1
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Li D, Cai Y, Guo J, Liu Y, Lu F, Li Q, Liu Y, Li Y. Screening signal peptidase based on split-GFP assembly technology to promote the secretion of alkaline protease AprE in Bacillus amyloliquefaciens. Int J Biol Macromol 2024; 269:132166. [PMID: 38723822 DOI: 10.1016/j.ijbiomac.2024.132166] [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: 02/04/2024] [Revised: 04/04/2024] [Accepted: 05/05/2024] [Indexed: 05/13/2024]
Abstract
Improving the ability of bacteria to secrete protein is essential for large-scale production of food enzymes. However, due to the lack of effective tracking technology for target proteins, the optimization of the secretory system is facing many problems. In this study, we utilized the split-GFP system to achieve self-assembly into mature GFP in Bacillus amyloliquefaciens and successfully tracked the alkaline protease AprE. The split-GFP system was employed to assess the signal peptidases, a crucial component in the secretory system, and signal peptidase sipA was identified as playing a role in the secretion of AprE. Deletion of sipA resulted in a higher accumulation of the precursor protein of AprE compared to other signal peptidase deletion strains. To explore the mechanism of signal peptidase on signal peptide, molecular docking and calculation of free energy were performed. The action strength of the signal peptidase is determined by its binding affinity with the tripeptides at the C-terminal of the signal peptide. The functions of signal peptides YdbK and NucB rely on sipA, and overexpression of sipA by integrating it into genome of B. amyloliquefaciens increased the activity of extracellular AprE by 19.9 %. These findings provide insights into enhancing the secretion efficiency of chassis strains.
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Affiliation(s)
- Dengke Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Yian Cai
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Jiejie Guo
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Yihan Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Qinggang Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Yexue Liu
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Yu Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
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2
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Jiang J, Yang G, Ma F. Fluorescence coupling strategies in fluorescence-activated droplet sorting (FADS) for ultrahigh-throughput screening of enzymes, metabolites, and antibodies. Biotechnol Adv 2023; 66:108173. [PMID: 37169102 DOI: 10.1016/j.biotechadv.2023.108173] [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: 01/11/2023] [Revised: 04/17/2023] [Accepted: 05/06/2023] [Indexed: 05/13/2023]
Abstract
Fluorescence-activated droplet sorting (FADS) has emerged as a powerful tool for ultrahigh-throughput screening of enzymes, metabolites, and antibodies. Fluorescence coupling strategies (FCSs) are key to the development of new FADS methods through their coupling of analyte properties such as concentration, activities, and affinity with fluorescence signals. Over the last decade, a series of FCSs have been developed, greatly expanding applications of FADS. Here, we review recent advances in FCS for different analyte types, providing a critical comparison of the available FCSs and further classification into four categories according to their principles. We also summarize successful FADS applications employing FCSs in enzymes, metabolites, and antibodies. Further, we outline possible future developments in this area.
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Affiliation(s)
- Jingjie Jiang
- Medical Enzyme Engineering Center, CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China
| | - Guangyu Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Fuqiang Ma
- Medical Enzyme Engineering Center, CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China.
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3
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Characterization of putative mannoprotein in Kluyveromyces lactis for lactase production. Synth Syst Biotechnol 2023; 8:168-175. [PMID: 36733311 PMCID: PMC9880975 DOI: 10.1016/j.synbio.2023.01.001] [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: 10/20/2022] [Revised: 12/24/2022] [Accepted: 01/01/2023] [Indexed: 01/07/2023] Open
Abstract
Lactase is a member of the β-galactosidase family of enzymes that can hydrolyze lactose into galactose and glucose. However, extracellular lactase production was still restricted to the process of cell lysis. In this study, lactase-producing Kluyveromyces lactis JNXR-2101 was obtained using a rapid and sensitive method based on the fluorescent substrate 4-methylumbelliferyl-β-d-galactopyranoside. The purified enzyme was identified as a neutral lactase with an optimum pH of 9. To facilitate extracellular production of lactase, a putative mannoprotein KLLA0_E01057g of K. lactis was knocked out. It could effectively promote cell wall degradation and lactase production after lyticase treatment, which showed potential on other extracellular enzyme preparation. After optimizing the fermentation conditions, the lactase yield from mannoprotein-deficient K. lactis JNXR-2101ΔE01057g reached 159.62 U/mL in a 5-L fed-batch bioreactor.
