1
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Nur A, Lai JY, Ch'ng ACW, Choong YS, Wan Isa WYH, Lim TS. A review of in vitro stochastic and non-stochastic affinity maturation strategies for phage display derived monoclonal antibodies. Int J Biol Macromol 2024; 277:134217. [PMID: 39069045 DOI: 10.1016/j.ijbiomac.2024.134217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/24/2024] [Accepted: 07/25/2024] [Indexed: 07/30/2024]
Abstract
Monoclonal antibodies identified using display technologies like phage display occasionally suffers from a lack of affinity making it unsuitable for application. This drawback is circumvented with the application of affinity maturation. Affinity maturation is an essential step in the natural evolution of antibodies in the immune system. The evolution of molecular based methods has seen the development of various mutagenesis approaches. This allows for the natural evolutionary process during somatic hypermutation to be replicated in the laboratories for affinity maturation to fine-tune the affinity and selectivity of antibodies. In this review, we will discuss affinity maturation strategies for mAbs generated through phage display systems. The review will highlight various in vitro stochastic and non-stochastic affinity maturation approaches that includes but are not limited to random mutagenesis, site-directed mutagenesis, and gene synthesis.
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Affiliation(s)
- Alia Nur
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Wan Yus Haniff Wan Isa
- School of Medical Sciences, Department of Medicine, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Penang, Malaysia.
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2
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Mighell TL, Toledano I, Lehner B. SUNi mutagenesis: Scalable and uniform nicking for efficient generation of variant libraries. PLoS One 2023; 18:e0288158. [PMID: 37418460 DOI: 10.1371/journal.pone.0288158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 06/20/2023] [Indexed: 07/09/2023] Open
Abstract
Multiplexed assays of variant effects (MAVEs) have made possible the functional assessment of all possible mutations to genes and regulatory sequences. A core pillar of the approach is generation of variant libraries, but current methods are either difficult to scale or not uniform enough to enable MAVEs at the scale of gene families or beyond. We present an improved method called Scalable and Uniform Nicking (SUNi) mutagenesis that combines massive scalability with high uniformity to enable cost-effective MAVEs of gene families and eventually genomes.
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Affiliation(s)
- Taylor L Mighell
- The Barcelona Institute of Science and Technology, Center for Genomic Regulation (CRG), Barcelona, Spain
| | - Ignasi Toledano
- The Barcelona Institute of Science and Technology, Center for Genomic Regulation (CRG), Barcelona, Spain
| | - Ben Lehner
- The Barcelona Institute of Science and Technology, Center for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
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3
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Flynn J, Samant N, Schneider-Nachum G, Tenzin T, Bolon DNA. Mutational fitness landscape and drug resistance. Curr Opin Struct Biol 2023; 78:102525. [PMID: 36621152 PMCID: PMC10243218 DOI: 10.1016/j.sbi.2022.102525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/29/2022] [Accepted: 12/06/2022] [Indexed: 01/08/2023]
Abstract
Robust technology has been developed to systematically quantify fitness landscapes that provide valuable opportunities to improve our understanding of drug resistance and define new avenues to develop drugs with reduced resistance susceptibility. We outline the critical importance of drug resistance studies and the potential for fitness landscape approaches to contribute to this effort. We describe the major technical advancements in mutational scanning, which is the primary approach used to quantify protein fitness landscapes. There are many complex steps to consider in planning and executing mutational scanning projects including developing a selection scheme, generating mutant libraries, tracking the frequency of variants using next-generation sequencing, and processing and interpreting the data. Key experimental parameters impacting each of these steps are discussed to aid in planning fitness landscape studies. There is a strong need for improved understanding of drug resistance, and fitness landscapes provide a promising new approach.
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Affiliation(s)
- Julia Flynn
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Neha Samant
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Gily Schneider-Nachum
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Tsepal Tenzin
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Daniel N A Bolon
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
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4
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Dewachter L, Brooks AN, Noon K, Cialek C, Clark-ElSayed A, Schalck T, Krishnamurthy N, Versées W, Vranken W, Michiels J. Deep mutational scanning of essential bacterial proteins can guide antibiotic development. Nat Commun 2023; 14:241. [PMID: 36646716 PMCID: PMC9842644 DOI: 10.1038/s41467-023-35940-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 01/09/2023] [Indexed: 01/18/2023] Open
Abstract
Deep mutational scanning is a powerful approach to investigate a wide variety of research questions including protein function and stability. Here, we perform deep mutational scanning on three essential E. coli proteins (FabZ, LpxC and MurA) involved in cell envelope synthesis using high-throughput CRISPR genome editing, and study the effect of the mutations in their original genomic context. We use more than 17,000 variants of the proteins to interrogate protein function and the importance of individual amino acids in supporting viability. Additionally, we exploit these libraries to study resistance development against antimicrobial compounds that target the selected proteins. Among the three proteins studied, MurA seems to be the superior antimicrobial target due to its low mutational flexibility, which decreases the chance of acquiring resistance-conferring mutations that simultaneously preserve MurA function. Additionally, we rank anti-LpxC lead compounds for further development, guided by the number of resistance-conferring mutations against each compound. Our results show that deep mutational scanning studies can be used to guide drug development, which we hope will contribute towards the development of novel antimicrobial therapies.
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Affiliation(s)
- Liselot Dewachter
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium. .,VIB-KU Leuven Center for Microbiology, Leuven, Belgium.
| | | | | | | | | | - Thomas Schalck
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | | | - Wim Versées
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,VIB-VUB Center for Structural Biology, Brussels, Belgium
| | - Wim Vranken
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,VIB-VUB Center for Structural Biology, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium. .,VIB-KU Leuven Center for Microbiology, Leuven, Belgium.
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5
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Wei H, Li X. Deep mutational scanning: A versatile tool in systematically mapping genotypes to phenotypes. Front Genet 2023; 14:1087267. [PMID: 36713072 PMCID: PMC9878224 DOI: 10.3389/fgene.2023.1087267] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/02/2023] [Indexed: 01/13/2023] Open
Abstract
Unveiling how genetic variations lead to phenotypic variations is one of the key questions in evolutionary biology, genetics, and biomedical research. Deep mutational scanning (DMS) technology has allowed the mapping of tens of thousands of genetic variations to phenotypic variations efficiently and economically. Since its first systematic introduction about a decade ago, we have witnessed the use of deep mutational scanning in many research areas leading to scientific breakthroughs. Also, the methods in each step of deep mutational scanning have become much more versatile thanks to the oligo-synthesizing technology, high-throughput phenotyping methods and deep sequencing technology. However, each specific possible step of deep mutational scanning has its pros and cons, and some limitations still await further technological development. Here, we discuss recent scientific accomplishments achieved through the deep mutational scanning and describe widely used methods in each step of deep mutational scanning. We also compare these different methods and analyze their advantages and disadvantages, providing insight into how to design a deep mutational scanning study that best suits the aims of the readers' projects.
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Affiliation(s)
- Huijin Wei
- Zhejiang University—University of Edinburgh Institute, Zhejiang University, Haining, Zhejiang, China
| | - Xianghua Li
- Zhejiang University—University of Edinburgh Institute, Zhejiang University, Haining, Zhejiang, China
- Deanery of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
- The Second Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang, China
- Biomedical and Health Translational Centre of Zhejiang Province, Haining, Zhejiang, China
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6
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Huang RR, Kierny M, Volgina V, Iwashima M, Miller C, Kay BK. Construction of an Ultra-Large Phage Display Library by Kunkel Mutagenesis and Rolling Circle Amplification. Methods Mol Biol 2023; 2702:205-226. [PMID: 37679621 DOI: 10.1007/978-1-0716-3381-6_10] [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] [Indexed: 09/09/2023]
Abstract
An important contributor to the successful generation of recombinant affinity reagents via phage display is a large and diverse library. We describe, herein, the application of Kunkel mutagenesis and rolling circle amplification (RCA) to the construction of a 1.1 × 1011 member library, with only 26 electroporations, and isolation of low- to sub-nanomolar monobodies to a number of protein targets, including human COP9 signalosome subunit 5 (COPS5), HIV-1 Rev. binding protein-like protein (HRBL), X-ray repair cross-complementing 5/6 (Ku70/80) heterodimer, the receptor-binding domain (RBD) of SARS-CoV-2, and transforming growth factor beta 1 (TGF-β1).
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Affiliation(s)
| | | | - Veronica Volgina
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
| | - Makio Iwashima
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
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7
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Tabet D, Parikh V, Mali P, Roth FP, Claussnitzer M. Scalable Functional Assays for the Interpretation of Human Genetic Variation. Annu Rev Genet 2022; 56:441-465. [PMID: 36055970 DOI: 10.1146/annurev-genet-072920-032107] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Scalable sequence-function studies have enabled the systematic analysis and cataloging of hundreds of thousands of coding and noncoding genetic variants in the human genome. This has improved clinical variant interpretation and provided insights into the molecular, biophysical, and cellular effects of genetic variants at an astonishing scale and resolution across the spectrum of allele frequencies. In this review, we explore current applications and prospects for the field and outline the principles underlying scalable functional assay design, with a focus on the study of single-nucleotide coding and noncoding variants.
