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High-throughput screening of enzyme mutants by comparison of their activity ratios to an enzyme tag. Anal Biochem 2020; 588:113474. [PMID: 31614116 DOI: 10.1016/j.ab.2019.113474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 10/01/2019] [Accepted: 10/08/2019] [Indexed: 12/16/2022]
Abstract
With Escherichia coli alkaline phosphatase (ECAP) as the tag fused to the N-terminus of Pseudomonas Aeruginosa arylsulfatase (PAAS) and its mutants via a flexible linker, the comparison of the activity ratios of an applicable enzyme and its mutants to a suitable enzyme tag in cell lysates of their fused forms was tested for high-throughput (HTP) screening of mutants. After both the induced expression of a fused form and alkaline lysis of the transformed cells in microplate wells, HTP assay of the activities of ECAP and PAAS/mutant was realized via spectrophotometric-dual-enzyme-simultaneous-assay to derive their activity ratio. The successful induced expression of fused forms required ECAP activities higher than 5.3 U/L in cell lysates. Of three representative fused PAAS/mutants in cell lysates, there were similar proteolytic fragments and the comparison of their activity ratios greatly enhanced the recognition of weakly positive mutants. After saturation mutagenesis at M72 of the fused PAAS, the activity ratios of PAAS/mutants to ECAP in cell lysates of their fused forms were proportional to specific activities of their non-fused counterparts in cell lysates by an immunoturbidimetric assay. Therefore, the proposed strategy was absorbing for both HTP screening of mutants and HTP elucidation of sequence-activity relationship of applicable enzymes.
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2
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Abstract
Saturation mutagenesis is conveniently located between the two extremes of protein engineering, namely random mutagenesis, and rational design. It involves mutating a confined number of target residues to other amino acids, and hence requires knowledge regarding the sites for mutagenesis, but not their final identity. There are many different strategies for performing and designing such experiments, ranging from simple single degenerate codons to codon collections that code for distinct sets of amino acids. Here, we provide detailed information on the Dynamic Management for Codon Compression (DYNAMCC) approaches that allow us to precisely define the desired amino acid composition to be introduced to a specific target site. DYNAMCC allows us to set usage thresholds and to eliminate undesirable stop and wild-type codons, thus allowing us to control library size and subsequently downstream screening efforts. The DYNAMCC algorithms are free of charge and are implemented in a website for easy access and usage: www.dynamcc.com .
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Affiliation(s)
- Gur Pines
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, CO, USA. .,Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA.
| | - Ryan T Gill
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, CO, USA.,Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
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3
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Optimization of design and production strategies for novel adeno-associated viral display peptide libraries. Gene Ther 2017. [PMID: 28622288 DOI: 10.1038/gt.2017.51] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Libraries displaying random peptides on the surface of adeno-associated virus (AAV) are powerful tools for the generation of target-specific gene therapy vectors. However, for unknown reasons the success rate of AAV library screenings is variable and the influence of the production procedure has not been thoroughly evaluated. During library screenings, the capsid variants with the most favorable tropism are enriched over several selection rounds on a target of choice and identified by subsequent sequencing of the encapsidated viral genomes encoding the library capsids with targeting peptide insertions. Thus, a high capsid-genome correlation is crucial to obtain the correct information about the selected capsid variants. Producing AAV libraries by a two-step protocol with pseudotyped library transfer shuttles has been proposed as one way to ensure such a correlation. Here we show that AAV2 libraries produced by such a protocol via transfer shuttles display an unexpected additional bias in the amino-acid composition which confers increased heparin affinity and thus similarity to wildtype AAV2 tropism. This bias may fundamentally impair the intended use of AAV libraries, discouraging the use of transfer shuttles for the production of AAV libraries in the future.
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Pines G, Pines A, Garst AD, Zeitoun RI, Lynch SA, Gill RT. Codon compression algorithms for saturation mutagenesis. ACS Synth Biol 2015; 4:604-14. [PMID: 25303315 DOI: 10.1021/sb500282v] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Saturation mutagenesis is employed in protein engineering and genome-editing efforts to generate libraries that span amino acid design space. Traditionally, this is accomplished by using degenerate/compressed codons such as NNK (N = A/C/G/T, K = G/T), which covers all amino acids and one stop codon. These solutions suffer from two types of redundancy: (a) different codons for the same amino acid lead to bias, and (b) wild type amino acid is included within the library. These redundancies increase library size and downstream screening efforts. Here, we present a dynamic approach to compress codons for any desired list of amino acids, taking into account codon usage. This results in a unique codon collection for every amino acid to be mutated, with the desired redundancy level. Finally, we demonstrate that this approach can be used to design precise oligo libraries amendable to recombineering and CRISPR-based genome editing to obtain a diverse population with high efficiency.