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4
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Xiong J, Chu JCH, Fong WP, Wong CTT, Ng DKP. Specific Activation of Photosensitizer with Extrinsic Enzyme for Precisive Photodynamic Therapy. J Am Chem Soc 2022; 144:10647-10658. [PMID: 35639988 DOI: 10.1021/jacs.2c04017] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Delivery of functional proteins into the intracellular space has been a challenging task that could lead to a myriad of therapeutic applications. We report herein a novel bioconjugation strategy for enzyme modification and selective delivery into cancer cells for lock-and-key-type activation of photosensitizers. Using a bifunctional linker containing a bis(bromomethyl)phenyl group and an o-phthalaldehyde moiety, it could induce cyclization of the peptide sequence Ac-NH-CRGDfC-CONH2 through site-specific dibenzylation with the two cysteine residues and further coupling with β-galactosidase via the phthalaldehyde-amine capture reaction. This facile two-step one-pot procedure enabled the preparation of cyclic RGD-modified β-galactosidase readily, which could be internalized selectively into αvβ3 integrin-overexpressed cancer cells. Upon encountering an intrinsically quenched distyryl boron dipyrromethene-based photosensitizer conjugated with a galactose moiety through a self-immolative linker inside the cells, the extrinsic enzyme induced specific cleavage of the β-galactosidic bond followed by self-immolation to release an activated derivative, thereby restoring the photodynamic activities and causing cell death effectively. The high specificity of this extrinsic enzyme-activated photosensitizing system was also demonstrated in vivo using nude mice bearing an αvβ3 integrin-positive U87-MG tumor. The specific activation at the tumor site resulted in lighting up and complete eradication of the tumor upon laser irradiation, while by using the native β-galactosidase, the effects were largely reduced. In contrast to the conventional activation using intrinsic enzymes, this extrinsic enzyme activatable approach can further minimize the nonspecific activation toward precisive photodynamic therapy.
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Affiliation(s)
- Junlong Xiong
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Jacky C H Chu
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Wing-Ping Fong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Clarence T T Wong
- Department of Applied Biology and Chemical Technology and State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Dennis K P Ng
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
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5
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Vanella R, Kovacevic G, Doffini V, Fernández de Santaella J, Nash MA. High-throughput screening, next generation sequencing and machine learning: advanced methods in enzyme engineering. Chem Commun (Camb) 2022; 58:2455-2467. [PMID: 35107442 PMCID: PMC8851469 DOI: 10.1039/d1cc04635g] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Enzyme engineering is an important biotechnological process capable of generating tailored biocatalysts for applications in industrial chemical conversion and biopharma. Typical enhancements sought in enzyme engineering and in vitro evolution campaigns include improved folding stability, catalytic activity, and/or substrate specificity. Despite significant progress in recent years in the areas of high-throughput screening and DNA sequencing, our ability to explore the vast space of functional enzyme sequences remains severely limited. Here, we review the currently available suite of modern methods for enzyme engineering, with a focus on novel readout systems based on enzyme cascades, and new approaches to reaction compartmentalization including single-cell hydrogel encapsulation techniques to achieve a genotype–phenotype link. We further summarize systematic scanning mutagenesis approaches and their merger with deep mutational scanning and massively parallel next-generation DNA sequencing technologies to generate mutability landscapes. Finally, we discuss the implementation of machine learning models for computational prediction of enzyme phenotypic fitness from sequence. This broad overview of current state-of-the-art approaches for enzyme engineering and evolution will aid newcomers and experienced researchers alike in identifying the important challenges that should be addressed to move the field forward. Enzyme engineering is an important biotechnological process capable of generating tailored biocatalysts for applications in industrial chemical conversion and biopharma.![]()
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Affiliation(s)
- Rosario Vanella
- Department of Chemistry, University of Basel, 4058 Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.
