1
|
Vanella R, Küng C, Schoepfer AA, Doffini V, Ren J, Nash MA. Understanding activity-stability tradeoffs in biocatalysts by enzyme proximity sequencing. Nat Commun 2024; 15:1807. [PMID: 38418512 PMCID: PMC10902396 DOI: 10.1038/s41467-024-45630-3] [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: 03/24/2023] [Accepted: 01/26/2024] [Indexed: 03/01/2024] Open
Abstract
Understanding the complex relationships between enzyme sequence, folding stability and catalytic activity is crucial for applications in industry and biomedicine. However, current enzyme assay technologies are limited by an inability to simultaneously resolve both stability and activity phenotypes and to couple these to gene sequences at large scale. Here we present the development of enzyme proximity sequencing, a deep mutational scanning method that leverages peroxidase-mediated radical labeling with single cell fidelity to dissect the effects of thousands of mutations on stability and catalytic activity of oxidoreductase enzymes in a single experiment. We use enzyme proximity sequencing to analyze how 6399 missense mutations influence folding stability and catalytic activity in a D-amino acid oxidase from Rhodotorula gracilis. The resulting datasets demonstrate activity-based constraints that limit folding stability during natural evolution, and identify hotspots distant from the active site as candidates for mutations that improve catalytic activity without sacrificing stability. Enzyme proximity sequencing can be extended to other enzyme classes and provides valuable insights into biophysical principles governing enzyme structure and function.
Collapse
Affiliation(s)
- Rosario Vanella
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland.
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.
| | - Christoph Küng
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Alexandre A Schoepfer
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
- National Center for Competence in Research (NCCR), Catalysis, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Vanni Doffini
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Jin Ren
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Michael A Nash
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland.
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.
- National Center for Competence in Research (NCCR), Molecular Systems Engineering, 4058, Basel, Switzerland.
- Swiss Nanoscience Institute, 4056, Basel, Switzerland.
| |
Collapse
|
2
|
Eenink BDG, Kaminski TS, Bornberg-Bauer E, Jose J, Hollfelder F, van Loo B. Vector redesign and in-droplet cell-growth improves enrichment and recovery in live Escherichia coli. Microb Biotechnol 2022; 15:2845-2853. [PMID: 36099491 PMCID: PMC9618318 DOI: 10.1111/1751-7915.14144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 08/23/2022] [Accepted: 09/01/2022] [Indexed: 11/21/2022] Open
Abstract
Directed evolution (DE) is a widely used method for improving the function of biomolecules via multiple rounds of mutation and selection. Microfluidic droplets have emerged as an important means to screen the large libraries needed for DE, but this approach was so far partially limited by the need to lyse cells, recover DNA, and retransform into cells for the next round, necessitating the use of a high‐copy number plasmid or oversampling. The recently developed live cell recovery avoids some of these limitations by directly regrowing selected cells after sorting. However, repeated sorting cycles used to further enrich the most active variants ultimately resulted in unfavourable recovery of empty plasmid vector‐containing cells over those expressing the protein of interest. In this study, we found that engineering of the original expression vector solved the problem of false positives (i.e. plasmids lacking an insert) cells containing empty vectors. Five approaches to measure activity of cell‐displayed enzymes in microdroplets were compared. By comparing various cell treatment methods prior to droplet sorting two things were found. Substrate encapsulation from the start, that is prior to expression of enzyme, showed no disadvantage to post‐induction substrate addition by pico‐injection with respect to recovery of true positive variants. Furthermore in‐droplet cell growth prior to induction of enzyme production improves the total amount of cells retrieved (recovery) and proportion of true positive variants (enrichment) after droplet sorting.
Collapse
Affiliation(s)
- Bernard D G Eenink
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Tomasz S Kaminski
- Department of Biochemistry, University of Cambridge, Cambridge, UK.,Department of Environmental Microbiology and Biotechnology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.,Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Joachim Jose
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Münster, Germany
| | | | - Bert van Loo
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.,Department of Applied Sciences, Northumbria University, Newcastle-upon-Tyne, UK
| |
Collapse
|
3
|
Vanella R, Kovacevic G, Doffini V, Fernández de Santaella J, Nash MA. High-throughput screening, next generation sequencing and machine learning: advanced methods in enzyme engineering. Chem Commun (Camb) 2022; 58:2455-2467. [PMID: 35107442 PMCID: PMC8851469 DOI: 10.1039/d1cc04635g] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 01/23/2022] [Indexed: 12/29/2022]
Abstract
Enzyme engineering is an important biotechnological process capable of generating tailored biocatalysts for applications in industrial chemical conversion and biopharma. Typical enhancements sought in enzyme engineering and in vitro evolution campaigns include improved folding stability, catalytic activity, and/or substrate specificity. Despite significant progress in recent years in the areas of high-throughput screening and DNA sequencing, our ability to explore the vast space of functional enzyme sequences remains severely limited. Here, we review the currently available suite of modern methods for enzyme engineering, with a focus on novel readout systems based on enzyme cascades, and new approaches to reaction compartmentalization including single-cell hydrogel encapsulation techniques to achieve a genotype-phenotype link. We further summarize systematic scanning mutagenesis approaches and their merger with deep mutational scanning and massively parallel next-generation DNA sequencing technologies to generate mutability landscapes. Finally, we discuss the implementation of machine learning models for computational prediction of enzyme phenotypic fitness from sequence. This broad overview of current state-of-the-art approaches for enzyme engineering and evolution will aid newcomers and experienced researchers alike in identifying the important challenges that should be addressed to move the field forward.
Collapse
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.
| |
Collapse
|
4
|
Green L, Scrutton NS, Currin A. GeneORator: An Efficient Method for the Systematic Mutagenesis of Entire Genes. Methods Mol Biol 2022; 2461:111-122. [PMID: 35727446 DOI: 10.1007/978-1-0716-2152-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Directed evolution is a powerful tool for the rapid improvement of a target protein toward a desired fitness criteria, such as activity, specificity, or stability. In order to achieve these desired improvements, it is often beneficial to subject the entirety of the protein to mutagenesis. However, the creation of such libraries by targeted methods (i.e. site-directed mutagenesis) can be a laborious and costly task. Here we outline the GeneORator method, which uses Boolean "OR" logic to introduce specific codon mutations at multiple loci in a single reaction, thereby greatly reducing the experimental workload. The method describes library synthesis using asymmetric PCR, in which mutagenic primers are designed to create OR-type mutations at multiple sites of variation in a two-step protocol. As an example, we show how this can be utilized for controlled and economical mutagenesis of every amino acid codon in a gene.
