1
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Shishparenok AN, Gladilina YA, Zhdanov DD. Engineering and Expression Strategies for Optimization of L-Asparaginase Development and Production. Int J Mol Sci 2023; 24:15220. [PMID: 37894901 PMCID: PMC10607044 DOI: 10.3390/ijms242015220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Genetic engineering for heterologous expression has advanced in recent years. Model systems such as Escherichia coli, Bacillus subtilis and Pichia pastoris are often used as host microorganisms for the enzymatic production of L-asparaginase, an enzyme widely used in the clinic for the treatment of leukemia and in bakeries for the reduction of acrylamide. Newly developed recombinant L-asparaginase (L-ASNase) may have a low affinity for asparagine, reduced catalytic activity, low stability, and increased glutaminase activity or immunogenicity. Some successful commercial preparations of L-ASNase are now available. Therefore, obtaining novel L-ASNases with improved properties suitable for food or clinical applications remains a challenge. The combination of rational design and/or directed evolution and heterologous expression has been used to create enzymes with desired characteristics. Computer design, combined with other methods, could make it possible to generate mutant libraries of novel L-ASNases without costly and time-consuming efforts. In this review, we summarize the strategies and approaches for obtaining and developing L-ASNase with improved properties.
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Affiliation(s)
- Anastasiya N. Shishparenok
- Laboratory of Medical Biotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.N.S.); (Y.A.G.)
| | - Yulia A. Gladilina
- Laboratory of Medical Biotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.N.S.); (Y.A.G.)
| | - Dmitry D. Zhdanov
- Laboratory of Medical Biotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.N.S.); (Y.A.G.)
- Department of Biochemistry, Peoples’ Friendship University of Russia named after Patrice Lumumba (RUDN University), Miklukho—Maklaya St. 6, 117198 Moscow, Russia
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2
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Tan DZJ, Fung V, Sun T, Tian K, Li Z, Zhou K. Developing a Nanopore Sequencing Workflow for Protein Engineering Applications. ACS Synth Biol 2023; 12:2041-2050. [PMID: 37403232 DOI: 10.1021/acssynbio.3c00087] [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: 07/06/2023]
Abstract
Sequencing plays a critical role in protein engineering, where the genetic information encoding for a desired mutation can be identified. We evaluated the performance of two commercially available NGS technologies (Illumina NGS and nanopore sequencing) on the available mutant libraries that were either previously constructed for other protein engineering projects or constructed in-house for this study. The sequencing results from Illumina sequencing indicated that a substantial proportion of the reads exhibited strand exchange, which mixed information of different mutants. When nanopore sequencing was used, the occurrence of strand exchange was substantially reduced compared with that of Illumina sequencing. We then developed a new library preparation workflow for nanopore sequencing and were successful in further reducing the incidence of strand exchange. The optimized workflow was successfully used to aid selection of improved alcohol dehydrogenase mutants in cells where their activities were coupled with the cell growth rate. The workflow quantified the enrichment fold change of most mutants in the library (size = 1728) in the growth-based selection passaging. A mutant that was >500% more active than its parent variant was identified based on the fold change data but not with the absolute abundance data (random sampling of the passaged cells), highlighting the usefulness of this rapid and affordable sequencing workflow in protein engineering.