| | - Gordana Kovacevic
- Department of Chemistry, University of Basel, 4058 Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.
| | - Vanni Doffini
- Department of Chemistry, University of Basel, 4058 Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.
| | - Jaime Fernández de Santaella
- Department of Chemistry, University of Basel, 4058 Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.
| | - Michael A Nash
- Department of Chemistry, University of Basel, 4058 Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.
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6
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Nakamura A, Honma N, Tanaka Y, Suzuki Y, Shida Y, Tsuda Y, Hidaka K, Ogasawara W. 7-Aminocoumarin-4-acetic Acid as a Fluorescent Probe for Detecting Bacterial Dipeptidyl Peptidase Activities in Water-in-Oil Droplets and in Bulk. Anal Chem 2021; 94:2416-2424. [PMID: 34963280 PMCID: PMC8886566 DOI: 10.1021/acs.analchem.1c04108] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Droplet-based
microfluidic systems are a powerful tool for biological
assays with high throughput. Water-in-oil droplets (WODLs) are typically
used in droplet-based microfluidic systems to culture microorganisms
and perform enzyme assays. However, because of the oil surrounding
the nanoliter and picoliter volumes of WODLs, availability of suitable
substrates is limited. For instance, although 7-amino-4-methylcoumarin
(AMC) is commonly used as a fluorescent probe of the substrate to
detect peptidase activity, AMC leaks from WODLs to the oil phase due
to its high hydrophobicity. Thus, AMC substrates cannot be used in
droplet-based microfluidic systems with WODLs. In this study, we developed
a peptidase substrate consisting of a dipeptide and 7-aminocoumarin-4-acetic
acid (ACA), an AMC-derived fluorogenic compound. ACA was retained
in the WODL for more than 7 days, and the dipeptidyl ACA substrate
detected dipeptidyl peptidase (DPP) activity in the WODL. Compared
to AMC substrates, the substrate specificity constants of DPPs for
ACA substrates increased up to 4.7-fold. Fluorescence-activated droplet
sorting made high-throughput screening of microorganisms based on
DPP activity using the dipeptidyl ACA substrate possible. Since ACA
could be applied to various substrates as a fluorescent probe, detectable
microbial enzyme activities for droplet-based microfluidic systems
can be largely expanded.
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Affiliation(s)
- Akihiro Nakamura
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Nobuyuki Honma
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Yuma Tanaka
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Yoshiyuki Suzuki
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Yosuke Shida
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Yuko Tsuda
- Faculty of Pharmaceutical Sciences, Cooperative Research Center of Life Sciences, Kobe Gakuin University, 1-1-3 Minatojima, Chuo-ku, Kobe, Hyogo 650-8586, Japan
| | - Koushi Hidaka
- Graduate School of Health Sciences, Kobe University, 7-10-2 Tomogaoka, Suma-ku, Kobe, Hyogo 654-0142, Japan
| | - Wataru Ogasawara
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan.,Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
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7
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Stucki A, Vallapurackal J, Ward TR, Dittrich PS. Droplet Microfluidics and Directed Evolution of Enzymes: An Intertwined Journey. Angew Chem Int Ed Engl 2021; 60:24368-24387. [PMID: 33539653 PMCID: PMC8596820 DOI: 10.1002/anie.202016154] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Indexed: 12/12/2022]
Abstract
Evolution is essential to the generation of complexity and ultimately life. It relies on the propagation of the properties, traits, and characteristics that allow an organism to survive in a challenging environment. It is evolution that shaped our world over about four billion years by slow and iterative adaptation. While natural evolution based on selection is slow and gradual, directed evolution allows the fast and streamlined optimization of a phenotype under selective conditions. The potential of directed evolution for the discovery and optimization of enzymes is mostly limited by the throughput of the tools and methods available for screening. Over the past twenty years, versatile tools based on droplet microfluidics have been developed to address the need for higher throughput. In this Review, we provide a chronological overview of the intertwined development of microfluidics droplet-based compartmentalization methods and in vivo directed evolution of enzymes.