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Affiliation(s)
- Daniel Tabet
- Donnelly Centre, Department of Molecular Genetics, and Department of Computer Science, University of Toronto, Toronto, Ontario, Canada;
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Victoria Parikh
- Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Prashant Mali
- Department of Bioengineering, University of California, San Diego, California, USA
| | - Frederick P Roth
- Donnelly Centre, Department of Molecular Genetics, and Department of Computer Science, University of Toronto, Toronto, Ontario, Canada;
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Melina Claussnitzer
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Genomic Medicine and Endocrine Division, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Harvard University, Boston, Massachusetts, USA;
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8
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Blazeck J, Karamitros CS, Ford K, Somody C, Qerqez A, Murray K, Burkholder NT, Marshall N, Sivakumar A, Lu WC, Tan B, Lamb C, Tanno Y, Siddiqui MY, Ashoura N, Coma S, Zhang XM, McGovern K, Kumada Y, Zhang YJ, Manfredi M, Johnson KA, D’Arcy S, Stone E, Georgiou G. Bypassing evolutionary dead ends and switching the rate-limiting step of a human immunotherapeutic enzyme. Nat Catal 2022; 5:952-967. [PMID: 36465553 PMCID: PMC9717613 DOI: 10.1038/s41929-022-00856-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 09/09/2022] [Indexed: 11/08/2022]
Abstract
The Trp metabolite kynurenine (KYN) accumulates in numerous solid tumours and mediates potent immunosuppression. Bacterial kynureninases (KYNases), which preferentially degrade kynurenine, can relieve immunosuppression in multiple cancer models, but immunogenicity concerns preclude their clinical use, while the human enzyme (HsKYNase) has very low activity for kynurenine and shows no therapeutic effect. Using fitness selections, we evolved a HsKYNase variant with 27-fold higher activity, beyond which exploration of >30 evolutionary trajectories involving the interrogation of >109 variants led to no further improvements. Introduction of two amino acid substitutions conserved in bacterial KYNases reduced enzyme fitness but potentiated rapid evolution of variants with ~500-fold improved activity and reversed substrate specificity, resulting in an enzyme capable of mediating strong anti-tumour effects in mice. Pre-steady-state kinetics revealed a switch in rate-determining step attributable to changes in both enzyme structure and conformational dynamics. Apart from its clinical significance, our work highlights how rationally designed substitutions can potentiate trajectories that overcome barriers in protein evolution.
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Affiliation(s)
- John Blazeck
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Christos S. Karamitros
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Kyle Ford
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Catrina Somody
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Ahlam Qerqez
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Kyle Murray
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas, USA
| | - Nathaniel T. Burkholder
- Department of Molecular Biosciences, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Nicholas Marshall
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Anirudh Sivakumar
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Wei-Cheng Lu
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Bing Tan
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Candice Lamb
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Yuri Tanno
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Menna Y. Siddiqui
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Norah Ashoura
- Department of Molecular Biosciences, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Silvia Coma
- Ikena Oncology, Cambridge, Massachusetts, USA
| | | | | | - Yoichi Kumada
- Department of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Kyoto, Japan
| | - Yan Jessie Zhang
- Department of Molecular Biosciences, University of Texas at Austin (UT Austin), Austin, Texas, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin (UT Austin), Austin, Texas, USA
| | | | - Kenneth A. Johnson
- Department of Molecular Biosciences, University of Texas at Austin (UT Austin), Austin, Texas, USA
| | - Sheena D’Arcy
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas, USA
| | - Everett Stone
- Department of Molecular Biosciences, University of Texas at Austin (UT Austin), Austin, Texas, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin (UT Austin), Austin, Texas, USA
- Department of Oncology, University of Texas Dell Medical School, LiveSTRONG Cancer Institutes, Austin, Texas, USA
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, Texas, USA
- Department of Molecular Biosciences, University of Texas at Austin (UT Austin), Austin, Texas, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin (UT Austin), Austin, Texas, USA
- Department of Oncology, University of Texas Dell Medical School, LiveSTRONG Cancer Institutes, Austin, Texas, USA
- Department of Biomedical Engineering, University of Texas at Austin (UT Austin), Austin, TX, USA
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9
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Iqbal Z, Sadaf S. A patent-based consideration of latest platforms in the art of directed evolution: a decade long untold story. Biotechnol Genet Eng Rev 2022; 38:133-246. [PMID: 35200115 DOI: 10.1080/02648725.2021.2017638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Directed (or in vitro) evolution of proteins and metabolic pathways requires tools for creating genetic diversity and identifying protein variants with new or improved functional properties. Besides simplicity, reliability, speed, versatility, universal applicability and economy of the technique, the new science of synthetic biology requires improved means for construction of smart and high-quality mutant libraries to better navigate the sequence diversity. In vitro CRISPR/Cas9-mediated mutagenic (ICM) system and machine-learning (ML)-assisted approaches to directed evolution are now in the field to achieve the goal. This review describes the gene diversification strategies, screening and selection methods, in silico (computer-aided), Cas9-mediated and ML-based approaches to mutagenesis, developed especially in the last decade, and their patent position. The objective behind is to emphasize researchers the need for noting which mutagenesis, screening or selection method is patented and then selecting a suitable restriction-free approach to sequence diversity. Techniques and evolved products subject to patent rights need commercial license if their use is for purposes other than private or experimental research.
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Affiliation(s)
- Zarina Iqbal
- IP Litigation Department, PakPat World Intellectual Property Protection Services, Lahore, Pakistan
| | - Saima Sadaf
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
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10
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OverFlap PCR: A reliable approach for generating plasmid DNA libraries containing random sequences without a template bias. PLoS One 2022; 17:e0262968. [PMID: 35939421 PMCID: PMC9359533 DOI: 10.1371/journal.pone.0262968] [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: 01/03/2022] [Accepted: 07/17/2022] [Indexed: 11/19/2022] Open
Abstract
Over the decades, practical biotechnology researchers have aimed to improve naturally occurring proteins and create novel ones. It is widely recognized that coupling protein sequence randomization with various effect screening methodologies is one of the most powerful techniques for quickly, efficiently, and purposefully acquiring these desired improvements. Over the years, considerable advancements have been made in this field. However, developing PCR-based or template-guided methodologies has been hampered by resultant template sequence biases. Here, we present a novel whole plasmid amplification-based approach, which we named OverFlap PCR, for randomizing virtually any region of plasmid DNA without introducing a template sequence bias.
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11
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Zhao F, Chen F, Yu H, Fan S, Bai M, Xue J, Zhao Y, Zuo X, Fan C, Zhao Y. CRISPR/Cas system-guided plasmid mutagenesis without sequence restriction. FUNDAMENTAL RESEARCH 2022. [DOI: 10.1016/j.fmre.2022.06.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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12
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Local and Global Protein Interactions Contribute to Residue Entrenchment in Beta-Lactamase TEM-1. Antibiotics (Basel) 2022; 11:antibiotics11050652. [PMID: 35625296 PMCID: PMC9137480 DOI: 10.3390/antibiotics11050652] [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: 03/12/2022] [Revised: 04/29/2022] [Accepted: 05/05/2022] [Indexed: 11/22/2022] Open
Abstract
Due to their rapid evolution and their impact on healthcare, beta-lactamases, protein degrading beta-lactam antibiotics, are used as generic models of protein evolution. Therefore, we investigated the mutation effects in two distant beta-lactamases, TEM-1 and CTX-M-15. Interestingly, we found a site with a complex pattern of genetic interactions. Mutation G251W in TEM-1 inactivates the protein’s function, just as the reciprocal mutation, W251G, does in CTX-M-15. The phylogenetic analysis revealed that mutation G has been entrenched in TEM-1’s background: while rarely observed throughout the phylogeny, it is essential in TEM-1. Using a rescue experiment, in the TEM-1 G251W mutant, we identified sites that alleviate the deviation from G to W. While few of these mutations could potentially involve local interactions, most of them were found on distant residues in the 3D structure. Many well-known mutations that have an impact on protein stability, such as M182T, were recovered. Our results therefore suggest that entrenchment of an amino acid may rely on diffuse interactions among multiple sites, with a major impact on protein stability.
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13
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Lin WC, Tang HC, Wang HY, Kao CY, Chang YC, Li AH, Yang SB, Mou KY. Fragment-Directed Random Mutagenesis by the Reverse Kunkel Method. ACS Synth Biol 2022; 11:1658-1668. [PMID: 35324156 DOI: 10.1021/acssynbio.2c00086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Two fundamentally different approaches are routinely used for protein engineering: user-defined mutagenesis and random mutagenesis, each with its own strengths and weaknesses. Here, we invent a unique mutagenesis protocol, which combines the advantages of user-defined mutagenesis and random mutagenesis. The new method, termed the reverse Kunkel method, allows the user to create random mutations at multiple specified regions in a one-pot reaction. We demonstrated the reverse Kunkel method by mimicking the somatic hypermutation in antibodies that introduces random mutations concentrated in complementarity-determining regions. Coupling with the phage display and yeast display selections, we successfully generated dramatically improved antibodies against a model protein and a neurotransmitter peptide in terms of affinity and immunostaining performance. The reverse Kunkel method is especially suitable for engineering proteins whose activities are determined by multiple variable regions, such as antibodies and adeno-associated virus capsids, or whose functional domains are composed of several discontinuous sequences, such as Cas9 and Cas12a.
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Affiliation(s)
- Wen-Ching Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Hao-Cheng Tang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Han Ying Wang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Chia-Yi Kao
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
- Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 11529, Taiwan
| | - You-Chiun Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
- Taiwan International Graduate Program in Chemical Biology and Molecular Biophysics, National Taiwan University and Academia Sinica, Taipei 11529, Taiwan
| | - Athena Hsu Li
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 11529, Taiwan
| | - Shi-Bing Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Kurt Yun Mou
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
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14
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Gasperin-Bulbarela J, Cabanillas-Bernal O, Dueñas S, Licea-Navarro AF. Preparation of Immune and Synthetic VNAR Libraries as Sources of High-Affinity Binders. Methods Mol Biol 2022; 2446:71-93. [PMID: 35157269 DOI: 10.1007/978-1-0716-2075-5_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The shark-derived autonomous variable antibody domains known as VNARs are attractive tools for therapeutic and diagnostic applications due to their favorable properties like small size (approximately 12 kDa), high thermal and chemical stability, and good tissue penetration. Currently, different techniques have been reported to generate VNAR domains against targets of therapeutic interest. Here, we describe methods for the preparation of an immune VNAR library based on bacteriophage display, and for the preparation of a synthetic library of VNAR domains using a modified protocol based on Kunkel mutagenesis. Finally, we describe procedures for in silico maturation of a VNAR using a bioinformatic approach to obtain higher affinity binders.