Collapse
Affiliation(s)
- Lucy Green
- Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, University of Manchester, Manchester, UK
| | - Nigel S Scrutton
- Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, University of Manchester, Manchester, UK
| | - Andrew Currin
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Ortseifen V, Viefhues M, Wobbe L, Grünberger A. Microfluidics for Biotechnology: Bridging Gaps to Foster Microfluidic Applications. Front Bioeng Biotechnol 2020; 8:589074. [PMID: 33282849 PMCID: PMC7691494 DOI: 10.3389/fbioe.2020.589074] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/26/2020] [Indexed: 12/15/2022] Open
Abstract
Microfluidics and novel lab-on-a-chip applications have the potential to boost biotechnological research in ways that are not possible using traditional methods. Although microfluidic tools were increasingly used for different applications within biotechnology in recent years, a systematic and routine use in academic and industrial labs is still not established. For many years, absent innovative, ground-breaking and “out-of-the-box” applications have been made responsible for the missing drive to integrate microfluidic technologies into fundamental and applied biotechnological research. In this review, we highlight microfluidics’ offers and compare them to the most important demands of the biotechnologists. Furthermore, a detailed analysis in the state-of-the-art use of microfluidics within biotechnology was conducted exemplarily for four emerging biotechnological fields that can substantially benefit from the application of microfluidic systems, namely the phenotypic screening of cells, the analysis of microbial population heterogeneity, organ-on-a-chip approaches and the characterisation of synthetic co-cultures. The analysis resulted in a discussion of potential “gaps” that can be responsible for the rare integration of microfluidics into biotechnological studies. Our analysis revealed six major gaps, concerning the lack of interdisciplinary communication, mutual knowledge and motivation, methodological compatibility, technological readiness and missing commercialisation, which need to be bridged in the future. We conclude that connecting microfluidics and biotechnology is not an impossible challenge and made seven suggestions to bridge the gaps between those disciplines. This lays the foundation for routine integration of microfluidic systems into biotechnology research procedures.
Collapse
Affiliation(s)
- Vera Ortseifen
- Proteome and Metabolome Research, Faculty of Biology, Center for Biotechnology/CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Martina Viefhues
- Experimental Biophysics and Applied Nanosciences, Faculty of Physics, Bielefeld University, Bielefeld, Germany
| | - Lutz Wobbe
- Algae Biotechnology and Bioenergy Group, Faculty of Biology, Center for Biotechnology/CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Alexander Grünberger
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| |
Collapse
|
7
|
Ding Q, Diao W, Gao C, Chen X, Liu L. Microbial cell engineering to improve cellular synthetic capacity. Biotechnol Adv 2020; 45:107649. [PMID: 33091485 DOI: 10.1016/j.biotechadv.2020.107649] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/02/2020] [Accepted: 10/13/2020] [Indexed: 01/21/2023]
Abstract
Rapid technological progress in gene assembly, biosensors, and genetic circuits has led to reinforce the cellular synthetic capacity for chemical production. However, overcoming the current limitations of these techniques in maintaining cellular functions and enhancing the cellular synthetic capacity (e.g., catalytic efficiency, strain performance, and cell-cell communication) remains challenging. In this review, we propose a strategy for microbial cell engineering to improve the cellular synthetic capacity by utilizing biotechnological tools along with system biology methods to regulate cellular functions during chemical production. Current strategies in microbial cell engineering are mainly focused on the organelle, cell, and consortium levels. This review highlights the potential of using biotechnology to further develop the field of microbial cell engineering and provides guidance for utilizing microorganisms as attractive regulation targets.
Collapse
Affiliation(s)
- Qiang Ding
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Wenwen Diao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.
| |
Collapse
|
8
|
van Loo B, Heberlein M, Mair P, Zinchenko A, Schüürmann J, Eenink BDG, Holstein JM, Dilkaute C, Jose J, Hollfelder F, Bornberg-Bauer E. High-Throughput, Lysis-Free Screening for Sulfatase Activity Using Escherichia coli Autodisplay in Microdroplets. ACS Synth Biol 2019; 8:2690-2700. [PMID: 31738524 DOI: 10.1021/acssynbio.9b00274] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Directed evolution of enzymes toward improved catalytic performance has become a powerful tool in protein engineering. To be effective, a directed evolution campaign requires the use of high-throughput screening. In this study we describe the development of an ultra high-throughput lysis-free procedure to screen for improved sulfatase activity by combining microdroplet-based single-variant activity sorting with E. coli autodisplay. For the first step in a 4-step screening procedure, we quantitatively screened >105 variants of the homodimeric arylsulfatase from Silicibacter pomeroyi (SpAS1), displayed on the E. coli cell surface, for improved sulfatase activity using fluorescence activated droplet sorting. Compartmentalization of the fluorescent reaction product with living E. coli cells autodisplaying the sulfatase variants ensured the continuous linkage of genotype and phenotype during droplet sorting and allowed for direct recovery by simple regrowth of the sorted cells. The use of autodisplay on living cells simplified and reduced the degree of liquid handling during all steps in the screening procedure to the single event of simply mixing substrate and cells. The percentage of apparent improved variants was enriched >10-fold as a result of droplet sorting. We ultimately identified 25 SpAS1 variants with improved performance toward 4-nitrophenyl sulfate (up to 6.2-fold) and/or fluorescein disulfate (up to 30-fold). In SpAS1 variants with improved performance toward the bulky fluorescein disulfate, many of the beneficial mutations occur in residues that form hydrogen bonds between α-helices in the C-terminal oligomerization region, suggesting a previously unknown role for the dimer interface in shaping the substrate binding site of SpAS1.