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Affiliation(s)
- Ariane Stucki
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26CH-4058BaselSwitzerland
- National Competence Center in Research (NCCR)Molecular Systems EngineeringBaselSwitzerland
| | - Jaicy Vallapurackal
- Department of ChemistryUniversity of BaselMattenstrasse 24aCH-4058BaselSwitzerland
- National Competence Center in Research (NCCR)Molecular Systems EngineeringBaselSwitzerland
| | - Thomas R. Ward
- Department of ChemistryUniversity of BaselMattenstrasse 24aCH-4058BaselSwitzerland
- National Competence Center in Research (NCCR)Molecular Systems EngineeringBaselSwitzerland
| | - Petra S. Dittrich
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26CH-4058BaselSwitzerland
- National Competence Center in Research (NCCR)Molecular Systems EngineeringBaselSwitzerland
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8
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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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9
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Stucki A, Vallapurackal J, Ward TR, Dittrich PS. Droplet Microfluidics and Directed Evolution of Enzymes: An Intertwined Journey. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016154] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ariane Stucki
- Department of Biosystems Science and Engineering ETH Zurich Mattenstrasse 26 CH-4058 Basel Switzerland
- National Competence Center in Research (NCCR) Molecular Systems Engineering Basel Switzerland
| | - Jaicy Vallapurackal
- Department of Chemistry University of Basel Mattenstrasse 24a CH-4058 Basel Switzerland
- National Competence Center in Research (NCCR) Molecular Systems Engineering Basel Switzerland
| | - Thomas R. Ward
- Department of Chemistry University of Basel Mattenstrasse 24a CH-4058 Basel Switzerland
- National Competence Center in Research (NCCR) Molecular Systems Engineering Basel Switzerland
| | - Petra S. Dittrich
- Department of Biosystems Science and Engineering ETH Zurich Mattenstrasse 26 CH-4058 Basel Switzerland
- National Competence Center in Research (NCCR) Molecular Systems Engineering Basel Switzerland
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10
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Li M, Liu H, Zhuang S, Goda K. Droplet flow cytometry for single-cell analysis. RSC Adv 2021; 11:20944-20960. [PMID: 35479393 PMCID: PMC9034116 DOI: 10.1039/d1ra02636d] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 06/06/2021] [Indexed: 01/22/2023] Open
Abstract
The interrogation of single cells has revolutionised biology and medicine by providing crucial unparalleled insights into cell-to-cell heterogeneity. Flow cytometry (including fluorescence-activated cell sorting) is one of the most versatile and high-throughput approaches for single-cell analysis by detecting multiple fluorescence parameters of individual cells in aqueous suspension as they flow past through a focus of excitation lasers. However, this approach relies on the expression of cell surface and intracellular biomarkers, which inevitably lacks spatial and temporal phenotypes and activities of cells, such as secreted proteins, extracellular metabolite production, and proliferation. Droplet microfluidics has recently emerged as a powerful tool for the encapsulation and manipulation of thousands to millions of individual cells within pico-litre microdroplets. Integrating flow cytometry with microdroplet architectures surrounded by aqueous solutions (e.g., water-in-oil-in-water (W/O/W) double emulsion and hydrogel droplets) opens avenues for new cellular assays linking cell phenotypes to genotypes at the single-cell level. In this review, we discuss the capabilities and applications of droplet flow cytometry (DFC). This unique technique uses standard commercially available flow cytometry instruments to characterise or select individual microdroplets containing single cells of interest. We explore current challenges associated with DFC and present our visions for future development.
