescent proteins. We employed the OxyR sensor to monitor the oxidation of glycerol to glyceraldehyde and of toluene to o-cresol catalysed by recombinant E. coli expressing an alcohol oxidase and a P450 monooxygenase, respectively. In case of the P450 BM3-catalysed reaction, we additionally monitored o-cresol formation via a second genetically encoded sensor based on the phenol-sensitive transcriptional activator, DmpR, and an orthogonal fluorescent reporter protein. Single round screens of mutant libraries by flow cytometry or by visual inspection of colonies on agar plates yielded significantly improved oxidase and oxygenase variants thus exemplifying the suitability of the sensor system to accurately assess whole-cell oxidations in a high-throughput manner.
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Affiliation(s)
- Tsvetan Kardashliev
- Department of Biosystems Science and Engineering ETH Zurich, Mattenstrasse 26 4058 Basel Switzerland
| | - Alexandra Weingartner
- Institute of Biotechnology, RWTH Aachen University Worringerweg 3 52074 Aachen Germany
| | - Elvira Romero
- Faculty of Science and Engineering, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University Worringerweg 3 52074 Aachen Germany
| | - Marco Fraaije
- Faculty of Science and Engineering, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Sven Panke
- Department of Biosystems Science and Engineering ETH Zurich, Mattenstrasse 26 4058 Basel Switzerland
| | - Martin Held
- Department of Biosystems Science and Engineering ETH Zurich, Mattenstrasse 26 4058 Basel Switzerland
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29
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Kumari M, Padhi S, Sharma S, Phukon LC, Singh SP, Rai AK. Biotechnological potential of psychrophilic microorganisms as the source of cold-active enzymes in food processing applications. 3 Biotech 2021; 11:479. [PMID: 34790503 DOI: 10.1007/s13205-021-03008-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/29/2021] [Indexed: 12/13/2022] Open
Abstract
Microorganisms striving in extreme environments and exhibiting optimal growth and reproduction at low temperatures, otherwise known as psychrophilic microorganisms, are potential sources of cold-active enzymes. Owing to higher stability and cold activity, these enzymes are gaining enormous attention in numerous industrial bioprocesses. Applications of several cold-active enzymes have been established in the food industry, e.g., β-galactosidase, pectinase, proteases, amylases, xylanases, pullulanases, lipases, and β-mannanases. The enzyme engineering approaches and the accumulating knowledge of protein structure and function have made it possible to improve the catalytic properties of interest and express the candidate enzyme in a heterologous host for a higher level of enzyme production. This review compiles the relevant and recent information on the potential uses of different cold-active enzymes in the food industry.
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Affiliation(s)
- Megha Kumari
- Institute of Bioresources and Sustainable Development, Regional Centre, Sikkim, India
| | - Srichandan Padhi
- Institute of Bioresources and Sustainable Development, Regional Centre, Sikkim, India
| | - Swati Sharma
- Institute of Bioresources and Sustainable Development, Regional Centre, Sikkim, India
| | - Loreni Chiring Phukon
- Institute of Bioresources and Sustainable Development, Regional Centre, Sikkim, India
| | - Sudhir P Singh
- Centre of Innovative and Applied Bioprocessing, Mohali, India
| | - Amit Kumar Rai
- Institute of Bioresources and Sustainable Development, Regional Centre, Sikkim, India
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30
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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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31
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Li L, Wu E, Jia K, Yang K. Temperature field regulation of a droplet using an acoustothermal heater. LAB ON A CHIP 2021; 21:3184-3194. [PMID: 34195725 DOI: 10.1039/d1lc00267h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Heating a droplet without contamination is desired for the emerging applications of microfluidic devices in life science and materials science, especially in the form of controllable temperature distribution. Microfluidic heaters using surface acoustic waves have been recently demonstrated, which highlights an urgent need for an insight into the detailed heating mechanism to guide the development of temperature regulation methodologies. Here, we show that the temperature field of a droplet on the path of a travelling wave can be regulated by modulating the heat source distribution and thermal conduction inside the target. We model the acoustothermal process of the droplet including the effects of electric dissipation, acoustic dissipation, and acoustic-induced steady flow. The electric-mechanical-acoustic coupling contributes to the dominant heat source, and we call it acoustic heat source. The nonlinear effects of incident waves generate acoustic vortexes with a velocity of up to 20 mm s-1, inducing forced convection inside the droplet to enhance heat transfer. The equilibrium temperature field of a droplet is determined by a synergy of dissipative acoustic attenuation and acoustic streaming. We demonstrate that the distribution of the acoustic heat source and the patterns of acoustic streaming can be modulated by fluid viscosity and droplet size. Various spatial combinations of the acoustic heat source and steady streaming make different temperature fields in the droplet. We also propose a phase diagram of the temperature distribution in the droplet. This methodology enables opportunities for temperature-related processing inside a droplet bioparticle carrier or microreactor.