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Affiliation(s)
- Gur Pines
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | | | - Andrew D. Garst
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Ramsey I. Zeitoun
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Sean A. Lynch
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
- Biosciences Center,
National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Ryan T. Gill
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
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Xu M, Hu S, Ding B, Fei C, Wan W, Hu D, Du R, Zhou X, Hong J, Liu H, Gao X, Liu J. Design and construction of small perturbation mutagenesis libraries for antibody affinity maturation using massive microchip-synthesized oligonucleotides. J Biotechnol 2014; 194:27-36. [PMID: 25444869 DOI: 10.1016/j.jbiotec.2014.11.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 10/14/2014] [Accepted: 11/07/2014] [Indexed: 12/20/2022]
Abstract
We report a rational strategy to design and construct multiple small perturbation mutagenesis (SPM) libraries using massively parallel synthesis of oligonucleotides on a microchip for affinity maturation of an engineered anti-ErbB2 antibody chA21. On the basis of a comprehensive analysis of the sequence and structural relationships of six complementary determination regions (CDRs) in the Kabatman database, a computational algorithm was developed to introduce single-site and double-site mutations into variable CDR positions using ambiguous nucleotides. The six SPM libraries were composed of 419 degenerate oligonucleotides that can be expanded into 161,832 unique CDR sequences with a high coverage ratio of 95% natural amino acid diversity. We used Illumina next-generation sequencing to demonstrate that the synthetic CDR library sequences, as well as relative quantities per sequence, can be controlled precisely by adjusting reaction chamber assignment and input nucleoside composition. The microchip-synthesized oligonucleotides were used for construction of single-chain antibody fragment (scFv) phage libraries through one-step mutagenic PCR of double-stranded plasmids with >10(6)E. coli transformants. A variant with combinatorial mutations from four individual CDRs achieved more than 19-fold affinity increase. The strategy described herein should be broadly applicable to affinity and selectivity studies of antibodies and other proteins.
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Affiliation(s)
- Man Xu
- School of Life Sciences, University of Science and Technology of China, 443 Huangshan Rd, Hefei, Anhui 230027, China
| | - Siyi Hu
- School of Life Sciences, University of Science and Technology of China, 443 Huangshan Rd, Hefei, Anhui 230027, China
| | - Bo Ding
- School of Life Sciences, University of Science and Technology of China, 443 Huangshan Rd, Hefei, Anhui 230027, China
| | - Caiyi Fei
- School of Life Sciences, University of Science and Technology of China, 443 Huangshan Rd, Hefei, Anhui 230027, China
| | - Wen Wan
- School of Life Sciences, University of Science and Technology of China, 443 Huangshan Rd, Hefei, Anhui 230027, China
| | - Dongmei Hu
- School of Life Sciences, University of Science and Technology of China, 443 Huangshan Rd, Hefei, Anhui 230027, China
| | - Ruikai Du
- School of Life Sciences, University of Science and Technology of China, 443 Huangshan Rd, Hefei, Anhui 230027, China
| | - Xiaochuan Zhou
- LC Sciences, 2575 West Bellfort St. STE 270, Houston, TX 77054, USA
| | - Jiong Hong
- School of Life Sciences, University of Science and Technology of China, 443 Huangshan Rd, Hefei, Anhui 230027, China
| | - Haiyan Liu
- School of Life Sciences, University of Science and Technology of China, 443 Huangshan Rd, Hefei, Anhui 230027, China
| | - Xiaolian Gao
- School of Life Sciences, University of Science and Technology of China, 443 Huangshan Rd, Hefei, Anhui 230027, China; Department of Biology and Biochemistry, University of Houston, 4800 Calhoun Rd, Houston, TX 77004, USA.
| | - Jing Liu
- School of Life Sciences, University of Science and Technology of China, 443 Huangshan Rd, Hefei, Anhui 230027, China.