Collapse
Affiliation(s)
- Bert van Loo
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - Magdalena Heberlein
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Philip Mair
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Anastasia Zinchenko
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Jan Schüürmann
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, 48149 Münster, Germany
| | - Bernard D. G. Eenink
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - Josephin M. Holstein
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Carina Dilkaute
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, 48149 Münster, Germany
| | - Joachim Jose
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, 48149 Münster, Germany
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| |
Collapse
|
9
|
Enzymatic Synthesis of Nucleoside Triphosphates and Deoxynucleoside Triphosphates by Surface-Displayed Kinases. Appl Biochem Biotechnol 2019; 190:1271-1288. [PMID: 31745822 DOI: 10.1007/s12010-019-03138-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/12/2019] [Indexed: 02/07/2023]
Abstract
Nucleoside triphosphates and deoxynucleoside triphosphates are important biochemical molecules. In this study, recombinant Escherichia coli that could display nucleotide kinases (INP-N-NMKases) and acetate kinase (INP-N-ACKase) on the cell surface were constructed by fusing an enzyme (NMKase/ACKase) to the N-terminus of ice nucleation protein (INP-N). By using intact recombinant bacteria cells as a catalyst coupled with an ACKase-catalyzed adenosine-5'-triphosphate (ATP) regeneration system, nucleoside triphosphates (NTPs) and deoxynucleoside triphosphates (dNTPs) could be synthesized efficiently. In a reaction system with 5 mmol/l substrate, the conversion rates of cytidine-5'-triphosphate (CTP) and deoxycytidine-5'-triphosphate (dCTP) were 96% and 93%, respectively, the conversion rate of ATP and deoxyadenosine-5'-triphosphate (dATP) was 96%, the conversion rate of deoxythymidine-5'-triphosphate (dTTP) was 91%, and the conversion rate of uridine-5'-triphosphate (UTP) was 80%. There was no obvious degradation. At 37 °C, the stability of the surface-displayed fusion protein, especially in the presence of the substrate, was significantly improved. Each whole cell could be reused more than 8 times.
Collapse
|
10
|
Enzymes from Marine Polar Regions and Their Biotechnological Applications. Mar Drugs 2019; 17:md17100544. [PMID: 31547548 PMCID: PMC6835263 DOI: 10.3390/md17100544] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 12/27/2022] Open
Abstract
The microorganisms that evolved at low temperatures express cold-adapted enzymes endowed with unique catalytic properties in comparison to their mesophilic homologues, i.e., higher catalytic efficiency, improved flexibility, and lower thermal stability. Cold environments are therefore an attractive research area for the discovery of enzymes to be used for investigational and industrial applications in which such properties are desirable. In this work, we will review the literature on cold-adapted enzymes specifically focusing on those discovered in the bioprospecting of polar marine environments, so far largely neglected because of their limited accessibility. We will discuss their existing or proposed biotechnological applications within the framework of the more general applications of cold-adapted enzymes.
Collapse
|
11
|
Chiu FWY, Stavrakis S. High-throughput droplet-based microfluidics for directed evolution of enzymes. Electrophoresis 2019; 40:2860-2872. [PMID: 31433062 PMCID: PMC6899980 DOI: 10.1002/elps.201900222] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/10/2019] [Accepted: 08/12/2019] [Indexed: 01/12/2023]
Abstract
Natural enzymes have evolved over millions of years to allow for their effective operation within specific environments. However, it is significant to note that despite their wide structural and chemical diversity, relatively few natural enzymes have been successfully applied to industrial processes. To address this limitation, directed evolution (DE) (a method that mimics the process of natural selection to evolve proteins toward a user‐defined goal) coupled with droplet‐based microfluidics allows the detailed analysis of millions of enzyme variants on ultra‐short timescales, and thus the design of novel enzymes with bespoke properties. In this review, we aim at presenting the development of DE over the last years and highlighting the most important advancements in droplet‐based microfluidics, made in this context towards the high‐throughput demands of enzyme optimization. Specifically, an overview of the range of microfluidic unit operations available for the construction of DE platforms is provided, focusing on their suitability and benefits for cell‐based assays, as in the case of directed evolution experimentations.
Collapse
Affiliation(s)
- Flora W Y Chiu
- Institute for Chemical and Bioengineering, ETH Zürich, Zürich, Switzerland
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, ETH Zürich, Zürich, Switzerland
| |
Collapse
|
12
|
Tan Z, Heemstra JM. High-Throughput Measurement of Small-Molecule Enantiopurity by Using Flow Cytometry. Chembiochem 2018; 19:1853-1857. [PMID: 30126025 DOI: 10.1002/cbic.201800341] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Indexed: 12/18/2022]
Abstract
Fluorescence-activated cell sorting (FACS) offers a powerful approach to high-throughput library screening in directed evolution experiments. However, FACS is rarely used in the evolution of stereoselective enzymes, due to the difficulty of designing fluorescence-based assays for measuring enantiopurity. Here, we describe a new FACS-based enantiopurity analysis approach that overcomes these limitations by using enantiomeric DNA biosensors labeled with orthogonal fluorophores. By co-encapsulating the biosensors with a mixture of target enantiomers in microfluidic droplets, we could demonstrate the use of FACS to differentiate between droplets having various levels of target enantiopurity. We envision the utility of this method for high-throughput screening of enantiopurity in the directed evolution of stereoselective enzymes, thereby facilitating the discovery of new asymmetric biocatalysts for the synthesis of pharmaceuticals and other high-value chemicals.
Collapse
Affiliation(s)
- Zhesen Tan
- Department of Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - Jennifer M Heemstra
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA.,Department of Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| |
Collapse
|
13
|
Bilal M, Iqbal HMN, Guo S, Hu H, Wang W, Zhang X. State-of-the-art protein engineering approaches using biological macromolecules: A review from immobilization to implementation view point. Int J Biol Macromol 2018; 108:893-901. [PMID: 29102791 DOI: 10.1016/j.ijbiomac.2017.10.182] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 10/18/2017] [Accepted: 10/31/2017] [Indexed: 02/05/2023]
Abstract
Over the past years, technological and scientific advances have proven biocatalysis as a sustainable alternative than traditional chemical catalysis including organo- or metallocatalysis. In this context, immobilization based approaches represent simple but effective routes for engineering enzyme catalysts with higher activities than wild-type derivatives. Many enzymes including oxidoreductases have been engineered by rational and directed evolution, to realize the catalytic activity, enantioselectivity, and stability attributes which are essential for their biotechnological exploitation. Induce yet stable activity in enzyme catalysis offer new insights and motivation to engineer efficient catalysts for practical and commercial purposes. It has now become possible to envisage substrate accessibility to the catalytic site of the enzyme by current computational capabilities that reduce the experimental work related to the enzyme selection, screening, and engineering. Herein, state-of-the-art protein engineering approaches for improving enzymatic activities including chemical modification, directed evolution, and rational design or their combination methods are discussed. The emphasis is also given to the applications of the resulting tailored catalysts ranging from fine chemicals to novel pharmaceutical compounds that use biocatalysts as a vital step.