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Affiliation(s)
- Liqiang Li
- State Key Laboratory of Fluid Power and Mechatronic Systems, School of Mechanical Engineering, Zhejiang University, No. 38 Zheda Road, Hangzhou, 310027, P. R. China
| | - Eryong Wu
- State Key Laboratory of Fluid Power and Mechatronic Systems, School of Mechanical Engineering, Zhejiang University, No. 38 Zheda Road, Hangzhou, 310027, P. R. China
| | - Kun Jia
- State Key Laboratory for Strength and Vibration of Mechanical Structures, School of Aerospace, Xi'an Jiaotong University, No. 28 West Xianning Road, 710049, Xi'an, P. R. China.
| | - Keji Yang
- State Key Laboratory of Fluid Power and Mechatronic Systems, School of Mechanical Engineering, Zhejiang University, No. 38 Zheda Road, Hangzhou, 310027, P. R. China
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32
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Consolidated Bioprocessing: Synthetic Biology Routes to Fuels and Fine Chemicals. Microorganisms 2021; 9:microorganisms9051079. [PMID: 34069865 PMCID: PMC8157379 DOI: 10.3390/microorganisms9051079] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/27/2021] [Accepted: 05/14/2021] [Indexed: 11/17/2022] Open
Abstract
The long road from emerging biotechnologies to commercial “green” biosynthetic routes for chemical production relies in part on efficient microbial use of sustainable and renewable waste biomass feedstocks. One solution is to apply the consolidated bioprocessing approach, whereby microorganisms convert lignocellulose waste into advanced fuels and other chemicals. As lignocellulose is a highly complex network of polymers, enzymatic degradation or “saccharification” requires a range of cellulolytic enzymes acting synergistically to release the abundant sugars contained within. Complications arise from the need for extracellular localisation of cellulolytic enzymes, whether they be free or cell-associated. This review highlights the current progress in the consolidated bioprocessing approach, whereby microbial chassis are engineered to grow on lignocellulose as sole carbon sources whilst generating commercially useful chemicals. Future perspectives in the emerging biofoundry approach with bacterial hosts are discussed, where solutions to existing bottlenecks could potentially be overcome though the application of high throughput and iterative Design-Build-Test-Learn methodologies. These rapid automated pathway building infrastructures could be adapted for addressing the challenges of increasing cellulolytic capabilities of microorganisms to commercially viable levels.
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33
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Robotics for enzyme technology: innovations and technological perspectives. Appl Microbiol Biotechnol 2021; 105:4089-4097. [PMID: 33970318 DOI: 10.1007/s00253-021-11302-1] [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: 12/12/2020] [Revised: 04/09/2021] [Accepted: 04/17/2021] [Indexed: 10/21/2022]
Abstract
The use of robotics in the life science sector has created a considerable and significant impact on a wide range of research areas, including enzyme technology due to their immense applications in enzyme and microbial engineering as an indispensable tool in high-throughput screening applications. Scientists are experiencing the advanced applications of various biological robots (nanobots), fabricated based on bottom-up or top-down approaches for making nanotechnology scaffolds. Nanobots and enzyme-powered nanomotors are particularly attractive because they are self-propelled vehicles, which consume biocompatible fuels. These smart nanostructures are widely used as drug delivery systems for the efficient treatment of various diseases. This review gives insights into the escalating necessity of robotics and nanobots and their ever-widening applications in enzyme technology, including biofuel production and biomedical applications. It also offers brief insights into high-throughput robotic platforms that are currently being used in enzyme screening applications for monitoring and control of microbial growth conditions. KEY POINTS: • Robotics and their applications in biotechnology are highlighted. • Robotics for high-throughput enzyme screening and microbial engineering are described. • Nanobots and enzyme-powered nanomotors as controllable drug delivery systems are reviewed.