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Affiliation(s)
- Daniel Zhi Jun Tan
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Vincent Fung
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Tao Sun
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Kaiyuan Tian
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Zhi Li
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Kang Zhou
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
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3
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Wu J, Chen S, Xu J, Xu W, Zheng S, Tian Q, Luo C, Chen X, Shentu X. Insight into Pathogenic Mechanism Underlying the Hereditary Cataract Caused by βB2-G149V Mutation. Biomolecules 2023; 13:biom13050864. [PMID: 37238733 DOI: 10.3390/biom13050864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 04/17/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Congenital cataracts account for approximately 5-20% of childhood blindness worldwide and 22-30% of childhood blindness in developing countries. Genetic disorders are the primary cause of congenital cataracts. In this work, we investigated the underlying molecular mechanism of G149V point missense mutation in βB2-crystallin, which was first identified in a three-generation Chinese family with two affected members diagnosed with congenital cataracts. Spectroscopic experiments were performed to determine the structural differences between the wild type (WT) and the G149V mutant of βB2-crystallin. The results showed that the G149V mutation significantly changed the secondary and tertiary structure of βB2-crystallin. The polarity of the tryptophan microenvironment and the hydrophobicity of the mutant protein increased. The G149V mutation made the protein structure loose and the interaction between oligomers was reduced, which decreased the stability of the protein. Furthermore, we compared βB2-crystallin WT and the G149V mutant with their biophysical properties under environmental stress. We found that the G149V mutation makes βB2-crystallin more sensitive to environmental stresses (oxidative stress, UV irradiation, and heat shock) and more likely to aggregate and form precipitation. These features might be important to the pathogenesis of βB2-crystallin G149V mutant related to congenital cataracts.
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Affiliation(s)
- Jing Wu
- Department of Ophthalmology, The Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou 310030, China
- Department of Ophthalmology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, 158 Shangtang Road, Hangzhou 310053, China
| | - Silong Chen
- Department of Ophthalmology, The Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou 310030, China
| | - Jingjie Xu
- Department of Ophthalmology, The Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou 310030, China
| | - Wanyue Xu
- Institute of Translational Medicine, Zhejiang University School of Medicine, 268 Kaixuan Road, Hangzhou 310030, China
| | - Sifan Zheng
- GKT School of Medical Education, King's College London, London SE1 1UL, UK
| | - Qing Tian
- Institute of Translational Medicine, Zhejiang University School of Medicine, 268 Kaixuan Road, Hangzhou 310030, China
| | - Chenqi Luo
- Department of Ophthalmology, The Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou 310030, China
| | - Xiangjun Chen
- Department of Ophthalmology, The Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou 310030, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, 268 Kaixuan Road, Hangzhou 310030, China
| | - Xingchao Shentu
- Department of Ophthalmology, The Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou 310030, China
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4
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Chung CZ, Söll D, Krahn N. Using selenocysteine-specific reporters to screen for efficient tRNA Sec variants. Methods Enzymol 2022; 662:63-93. [PMID: 35101219 DOI: 10.1016/bs.mie.2021.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The unique properties of selenocysteine (Sec) have generated an interest in the scientific community to site-specifically incorporate Sec into a protein of choice. Current technologies have rewired the natural Sec-specific translation factor-dependent selenoprotein biosynthesis pathway by harnessing the canonical elongation factor (EF-Tu) to simplify the requirements for Sec incorporation in Escherichia coli. This strategy is versatile and can be applied to Sec incorporation at any position in a protein of interest. However, selenoprotein production is still limited by yield and serine misincorporation. This protocol outlines a method in E. coli to design and optimize tRNA libraries which can be selected and screened for by the use of Sec-specific intein-based reporters. This provides a fast and simple way to engineer tRNAs with enhanced Sec-incorporation ability.
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Affiliation(s)
- Christina Z Chung
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States
| | - Dieter Söll
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States; Department of Chemistry, Yale University, New Haven, CT, United States.
| | - Natalie Krahn
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States
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5
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Chen W, She W, Li A, Zhai C, Ma L. Site-Directed Mutagenesis Method Mediated by Cas9. Methods Mol Biol 2022; 2461:165-174. [PMID: 35727450 DOI: 10.1007/978-1-0716-2152-3_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: 04/18/2023]
Abstract
This study presents an in vitro CRISPR/Cas9-mediated mutagenic (ICM) system that allows rapid construction of designed mutants or site-saturation mutagenesis libraries in a PCR-independent manner. The plasmid DNA is double digested with Cas9 bearing specific single guide RNAs to remove the target nucleotides. Next, T5 exonuclease excises both 5'-ends of the linearized plasmid to generate homologous regions of approximately 15 nt. Subsequently, a short dsDNA of approximately 30-50 bp containing the desired mutation cyclizes the plasmid through base pairing and introduces the mutation into the plasmid. The gaps are repaired in Escherichia coli host cells after transformation. This method is highly efficient and accurate. Both single and multiple site-directed mutagenesis can be successfully performed, especially to large sized plasmids. This method demonstrates the great potential 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)
- Wanping Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, School of Life Sciences, Hubei University, Wuhan, People's Republic of China
| | - Wenwen She
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, School of Life Sciences, Hubei University, Wuhan, People's Republic of China
| | - Aitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, School of Life Sciences, Hubei University, Wuhan, People's Republic of China
| | - Chao Zhai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, School of Life Sciences, Hubei University, Wuhan, People's Republic of China.