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Affiliation(s)
| | | | - Salvador Dueñas
- Biomedical Innovation Department, CICESE, Zona Playitas, Ensenada, Mexico
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15
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Hanning KR, Minot M, Warrender AK, Kelton W, Reddy ST. Deep mutational scanning for therapeutic antibody engineering. Trends Pharmacol Sci 2021; 43:123-135. [PMID: 34895944 DOI: 10.1016/j.tips.2021.11.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/02/2021] [Accepted: 11/10/2021] [Indexed: 12/24/2022]
Abstract
The biophysical and functional properties of monoclonal antibody (mAb) drug candidates are often improved by protein engineering methods to increase the probability of clinical efficacy. One emerging method is deep mutational scanning (DMS) which combines the power of exhaustive protein mutagenesis and functional screening with deep sequencing and bioinformatics. The application of DMS has yielded significant improvements to the affinity, specificity, and stability of several preclinical antibodies alongside novel applications such as introducing multi-specific binding properties. DMS has also been applied directly on target antigens to precisely map antibody-binding epitopes and notably to profile the mutational escape potential of viral targets (e.g., SARS-CoV-2 variants). Finally, DMS combined with machine learning is enabling advances in the computational screening and engineering of therapeutic antibodies.
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Affiliation(s)
- Kyrin R Hanning
- Te Huataki Waiora School of Health, University of Waikato, Hamilton 3240, New Zealand
| | - Mason Minot
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel 4058, Switzerland
| | - Annmaree K Warrender
- Te Huataki Waiora School of Health, University of Waikato, Hamilton 3240, New Zealand
| | - William Kelton
- Te Huataki Waiora School of Health, University of Waikato, Hamilton 3240, New Zealand.
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel 4058, Switzerland.
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16
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Francino-Urdaniz IM, Whitehead TA. An overview of methods for the structural and functional mapping of epitopes recognized by anti-SARS-CoV-2 antibodies. RSC Chem Biol 2021; 2:1580-1589. [PMID: 34977572 PMCID: PMC8637828 DOI: 10.1039/d1cb00169h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 09/25/2021] [Indexed: 12/20/2022] Open
Abstract
This mini-review presents a critical survey of techniques used for epitope mapping on the SARS-CoV-2 Spike protein. The sequence and structures for common neutralizing and non-neutralizing epitopes on the Spike protein are described as determined by X-ray crystallography, electron microscopy and linear peptide epitope mapping, among other methods. An additional focus of this mini-review is an analytical appraisal of different deep mutational scanning workflows for conformational epitope mapping and identification of mutants on the Spike protein which escape antibody neutralization. Such a focus is necessary as a critical review of deep mutational scanning for conformational epitope mapping has not been published. A perspective is presented on the use of different epitope determination methods for development of broadly potent antibody therapies and vaccines against SARS-CoV-2.
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Affiliation(s)
- Irene M Francino-Urdaniz
- Department of Chemical and Biological Engineering, University of Colorado JSC Biotechnology Building, 3415 Colorado Avenue Boulder CO 80305 USA +1 303-735-2145
| | - Timothy A Whitehead
- Department of Chemical and Biological Engineering, University of Colorado JSC Biotechnology Building, 3415 Colorado Avenue Boulder CO 80305 USA +1 303-735-2145
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17
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Kuiper BP, Prins RC, Billerbeck S. Oligo Pools as an Affordable Source of Synthetic DNA for Cost-Effective Library Construction in Protein- and Metabolic Pathway Engineering. Chembiochem 2021; 23:e202100507. [PMID: 34817110 PMCID: PMC9300125 DOI: 10.1002/cbic.202100507] [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: 09/23/2021] [Revised: 11/23/2021] [Indexed: 11/11/2022]
Abstract
The construction of custom libraries is critical for rational protein engineering and directed evolution. Array‐synthesized oligo pools of thousands of user‐defined sequences (up to ∼350 bases in length) have emerged as a low‐cost commercially available source of DNA. These pools cost ≤10 % (depending on error rate and length) of other commercial sources of custom DNA, and this significant cost difference can determine whether an enzyme engineering project can be realized on a given research budget. However, while being cheap, oligo pools do suffer from a low concentration of individual oligos and relatively high error rates. Several powerful techniques that specifically make use of oligo pools have been developed and proven valuable or even essential for next‐generation protein and pathway engineering strategies, such as sequence‐function mapping, enzyme minimization, or de‐novo design. Here we consolidate the knowledge on these techniques and their applications to facilitate the use of oligo pools within the protein engineering community.
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Affiliation(s)
- Bastiaan P Kuiper
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Rianne C Prins
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Sonja Billerbeck
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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18
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Appel M, Longwell SA, Morri M, Neff N, Herschlag D, Fordyce PM. uPIC-M: Efficient and Scalable Preparation of Clonal Single Mutant Libraries for High-Throughput Protein Biochemistry. ACS OMEGA 2021; 6:30542-30554. [PMID: 34805683 PMCID: PMC8600632 DOI: 10.1021/acsomega.1c04180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/05/2021] [Indexed: 06/13/2023]
Abstract
New high-throughput biochemistry techniques complement selection-based approaches and provide quantitative kinetic and thermodynamic data for thousands of protein variants in parallel. With these advances, library generation rather than data collection has become rate-limiting. Unlike pooled selection approaches, high-throughput biochemistry requires mutant libraries in which individual sequences are rationally designed, efficiently recovered, sequence-validated, and separated from one another, but current strategies are unable to produce these libraries at the needed scale and specificity at reasonable cost. Here, we present a scalable, rapid, and inexpensive approach for creating User-designed Physically Isolated Clonal-Mutant (uPIC-M) libraries that utilizes recent advances in oligo synthesis, high-throughput sample preparation, and next-generation sequencing. To demonstrate uPIC-M, we created a scanning mutant library of SpAP, a 541 amino acid alkaline phosphatase, and recovered 94% of desired mutants in a single iteration. uPIC-M uses commonly available equipment and freely downloadable custom software and can produce a 5000 mutant library at 1/3 the cost and 1/5 the time of traditional techniques.
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Affiliation(s)
- Mason
J. Appel
- Department
of Biochemistry, Stanford University, Stanford, California 94305, United States
| | - Scott A. Longwell
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Maurizio Morri
- Chan
Zuckerberg Biohub, San Francisco, California 94110, United States
| | - Norma Neff
- Chan
Zuckerberg Biohub, San Francisco, California 94110, United States
| | - Daniel Herschlag
- Department
of Biochemistry, Stanford University, Stanford, California 94305, United States
| | - Polly M. Fordyce
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
- Chan
Zuckerberg Biohub, San Francisco, California 94110, United States
- Department
of Genetics, Stanford University, Stanford, California 94305, United States
- ChEM-H
Institute, Stanford University, Stanford, California 94305, United States
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19
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Tietze L, Lale R. Importance of the 5' regulatory region to bacterial synthetic biology applications. Microb Biotechnol 2021; 14:2291-2315. [PMID: 34171170 PMCID: PMC8601185 DOI: 10.1111/1751-7915.13868] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 01/02/2023] Open
Abstract
The field of synthetic biology is evolving at a fast pace. It is advancing beyond single-gene alterations in single hosts to the logical design of complex circuits and the development of integrated synthetic genomes. Recent breakthroughs in deep learning, which is increasingly used in de novo assembly of DNA components with predictable effects, are also aiding the discipline. Despite advances in computing, the field is still reliant on the availability of pre-characterized DNA parts, whether natural or synthetic, to regulate gene expression in bacteria and make valuable compounds. In this review, we discuss the different bacterial synthetic biology methodologies employed in the creation of 5' regulatory regions - promoters, untranslated regions and 5'-end of coding sequences. We summarize methodologies and discuss their significance for each of the functional DNA components, and highlight the key advances made in bacterial engineering by concentrating on their flaws and strengths. We end the review by outlining the issues that the discipline may face in the near future.
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Affiliation(s)
- Lisa Tietze
- PhotoSynLabDepartment of BiotechnologyFaculty of Natural SciencesNorwegian University of Science and TechnologyTrondheimN‐7491Norway
| | - Rahmi Lale
- PhotoSynLabDepartment of BiotechnologyFaculty of Natural SciencesNorwegian University of Science and TechnologyTrondheimN‐7491Norway
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20
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Alejaldre L, Pelletier JN, Quaglia D. Methods for enzyme library creation: Which one will you choose?: A guide for novices and experts to introduce genetic diversity. Bioessays 2021; 43:e2100052. [PMID: 34263468 DOI: 10.1002/bies.202100052] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/28/2021] [Accepted: 06/02/2021] [Indexed: 12/15/2022]
Abstract
Enzyme engineering allows to explore sequence diversity in search for new properties. The scientific literature is populated with methods to create enzyme libraries for engineering purposes, however, choosing a suitable method for the creation of mutant libraries can be daunting, in particular for the novices. Here, we address both novices and experts: how can one enter the arena of enzyme library design and what guidelines can advanced users apply to select strategies best suited to their purpose? Section I is dedicated to the novices and presents an overview of established and standard methods for library creation, as well as available commercial solutions. The expert will discover an up-to-date tool to freshen up their repertoire (Section I) and learn of the newest methods that are likely to become a mainstay (Section II). We focus primarily on in vitro methods, presenting the advantages of each method. Our ultimate aim is to offer a selection of methods/strategies that we believe to be most useful to the enzyme engineer, whether a first-timer or a seasoned user.