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34
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Rapid in vitro prototyping of O-methyltransferases for pathway applications in Escherichia coli. Cell Chem Biol 2021; 28:876-886.e4. [PMID: 33957079 DOI: 10.1016/j.chembiol.2021.04.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 02/20/2021] [Accepted: 04/16/2021] [Indexed: 11/22/2022]
Abstract
O-Methyltransferases are ubiquitous enzymes involved in biosynthetic pathways for secondary metabolites such as bacterial antibiotics, human catecholamine neurotransmitters, and plant phenylpropanoids. While thousands of putative O-methyltransferases are found in sequence databases, few examples are functionally characterized. From a pathway engineering perspective, however, it is crucial to know the substrate and product ranges of the respective enzymes to fully exploit their catalytic power. In this study, we developed an in vitro prototyping workflow that allowed us to screen ∼30 enzymes against five substrates in 3 days with high reproducibility. We combined in vitro transcription/translation of the genes of interest with a microliter-scale enzymatic assay in 96-well plates. The substrate conversion was indirectly measured by quantifying the consumption of the S-adenosyl-L-methionine co-factor by time-resolved fluorescence resonance energy transfer rather than time-consuming product analysis by chromatography. This workflow allowed us to rapidly prototype thus far uncharacterized O-methyltransferases for future use as biocatalysts.
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35
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Pagar AD, Patil MD, Flood DT, Yoo TH, Dawson PE, Yun H. Recent Advances in Biocatalysis with Chemical Modification and Expanded Amino Acid Alphabet. Chem Rev 2021; 121:6173-6245. [PMID: 33886302 DOI: 10.1021/acs.chemrev.0c01201] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The two main strategies for enzyme engineering, directed evolution and rational design, have found widespread applications in improving the intrinsic activities of proteins. Although numerous advances have been achieved using these ground-breaking methods, the limited chemical diversity of the biopolymers, restricted to the 20 canonical amino acids, hampers creation of novel enzymes that Nature has never made thus far. To address this, much research has been devoted to expanding the protein sequence space via chemical modifications and/or incorporation of noncanonical amino acids (ncAAs). This review provides a balanced discussion and critical evaluation of the applications, recent advances, and technical breakthroughs in biocatalysis for three approaches: (i) chemical modification of cAAs, (ii) incorporation of ncAAs, and (iii) chemical modification of incorporated ncAAs. Furthermore, the applications of these approaches and the result on the functional properties and mechanistic study of the enzymes are extensively reviewed. We also discuss the design of artificial enzymes and directed evolution strategies for enzymes with ncAAs incorporated. Finally, we discuss the current challenges and future perspectives for biocatalysis using the expanded amino acid alphabet.
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Affiliation(s)
- Amol D Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Mahesh D Patil
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Dillon T Flood
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Korea
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
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Yang J, Tu R, Yuan H, Wang Q, Zhu L. Recent advances in droplet microfluidics for enzyme and cell factory engineering. Crit Rev Biotechnol 2021; 41:1023-1045. [PMID: 33730939 DOI: 10.1080/07388551.2021.1898326] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Enzymes and cell factories play essential roles in industrial biotechnology for the production of chemicals and fuels. The properties of natural enzymes and cells often cannot meet the requirements of different industrial processes in terms of cost-effectiveness and high durability. To rapidly improve their properties and performances, laboratory evolution equipped with high-throughput screening methods and facilities is commonly used to tailor the desired properties of enzymes and cell factories, addressing the challenges of achieving high titer and the yield of the target products at high/low temperatures or extreme pH, in unnatural environments or in the presence of unconventional media. Droplet microfluidic screening (DMFS) systems have demonstrated great potential for exploring vast genetic diversity in a high-throughput manner (>106/h) for laboratory evolution and have been increasingly used in recent years, contributing to the identification of extraordinary mutants. This review highlights the recent advances in concepts and methods of DMFS for library screening, including the key factors in droplet generation and manipulation, signal sources for sensitive detection and sorting, and a comprehensive summary of success stories of DMFS implementation for engineering enzymes and cell factories during the past decade.