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Affiliation(s)
- Ming Li
- School of Engineering, Macquarie University Sydney NSW 2109 Australia
- Biomolecular Discovery Research Centre, Macquarie University Sydney NSW 2109 Australia
| | - Hangrui Liu
- Department of Physics and Astronomy, Macquarie University Sydney NSW 2109 Australia
| | - Siyuan Zhuang
- School of Engineering, Macquarie University Sydney NSW 2109 Australia
| | - Keisuke Goda
- Department of Chemistry, The University of Tokyo Tokyo 113-0033 Japan
- Institute of Technological Sciences, Wuhan University 430072 Hubei PR China
- Department of Bioengineering, University of California Los Angeles CA 90095 USA
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11
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Xu W, Zhao S, Zhang W, Wu H, Guang C, Mu W. Recent advances and future prospective of organophosphorus-degrading enzymes: identification, modification, and application. Crit Rev Biotechnol 2021; 41:1096-1113. [PMID: 33906533 DOI: 10.1080/07388551.2021.1898331] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The organophosphorus-based OPs) nerve agents and pesticides have been applied in the agriculture industry for a long time. However, they were found to have a persistent effect on the environment and threaten human health. Traditional methods, including incineration and landfilling, could not thoroughly remove these organophosphorus compounds (OPs). Meanwhile, chemical hydrolysis for decontamination was also inhibited due to the presence of corrosive materials and high costs. Biological remediation for OPs employing microorganisms and organophosphorus-degrading enzymes is promising due to a mild and controllable procedure, environmental-friendly reactions, and high efficacy. A wide variety of enzymes have shown latent ability in degrading OPs hazards like organophosphorus hydrolase (OPH), organophosphorus acid anhydrolase (OPAA), the diisopropylfluorophosphatase (DFPase), and mammalian paraoxonase 1 (PON 1). To this end, increasing efforts have been made on these intriguing enzymes to increase their expression level, enhance the catalytic activity, modify the optimal substrate, and expand the practical application. In this review, the enzyme resource, crystal structure, molecular modification, and industry application were compared and discussed in detail. Moreover, the proposed ideas and positive results could be useful for the other relevant OPs-degrading enzymes.
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Affiliation(s)
- Wei Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Sumao Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hao Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Cuie Guang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
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12
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Vitelli M, Budman H, Pritzker M, Tamer M. Applications of flow cytometry sorting in the pharmaceutical industry: A review. Biotechnol Prog 2021; 37:e3146. [PMID: 33749147 DOI: 10.1002/btpr.3146] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/12/2021] [Accepted: 03/12/2021] [Indexed: 12/17/2022]
Abstract
The article reviews applications of flow cytometry sorting in manufacturing of pharmaceuticals. Flow cytometry sorting is an extremely powerful tool for monitoring, screening and separating single cells based on any property that can be measured by flow cytometry. Different applications of flow cytometry sorting are classified into groups and discussed in separate sections as follows: (a) isolation of cell types, (b) high throughput screening, (c) cell surface display, (d) droplet fluorescent-activated cell sorting (FACS). Future opportunities are identified including: (a) sorting of particular fractions of the cell population based on a property of interest for generating inoculum that will result in improved outcomes of cell cultures and (b) the use of population balance models in combination with FACS to design and optimize cell cultures.