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Affiliation(s)
- Lorea Alejaldre
- Département de biochimie and Center for Green Chemistry and Catalysis (CGCC), Université de Montréal, Montréal, Quebec, Canada.,PROTEO, The Québec Network for Research on Protein Function, Engineering and Applications, Québec, Quebec, Canada
| | - Joelle N Pelletier
- Département de biochimie and Center for Green Chemistry and Catalysis (CGCC), Université de Montréal, Montréal, Quebec, Canada.,PROTEO, The Québec Network for Research on Protein Function, Engineering and Applications, Québec, Quebec, Canada.,Département de chimie, Université de Montréal, Montréal, Quebec, Canada
| | - Daniela Quaglia
- Département de chimie, Université de Montréal, Montréal, Quebec, Canada.,School of Chemistry, University of Nottingham, Nottingham, UK
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21
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Alejaldre L, Lemay-St-Denis C, Perez Lopez C, Sancho Jodar F, Guallar V, Pelletier JN. Known Evolutionary Paths Are Accessible to Engineered ß-Lactamases Having Altered Protein Motions at the Timescale of Catalytic Turnover. Front Mol Biosci 2020; 7:599298. [PMID: 33330628 PMCID: PMC7716773 DOI: 10.3389/fmolb.2020.599298] [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: 08/26/2020] [Accepted: 10/23/2020] [Indexed: 11/26/2022] Open
Abstract
The evolution of new protein functions is dependent upon inherent biophysical features of proteins. Whereas, it has been shown that changes in protein dynamics can occur in the course of directed molecular evolution trajectories and contribute to new function, it is not known whether varying protein dynamics modify the course of evolution. We investigate this question using three related ß-lactamases displaying dynamics that differ broadly at the slow timescale that corresponds to catalytic turnover yet have similar fast dynamics, thermal stability, catalytic, and substrate recognition profiles. Introduction of substitutions E104K and G238S, that are known to have a synergistic effect on function in the parent ß-lactamase, showed similar increases in catalytic efficiency toward cefotaxime in the related ß-lactamases. Molecular simulations using Protein Energy Landscape Exploration reveal that this results from stabilizing the catalytically-productive conformations, demonstrating the dominance of the synergistic effect of the E014K and G238S substitutions in vitro in contexts that vary in terms of sequence and dynamics. Furthermore, three rounds of directed molecular evolution demonstrated that known cefotaximase-enhancing mutations were accessible regardless of the differences in dynamics. Interestingly, specific sequence differences between the related ß-lactamases were shown to have a higher effect in evolutionary outcomes than did differences in dynamics. Overall, these ß-lactamase models show tolerance to protein dynamics at the timescale of catalytic turnover in the evolution of a new function.
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Affiliation(s)
- Lorea Alejaldre
- Biochemistry Department, Université de Montréal, Montréal, QC, Canada
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec City, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC, Canada
| | - Claudèle Lemay-St-Denis
- Biochemistry Department, Université de Montréal, Montréal, QC, Canada
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec City, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC, Canada
| | | | | | - Victor Guallar
- Barcelona Supercomputing Center, Barcelona, Spain
- ICREA: Institució Catalana de Recerca i Estudis Avancats, Barcelona, Spain
| | - Joelle N. Pelletier
- Biochemistry Department, Université de Montréal, Montréal, QC, Canada
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec City, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC, Canada
- Chemistry Department, Université de Montréal, Montréal, QC, Canada
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22
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Oh EJ, Liu R, Liang L, Freed EF, Eckert CA, Gill RT. Multiplex Evolution of Antibody Fragments Utilizing a Yeast Surface Display Platform. ACS Synth Biol 2020; 9:2197-2202. [PMID: 32551581 DOI: 10.1021/acssynbio.0c00159] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Advances in high-throughput synthetic biology technologies based on the CRISPR/Cas9 system have enabled a comprehensive assessment of mutations conferring desired phenotypes, as well as a better understanding of genotype-phenotype correlations in protein engineering. Engineering antibodies to enhance properties such as binding affinity and stability plays an essential role in therapeutic applications. Here we report a method, multiplex navigation of antibody structure (MINAS), that combines a CRISPR/Cas9-based trackable editing method and fluorescent-activated cell sorting (FACS) of yeast-displayed libraries. We designed mutations in all of the complementarity-determining and framework regions of a well-characterized scFv antibody and mapped the contribution of these regions to enhanced properties. We identified specific mutants that showed higher binding affinities up to 100-fold compared to the wild-type. This study expands the applicability of CRISPR/Cas9-based trackable protein engineering by combining it with a surface display platform.
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Affiliation(s)
- Eun Joong Oh
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Rongming Liu
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Liya Liang
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Emily F. Freed
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Carrie A. Eckert
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80303, United States
- National Renewable Energy Laboratory (NREL), Bioscience Center, Golden, Colorado 80401, United States
| | - Ryan T. Gill
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80303, United States
- Novo Nordisk Foundation Center for Biosustainability, Danish Technical University, Lyngby, Denmark
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23
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Steiner PJ, Baumer ZT, Whitehead TA. A Method for User-defined Mutagenesis by Integrating Oligo Pool Synthesis Technology with Nicking Mutagenesis. Bio Protoc 2020; 10:e3697. [PMID: 33659364 DOI: 10.21769/bioprotoc.3697] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/20/2020] [Accepted: 05/26/2020] [Indexed: 11/02/2022] Open
Abstract
Saturation mutagenesis is a fundamental enabling technology for protein engineering and epitope mapping. Nicking mutagenesis (NM) allows the user to rapidly construct libraries of all possible single mutations in a target protein sequence from plasmid DNA in a one-pot procedure. Briefly, one strand of the plasmid DNA is degraded using a nicking restriction endonuclease and exonuclease treatment. Mutagenic primers encoding the desired mutations are annealed to the resulting circular single-stranded DNA, extended with high-fidelity polymerase, and ligated into covalently closed circular DNA by Taq DNA ligase. The heteroduplex DNA is resolved by selective degradation of the template strand. The complementary strand is synthesized and ligated, resulting in a library of mutated covalently closed circular plasmids. It was later shown that because very little primer is used in the procedure, resuspended oligo pools, which normally require amplification before use, can be used directly in the mutagenesis procedure. Because oligo pools can contain tens of thousands of unique oligos, this enables the construction of libraries of tens of thousands of user-defined mutations in a single-pot mutagenesis reaction, which significantly improves the utility of NM as described below. Use of oligo pools afford an economically advantageous approach to mutagenic experiments. First, oligo pool synthesis is much less expensive per nucleotide synthesized than conventional synthesis. Second, a mixed pool may be generated and used for mutagenesis of multiple different genes. To use the same oligo-pool for mutagenesis of a variety of genes, the user must only quantify the fraction of the oligo-pool specific to her mutagenic experiment and adjust the volume and effective concentration of the oligo-pool for use in nicking mutagenesis.
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Affiliation(s)
- Paul J Steiner
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Colorado, USA
| | - Zachary T Baumer
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Colorado, USA
| | - Timothy A Whitehead
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Colorado, USA
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24
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Klesmith JR, Hackel BJ. Improved mutant function prediction via PACT: Protein Analysis and Classifier Toolkit. Bioinformatics 2020; 35:2707-2712. [PMID: 30590444 DOI: 10.1093/bioinformatics/bty1042] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 12/06/2018] [Accepted: 12/19/2018] [Indexed: 12/31/2022] Open
Abstract
MOTIVATION Deep mutational scanning experiments have enabled the measurement of the sequence-function relationship for thousands of mutations in a single experiment. The Protein Analysis and Classifier Toolkit (PACT) is a Python software package that marries the fitness metric of a given mutation within these experiments to sequence and structural features enabling downstream analyses. PACT enables the easy development of user sharable protocols for custom deep mutational scanning experiments as all code is modular and reusable between protocols. Protocols for mutational libraries with single or multiple mutations are included. To exemplify its utility, PACT assessed two deep mutational scanning datasets that measured the tradeoff of enzyme activity and enzyme stability. RESULTS PACT efficiently evaluated classifiers that predict protein mutant function tested on deep mutational scanning screens. We found that the classifiers with the lowest false positive and highest true positive rate assesses sequence homology, contact number and if mutation involves proline. AVAILABILITY AND IMPLEMENTATION PACT and the processed datasets are distributed freely under the terms of the GPL-3 license. The source code is available at GitHub (https://github.com/JKlesmith/PACT). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Justin R Klesmith
- Department of Chemical Engineering and Materials Science, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota, Twin Cities, Minneapolis, MN, USA
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25
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Chen JZ, Fowler DM, Tokuriki N. Comprehensive exploration of the translocation, stability and substrate recognition requirements in VIM-2 lactamase. eLife 2020; 9:e56707. [PMID: 32510322 PMCID: PMC7308095 DOI: 10.7554/elife.56707] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/06/2020] [Indexed: 12/12/2022] Open
Abstract
Metallo-β-lactamases (MBLs) degrade a broad spectrum of β-lactam antibiotics, and are a major disseminating source for multidrug resistant bacteria. Despite many biochemical studies in diverse MBLs, molecular understanding of the roles of residues in the enzyme's stability and function, and especially substrate specificity, is lacking. Here, we employ deep mutational scanning (DMS) to generate comprehensive single amino acid variant data on a major clinical MBL, VIM-2, by measuring the effect of thousands of VIM-2 mutants on the degradation of three representative classes of β-lactams (ampicillin, cefotaxime, and meropenem) and at two different temperatures (25°C and 37°C). We revealed residues responsible for expression and translocation, and mutations that increase resistance and/or alter substrate specificity. The distribution of specificity-altering mutations unveiled distinct molecular recognition of the three substrates. Moreover, these function-altering mutations are frequently observed among naturally occurring variants, suggesting that the enzymes have continuously evolved to become more potent resistance genes.