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Affiliation(s)
- Jianhua Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Ran Tu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Huiling Yuan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Qinhong Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Leilei Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
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Zhu B, Wang D, Wei N. Enzyme Discovery and Engineering for Sustainable Plastic Recycling. Trends Biotechnol 2021; 40:22-37. [PMID: 33676748 DOI: 10.1016/j.tibtech.2021.02.008] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 10/22/2022]
Abstract
The drastically increasing amount of plastic waste is causing an environmental crisis that requires innovative technologies for recycling post-consumer plastics to achieve waste valorization while meeting environmental quality goals. Biocatalytic depolymerization mediated by enzymes has emerged as an efficient and sustainable alternative for plastic treatment and recycling. A variety of plastic-degrading enzymes have been discovered from microbial sources. Meanwhile, protein engineering has been exploited to modify and optimize plastic-degrading enzymes. This review highlights the recent trends and up-to-date advances in mining novel plastic-degrading enzymes through state-of-the-art omics-based techniques and improving the enzyme catalytic efficiency and stability via various protein engineering strategies. Future research prospects and challenges are also discussed.
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Affiliation(s)
- Baotong Zhu
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, Indiana 46556, USA
| | - Dong Wang
- Department of Computer Science and Engineering, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, Indiana 46556, USA
| | - Na Wei
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, Indiana 46556, USA.
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38
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Rollin JA, Bomble YJ, St. John PC, Stark AK. Biochemical Production with Purified Cell-Free Systems. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2018.07.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Rembeza E, Engqvist MKM. Adaptation of a Microfluidic qPCR System for Enzyme Kinetic Studies. ACS OMEGA 2021; 6:1985-1990. [PMID: 33521438 PMCID: PMC7841792 DOI: 10.1021/acsomega.0c04918] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/21/2020] [Indexed: 05/11/2023]
Abstract
Microfluidic platforms offer a drastic increase in throughput while minimizing sample usage and hands-on time, which make them important tools for large-scale biological studies. A range of such systems have been developed for enzyme activity studies, although their complexity largely hinders their application to the wider scientific community. Here, we present adaptation of an easy-to-use commercial microfluidic qPCR system for performing enzyme kinetic studies. We demonstrate the functionality of the Fluidigm Biomark HD system (the Fluidigm system) by determining the kinetic properties of three oxidases in a resorufin-based fluorescence assay. The results obtained in the microfluidic system proved reproducible and comparable to the ones obtained in a standard microplate-based assay. With a wide range of easy-to-use, off-the-shelf components, the microfluidic system presents itself as a simple and customizable platform for high-throughput enzyme activity studies.
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40
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Daletos G, Stephanopoulos G. Protein engineering strategies for microbial production of isoprenoids. Metab Eng Commun 2020; 11:e00129. [PMID: 32612930 PMCID: PMC7322351 DOI: 10.1016/j.mec.2020.e00129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 04/06/2020] [Accepted: 04/24/2020] [Indexed: 01/16/2023] Open
Abstract
Isoprenoids comprise one of the most chemically diverse family of natural products with high commercial interest. The structural diversity of isoprenoids is mainly due to the modular activity of three distinct classes of enzymes, including prenyl diphosphate synthases, terpene synthases, and cytochrome P450s. The heterologous expression of these enzymes in microbial systems is suggested to be a promising sustainable way for the production of isoprenoids. Several limitations are associated with native enzymes, such as low stability, activity, and expression profiles. To address these challenges, protein engineering has been applied to improve the catalytic activity, selectivity, and substrate turnover of enzymes. In addition, the natural promiscuity and modular fashion of isoprenoid enzymes render them excellent targets for combinatorial studies and the production of new-to-nature metabolites. In this review, we discuss key individual and multienzyme level strategies for the successful implementation of enzyme engineering towards efficient microbial production of high-value isoprenoids. Challenges and future directions of protein engineering as a complementary strategy to metabolic engineering are likewise outlined.