Collapse
Affiliation(s)
- Muhammad Bilal
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, N.L., CP 64849, Mexico
| | - Shuqi Guo
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongbo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China; National Experimental Teaching Center for Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| |
Collapse
|
14
|
Bunzel HA, Garrabou X, Pott M, Hilvert D. Speeding up enzyme discovery and engineering with ultrahigh-throughput methods. Curr Opin Struct Biol 2018; 48:149-156. [PMID: 29413955 DOI: 10.1016/j.sbi.2017.12.010] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 12/26/2017] [Indexed: 01/24/2023]
Abstract
Exploring the sequence space of enzyme catalysts is ultimately a numbers game. Ultrahigh-throughput screening methods for rapid analysis of millions of variants are therefore increasingly important for investigating sequence-function relationships, searching large metagenomic libraries for interesting activities, and accelerating enzyme evolution in the laboratory. Recent applications of such technologies are reviewed here, with a particular focus on the practical benefits of droplet-based microfluidics for the directed evolution of natural and artificial enzymes. Broader implementation of such rapid, cost-effective screening technologies is likely to redefine the way enzymes are studied and engineered for academic and industrial purposes.
Collapse
Affiliation(s)
- Hans Adrian Bunzel
- Laboratory of Organic Chemistry, ETH Zurich, Zurich CH-8093, Switzerland
| | - Xavier Garrabou
- Laboratory of Organic Chemistry, ETH Zurich, Zurich CH-8093, Switzerland
| | - Moritz Pott
- Laboratory of Organic Chemistry, ETH Zurich, Zurich CH-8093, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, Zurich CH-8093, Switzerland.
| |
Collapse
|
15
|
Fulton A, Hayes MR, Schwaneberg U, Pietruszka J, Jaeger KE. High-Throughput Screening Assays for Lipolytic Enzymes. Methods Mol Biol 2018; 1685:209-231. [PMID: 29086311 DOI: 10.1007/978-1-4939-7366-8_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Screening is defined as the identification of hits within a large library of variants of an enzyme or protein with a predefined property. In theory, each variant present in the respective library needs to be assayed; however, to save time and consumables, many screening regimes involve a primary round to identify clones producing active enzymes. Such primary or prescreenings for lipolytic enzyme activity are often carried out on agar plates containing pH indicators or substrates as triolein or tributyrin. Subsequently, high-throughput screening assays are usually performed in microtiter plate (MTP) format using chromogenic or fluorogenic substrates and, if available, automated liquid handling robotics. Here, we describe different assay systems to determine the activity and enantioselectivity of lipases and esterases as well as the synthesis of several substrates. We also report on the construction of a complete site saturation library derived from lipase A of Bacillus subtilis and its testing for detergent tolerance. This approach allows for the identification of amino acids affecting sensitivity or resistance against different detergents.
Collapse
Affiliation(s)
- Alexander Fulton
- Institute of Molecular Enzyme Technology, Heinrich-Heine - Universität Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany
- Novozymes A/S, Krogshoejvej 36, 2880, Bagsvaerd, Denmark
| | - Marc R Hayes
- Institute of Bioorganic Chemistry, Heinrich-Heine - Universität Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, 52074, Aachen, Germany
- DWI Leibniz-Institute for Interactive Materials at RWTH Aachen University, 52056, Aachen, Germany
| | - Jörg Pietruszka
- Institute of Bioorganic Chemistry, Heinrich-Heine - Universität Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52428, Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich-Heine - Universität Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany.
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52428, Jülich, Germany.
| |
Collapse
|
16
|
From molecular engineering to process engineering: development of high-throughput screening methods in enzyme directed evolution. Appl Microbiol Biotechnol 2017; 102:559-567. [PMID: 29181567 DOI: 10.1007/s00253-017-8568-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/29/2017] [Accepted: 10/03/2017] [Indexed: 01/17/2023]
Abstract
With increasing concerns in sustainable development, biocatalysis has been recognized as a competitive alternative to traditional chemical routes in the past decades. As nature's biocatalysts, enzymes are able to catalyze a broad range of chemical transformations, not only with mild reaction conditions but also with high activity and selectivity. However, the insufficient activity or enantioselectivity of natural enzymes toward non-natural substrates limits their industrial application, while directed evolution provides a potent solution to this problem, thanks to its independence on detailed knowledge about the relationship between sequence, structure, and mechanism/function of the enzymes. A proper high-throughput screening (HTS) method is the key to successful and efficient directed evolution. In recent years, huge varieties of HTS methods have been developed for rapid evaluation of mutant libraries, ranging from in vitro screening to in vivo selection, from indicator addition to multi-enzyme system construction, and from plate screening to computation- or machine-assisted screening. Recently, there is a tendency to integrate directed evolution with metabolic engineering in biosynthesis, using metabolites as HTS indicators, which implies that directed evolution has transformed from molecular engineering to process engineering. This paper aims to provide an overview of HTS methods categorized based on the reaction principles or types by summarizing related studies published in recent years including the work from our group, to discuss assay design strategies and typical examples of HTS methods, and to share our understanding on HTS method development for directed evolution of enzymes involved in specific catalytic reactions or metabolic pathways.
Collapse
|
17
|
Dobler L, de Carvalho BR, Alves WDS, Neves BC, Freire DMG, Almeida RV. Enhanced rhamnolipid production by Pseudomonas aeruginosa overexpressing estA in a simple medium. PLoS One 2017; 12:e0183857. [PMID: 28837648 PMCID: PMC5570425 DOI: 10.1371/journal.pone.0183857] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 08/11/2017] [Indexed: 11/18/2022] Open
Abstract
A modified Pseudomonas aeruginosa strain capable of overexpressing the estA gene, an encoding gene for a membrane-bound esterase, was constructed and its rhamnolipid (RML) production was studied. Fermentations using wild-type (WT) and modified P. aeruginosa strains were conducted until exhaustion of glycerol in Medium Salt Production, using two different C/N ratios. At a C/N of 83.2, the modified strain produced up to 3.9 times more RMLs than the WT, yielding a maximum concentration of 14.62 g/L RML when measured by HPLC and 22 g/L by the orcinol assay. Cell-free supernatant from the modified strain reduced surface tension to 29.4 mN/m and had a CMC of 240 mg/L and CMD of 56.05. This is the first report on the construction of an estA-based recombinant strain for RML production.