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Affiliation(s)
- John Z Chen
- Michael Smith Laboratories, University of British ColumbiaVancouverCanada
| | - Douglas M Fowler
- Department of Genome Sciences, University of WashingtonSeattleUnited States
- Department of Bioengineering, University of WashingtonSeattleUnited States
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British ColumbiaVancouverCanada
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26
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Kemble H, Eisenhauer C, Couce A, Chapron A, Magnan M, Gautier G, Le Nagard H, Nghe P, Tenaillon O. Flux, toxicity, and expression costs generate complex genetic interactions in a metabolic pathway. SCIENCE ADVANCES 2020; 6:eabb2236. [PMID: 32537514 PMCID: PMC7269641 DOI: 10.1126/sciadv.abb2236] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 03/31/2020] [Indexed: 05/31/2023]
Abstract
Our ability to predict the impact of mutations on traits relevant for disease and evolution remains severely limited by the dependence of their effects on the genetic background and environment. Even when molecular interactions between genes are known, it is unclear how these translate to organism-level interactions between alleles. We therefore characterized the interplay of genetic and environmental dependencies in determining fitness by quantifying ~4000 fitness interactions between expression variants of two metabolic genes, starting from various environmentally modulated expression levels. We detect a remarkable variety of interactions dependent on initial expression levels and demonstrate that they can be quantitatively explained by a mechanistic model accounting for catabolic flux, metabolite toxicity, and expression costs. Complex fitness interactions between mutations can therefore be predicted simply from their simultaneous impact on a few connected molecular phenotypes.
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Affiliation(s)
- Harry Kemble
- IAME, INSERM, Université de Paris, Université Paris Nord, 75018 Paris, France
- Laboratory of Biochemistry (LBC), Chimie Biologie et Innovation, ESPCI Paris, PSL University, CNRS, 75005 Paris, France
| | | | - Alejandro Couce
- IAME, INSERM, Université de Paris, Université Paris Nord, 75018 Paris, France
- Department of Life Sciences, Imperial College, London SW7 2AZ, UK
| | - Audrey Chapron
- IAME, INSERM, Université de Paris, Université Paris Nord, 75018 Paris, France
| | - Mélanie Magnan
- IAME, INSERM, Université de Paris, Université Paris Nord, 75018 Paris, France
| | - Gregory Gautier
- Centre de Recherche sur l'Inflammation, INSERM, UMRS 1149, 75018 Paris, France
- Laboratoire d’Excellence INFLAMEX, Université de Paris, Sorbonne Paris Cité, 75018 Paris, France
| | - Hervé Le Nagard
- IAME, INSERM, Université de Paris, Université Paris Nord, 75018 Paris, France
| | - Philippe Nghe
- Laboratory of Biochemistry (LBC), Chimie Biologie et Innovation, ESPCI Paris, PSL University, CNRS, 75005 Paris, France
| | - Olivier Tenaillon
- IAME, INSERM, Université de Paris, Université Paris Nord, 75018 Paris, France
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27
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Pines G, Fankhauser RG, Eckert CA. Predicting Drug Resistance Using Deep Mutational Scanning. Molecules 2020; 25:E2265. [PMID: 32403408 PMCID: PMC7248951 DOI: 10.3390/molecules25092265] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/05/2020] [Accepted: 05/05/2020] [Indexed: 12/12/2022] Open
Abstract
Drug resistance is a major healthcare challenge, resulting in a continuous need to develop new inhibitors. The development of these inhibitors requires an understanding of the mechanisms of resistance for a critical mass of occurrences. Recent genome editing technologies based on high-throughput DNA synthesis and sequencing may help to predict mutations resulting in resistance by testing large mutagenesis libraries. Here we describe the rationale of this approach, with examples and relevance to drug development and resistance in malaria.
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Affiliation(s)
- Gur Pines
- Department of Entomology, Agricultural Research Organization, Volcani Center, P.O.B 15159, Rishon LeZion 7505101, Israel
| | - Reilly G. Fankhauser
- Department of Dermatology, Oregon Health & Science University, Baird Hall 3225 SW Pavilion Loop, Portland, OR 97239, USA;
| | - Carrie A. Eckert
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, 027 UCB, Boulder, CO 80309, USA
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
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28
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Medina-Cucurella AV, Steiner PJ, Faber MS, Beltrán J, Borelli AN, Kirby MB, Cutler SR, Whitehead TA. User-defined single pot mutagenesis using unamplified oligo pools. Protein Eng Des Sel 2020; 32:41-45. [PMID: 31297523 DOI: 10.1093/protein/gzz013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/17/2019] [Accepted: 06/11/2019] [Indexed: 11/13/2022] Open
Abstract
User-defined mutagenic libraries are fundamental for applied protein engineering workflows. Here we show that unamplified oligo pools can be used to prepare site saturation mutagenesis libraries from plasmid DNA with near-complete coverage of desired mutations and few off-target mutations. We find that oligo pools yield higher quality libraries when compared to individually synthesized degenerate oligos. We also show that multiple libraries can be multiplexed into a single oligo pool, making preparation of multiple libraries less expensive and more convenient. We provide software for automatic oligo pool design that can generate mutagenic oligos for saturating or focused libraries.
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Affiliation(s)
| | - Paul J Steiner
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, USA
| | - Matthew S Faber
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Jesús Beltrán
- Department of Plant Cell Biology, University of California, Riverside, CA, USA
| | - Alexandra N Borelli
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, USA
| | - Monica B Kirby
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, USA
| | - Sean R Cutler
- Department of Plant Cell Biology, University of California, Riverside, CA, USA
| | - Timothy A Whitehead
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA.,Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, USA
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29
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Bozovičar K, Bratkovič T. Evolving a Peptide: Library Platforms and Diversification Strategies. Int J Mol Sci 2019; 21:E215. [PMID: 31892275 PMCID: PMC6981544 DOI: 10.3390/ijms21010215] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 12/22/2019] [Accepted: 12/25/2019] [Indexed: 12/22/2022] Open
Abstract
Peptides are widely used in pharmaceutical industry as active pharmaceutical ingredients, versatile tools in drug discovery, and for drug delivery. They find themselves at the crossroads of small molecules and proteins, possessing favorable tissue penetration and the capability to engage into specific and high-affinity interactions with endogenous receptors. One of the commonly employed approaches in peptide discovery and design is to screen combinatorial libraries, comprising a myriad of peptide variants of either chemical or biological origin. In this review, we focus mainly on recombinant peptide libraries, discussing different platforms for their display or expression, and various diversification strategies for library design. We take a look at well-established technologies as well as new developments and future directions.
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Affiliation(s)
| | - Tomaž Bratkovič
- Department of Pharmaceutical Biology, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, SI-1000 Ljubljana, Slovenia;
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30
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Hu FJ, Lundqvist M, Uhlén M, Rockberg J. SAMURAI (Solid-phase Assisted Mutagenesis by Uracil Restriction for Accurate Integration) for antibody affinity maturation and paratope mapping. Nucleic Acids Res 2019; 47:e34. [PMID: 30715449 PMCID: PMC6451119 DOI: 10.1093/nar/gkz050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 01/08/2019] [Accepted: 01/24/2019] [Indexed: 12/31/2022] Open
Abstract
Mutagenesis libraries are essential for combinatorial protein engineering. Despite improvements in gene synthesis and directed mutagenesis, current methodologies still have limitations regarding the synthesis of complete antibody single-chain variable fragment (scFv) genes and simultaneous diversification of all six CDRs. Here, we describe the generation of mutagenesis libraries for antibody affinity maturation using a cell-free solid-phase technique for annealing of single-strand mutagenic oligonucleotides. The procedure consists of PCR-based incorporation of uracil into a wild-type template, bead-based capture, elution of single-strand DNA, and in vitro uracil excision enzyme based degradation of the template DNA. Our approach enabled rapid (8 hours) mutagenesis and automated cloning of 50 position-specific alanine mutants for mapping of a scFv antibody paratope. We further exemplify our method by generating affinity maturation libraries with diversity introduced in critical, nonessential, or all CDR positions randomly. Assessment with Illumina deep sequencing showed less than 1% wild-type in two libraries and the ability to diversify all CDR positions simultaneously. Selections of the libraries with bacterial display and deep sequencing evaluation of the selection output showed that diversity introduced in non-essential positions allowed for a more effective enrichment of improved binders compared to the other two diversification strategies.