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Affiliation(s)
- Georgios Daletos
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
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41
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Puentes PR, Henao MC, Torres CE, Gómez SC, Gómez LA, Burgos JC, Arbeláez P, Osma JF, Muñoz-Camargo C, Reyes LH, Cruz JC. Design, Screening, and Testing of Non-Rational Peptide Libraries with Antimicrobial Activity: In Silico and Experimental Approaches. Antibiotics (Basel) 2020; 9:E854. [PMID: 33265897 PMCID: PMC7759991 DOI: 10.3390/antibiotics9120854] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022] Open
Abstract
One of the challenges of modern biotechnology is to find new routes to mitigate the resistance to conventional antibiotics. Antimicrobial peptides (AMPs) are an alternative type of biomolecules, naturally present in a wide variety of organisms, with the capacity to overcome the current microorganism resistance threat. Here, we reviewed our recent efforts to develop a new library of non-rationally produced AMPs that relies on bacterial genome inherent diversity and compared it with rationally designed libraries. Our approach is based on a four-stage workflow process that incorporates the interplay of recent developments in four major emerging technologies: artificial intelligence, molecular dynamics, surface-display in microorganisms, and microfluidics. Implementing this framework is challenging because to obtain reliable results, the in silico algorithms to search for candidate AMPs need to overcome issues of the state-of-the-art approaches that limit the possibilities for multi-space data distribution analyses in extremely large databases. We expect to tackle this challenge by using a recently developed classification algorithm based on deep learning models that rely on convolutional layers and gated recurrent units. This will be complemented by carefully tailored molecular dynamics simulations to elucidate specific interactions with lipid bilayers. Candidate AMPs will be recombinantly-expressed on the surface of microorganisms for further screening via different droplet-based microfluidic-based strategies to identify AMPs with the desired lytic abilities. We believe that the proposed approach opens opportunities for searching and screening bioactive peptides for other applications.
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Affiliation(s)
- Paola Ruiz Puentes
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogota DC 111711, Colombia; (P.R.P.); (P.A.)
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - María C. Henao
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogota DC 111711, Colombia;
| | - Carlos E. Torres
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Saúl C. Gómez
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Laura A. Gómez
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Juan C. Burgos
- Chemical Engineering Program, Universidad de Cartagena, Cartagena 130015, Colombia;
| | - Pablo Arbeláez
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogota DC 111711, Colombia; (P.R.P.); (P.A.)
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Johann F. Osma
- Department of Electrical and Electronic Engineering, Universidad de los Andes, Bogota DC 111711, Colombia;
| | - Carolina Muñoz-Camargo
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Luis H. Reyes
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogota DC 111711, Colombia;
| | - Juan C. Cruz
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide 5005, Australia
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Di Girolamo S, Puorger C, Lipps G. Stable and selective permeable hydrogel microcapsules for high-throughput cell cultivation and enzymatic analysis. Microb Cell Fact 2020; 19:170. [PMID: 32854709 PMCID: PMC7451113 DOI: 10.1186/s12934-020-01427-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 08/17/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Miniaturization of biochemical reaction volumes within artificial microcompartments has been the key driver for directed evolution of several catalysts in the past two decades. Typically, single cells are co-compartmentalized within water-in-oil emulsion droplets with a fluorogenic substrate whose conversion allows identification of catalysts with improved performance. However, emulsion droplet-based technologies prevent cell proliferation to high density and preclude the feasibility of biochemical reactions that require the exchange of small molecule substrates. Here, we report on the development of a high-throughput screening method that addresses these shortcomings and that relies on a novel selective permeable polymer hydrogel microcapsule. RESULTS Hollow-core polyelectrolyte-coated chitosan alginate microcapsules (HC-PCAMs) with selective permeability were successfully constructed by jet break-up and layer-by-layer (LBL) technology. We showed that HC-PCAMs serve as miniaturized vessels for single cell encapsulation, enabling cell growth to high density and cell lysis to generate monoclonal cell lysate compartments suitable for high-throughput analysis using a large particle sorter (COPAS). The feasibility of using HC-PCAMs as reaction compartments which exchange small molecule substrates was demonstrated using the transpeptidation reaction catalyzed by the bond-forming enzyme sortase F from P. acnes. The polyelectrolyte shell surrounding microcapsules allowed a fluorescently labelled peptide substrate to enter the microcapsule and take part in the transpeptidation reaction catalyzed by the intracellularly expressed sortase enzyme retained within the capsule upon cell lysis. The specific retention of fluorescent transpeptidation products inside microcapsules enabled the sortase activity to be linked with a fluorescent readout and allowed clear separation of microcapsules expressing the wild type SrtF from those expressing the inactive variant. CONCLUSION A novel polymer hydrogel microcapsule-based method, which allows for high-throughput analysis based on encapsulation of single cells has been developed. The method has been validated for the transpeptidation activity of sortase enzymes and represents a powerful tool for screening of libraries of sortases, other bond-forming enzymes, as well as of binding affinities in directed evolution experiments. Moreover, selective permeable microcapsules encapsulating microcolonies provide a new and efficient means for preparing novel caged biocatalyst and biosensor agents.