Collapse
Affiliation(s)
- Leticia Dobler
- LaMMP–Laboratório de Microbiologia Molecular e de Proteínas, Chemistry Institute, Federal University from Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail: (LD); (DMGF); (RVA)
| | - Bruna Rocha de Carvalho
- LaMMP–Laboratório de Microbiologia Molecular e de Proteínas, Chemistry Institute, Federal University from Rio de Janeiro, Rio de Janeiro, Brazil
| | - Wilber de Sousa Alves
- LaMMP–Laboratório de Microbiologia Molecular e de Proteínas, Chemistry Institute, Federal University from Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bianca Cruz Neves
- LaMMP–Laboratório de Microbiologia Molecular e de Proteínas, Chemistry Institute, Federal University from Rio de Janeiro, Rio de Janeiro, Brazil
| | - Denise Maria Guimarães Freire
- LaBiM–Laboratório de Biotecnologia Microbiana, Chemistry Institute, Federal University from Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail: (LD); (DMGF); (RVA)
| | - Rodrigo Volcan Almeida
- LaMMP–Laboratório de Microbiologia Molecular e de Proteínas, Chemistry Institute, Federal University from Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail: (LD); (DMGF); (RVA)
| |
Collapse
|
18
|
Abstract
Life on Earth is incredibly diverse. Yet, underneath that diversity, there are a number of constants and highly conserved processes: all life is based on DNA and RNA; the genetic code is universal; biology is limited to a small subset of potential chemistries. A vast amount of knowledge has been accrued through describing and characterizing enzymes, biological processes and organisms. Nevertheless, much remains to be understood about the natural world. One of the goals in Synthetic Biology is to recapitulate biological complexity from simple systems made from biological molecules-gaining a deeper understanding of life in the process. Directed evolution is a powerful tool in Synthetic Biology, able to bypass gaps in knowledge and capable of engineering even the most highly conserved biological processes. It encompasses a range of methodologies to create variation in a population and to select individual variants with the desired function-be it a ligand, enzyme, pathway or even whole organisms. Here, we present some of the basic frameworks that underpin all evolution platforms and review some of the recent contributions from directed evolution to synthetic biology, in particular methods that have been used to engineer the Central Dogma and the genetic code.
Collapse
|
19
|
Peschke T, Rabe KS, Niemeyer CM. Orthogonale Oberflächenmarkierungen für die Ganzzellkatalyse. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609590] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Theo Peschke
- Karlsruher Institut für Technologie (KIT); Institut für Biologische Grenzflächen-1 (IBG-1); Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Deutschland
| | - Kersten S. Rabe
- Karlsruher Institut für Technologie (KIT); Institut für Biologische Grenzflächen-1 (IBG-1); Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Deutschland
| | - Christof M. Niemeyer
- Karlsruher Institut für Technologie (KIT); Institut für Biologische Grenzflächen-1 (IBG-1); Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Deutschland
| |
Collapse
|
20
|
Peschke T, Rabe KS, Niemeyer CM. Orthogonal Surface Tags for Whole-Cell Biocatalysis. Angew Chem Int Ed Engl 2017; 56:2183-2186. [PMID: 28105787 DOI: 10.1002/anie.201609590] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/10/2016] [Indexed: 01/07/2023]
Abstract
We herein describe the engineering of E. coli strains that display orthogonal tags for immobilization on their surface and overexpress a functional heterologous "protein content" in their cytosol at the same time. Using the outer membrane protein Lpp-ompA, cell-surface display of the streptavidin-binding peptide, the SpyTag/SpyCatcher system, or a HaloTag variant allowed us to generate bacterial strains that can selectively bind to solid substrates, as demonstrated with magnetic microbeads. The simultaneous cytosolic expression of functional content was demonstrated for fluorescent proteins or stereoselective ketoreductase enzymes. The latter strains gave high selectivities for specific immobilization onto complementary surfaces and also in the whole-cell stereospecific transformation of a prochiral CS -symmetric nitrodiketone.
Collapse
Affiliation(s)
- Theo Peschke
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz, 76344, Eggenstein-Leopoldshafen, Germany
| | - Kersten S Rabe
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz, 76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz, 76344, Eggenstein-Leopoldshafen, Germany
| |
Collapse
|
21
|
High-throughput strategies for the discovery and engineering of enzymes for biocatalysis. Bioprocess Biosyst Eng 2016; 40:161-180. [DOI: 10.1007/s00449-016-1690-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 10/05/2016] [Indexed: 12/16/2022]
|
22
|
Körfer G, Pitzler C, Vojcic L, Martinez R, Schwaneberg U. In vitro flow cytometry-based screening platform for cellulase engineering. Sci Rep 2016; 6:26128. [PMID: 27184298 PMCID: PMC4869107 DOI: 10.1038/srep26128] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 04/15/2016] [Indexed: 01/08/2023] Open
Abstract
Ultrahigh throughput screening (uHTS) plays an essential role in directed evolution for tailoring biocatalysts for industrial applications. Flow cytometry-based uHTS provides an efficient coverage of the generated protein sequence space by analysis of up to 107 events per hour. Cell-free enzyme production overcomes the challenge of diversity loss during the transformation of mutant libraries into expression hosts, enables directed evolution of toxic enzymes, and holds the promise to efficiently design enzymes of human or animal origin. The developed uHTS cell-free compartmentalization platform (InVitroFlow) is the first report in which a flow cytometry-based screened system has been combined with compartmentalized cell-free expression for directed cellulase enzyme evolution. InVitroFlow was validated by screening of a random cellulase mutant library employing a novel screening system (based on the substrate fluorescein-di-β-D-cellobioside), and yielded significantly improved cellulase variants (e.g. CelA2-H288F-M1 (N273D/H288F/N468S) with 13.3-fold increased specific activity (220.60 U/mg) compared to CelA2 wildtype: 16.57 U/mg).