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Affiliation(s)
- Francis Jingxin Hu
- KTH - Royal Institute of Technology, Department of Protein Science, 106 91 Stockholm, Sweden
| | - Magnus Lundqvist
- KTH - Royal Institute of Technology, Department of Protein Science, 106 91 Stockholm, Sweden
| | - Mathias Uhlén
- KTH - Royal Institute of Technology, Department of Protein Science, 106 91 Stockholm, Sweden.,KTH - Royal Institute of Technology, Science for Life Laboratory, Solna 171 65, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark
| | - Johan Rockberg
- KTH - Royal Institute of Technology, Department of Protein Science, 106 91 Stockholm, Sweden
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31
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Rogers OC, Johnson DM, Firnberg E. mRhubarb: Engineering of monomeric, red-shifted, and brighter variants of iRFP using structure-guided multi-site mutagenesis. Sci Rep 2019; 9:15653. [PMID: 31666599 PMCID: PMC6821797 DOI: 10.1038/s41598-019-52123-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 10/14/2019] [Indexed: 11/23/2022] Open
Abstract
Far-red and near-infrared fluorescent proteins (FPs) enable in vivo tissue imaging with greater depth and clarity compared to FPs in the visible spectrum due to reduced light absorbance and scatter by tissues. However current tools are limited by low brightness, limited red-shifting, and a non-ideal dimeric oligomerization state. In this study we developed a monomeric variant of iRFP, termed mRhubarb713, and subsequently used a targeted and expansive multi-site mutagenesis approach to screen for variants with red-shifted spectral activity. Two monomeric variants were discovered, deemed mRhubarb719 and mRhubarb720, with red-shifted spectra and increased quantum yield compared to iRFP. These tools build on previously developed near-IR FPs and should enable improved in vivo imaging studies with a genetically encoded reporter.
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32
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Engineering selective competitors for the discrimination of highly conserved protein-protein interaction modules. Nat Commun 2019; 10:4521. [PMID: 31586061 PMCID: PMC6778148 DOI: 10.1038/s41467-019-12528-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 09/14/2019] [Indexed: 12/13/2022] Open
Abstract
Designing highly specific modulators of protein-protein interactions (PPIs) is especially challenging in the context of multiple paralogs and conserved interaction surfaces. In this case, direct generation of selective and competitive inhibitors is hindered by high similarity within the evolutionary-related protein interfaces. We report here a strategy that uses a semi-rational approach to separate the modulator design into two functional parts. We first achieve specificity toward a region outside of the interface by using phage display selection coupled with molecular and cellular validation. Highly selective competition is then generated by appending the more degenerate interaction peptide to contact the target interface. We apply this approach to specifically bind a single PDZ domain within the postsynaptic protein PSD-95 over highly similar PDZ domains in PSD-93, SAP-97 and SAP-102. Our work provides a paralog-selective and domain specific inhibitor of PSD-95, and describes a method to efficiently target other conserved PPI modules. Developing inhibitors that target specific protein-protein interactions (PPIs) is challenging. Here, the authors show that target selectivity and PPI blocking can be achieved simultaneously with PPI inhibitors that contain two functional modules, and create a paralog-selective PSD-95 inhibitor as proof-of-concept.
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33
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Ribeiro LF, Amarelle V, Alves LDF, Viana de Siqueira GM, Lovate GL, Borelli TC, Guazzaroni ME. Genetically Engineered Proteins to Improve Biomass Conversion: New Advances and Challenges for Tailoring Biocatalysts. Molecules 2019; 24:molecules24162879. [PMID: 31398877 PMCID: PMC6719137 DOI: 10.3390/molecules24162879] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 07/30/2019] [Accepted: 08/06/2019] [Indexed: 01/02/2023] Open
Abstract
Protein engineering emerged as a powerful approach to generate more robust and efficient biocatalysts for bio-based economy applications, an alternative to ecologically toxic chemistries that rely on petroleum. On the quest for environmentally friendly technologies, sustainable and low-cost resources such as lignocellulosic plant-derived biomass are being used for the production of biofuels and fine chemicals. Since most of the enzymes used in the biorefinery industry act in suboptimal conditions, modification of their catalytic properties through protein rational design and in vitro evolution techniques allows the improvement of enzymatic parameters such as specificity, activity, efficiency, secretability, and stability, leading to better yields in the production lines. This review focuses on the current application of protein engineering techniques for improving the catalytic performance of enzymes used to break down lignocellulosic polymers. We discuss the use of both classical and modern methods reported in the literature in the last five years that allowed the boosting of biocatalysts for biomass degradation.
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Affiliation(s)
- Lucas Ferreira Ribeiro
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-901, Brazil.
| | - Vanesa Amarelle
- Department of Microbial Biochemistry and Genomics, Biological Research Institute Clemente Estable, Montevideo, PC 11600, Uruguay
| | - Luana de Fátima Alves
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Ribeirão Preto 14049-900, Brazil
| | | | - Gabriel Lencioni Lovate
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Ribeirão Preto 14049-900, Brazil
| | - Tiago Cabral Borelli
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-901, Brazil
| | - María-Eugenia Guazzaroni
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-901, Brazil.
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34
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Thisted T, Biesova Z, Walmacq C, Stone E, Rodnick-Smith M, Ahmed SS, Horrigan SK, Van Engelen B, Reed C, Kalnik MW. Optimization of a nicotine degrading enzyme for potential use in treatment of nicotine addiction. BMC Biotechnol 2019; 19:56. [PMID: 31375100 PMCID: PMC6679477 DOI: 10.1186/s12896-019-0551-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/23/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Smoking and tobacco use continue to be the largest preventable causes of death globally. A novel therapeutic approach has recently been proposed: administration of an enzyme that degrades nicotine, the main addictive component of tobacco, minimizing brain exposure and reducing its reinforcing effects. Pre-clinical proof of concept has been previously established through dosing the amine oxidase NicA2 from Pseudomonas putida in rat nicotine self-administration models of addiction. RESULTS This paper describes efforts towards optimizing NicA2 for potential therapeutic use: enhancing potency, improving its pharmacokinetic profile, and attenuating immunogenicity. Libraries randomizing residues located in all 22 active site positions of NicA2 were screened. 58 single mutations with 2- to 19-fold enhanced catalytic activity compared to wt at 10 μM nicotine were identified. A novel nicotine biosensor assay allowed efficient screening of the many primary hits for activity at nicotine concentrations typically found in smokers. 10 mutants with improved activity in rat serum at or below 250 nM were identified. These catalytic improvements translated to increased potency in vivo in the form of further lowering of nicotine blood levels and nicotine accumulation in the brains of Sprague-Dawley rats. Examination of the X-ray crystal structure suggests that these mutants may accelerate the rate limiting re-oxidation of the flavin adenine dinucleotide cofactor by enhancing molecular oxygen's access. PEGylation of NicA2 led to prolonged serum half-life and lowered immunogenicity observed in a human HLA DR4 transgenic mouse model, without impacting nicotine degrading activity. CONCLUSIONS Systematic mutational analysis of the active site of the nicotine-degrading enzyme NicA2 has yielded 10 variants that increase the catalytic activity and its effects on nicotine distribution in vivo at nicotine plasma concentrations found in smokers. In addition, PEGylation substantially increases circulating half-life and reduces the enzyme's immunogenic potential. Taken together, these results provide a viable path towards generation of a drug candidate suitable for human therapeutic use in treating nicotine addiction.
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Affiliation(s)
- Thomas Thisted
- Antidote Therapeutics, Inc, 708 Quince Orchard Road, Suite 250-C, Gaithersburg, MD 20878 USA
| | - Zuzana Biesova
- Antidote Therapeutics, Inc, 708 Quince Orchard Road, Suite 250-C, Gaithersburg, MD 20878 USA
| | - Celine Walmacq
- Antidote Therapeutics, Inc, 708 Quince Orchard Road, Suite 250-C, Gaithersburg, MD 20878 USA
| | - Everett Stone
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX USA
| | - Max Rodnick-Smith
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX USA
| | - Shaheda S. Ahmed
- Alcyomics Ltd, Bulman House, Regent Centre, Gosforth, Newcastle upon Tyne, NE3 3LS UK
| | | | - Bo Van Engelen
- Antidote Therapeutics, Inc, 708 Quince Orchard Road, Suite 250-C, Gaithersburg, MD 20878 USA
- Maastricht University, P. Debyeplein 1, 6229 HA, Maastricht, NL USA
| | - Charles Reed
- Antidote Therapeutics, Inc, 708 Quince Orchard Road, Suite 250-C, Gaithersburg, MD 20878 USA
| | - Matthew W. Kalnik
- Antidote Therapeutics, Inc, 708 Quince Orchard Road, Suite 250-C, Gaithersburg, MD 20878 USA
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35
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Cozens C, Pinheiro VB. Darwin Assembly: fast, efficient, multi-site bespoke mutagenesis. Nucleic Acids Res 2019; 46:e51. [PMID: 29409059 PMCID: PMC5934624 DOI: 10.1093/nar/gky067] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 01/24/2018] [Indexed: 12/15/2022] Open
Abstract
Engineering proteins for designer functions and biotechnological applications almost invariably requires (or at least benefits from) multiple mutations to non-contiguous residues. Several methods for multiple site-directed mutagenesis exist, but there remains a need for fast and simple methods to efficiently introduce such mutations – particularly for generating large, high quality libraries for directed evolution. Here, we present Darwin Assembly, which can deliver high quality libraries of >108 transformants, targeting multiple (>10) distal sites with minimal wild-type contamination (<0.25% of total population) and which takes a single working day from purified plasmid to library transformation. We demonstrate its efficacy with whole gene codon reassignment of chloramphenicol acetyl transferase, mutating 19 codons in a single reaction in KOD DNA polymerase and generating high quality, multiple-site libraries in T7 RNA polymerase and Tgo DNA polymerase. Darwin Assembly uses commercially available enzymes, can be readily automated, and offers a cost-effective route to highly complex and customizable library generation.