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Affiliation(s)
- Michael Vitelli
- Department of Chemical Engineering, University of Waterloo, Waterloo, Canada
| | - Hector Budman
- Department of Chemical Engineering, University of Waterloo, Waterloo, Canada
| | - Mark Pritzker
- Department of Chemical Engineering, University of Waterloo, Waterloo, Canada
| | - Melih Tamer
- Department of Manufacturing Technology, Sanofi Pasteur, Toronto, Canada
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13
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14
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Bowman EK, Alper HS. Microdroplet-Assisted Screening of Biomolecule Production for Metabolic Engineering Applications. Trends Biotechnol 2020; 38:701-714. [DOI: 10.1016/j.tibtech.2019.11.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/30/2019] [Accepted: 11/07/2019] [Indexed: 12/19/2022]
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15
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Brower KK, Carswell-Crumpton C, Klemm S, Cruz B, Kim G, Calhoun SGK, Nichols L, Fordyce PM. Double emulsion flow cytometry with high-throughput single droplet isolation and nucleic acid recovery. LAB ON A CHIP 2020; 20:2062-2074. [PMID: 32417874 PMCID: PMC7670282 DOI: 10.1039/d0lc00261e] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Droplet microfluidics has made large impacts in diverse areas such as enzyme evolution, chemical product screening, polymer engineering, and single-cell analysis. However, while droplet reactions have become increasingly sophisticated, phenotyping droplets by a fluorescent signal and sorting them to isolate individual variants-of-interest at high-throughput remains challenging. Here, we present sdDE-FACS (s[combining low line]ingle d[combining low line]roplet D[combining low line]ouble E[combining low line]mulsion-FACS), a new method that uses a standard flow cytometer to phenotype, select, and isolate individual double emulsion droplets of interest. Using a 130 μm nozzle at high sort frequency (12-14 kHz), we demonstrate detection of droplet fluorescence signals with a dynamic range spanning 5 orders of magnitude and robust post-sort recovery of intact double emulsion (DE) droplets using 2 commercially-available FACS instruments. We report the first demonstration of single double emulsion droplet isolation with post-sort recovery efficiencies >70%, equivalent to the capabilities of single-cell FACS. Finally, we establish complete downstream recovery of nucleic acids from single, sorted double emulsion droplets via qPCR with little to no cross-contamination. sdDE-FACS marries the full power of droplet microfluidics with flow cytometry to enable a variety of new droplet assays, including rare variant isolation and multiparameter single-cell analysis.
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Affiliation(s)
- Kara K Brower
- Department of Bioengineering, Stanford University, Stanford, California, USA.
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16
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Markel U, Essani KD, Besirlioglu V, Schiffels J, Streit WR, Schwaneberg U. Advances in ultrahigh-throughput screening for directed enzyme evolution. Chem Soc Rev 2020; 49:233-262. [PMID: 31815263 DOI: 10.1039/c8cs00981c] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enzymes are versatile catalysts and their synthetic potential has been recognized for a long time. In order to exploit their full potential, enzymes often need to be re-engineered or optimized for a given application. (Semi-) rational design has emerged as a powerful means to engineer proteins, but requires detailed knowledge about structure function relationships. In turn, directed evolution methodologies, which consist of iterative rounds of diversity generation and screening, can improve an enzyme's properties with virtually no structural knowledge. Current diversity generation methods grant us access to a vast sequence space (libraries of >1012 enzyme variants) that may hide yet unexplored catalytic activities and selectivity. However, the time investment for conventional agar plate or microtiter plate-based screening assays represents a major bottleneck in directed evolution and limits the improvements that are obtainable in reasonable time. Ultrahigh-throughput screening (uHTS) methods dramatically increase the number of screening events per time, which is crucial to speed up biocatalyst design, and to widen our knowledge about sequence function relationships. In this review, we summarize recent advances in uHTS for directed enzyme evolution. We shed light on the importance of compartmentalization to preserve the essential link between genotype and phenotype and discuss how cells and biomimetic compartments can be applied to serve this function. Finally, we discuss how uHTS can inspire novel functional metagenomics approaches to identify natural biocatalysts for novel chemical transformations.
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Affiliation(s)
- Ulrich Markel
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany.