Collapse
Affiliation(s)
| | | | - Ljubica Vojcic
- RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany
| | - Ronny Martinez
- RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany
| | - Ulrich Schwaneberg
- RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany.,DWI an der RWTH Aachen e.V, Forckenbeckstraße 50, 52056 Aachen, Germany
| |
Collapse
|
23
|
Krone KM, Warias R, Ritter C, Li A, Acevedo-Rocha CG, Reetz MT, Belder D. Analysis of Enantioselective Biotransformations Using a Few Hundred Cells on an Integrated Microfluidic Chip. J Am Chem Soc 2016; 138:2102-5. [DOI: 10.1021/jacs.5b12443] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Karin M. Krone
- Institute
of Analytical Chemistry, University of Leipzig, Linnéstrasse 3, 04103 Leipzig, Germany
| | - Rico Warias
- Institute
of Analytical Chemistry, University of Leipzig, Linnéstrasse 3, 04103 Leipzig, Germany
| | - Cornelia Ritter
- Faculty
of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35032 Marburg, Germany
| | - Aitao Li
- Faculty
of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35032 Marburg, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim/Ruhr, Germany
| | - Carlos G. Acevedo-Rocha
- Faculty
of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35032 Marburg, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim/Ruhr, Germany
| | - Manfred T. Reetz
- Faculty
of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35032 Marburg, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim/Ruhr, Germany
| | - Detlev Belder
- Institute
of Analytical Chemistry, University of Leipzig, Linnéstrasse 3, 04103 Leipzig, Germany
| |
Collapse
|
24
|
Abstract
Directed evolution has proved to be an effective strategy for improving or altering the activity of biomolecules for industrial, research and therapeutic applications. The evolution of proteins in the laboratory requires methods for generating genetic diversity and for identifying protein variants with desired properties. This Review describes some of the tools used to diversify genes, as well as informative examples of screening and selection methods that identify or isolate evolved proteins. We highlight recent cases in which directed evolution generated enzymatic activities and substrate specificities not known to exist in nature.
Collapse
Affiliation(s)
- Michael S Packer
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - David R Liu
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
| |
Collapse
|
25
|
Smith MR, Khera E, Wen F. Engineering Novel and Improved Biocatalysts by Cell Surface Display. Ind Eng Chem Res 2015; 54:4021-4032. [PMID: 29056821 PMCID: PMC5647830 DOI: 10.1021/ie504071f] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Biocatalysts, especially enzymes, have the ability to catalyze reactions with high product selectivity, utilize a broad range of substrates, and maintain activity at low temperature and pressure. Therefore, they represent a renewable, environmentally friendly alternative to conventional catalysts. Most current industrial-scale chemical production processes using biocatalysts employ soluble enzymes or whole cells expressing intracellular enzymes. Cell surface display systems differ by presenting heterologous enzymes extracellularly, overcoming some of the limitations associated with enzyme purification and substrate transport. Additionally, coupled with directed evolution, cell surface display is a powerful platform for engineering enzymes with enhanced properties. In this review, we will introduce the molecular and cellular principles of cell surface display and discuss how it has been applied to engineer enzymes with improved properties as well as to develop surface-engineered microbes as whole-cell biocatalysts.
Collapse
Affiliation(s)
- Mason R. Smith
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Eshita Khera
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Fei Wen
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
26
|
Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
Collapse
Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| |
Collapse
|
27
|
Pitzler C, Wirtz G, Vojcic L, Hiltl S, Böker A, Martinez R, Schwaneberg U. A Fluorescent Hydrogel-Based Flow Cytometry High-Throughput Screening Platform for Hydrolytic Enzymes. ACTA ACUST UNITED AC 2014; 21:1733-42. [DOI: 10.1016/j.chembiol.2014.10.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 10/16/2014] [Accepted: 10/23/2014] [Indexed: 01/12/2023]
|
28
|
Acevedo-Rocha CG, Agudo R, Reetz MT. Directed evolution of stereoselective enzymes based on genetic selection as opposed to screening systems. J Biotechnol 2014; 191:3-10. [DOI: 10.1016/j.jbiotec.2014.04.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 03/26/2014] [Accepted: 04/07/2014] [Indexed: 01/25/2023]
|
29
|
Fischlechner M, Schaerli Y, Mohamed MF, Patil S, Abell C, Hollfelder F. Evolution of enzyme catalysts caged in biomimetic gel-shell beads. Nat Chem 2014; 6:791-6. [DOI: 10.1038/nchem.1996] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 05/15/2014] [Indexed: 12/23/2022]
|
30
|
Stockinger S, Trapp O. Comparison of a Molecular and an Immobilized Gadolinium(III)-tris[(1R,4S)-3-heptafluorobutanoyl-camphor] as Catalyst in the Asymmetric Danishefsky-Hetero-Diels-Alder-Reaction. Chirality 2014; 26:243-8. [DOI: 10.1002/chir.22312] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 01/28/2014] [Accepted: 01/30/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Skrollan Stockinger
- Ruprecht-Karls-Universität Heidelberg; Organisch-Chemisches Institut; Heidelberg Germany
| | - Oliver Trapp
- Ruprecht-Karls-Universität Heidelberg; Organisch-Chemisches Institut; Heidelberg Germany
| |
Collapse
|
31
|
Maaß A, Heiseler T, Maaß F, Fritz J, Hofmeyer T, Glotzbach B, Becker S, Kolmar H. A general strategy for antibody library screening via conversion of transient target binding into permanent reporter deposition. Protein Eng Des Sel 2014; 27:41-7. [PMID: 24402333 DOI: 10.1093/protein/gzt060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We report here a generally applicable method for the selective covalent attachment of a reporter molecule to a replicating entity that allows one to obtain specific binders from a single round of library screening. We show that selective biotinylation of phage particles displaying a binder to any given target can be achieved by application of a coupled enzyme reaction on the surface of the target-binding phage particles that includes a peroxidase, an oxidase and a catalase. Due to the covalent linkage of biotin together with the tight and stable interaction of biotin with streptavidin, very stringent wash conditions for removal of nonspecific binders can be applied. The method termed (3)CARD (triple catalytic reporter deposition) was successfully applied to single-round screening of a phage display library of camelid single-domain antibodies against three different target proteins.