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Affiliation(s)
| | - Vitor B Pinheiro
- University College London, Gower Street, London WC1E 6BT, UK.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street WC1E 7HX, UK
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36
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Schmiedel JM, Lehner B. Determining protein structures using deep mutagenesis. Nat Genet 2019; 51:1177-1186. [PMID: 31209395 PMCID: PMC7610650 DOI: 10.1038/s41588-019-0431-x] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 04/29/2019] [Indexed: 12/12/2022]
Abstract
Determining the three-dimensional structures of macromolecules is a major goal of biological research, because of the close relationship between structure and function; however, thousands of protein domains still have unknown structures. Structure determination usually relies on physical techniques including X-ray crystallography, NMR spectroscopy and cryo-electron microscopy. Here we present a method that allows the high-resolution three-dimensional backbone structure of a biological macromolecule to be determined only from measurements of the activity of mutant variants of the molecule. This genetic approach to structure determination relies on the quantification of genetic interactions (epistasis) between mutations and the discrimination of direct from indirect interactions. This provides an alternative experimental strategy for structure determination, with the potential to reveal functional and in vivo structures.
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Affiliation(s)
- Jörn M Schmiedel
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ben Lehner
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- ICREA, Barcelona, Spain.
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37
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Synthetic libraries of shark vNAR domains with different cysteine numbers within the CDR3. PLoS One 2019; 14:e0213394. [PMID: 31206542 PMCID: PMC6576789 DOI: 10.1371/journal.pone.0213394] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 02/19/2019] [Indexed: 01/09/2023] Open
Abstract
The variable domain of New Antigen Receptors (vNAR) from sharks, present special characteristics in comparison to the conventional antibody molecules such as: small size (12–15 kDa), thermal and chemical stability and great tissue penetration, that makes them a good alternative source as therapeutic or diagnostic agents. Therefore, it is essential to improve techniques used for the development and selection of vNAR antibodies that recognize distinct antigens. The development of synthetic antibody libraries offers a fast option for the generation of antibodies with the desired characteristics. In this work three synthetic antibody libraries were constructed; without cysteines (Cys), with one Cys and with two Cys residues within its CDR3, with the objective of determining whether the presence or absence of Cys in the CDR3 favors the isolation of vNAR clones from a synthetic library. The libraries were validated selecting against six mammalian proteins. At least one vNAR was found for each of the antigens, and a clone coming from the library without Cys in the CDR3 was selected with all the antigens. In vitro angiogenesis assay with the isolated anti-VEGF antibodies, suggest that these vNARs are capable of inhibiting in vitro angiogenesis. In silico analysis of anti-VEGF antibodies showed that vNARs from synthetic libraries could rival antibodies with affinity maturation by in silico modeling.
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38
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Kinney JB, McCandlish DM. Massively Parallel Assays and Quantitative Sequence-Function Relationships. Annu Rev Genomics Hum Genet 2019; 20:99-127. [PMID: 31091417 DOI: 10.1146/annurev-genom-083118-014845] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over the last decade, a rich variety of massively parallel assays have revolutionized our understanding of how biological sequences encode quantitative molecular phenotypes. These assays include deep mutational scanning, high-throughput SELEX, and massively parallel reporter assays. Here, we review these experimental methods and how the data they produce can be used to quantitatively model sequence-function relationships. In doing so, we touch on a diverse range of topics, including the identification of clinically relevant genomic variants, the modeling of transcription factor binding to DNA, the functional and evolutionary landscapes of proteins, and cis-regulatory mechanisms in both transcription and mRNA splicing. We further describe a unified conceptual framework and a core set of mathematical modeling strategies that studies in these diverse areas can make use of. Finally, we highlight key aspects of experimental design and mathematical modeling that are important for the results of such studies to be interpretable and reproducible.
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Affiliation(s)
- Justin B Kinney
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; ,
| | - David M McCandlish
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; ,
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39
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Lim CC, Choong YS, Lim TS. Cognizance of Molecular Methods for the Generation of Mutagenic Phage Display Antibody Libraries for Affinity Maturation. Int J Mol Sci 2019; 20:E1861. [PMID: 30991723 PMCID: PMC6515083 DOI: 10.3390/ijms20081861] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/10/2019] [Accepted: 04/12/2019] [Indexed: 12/25/2022] Open
Abstract
Antibodies leverage on their unique architecture to bind with an array of antigens. The strength of interaction has a direct relation to the affinity of the antibodies towards the antigen. In vivo affinity maturation is performed through multiple rounds of somatic hypermutation and selection in the germinal centre. This unique process involves intricate sequence rearrangements at the gene level via molecular mechanisms. The emergence of in vitro display technologies, mainly phage display and recombinant DNA technology, has helped revolutionize the way antibody improvements are being carried out in the laboratory. The adaptation of molecular approaches in vitro to replicate the in vivo processes has allowed for improvements in the way recombinant antibodies are designed and tuned. Combinatorial libraries, consisting of a myriad of possible antibodies, are capable of replicating the diversity of the natural human antibody repertoire. The isolation of target-specific antibodies with specific affinity characteristics can also be accomplished through modification of stringent protocols. Despite the ability to screen and select for high-affinity binders, some 'fine tuning' may be required to enhance antibody binding in terms of its affinity. This review will provide a brief account of phage display technology used for antibody generation followed by a summary of different combinatorial library characteristics. The review will focus on available strategies, which include molecular approaches, next generation sequencing, and in silico approaches used for antibody affinity maturation in both therapeutic and diagnostic applications.
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Affiliation(s)
- Chia Chiu Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Penang 11800, Malaysia.
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40
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Acevedo‐Rocha CG, Sun Z, Reetz MT. Clarifying the Difference between Iterative Saturation Mutagenesis as a Rational Guide in Directed Evolution and OmniChange as a Gene Mutagenesis Technique. Chembiochem 2018; 19:2542-2544. [PMID: 30408315 DOI: 10.1002/cbic.201800372] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Indexed: 11/10/2022]
Affiliation(s)
| | - Zhoutong Sun
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Manfred T. Reetz
- Department of ChemistryPhilipps University 35032 Marburg Germany
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim Germany
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41
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She W, Ni J, Shui K, Wang F, He R, Xue J, Reetz MT, Li A, Ma L. Rapid and Error-Free Site-Directed Mutagenesis by a PCR-Free In Vitro CRISPR/Cas9-Mediated Mutagenic System. ACS Synth Biol 2018; 7:2236-2244. [PMID: 30075075 DOI: 10.1021/acssynbio.8b00245] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The quality and efficiency of any PCR-based mutagenesis technique may not be optimal due to, among other things, amino acid bias, which means that the development of efficient PCR-free methods is desirable. Here, we present a highly efficient in vitro CRISPR/Cas9-mediated mutagenic (ICM) system that allows rapid construction of designed mutants in a PCR-free manner. First, it involves plasmid digestion by utilizing a complex of Cas9 with specific single guide RNA (sgRNA) followed by degradation with T5 exonuclease to generate a 15 nt homologous region. Second, primers containing the desired mutations are annealed to form the double-stranded DNA fragments, which are then ligated into the linearized plasmid. In theory, neither the size of the target plasmid nor the unavailable restriction enzyme site poses any problems that may arise in traditional techniques. In this study, single and multiple site-directed mutagenesis were successfully performed even for a large size plasmid (up to 9.0 kb). Moreover, a PCR-free site-saturation mutagenesis library on single site and two adjacent sites of a green fluorescent protein was also generated with promising results. This demonstrates the great potential of the ICM system for creating high-quality mutant libraries in directed evolution as an alternative to PCR-based saturation mutagenesis, thus facilitating research on synthetic biology.
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Affiliation(s)
- Wenwen She
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 434200, China
| | - Jing Ni
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 434200, China
| | - Ke Shui
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Fei Wang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 434200, China
| | - Ruyi He
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 434200, China
| | - Jinhui Xue
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 434200, China
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Aitao Li
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 434200, China
| | - Lixin Ma
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 434200, China
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42
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Öling D, Lawenius L, Shaw W, Clark S, Kettleborough R, Ellis T, Larsson N, Wigglesworth M. Large Scale Synthetic Site Saturation GPCR Libraries Reveal Novel Mutations That Alter Glucose Signaling. ACS Synth Biol 2018; 7:2317-2321. [PMID: 30114904 DOI: 10.1021/acssynbio.8b00118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Site saturation mutagenesis (SSM) is a powerful mutagenesis strategy for protein engineering and directed evolution experiments. However, limiting factors using this method are either biased representation of variants, or limiting library size. To overcome these hurdles, we generated large scale targeted synthetic SSM libraries using massively parallel oligonucleotide synthesis and benchmarked this against an error-prone (epPCR) library. The yeast glucose activated GPCR-Gpr1 was chosen as a prototype to evolve novel glucose sensors. We demonstrate superior variant representation and several unique hits in the synthetic library compared to the PCR generated library. Application of this mutational approach further builds the possibilities of synthetic biology in tuning of a response to known ligands and in generating biosensors for novel ligands.
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Affiliation(s)
- David Öling
- Discovery Biology, Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D, 431 50 Mölndal, Sweden
| | - Lina Lawenius
- Discovery Biology, Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D, 431 50 Mölndal, Sweden
| | - William Shaw
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
- Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
| | - Sonya Clark
- Twist Bioscience, San Francisco, California 94158, United States
| | | | - Tom Ellis
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
- Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
| | - Niklas Larsson
- Discovery Biology, Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D, 431 50 Mölndal, Sweden
| | - Mark Wigglesworth
- Hit Identification, Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D, Macclesfield SK10 2NA, U.K
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43
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Multiplexed assays of variant effects contribute to a growing genotype-phenotype atlas. Hum Genet 2018; 137:665-678. [PMID: 30073413 PMCID: PMC6153521 DOI: 10.1007/s00439-018-1916-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 07/21/2018] [Indexed: 12/12/2022]
Abstract
Given the constantly improving cost and speed of genome sequencing, it is reasonable to expect that personal genomes will soon be known for many millions of humans. This stands in stark contrast with our limited ability to interpret the sequence variants which we find. Although it is, perhaps, easiest to interpret variants in coding regions, knowledge of functional impact is unknown for the vast majority of missense variants. While many computational approaches can predict the impact of coding variants, they are given a little weight in the current guidelines for interpreting clinical variants. Laboratory assays produce comparatively more trustworthy results, but until recently did not scale to the space of all possible mutations. The development of deep mutational scanning and other multiplexed assays of variant effect has now brought feasibility of this endeavour within view. Here, we review progress in this field over the last decade, break down the different approaches into their components, and compare methodological differences.