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Affiliation(s)
- Salvatore Di Girolamo
- University of Applied Sciences and Arts Northwestern Switzerland, Institute for Chemistry and Bioanalytics, Hofackerstrasse 30, 4132, Muttenz, Switzerland
| | - Chasper Puorger
- University of Applied Sciences and Arts Northwestern Switzerland, Institute for Chemistry and Bioanalytics, Hofackerstrasse 30, 4132, Muttenz, Switzerland
| | - Georg Lipps
- University of Applied Sciences and Arts Northwestern Switzerland, Institute for Chemistry and Bioanalytics, Hofackerstrasse 30, 4132, Muttenz, Switzerland.
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43
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High-throughput screening for efficient microbial biotechnology. Curr Opin Biotechnol 2020; 64:141-150. [DOI: 10.1016/j.copbio.2020.02.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/21/2020] [Accepted: 02/27/2020] [Indexed: 01/25/2023]
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44
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Billot R, Plener L, Jacquet P, Elias M, Chabrière E, Daudé D. Engineering acyl-homoserine lactone-interfering enzymes toward bacterial control. J Biol Chem 2020; 295:12993-13007. [PMID: 32690609 DOI: 10.1074/jbc.rev120.013531] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/17/2020] [Indexed: 12/20/2022] Open
Abstract
Enzymes able to degrade or modify acyl-homoserine lactones (AHLs) have drawn considerable interest for their ability to interfere with the bacterial communication process referred to as quorum sensing. Many proteobacteria use AHL to coordinate virulence and biofilm formation in a cell density-dependent manner; thus, AHL-interfering enzymes constitute new promising antimicrobial candidates. Among these, lactonases and acylases have been particularly studied. These enzymes have been isolated from various bacterial, archaeal, or eukaryotic organisms and have been evaluated for their ability to control several pathogens. Engineering studies on these enzymes were carried out and successfully modulated their capacity to interact with specific AHL, increase their catalytic activity and stability, or enhance their biotechnological potential. In this review, special attention is paid to the screening, engineering, and applications of AHL-modifying enzymes. Prospects and future opportunities are also discussed with a view to developing potent candidates for bacterial control.
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Affiliation(s)
- Raphaël Billot
- Gene&GreenTK, Marseille, France; IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix-Marseille Université, Marseille, France
| | | | | | - Mikael Elias
- Molecular Biology and Biophysics and Biotechnology Institute, Department of Biochemistry, University of Minnesota, St. Paul, Minnesota, USA
| | - Eric Chabrière
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix-Marseille Université, Marseille, France.
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45
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Recent advances in improving metabolic robustness of microbial cell factories. Curr Opin Biotechnol 2020; 66:69-77. [PMID: 32683192 DOI: 10.1016/j.copbio.2020.06.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/12/2020] [Accepted: 06/17/2020] [Indexed: 12/20/2022]
Abstract
Engineering microbial cell factories has been widely applied to produce compounds spanning from intricate natural products to bulk commodities. In each case, host robustness is essential to ensure the reliable and sustainable production of targeted metabolites. However, it can be negatively affected by metabolic burden, pathway toxicity, and harsh environment, resulting in a decreased titer and productivity. Enhanced robustness enables host to have better production performance under complicated growth circumstances. Here, we review current strategies for boosting host robustness, including metabolic balancing, genetic and phenotype stability enhancement, and tolerance engineering. In addition, we discuss the challenges and future perspectives on microbial host engineering for increased robustness.