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, School of Life Sciences, Hubei University, Wuhan, People's Republic of China.
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Wu J, Xu W, Wu W, Xu J, Zheng S, Shentu X, Chen X. Cataract-causing mutation R48C increases γA-crystallin susceptibility to oxidative stress and ultraviolet radiation. Int J Biol Macromol 2022; 194:688-694. [PMID: 34826455 DOI: 10.1016/j.ijbiomac.2021.11.113] [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] [Received: 09/09/2021] [Revised: 11/16/2021] [Accepted: 11/16/2021] [Indexed: 01/16/2023]
Abstract
Among all congenital cataracts caused by genetic mutations, approximately half are caused by a mutation in crystallin genes, and accounts the leading cause of blindness in children globally. In this study, we investigated the underlying molecular mechanism of R48C mutation (c.142C > T; p.[Arg48Cys]) of γA-crystallin in a Mexican-Mestizo descent family causing congenital cataracts. We purified γA-crystallin wild-type (WT) and R48C mutant and compared their structural characteristics and biophysical properties by Spectroscopic experiments and environmental stress (oxidative stress, ultraviolet irradiation, pH disorders, thermal shock, or chemical denaturation). The R48C mutant did not affect the secondary and tertiary structure of monomer γA-crystallin, nor did it affect its stability to heat shock and chemicals. However, the R48C mutant destroys the oxidative stability of γA-crystallin, which makes the protein more prone to aggregation and precipitation under oxidative conditions. These might be the pathogenesis of γA-crystallin R48C mutant related to congenital cataract and help to develop anti-cataract strategies from the perspective of γA-crystallin.
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Affiliation(s)
- Jing Wu
- Department of Ophthalmology, The Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, Zhejiang, China; Zhejiang Provincial Key Lab of Ophthalmology, 88 Jiefang Road, Hangzhou, Zhejiang, China; Department of Ophthalmology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, 158 Shangtang Road, Hangzhou, Zhejiang, China
| | - Wanyue Xu
- Institute of Translational Medicine, Zhejiang University School of Medicine, 268 Kaixuan Road, Hangzhou, Zhejiang, China
| | - Wei Wu
- Department of Ophthalmology, The Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, Zhejiang, China; Zhejiang Provincial Key Lab of Ophthalmology, 88 Jiefang Road, Hangzhou, Zhejiang, China
| | - Jingjie Xu
- Department of Ophthalmology, The Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, Zhejiang, China; Zhejiang Provincial Key Lab of Ophthalmology, 88 Jiefang Road, Hangzhou, Zhejiang, China
| | - Sifan Zheng
- GKT School of Medical Education, King's College London, London SE1 1UL, United Kingdom
| | - Xingchao Shentu
- Department of Ophthalmology, The Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, Zhejiang, China; Zhejiang Provincial Key Lab of Ophthalmology, 88 Jiefang Road, Hangzhou, Zhejiang, China.
| | - Xiangjun Chen
- Department of Ophthalmology, The Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, Zhejiang, China; Zhejiang Provincial Key Lab of Ophthalmology, 88 Jiefang Road, Hangzhou, Zhejiang, China; Institute of Translational Medicine, Zhejiang University School of Medicine, 268 Kaixuan Road, Hangzhou, Zhejiang, China.