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44
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Kawai F, Nakamura A, Visootsat A, Iino R. Plasmid-Based One-Pot Saturation Mutagenesis and Robot-Based Automated Screening for Protein Engineering. ACS OMEGA 2018; 3:7715-7726. [PMID: 30221239 PMCID: PMC6130897 DOI: 10.1021/acsomega.8b00663] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/27/2018] [Indexed: 05/24/2023]
Abstract
We evaluated a method for protein engineering using plasmid-based one-pot saturation mutagenesis and robot-based automated screening. When the biases in nucleotides and amino acids were assessed for a loss-of-function point mutation in green fluorescent protein, the ratios of gain-of-function mutants were not significantly different from the expected values for the primers among the three different suppliers. However, deep sequencing analysis revealed that the ratios of nucleotides in the primers were highly biased among the suppliers. Biases for NNB were less severe than for NNN. We applied this method to screen a fusion protein of two chitinases, ChiA and ChiB (ChiAB). Three NNB codons as well as tyrosine and serine (X1YSX2X3) were inserted to modify the surface structure of ChiAB. We observed significant amino acid bias at the X3 position in water-soluble, active ChiAB-X1YSX2X3 mutants. Examination of the crystal structure of one active mutant, ChiAB-FYSFV, revealed that the X3 residue plays an important role in structure stabilization.
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Affiliation(s)
- Fumihiro Kawai
- Institute
for Molecular Science, National Institutes
of Natural Sciences, 5-1 Higashiyama Myodaijicho, Okazaki, Aichi 444-8787, Japan
| | - Akihiko Nakamura
- Institute
for Molecular Science, National Institutes
of Natural Sciences, 5-1 Higashiyama Myodaijicho, Okazaki, Aichi 444-8787, Japan
- The
Graduate University for Advanced Studies (SOKENDAI), Shonan Village, Hayama, Kanagawa 240-0193, Japan
| | - Akasit Visootsat
- The
Graduate University for Advanced Studies (SOKENDAI), Shonan Village, Hayama, Kanagawa 240-0193, Japan
| | - Ryota Iino
- Institute
for Molecular Science, National Institutes
of Natural Sciences, 5-1 Higashiyama Myodaijicho, Okazaki, Aichi 444-8787, Japan
- The
Graduate University for Advanced Studies (SOKENDAI), Shonan Village, Hayama, Kanagawa 240-0193, Japan
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Ensari Y, Dhoke GV, Davari MD, Ruff AJ, Schwaneberg U. A Comparative Reengineering Study of cpADH5 through Iterative and Simultaneous Multisite Saturation Mutagenesis. Chembiochem 2018; 19:1563-1569. [DOI: 10.1002/cbic.201800159] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Yunus Ensari
- Lehrstuhl für BiotechnologieRWTH Aachen University Worringerweg 3 52074 Aachen Germany
- Kafkas UniversityFaculty of Engineering and ArchitectureDepartment of Bioengineering 36100 Kars Turkey
| | - Gaurao V. Dhoke
- Lehrstuhl für BiotechnologieRWTH Aachen University Worringerweg 3 52074 Aachen Germany
| | - Mehdi D. Davari
- Lehrstuhl für BiotechnologieRWTH Aachen University Worringerweg 3 52074 Aachen Germany
| | - Anna Joëlle Ruff
- Lehrstuhl für BiotechnologieRWTH Aachen University Worringerweg 3 52074 Aachen Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für BiotechnologieRWTH Aachen University Worringerweg 3 52074 Aachen Germany
- DWI-Leibniz Institut für Interaktive Materialien Forckenbeckstrasse 50 52056 Aachen Germany
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46
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Abstract
Directed evolution (DE) is a powerful tool for optimizing an enzyme's properties toward a particular objective, such as broader substrate scope, greater thermostability, or increased kcat. A successful DE project requires the generation of genetic diversity and subsequent screening or selection to identify variants with improved fitness. In contrast to random methods (error-prone PCR or DNA shuffling), site-directed mutagenesis enables the rational design of variant libraries and provides control over the nature and frequency of the encoded mutations. Knowledge of protein structure, dynamics, enzyme mechanisms, and natural evolution demonstrates that multiple (combinatorial) mutations are required to discover the most improved variants. To this end, we describe an experimentally straightforward and low-cost method for the preparation of combinatorial variant libraries. Our approach employs a two-step PCR protocol, first producing mutagenic megaprimers, which can then be combined in a "mix-and-match" fashion to generate diverse sets of combinatorial variant libraries both quickly and accurately.
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47
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Gupta K, Varadarajan R. Insights into protein structure, stability and function from saturation mutagenesis. Curr Opin Struct Biol 2018; 50:117-125. [PMID: 29505936 DOI: 10.1016/j.sbi.2018.02.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 02/09/2018] [Accepted: 02/17/2018] [Indexed: 12/20/2022]
Abstract
Where convenient phenotypic readouts are available, saturation mutagenesis coupled to deep sequencing provides a rapid and facile method to infer sequence determinants of protein structure, stability and function. We provide brief descriptions and currently available options for the various steps involved, and mention limitations of current implementations. We also highlight recent applications such as estimating relative stabilities and affinities of protein variants, mapping epitopes, protein model discrimination and prediction of mutant phenotypes. Most mutational scans have so far been applied to single genes and proteins. Additional methodological improvements are required to expand the scope to study intergenic epistasis and intermolecular interactions in macromolecular complexes.
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Affiliation(s)
- Kritika Gupta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India; Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur P.O., Bangalore 560 004, India.
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48
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Tian S, Das R. Primerize-2D: automated primer design for RNA multidimensional chemical mapping. Bioinformatics 2018; 33:1405-1406. [PMID: 28453672 DOI: 10.1093/bioinformatics/btw814] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 12/23/2016] [Indexed: 11/14/2022] Open
Abstract
Summary Rapid RNA synthesis of comprehensive single mutant libraries and targeted multiple mutant libraries is enabling new multidimensional chemical approaches to solve RNA structures. PCR assembly of DNA templates and in vitro transcription allow synthesis and purification of hundreds of RNA mutants in a cost-effective manner, with sharing of primers across constructs allowing significant reductions in expense. However, these protocols require organization of primer locations across numerous 96 well plates and guidance for pipetting, non-trivial tasks for which informatics and visualization tools can prevent costly errors. We report here an online tool to accelerate synthesis of large libraries of desired mutants through design and efficient organization of primers. The underlying program and graphical interface have been experimentally tested in our laboratory for RNA domains with lengths up to 300 nucleotides and libraries encompassing up to 960 variants. In addition to the freely available Primerize-2D server, the primer design code is available as a stand-alone Python package for broader applications. Availability and Implementation http://primerize2d.stanford.edu. Contact rhiju@stanford.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Rhiju Das
- Department of Biochemistry.,Department of Physics, Stanford University, Stanford, CA 94305, USA
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49
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Kang Z, Ding W, Jin P, Du G, Chen J. Combinatorial Evolution of DNA with RECODE. Methods Mol Biol 2018; 1772:205-212. [PMID: 29754230 DOI: 10.1007/978-1-4939-7795-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In past decades, DNA engineering protocols have led to the rapid development of synthetic biology. To engineer the natural proteins, many directed evolution methods based on molecular biology have been presented for generating genetic diversity or obtaining specific properties. Here, we provide a simple (PCR operation), efficient (larger amount of products), and powerful (multiple point mutations, deletions, insertions, and combinatorial multipoint mutagenesis) RECODE method, which is capable of reediting the target DNA flexibly to restructure regulatory regions and remodel enzymes by using the combined function of the thermostable DNA polymerase and DNA ligase in one pot. RECODE is expected to be an applicable choice to create diverse mutant libraries for rapid evolution and optimization of enzymes and synthetic pathways.
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Affiliation(s)
- Zhen Kang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu, China.
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.
| | - Wenwen Ding
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Peng Jin
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Guocheng Du
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu, China
| | - Jian Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu, China
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50
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Bratulic S, Badran AH. Modern methods for laboratory diversification of biomolecules. Curr Opin Chem Biol 2017; 41:50-60. [PMID: 29096324 PMCID: PMC6062405 DOI: 10.1016/j.cbpa.2017.10.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 10/03/2017] [Accepted: 10/08/2017] [Indexed: 11/29/2022]
Abstract
Genetic variation fuels Darwinian evolution, yet spontaneous mutation rates are maintained at low levels to ensure cellular viability. Low mutation rates preclude the exhaustive exploration of sequence space for protein evolution and genome engineering applications, prompting scientists to develop methods for efficient and targeted diversification of nucleic acid sequences. Directed evolution of biomolecules relies upon the generation of unbiased genetic diversity to discover variants with desirable properties, whereas genome-engineering applications require selective modifications on a genomic scale with minimal off-targets. Here, we review the current toolkit of mutagenesis strategies employed in directed evolution and genome engineering. These state-of-the-art methods enable facile modifications and improvements of single genes, multicomponent pathways, and whole genomes for basic and applied research, while simultaneously paving the way for genome editing therapeutic interventions.
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Affiliation(s)
- Sinisa Bratulic
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ahmed H Badran
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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