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Ma C, Tan ZL, Lin Y, Han S, Xing X, Zhang C. Gel microdroplet–based high-throughput screening for directed evolution of xylanase-producing Pichia pastoris. J Biosci Bioeng 2019; 128:662-668. [DOI: 10.1016/j.jbiosc.2019.05.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 05/11/2019] [Accepted: 05/13/2019] [Indexed: 01/24/2023]
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Chao L, Jongkees S. High-Throughput Approaches in Carbohydrate-Active Enzymology: Glycosidase and Glycosyl Transferase Inhibitors, Evolution, and Discovery. Angew Chem Int Ed Engl 2019; 58:12750-12760. [PMID: 30913359 PMCID: PMC6771893 DOI: 10.1002/anie.201900055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/05/2019] [Indexed: 01/13/2023]
Abstract
Carbohydrates are attached and removed in living systems through the action of carbohydrate-active enzymes such as glycosyl transferases and glycoside hydrolases. The molecules resulting from these enzymes have many important roles in organisms, such as cellular communication, structural support, and energy metabolism. In general, each carbohydrate transformation requires a separate catalyst, and so these enzyme families are extremely diverse. To make this diversity manageable, high-throughput approaches look at many enzymes at once. Similarly, high-throughput approaches can be a powerful way of finding inhibitors that can be used to tune the reactivity of these enzymes, either in an industrial, a laboratory, or a medicinal setting. In this review, we provide an overview of how these enzymes and inhibitors can be sought using techniques such as high-throughput natural product and combinatorial library screening, phage and mRNA display of (glyco)peptides, fluorescence-activated cell sorting, and metagenomics.
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Affiliation(s)
- Lemeng Chao
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3581AG, Utrecht, The Netherlands
| | - Seino Jongkees
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3581AG, Utrecht, The Netherlands
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Chao L, Jongkees S. High‐Throughput Approaches in Carbohydrate‐Active Enzymology: Glycosidase and Glycosyl Transferase Inhibitors, Evolution, and Discovery. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201900055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Lemeng Chao
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical Sciences Utrecht University Universiteitsweg 99 3581AG Utrecht The Netherlands
| | - Seino Jongkees
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical Sciences Utrecht University Universiteitsweg 99 3581AG Utrecht The Netherlands
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Vian A, Reuse B, Amstad E. Scalable production of double emulsion drops with thin shells. LAB ON A CHIP 2018; 18:1936-1942. [PMID: 29881836 DOI: 10.1039/c8lc00282g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Double emulsions are often used as containers to perform high throughput screening assays and as templates for capsules. These applications require double emulsions to be mechanically stable such that they do not coalesce during processing and storage. A possibility to increase their stability is to reduce the thickness of their shells to sufficiently low values that lubrication effects hinder coalescence. However, the controlled fabrication of double emulsions with such thin shells is difficult. Here, we introduce a new microfluidic device, the aspiration device, that reduces the shell thickness of double emulsions down to 240 nm at a high throughput; thereby, the shell volume is reduced by up to 95%. The shell thickness of the resulting double emulsions depends on the pressure profile in the device and hence on the fluid flow rates in the channels and is independent of the shell thickness of the injected double emulsions. Therefore, this device enables converting double emulsions with polydisperse shell thicknesses into double emulsions with well-defined, uniform thin shells.
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Affiliation(s)
- A Vian
- Soft Materials Laboratory, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
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21
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Choi A, Miller SC. Reductively-labile sulfonate ester protecting groups that are rapidly cleaved by physiological glutathione. Org Biomol Chem 2018; 15:1346-1349. [PMID: 28116407 DOI: 10.1039/c7ob00063d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Sulfonates are frequently used to endow water solubility on hydrophobic molecules, but the repertoire of sulfonate protecting groups remains limited. Here we describe the first sulfonate esters that can be unmasked by the mild reducing conditions found in live mammalian cells. Self-immolative cleavage releases the sulfonate and the two-electron reduction product of a thioquinone methide.
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Affiliation(s)
- Adam Choi
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St, Worcester, MA 01605, USA.
| | - Stephen C Miller
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St, Worcester, MA 01605, USA.