Collapse
Affiliation(s)
- Alexander Maaß
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, D-64287 Darmstadt, Germany
| | | | | | | | | | | | | | | |
Collapse
|
32
|
Abstract
Over the past three decades, a powerful array of techniques has been developed for expressing heterologous proteins and saccharides on the surface of bacteria. Surface-engineered bacteria, in turn, have proven useful in a variety of settings, including high-throughput screening, biofuel production, and vaccinology. In this chapter, we provide a comprehensive review of methods for displaying polypeptides and sugars on the bacterial cell surface, and discuss the many innovative applications these methods have found to date. While already an important biotechnological tool, we believe bacterial surface display may be further improved through integration with emerging methodology in other fields, such as protein engineering and synthetic chemistry. Ultimately, we envision bacterial display becoming a multidisciplinary platform with the potential to transform basic and applied research in bacteriology, biotechnology, and biomedicine.
Collapse
|
33
|
|
34
|
Protein Engineering as a Tool for the Development of Novel Bioproduction Systems. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 137:25-40. [DOI: 10.1007/10_2013_199] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
35
|
Pourmir A, Johannes TW. Directed evolution: selection of the host organism. Comput Struct Biotechnol J 2012; 2:e201209012. [PMID: 24688653 PMCID: PMC3962113 DOI: 10.5936/csbj.201209012] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 10/06/2012] [Accepted: 10/12/2012] [Indexed: 11/29/2022] Open
Abstract
Directed evolution has become a well-established tool for improving proteins and biological systems. A critical aspect of directed evolution is the selection of a suitable host organism for achieving functional expression of the target gene. To date, most directed evolution studies have used either Escherichia coli or Saccharomyces cerevisiae as a host; however, other bacterial and yeast species, as well as mammalian and insect cell lines, have also been successfully used. Recent advances in synthetic biology and genomics have opened the possibility of expanding the use of directed evolution to new host organisms such as microalgae. This review focuses on the different host organisms used in directed evolution and highlights some of the recent directed evolution strategies used in these organisms.
Collapse
Affiliation(s)
- Azadeh Pourmir
- Department of Chemical Engineering, The University of Tulsa, 800 S. Tucker Dr, Tulsa, OK 74104, United States
| | - Tyler W Johannes
- Department of Chemical Engineering, The University of Tulsa, 800 S. Tucker Dr, Tulsa, OK 74104, United States
| |
Collapse
|
36
|
Jose J, Maas RM, Teese MG. Autodisplay of enzymes—Molecular basis and perspectives. J Biotechnol 2012; 161:92-103. [DOI: 10.1016/j.jbiotec.2012.04.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2011] [Revised: 02/14/2012] [Accepted: 04/04/2012] [Indexed: 11/16/2022]
|
37
|
Directed Evolution of Proteins through In Vitro Protein Synthesis in Liposomes. J Nucleic Acids 2012; 2012:923214. [PMID: 22957209 PMCID: PMC3431101 DOI: 10.1155/2012/923214] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 07/10/2012] [Indexed: 11/17/2022] Open
Abstract
Directed evolution of proteins is a technique used to modify protein functions through "Darwinian selection." In vitro compartmentalization (IVC) is an in vitro gene screening system for directed evolution of proteins. IVC establishes the link between genetic information (genotype) and the protein translated from the information (phenotype), which is essential for all directed evolution methods, by encapsulating both in a nonliving microcompartment. Herein, we introduce a new liposome-based IVC system consisting of a liposome, the protein synthesis using recombinant elements (PURE) system and a fluorescence-activated cell sorter (FACS) used as a microcompartment, in vitro protein synthesis system, and high-throughput screen, respectively. Liposome-based IVC is characterized by in vitro protein synthesis from a single copy of a gene in a cell-sized unilamellar liposome and quantitative functional evaluation of the synthesized proteins. Examples of liposome-based IVC for screening proteins such as GFP and β-glucuronidase are described. We discuss the future directions for this method and its applications.
Collapse
|
38
|
MA FQ, FENG Y, YANG GY. Ultrahigh-throughput Enzymatic Screening Method Based on Fluorescence-activated Cell Sorting and Its Applications*. PROG BIOCHEM BIOPHYS 2012. [DOI: 10.3724/sp.j.1206.2011.00281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
39
|
|
40
|
Schlegel MK, Hütter J, Eriksson M, Lepenies B, Seeberger PH. Defined presentation of carbohydrates on a duplex DNA scaffold. Chembiochem 2011; 12:2791-800. [PMID: 22052782 DOI: 10.1002/cbic.201100511] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Indexed: 01/15/2023]
Abstract
A new method for the spatially defined alignment of carbohydrates on a duplex DNA scaffold is presented. The use of an N-hydroxysuccinimide (NHS)-ester phosphoramidite along with carbohydrates containing an alkylamine linker allows for on-column labeling during solid-phase oligonucleotide synthesis. This modification method during solid-phase synthesis only requires the use of minimal amounts of complex carbohydrates. The covalently attached carbohydrates are presented in the major groove of the B-form duplex DNA as potential substrates for murine type II C-type lectin receptors mMGL1 and mMGL2. CD spectroscopy and thermal melting revealed only minimal disturbance of the overall helical structure. Surface plasmon resonance and cellular uptake studies with bone-marrow-derived dendritic cells were used to assess the capability of these carbohydrate-modified duplexes to bind to mMGL receptors.