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Kille S, Acevedo-Rocha CG, Parra LP, Zhang ZG, Opperman DJ, Reetz MT, Acevedo JP. Reducing codon redundancy and screening effort of combinatorial protein libraries created by saturation mutagenesis. ACS Synth Biol 2013; 2:83-92. [PMID: 23656371 DOI: 10.1021/sb300037w] [Citation(s) in RCA: 199] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Saturation mutagenesis probes define sections of the vast protein sequence space. However, even if randomization is limited this way, the combinatorial numbers problem is severe. Because diversity is created at the codon level, codon redundancy is a crucial factor determining the necessary effort for library screening. Additionally, due to the probabilistic nature of the sampling process, oversampling is required to ensure library completeness as well as a high probability to encounter all unique variants. Our trick employs a special mixture of three primers, creating a degeneracy of 22 unique codons coding for the 20 canonical amino acids. Therefore, codon redundancy and subsequent screening effort is significantly reduced, and a balanced distribution of codon per amino acid is achieved, as demonstrated exemplarily for a library of cyclohexanone monooxygenase. We show that this strategy is suitable for any saturation mutagenesis methodology to generate less-redundant libraries.
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Affiliation(s)
- Sabrina Kille
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1,
45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße,
35043 Marburg, Germany
| | - Carlos G. Acevedo-Rocha
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1,
45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße,
35043 Marburg, Germany
| | - Loreto P. Parra
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1,
45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße,
35043 Marburg, Germany
| | - Zhi-Gang Zhang
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1,
45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße,
35043 Marburg, Germany
| | - Diederik J. Opperman
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1,
45470 Mülheim an der Ruhr, Germany
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1,
45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße,
35043 Marburg, Germany
| | - Juan Pablo Acevedo
- Facultad
de Medicina y Facultad
de Ingeniería de la Universidad de los Andes, Santiago, Chile
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Sheren J, Langer SJ, Leinwand LA. A randomized library approach to identifying functional lox site domains for the Cre recombinase. Nucleic Acids Res 2007; 35:5464-73. [PMID: 17702764 PMCID: PMC2018622 DOI: 10.1093/nar/gkm604] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The bacteriophage P1 Cre/loxP site-specific recombination system is a useful tool in a number of genetic engineering processes. The Cre recombinase has been shown to act on DNA sequences that vary considerably from that of its bacteriophage recognition sequence, loxP. However, little is known about the sequence requirements for functional lox-like sequences. In this study, we have implemented a randomized library approach to identify the sequence characteristics of functional lox site domains. We created a randomized spacer library and a randomized arm library, and then tested them for recombination in vivo and in vitro. Results from the spacer library show that, while there is great plasticity, identity between spacer pairs is the most important factor influencing function, especially in in vitro reactions. The presence of one completely randomized arm in a functional loxP recombination reaction revealed that only three wild-type loxP arms are necessary for successful recombination in Cre-expressing bacteria, and that there are nucleotide preferences at the first three and last three positions of the randomized arm for the most efficiently recombined sequences. Finally, we found that in vitro Cre recombination reactions are much more stringent for evaluating which sequences can support efficient recombination compared to the 294-CRE system.
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Affiliation(s)
- Jamie Sheren
- University of Colorado, Department of Molecular, Cellular and Developmental Biology, 347 UCB, Boulder, CO 80309-0347, USA.
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Neylon C. Chemical and biochemical strategies for the randomization of protein encoding DNA sequences: library construction methods for directed evolution. Nucleic Acids Res 2004; 32:1448-59. [PMID: 14990750 PMCID: PMC390300 DOI: 10.1093/nar/gkh315] [Citation(s) in RCA: 171] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2004] [Revised: 02/06/2004] [Accepted: 02/06/2004] [Indexed: 11/14/2022] Open
Abstract
Directed molecular evolution and combinatorial methodologies are playing an increasingly important role in the field of protein engineering. The general approach of generating a library of partially randomized genes, expressing the gene library to generate the proteins the library encodes and then screening the proteins for improved or modified characteristics has successfully been applied in the areas of protein-ligand binding, improving protein stability and modifying enzyme selectivity. A wide range of techniques are now available for generating gene libraries with different characteristics. This review will discuss these different methodologies, their accessibility and applicability to non-expert laboratories and the characteristics of the libraries they produce. The aim is to provide an up to date resource to allow groups interested in using directed evolution to identify the most appropriate methods for their purposes and to guide those moving on from initial experiments to more ambitious targets in the selection of library construction techniques. References are provided to original methodology papers and other recent examples from the primary literature that provide details of experimental methods.
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Affiliation(s)
- Cameron Neylon
- School of Chemistry, University of Southampton, Highfield SO17 1BJ, UK.
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9
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2001. [PMCID: PMC2447185 DOI: 10.1002/cfg.55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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