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46
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Winning the numbers game in enzyme evolution - fast screening methods for improved biotechnology proteins. Curr Opin Struct Biol 2020; 63:123-133. [PMID: 32615371 DOI: 10.1016/j.sbi.2020.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 04/28/2020] [Accepted: 05/08/2020] [Indexed: 01/02/2023]
Abstract
The booming demand for environmentally benign industrial processes relies on the ability to quickly find or engineer a biocatalyst suitable to ideal process conditions. Both metagenomic approaches and directed evolution involve the screening of huge libraries of protein variants, which can only be managed reasonably by flexible platforms for (ultra)high-throughput profiling against the desired criteria. Here, we review the most recent additions toward a growing toolbox of versatile assays using fluorescence, absorbance and mass spectrometry readouts. While conventional solution based high-throughput screening in microtiter plate formats is still important, the implementation of novel screening protocols for microfluidic cell or droplet sorting systems supports technological advances for ultra-high-frequency screening that now can dramatically reduce the timescale of engineering projects. We discuss practical issues of scope, scalability, sensitivity and stereoselectivity for the improvement of biotechnologically relevant enzymes from different classes.
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Li H, Fang W, Zhao Z, Li A, Li Z, Li M, Li Q, Feng X, Song Y. Droplet Precise Self‐Splitting on Patterned Adhesive Surfaces for Simultaneous Multidetection. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Huizeng Li
- Key Laboratory of Green Printing Institute of Chemistry Chinese Academy of Sciences (ICCAS) Beijing Engineering Research Center of Nanomaterials for Green Printing Technology National Laboratory for Molecular Sciences (BNLMS) Beijing 100190 P. R. China
| | - Wei Fang
- AML, CNMM, and Department of Engineering Mechanics, and State Key Laboratory of Tribology Tsinghua University Beijing 100084 P. R. China
| | - Zhipeng Zhao
- Key Laboratory of Green Printing Institute of Chemistry Chinese Academy of Sciences (ICCAS) Beijing Engineering Research Center of Nanomaterials for Green Printing Technology National Laboratory for Molecular Sciences (BNLMS) Beijing 100190 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - An Li
- Key Laboratory of Green Printing Institute of Chemistry Chinese Academy of Sciences (ICCAS) Beijing Engineering Research Center of Nanomaterials for Green Printing Technology National Laboratory for Molecular Sciences (BNLMS) Beijing 100190 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Zheng Li
- Key Laboratory of Green Printing Institute of Chemistry Chinese Academy of Sciences (ICCAS) Beijing Engineering Research Center of Nanomaterials for Green Printing Technology National Laboratory for Molecular Sciences (BNLMS) Beijing 100190 P. R. China
| | - Mingzhu Li
- Key Laboratory of Green Printing Institute of Chemistry Chinese Academy of Sciences (ICCAS) Beijing Engineering Research Center of Nanomaterials for Green Printing Technology National Laboratory for Molecular Sciences (BNLMS) Beijing 100190 P. R. China
| | - Qunyang Li
- AML, CNMM, and Department of Engineering Mechanics, and State Key Laboratory of Tribology Tsinghua University Beijing 100084 P. R. China
| | - Xiqiao Feng
- AML, CNMM, and Department of Engineering Mechanics, and State Key Laboratory of Tribology Tsinghua University Beijing 100084 P. R. China
| | - Yanlin Song
- Key Laboratory of Green Printing Institute of Chemistry Chinese Academy of Sciences (ICCAS) Beijing Engineering Research Center of Nanomaterials for Green Printing Technology National Laboratory for Molecular Sciences (BNLMS) Beijing 100190 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
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Ilić Đurđić K, Ece S, Ostafe R, Vogel S, Balaž AM, Schillberg S, Fischer R, Prodanović R. Flow cytometry-based system for screening of lignin peroxidase mutants with higher oxidative stability. J Biosci Bioeng 2020; 129:664-671. [DOI: 10.1016/j.jbiosc.2019.12.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 01/19/2023]