Collapse
Affiliation(s)
- Mark K Schlegel
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | | | | | | | | |
Collapse
|
41
|
Friest JA, Broussy S, Chung WJ, Berkowitz DB. Combinatorial catalysis employing a visible enzymatic beacon in real time: synthetically versatile (pseudo)halometalation/carbocyclizations. Angew Chem Int Ed Engl 2011; 50:8895-9. [PMID: 21905180 PMCID: PMC3517167 DOI: 10.1002/anie.201103365] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Indexed: 01/10/2023]
Affiliation(s)
- Jacob A. Friest
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588 (USA), Fax: (+001) 402-472-9402
| | - Sylvain Broussy
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588 (USA), Fax: (+001) 402-472-9402
| | - Woo Jin Chung
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588 (USA), Fax: (+001) 402-472-9402
| | - David B. Berkowitz
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588 (USA), Fax: (+001) 402-472-9402
| |
Collapse
|
42
|
Friest JA, Broussy S, Chung WJ, Berkowitz DB. Combinatorial Catalysis Employing a Visible Enzymatic Beacon in Real Time: Synthetically Versatile (Pseudo)Halometalation/Carbocyclizations. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103365] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
43
|
Fernández-Álvaro E, Snajdrova R, Jochens H, Davids T, Böttcher D, Bornscheuer UT. A Combination of In Vivo Selection and Cell Sorting for the Identification of Enantioselective Biocatalysts. Angew Chem Int Ed Engl 2011; 50:8584-7. [DOI: 10.1002/anie.201102360] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Indexed: 11/11/2022]
|
44
|
Fernández-Álvaro E, Snajdrova R, Jochens H, Davids T, Böttcher D, Bornscheuer UT. Eine Kombination aus In-vivo-Selektion und Zellsortierung zur Identifizierung enantioselektiver Biokatalysatoren. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201102360] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
45
|
Wilhelm S, Rosenau F, Kolmar H, Jaeger KE. Autotransporters with GDSL Passenger Domains: Molecular Physiology and Biotechnological Applications. Chembiochem 2011; 12:1476-85. [DOI: 10.1002/cbic.201100013] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Indexed: 12/12/2022]
|
46
|
Jochens H, Hesseler M, Stiba K, Padhi SK, Kazlauskas RJ, Bornscheuer UT. Protein Engineering of α/β-Hydrolase Fold Enzymes. Chembiochem 2011; 12:1508-17. [DOI: 10.1002/cbic.201000771] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Indexed: 01/01/2023]
|
47
|
Decorating microbes: surface display of proteins on Escherichia coli. Trends Biotechnol 2011; 29:79-86. [DOI: 10.1016/j.tibtech.2010.11.003] [Citation(s) in RCA: 165] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Revised: 11/05/2010] [Accepted: 11/12/2010] [Indexed: 11/22/2022]
|
48
|
Kwan DH, Chen H, Ratananikom K, Hancock SM, Watanabe Y, Kongsaeree PT, Samuels AL, Withers SG. Self‐Immobilizing Fluorogenic Imaging Agents of Enzyme Activity. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201005705] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- David H. Kwan
- Departments of Chemistry and Botany, University of British Columbia, Vancouver, B.C. V6T 1Z1 (Canada), Fax: (+1) 604‐822‐8869
| | - Hong‐Ming Chen
- Departments of Chemistry and Botany, University of British Columbia, Vancouver, B.C. V6T 1Z1 (Canada), Fax: (+1) 604‐822‐8869
| | | | - Susan M. Hancock
- Departments of Chemistry and Botany, University of British Columbia, Vancouver, B.C. V6T 1Z1 (Canada), Fax: (+1) 604‐822‐8869
| | - Yoichiro Watanabe
- Departments of Chemistry and Botany, University of British Columbia, Vancouver, B.C. V6T 1Z1 (Canada), Fax: (+1) 604‐822‐8869
| | | | - A. Lacey Samuels
- Departments of Chemistry and Botany, University of British Columbia, Vancouver, B.C. V6T 1Z1 (Canada), Fax: (+1) 604‐822‐8869
| | - Stephen G. Withers
- Departments of Chemistry and Botany, University of British Columbia, Vancouver, B.C. V6T 1Z1 (Canada), Fax: (+1) 604‐822‐8869
| |
Collapse
|
49
|
Kwan DH, Chen H, Ratananikom K, Hancock SM, Watanabe Y, Kongsaeree PT, Samuels AL, Withers SG. Self‐Immobilizing Fluorogenic Imaging Agents of Enzyme Activity. Angew Chem Int Ed Engl 2010; 50:300-3. [DOI: 10.1002/anie.201005705] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- David H. Kwan
- Departments of Chemistry and Botany, University of British Columbia, Vancouver, B.C. V6T 1Z1 (Canada), Fax: (+1) 604‐822‐8869
| | - Hong‐Ming Chen
- Departments of Chemistry and Botany, University of British Columbia, Vancouver, B.C. V6T 1Z1 (Canada), Fax: (+1) 604‐822‐8869
| | | | - Susan M. Hancock
- Departments of Chemistry and Botany, University of British Columbia, Vancouver, B.C. V6T 1Z1 (Canada), Fax: (+1) 604‐822‐8869
| | - Yoichiro Watanabe
- Departments of Chemistry and Botany, University of British Columbia, Vancouver, B.C. V6T 1Z1 (Canada), Fax: (+1) 604‐822‐8869
| | | | - A. Lacey Samuels
- Departments of Chemistry and Botany, University of British Columbia, Vancouver, B.C. V6T 1Z1 (Canada), Fax: (+1) 604‐822‐8869
| | - Stephen G. Withers
- Departments of Chemistry and Botany, University of British Columbia, Vancouver, B.C. V6T 1Z1 (Canada), Fax: (+1) 604‐822‐8869
| |
Collapse
|
50
|
Yang G, Rich JR, Gilbert M, Wakarchuk WW, Feng Y, Withers SG. Fluorescence activated cell sorting as a general ultra-high-throughput screening method for directed evolution of glycosyltransferases. J Am Chem Soc 2010; 132:10570-7. [PMID: 20662530 DOI: 10.1021/ja104167y] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glycosyltransferases (GTs) offer very attractive approaches to the synthesis of complex oligosaccharides. However, the limited number of available GTs, together with their instability and strict substrate specificity, have severely hampered the broad application of these enzymes. Previous attempts to broaden the range of substrate scope and to increase the activity of GTs via protein engineering have met with limited success, partially because of the lack of effective high-throughput screening methods. Recently, we reported an ultra-high-throughput screening method for sialyltransferases based on fluorescence-activated cell sorting (Aharoni et al. Nat. Methods 2006, 3, 609-614). Here, we considerably improve this method via the introduction of a two-color screening protocol to minimize the probability of false positive mutants and demonstrate its generality through directed evolution of a neutral sugar transferase, beta-1,3-galactosyltransferase CgtB. A variant with broader substrate tolerance than the wild-type enzyme and 300-fold higher activity was identified rapidly from a library of >10(7) CgtB mutants. Importantly, the variant effected much more efficient synthesis of G(M1a) and asialo G(M1) oligosaccharides, the building blocks of important therapeutic glycosphingolipids, than did the parent enzyme. This work not only establishes a new methodology for the directed evolution of galactosyltransferases, but also suggests a powerful strategy for the screening of almost all GT activities, thereby facilitating the engineering of glycosyltransferases.
Collapse
Affiliation(s)
- Guangyu Yang
- Centre for High-throughput Biology (CHiBi) and Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | | | | | | | | | | |
Collapse
|