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Carbohydrate active enzyme domains from extreme thermophiles: components of a modular toolbox for lignocellulose degradation. Extremophiles 2017; 22:1-12. [PMID: 29110088 DOI: 10.1007/s00792-017-0974-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/24/2017] [Indexed: 02/06/2023]
Abstract
Lignocellulosic biomass is a promising feedstock for the manufacture of biodegradable and renewable bioproducts. However, the complex lignocellulosic polymeric structure of woody tissue is difficult to access without extensive industrial pre-treatment. Enzyme processing of partly depolymerised biomass is an established technology, and there is evidence that high temperature (extremely thermophilic) lignocellulose degrading enzymes [carbohydrate active enzymes (CAZymes)] may enhance processing efficiency. However, wild-type thermophilic CAZymes will not necessarily be functionally optimal under industrial pre-treatment conditions. With recent advances in synthetic biology, it is now potentially possible to build CAZyme constructs from individual protein domains, tailored to the conditions of specific industrial processes. In this review, we identify a 'toolbox' of thermostable CAZyme domains from extremely thermophilic organisms and highlight recent advances in CAZyme engineering which will allow for the rational design of CAZymes tailored to specific aspects of lignocellulose digestion.
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Liu W, Gómez-Durán CFA, Smith BD. Fluorescent Neuraminidase Assay Based on Supramolecular Dye Capture After Enzymatic Cleavage. J Am Chem Soc 2017; 139:6390-6395. [PMID: 28426220 DOI: 10.1021/jacs.7b01628] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A conceptually new type of enzymatic cleavage assay is reported that utilizes in situ supramolecular capture of the fluorescent product. A squaraine-derived substrate with large blocking groups at each end of its structure cannot be threaded by a tetralactam macrocycle until the blocking groups are removed by enzyme cleavage. A prototype design responds to viral neuraminidase, an indicator of influenza infection, and also measures susceptibility of the sample to neuraminidase inhibitor drugs. The substrate structure incorporates three key features: (a) a bis(4-amino-3-hydroxyphenyl)squaraine core with bright deep-red fluorescence and excellent photostability, (b) an N-methyl group at each end of the squaraine core that ensures fast macrocycle threading kinetics, and (c) sialic acid blocking groups that prevent macrocycle threading until they are removed by viral neuraminidase. The enzyme assay can be conducted in aqueous solution where dramatic colorimetric and fluorescence changes are easily observed by the naked eye. Alternatively, affinity capture beads coated with macrocycle can be used to immobilize the liberated squaraine and enable a range of heterogeneous analysis options. With further optimization, this new type of neuraminidase assay may be useful in a point of care clinic to rapidly diagnose influenza infection and also determine which of the approved antiviral inhibitor drugs is likely to be the most effective treatment for an individual patient. The assay design is generalizable and can be readily modified to monitor virtually any type of enzyme-catalyzed cleavage reaction.
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Affiliation(s)
- Wenqi Liu
- Department of Chemistry and Biochemistry, University of Notre Dame , 236 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - César F A Gómez-Durán
- Department of Chemistry and Biochemistry, University of Notre Dame , 236 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - Bradley D Smith
- Department of Chemistry and Biochemistry, University of Notre Dame , 236 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
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Autour A, Ryckelynck M. Ultrahigh-Throughput Improvement and Discovery of Enzymes Using Droplet-Based Microfluidic Screening. MICROMACHINES 2017. [PMCID: PMC6189954 DOI: 10.3390/mi8040128] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Enzymes are extremely valuable tools for industrial, environmental, and biotechnological applications and there is a constant need for improving existing biological catalysts and for discovering new ones. Screening microbe or gene libraries is an efficient way of identifying new enzymes. In this view, droplet-based microfluidics appears to be one of the most powerful approaches as it allows inexpensive screenings in well-controlled conditions and an ultrahigh-throughput regime. This review aims to introduce the main microfluidic devices and concepts to be considered for such screening before presenting and discussing the latest successful applications of the technology for enzyme discovery.
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