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49
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Cao L, Chen R, Huang X, Li S, Zhang S, Yang X, Qin Z, Kong W, Xie W, Liu Y. Engineering of β-Glucosidase Bgl15 with Simultaneously Enhanced Glucose Tolerance and Thermostability To Improve Its Performance in High-Solid Cellulose Hydrolysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:5391-5401. [PMID: 32338906 DOI: 10.1021/acs.jafc.0c01817] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this study, a Petri-dish-based double-layer high-throughput screening method was established to improve glucose tolerance of β-glucosidase Bgl15. Two beneficial mutations were identified, and the joint mutant 2R1 improved the half-maximal inhibitory concentration of glucose from 0.04 to 2.1 M. The crystal structure of 2R1 was subsequently determined at 2.7 Å. Structure analysis revealed that enhancement of glucose tolerance may be due to improved transglycosylation activity made possible by a hydrophobic binding site for glucose as an acceptor and more stringent control of a putative water channel. To further ameliorate the application potential of the enzyme, it was engineered to increase the half-life at 50 °C from 0.8 h (Bgl15) to 180 h (mutant 5R1). Furthermore, supplementation of 5R1 to the cellulase cocktail significantly improved glucose production from pretreated sugar cane bagasse by 38%. Consequently, this study provided an efficient approach to enhance glucose tolerance and generated a promising catalyst for cellulose saccharification.
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50
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Li H, Fang W, Zhao Z, Li A, Li Z, Li M, Li Q, Feng X, Song Y. Droplet Precise Self‐Splitting on Patterned Adhesive Surfaces for Simultaneous Multidetection. Angew Chem Int Ed Engl 2020; 59:10535-10539. [DOI: 10.1002/anie.202003839] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Huizeng Li
- Key Laboratory of Green Printing Institute of Chemistry Chinese Academy of Sciences (ICCAS) Beijing Engineering Research Center of Nanomaterials for Green Printing Technology National Laboratory for Molecular Sciences (BNLMS) Beijing 100190 P. R. China
| | - Wei Fang
- AML, CNMM, and Department of Engineering Mechanics, and State Key Laboratory of Tribology Tsinghua University Beijing 100084 P. R. China
| | - Zhipeng Zhao
- Key Laboratory of Green Printing Institute of Chemistry Chinese Academy of Sciences (ICCAS) Beijing Engineering Research Center of Nanomaterials for Green Printing Technology National Laboratory for Molecular Sciences (BNLMS) Beijing 100190 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - An Li
- Key Laboratory of Green Printing Institute of Chemistry Chinese Academy of Sciences (ICCAS) Beijing Engineering Research Center of Nanomaterials for Green Printing Technology National Laboratory for Molecular Sciences (BNLMS) Beijing 100190 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Zheng Li
- Key Laboratory of Green Printing Institute of Chemistry Chinese Academy of Sciences (ICCAS) Beijing Engineering Research Center of Nanomaterials for Green Printing Technology National Laboratory for Molecular Sciences (BNLMS) Beijing 100190 P. R. China
| | - Mingzhu Li
- Key Laboratory of Green Printing Institute of Chemistry Chinese Academy of Sciences (ICCAS) Beijing Engineering Research Center of Nanomaterials for Green Printing Technology National Laboratory for Molecular Sciences (BNLMS) Beijing 100190 P. R. China
| | - Qunyang Li
- AML, CNMM, and Department of Engineering Mechanics, and State Key Laboratory of Tribology Tsinghua University Beijing 100084 P. R. China
| | - Xiqiao Feng
- AML, CNMM, and Department of Engineering Mechanics, and State Key Laboratory of Tribology Tsinghua University Beijing 100084 P. R. China
| | - Yanlin Song
- Key Laboratory of Green Printing Institute of Chemistry Chinese Academy of Sciences (ICCAS) Beijing Engineering Research Center of Nanomaterials for Green Printing Technology National Laboratory for Molecular Sciences (BNLMS) Beijing 100190 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
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