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7
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Currin A, Parker S, Robinson CJ, Takano E, Scrutton NS, Breitling R. The evolving art of creating genetic diversity: From directed evolution to synthetic biology. Biotechnol Adv 2021; 50:107762. [PMID: 34000294 PMCID: PMC8299547 DOI: 10.1016/j.biotechadv.2021.107762] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 04/21/2021] [Accepted: 04/25/2021] [Indexed: 12/31/2022]
Abstract
The ability to engineer biological systems, whether to introduce novel functionality or improved performance, is a cornerstone of biotechnology and synthetic biology. Typically, this requires the generation of genetic diversity to explore variations in phenotype, a process that can be performed at many levels, from single molecule targets (i.e., in directed evolution of enzymes) to whole organisms (e.g., in chassis engineering). Recent advances in DNA synthesis technology and automation have enhanced our ability to create variant libraries with greater control and throughput. This review highlights the latest developments in approaches to create such a hierarchy of diversity from the enzyme level to entire pathways in vitro, with a focus on the creation of combinatorial libraries that are required to navigate a target's vast design space successfully to uncover significant improvements in function.
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Affiliation(s)
- Andrew Currin
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom.
| | - Steven Parker
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Christopher J Robinson
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Eriko Takano
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Nigel S Scrutton
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Rainer Breitling
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom.
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8
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Hoque MA, Zhang Y, Li Z, Cui L, Feng Y. Remodeling enzyme active sites by stepwise loop insertion. Methods Enzymol 2020; 643:111-127. [PMID: 32896277 DOI: 10.1016/bs.mie.2020.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The remolding active site loops via residue insertion/deletion as well as substitution is thought to play a key role in enzyme divergent evolution. However, enzyme engineering by residue insertion in active site loops often severely perturbs the protein structural integrity and causes protein misfolding and activity loss. We have designed a stepwise loop insertion strategy (StLois), in which a pair of randomized residues is introduced in a stepwise manner, efficiently collating mutational fitness effects. The strategy of StLois constitutes three key steps. First, the target regions should be identified through structural and functional analysis on the counterpart enzymes. Second, pair residues can be introduced in loop regions through insertion with NNK codon degeneracy. Third, the best hit used as a template for the next round mutagenesis. The residue insertion process can repeat as many times as necessary. By using the StLois method, we have evolved the substrate preference of a lactonase to phosphotriesterase. In this chapter, we describe the detailed StLois technique, which efficiently expands the residue in the loop region and remolds the architecture of enzyme active site for novel catalytic properties.
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Affiliation(s)
- Md Anarul Hoque
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhi Li
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore
| | - Li Cui
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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9
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Lindenburg L, Huovinen T, van de Wiel K, Herger M, Snaith MR, Hollfelder F. Split & mix assembly of DNA libraries for ultrahigh throughput on-bead screening of functional proteins. Nucleic Acids Res 2020; 48:e63. [PMID: 32383757 PMCID: PMC7293038 DOI: 10.1093/nar/gkaa270] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/02/2020] [Accepted: 04/21/2020] [Indexed: 12/13/2022] Open
Abstract
Site-saturation libraries reduce protein screening effort in directed evolution campaigns by focusing on a limited number of rationally chosen residues. However, uneven library synthesis efficiency leads to amino acid bias, remedied at high cost by expensive custom synthesis of oligonucleotides, or through use of proprietary library synthesis platforms. To address these shortcomings, we have devised a method where DNA libraries are constructed on the surface of microbeads by ligating dsDNA fragments onto growing, surface-immobilised DNA, in iterative split-and-mix cycles. This method-termed SpliMLiB for Split-and-Mix Library on Beads-was applied towards the directed evolution of an anti-IgE Affibody (ZIgE), generating a 160,000-membered, 4-site, saturation library on the surface of 8 million monoclonal beads. Deep sequencing confirmed excellent library balance (5.1% ± 0.77 per amino acid) and coverage (99.3%). As SpliMLiB beads are monoclonal, they were amenable to direct functional screening in water-in-oil emulsion droplets with cell-free expression. A FACS-based sorting of the library beads allowed recovery of hits improved in Kd over wild-type ZIgE by up to 3.5-fold, while a consensus mutant of the best hits provided a 10-fold improvement. With SpliMLiB, directed evolution workflows are accelerated by integrating high-quality DNA library generation with an ultra-high throughput protein screening platform.
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Affiliation(s)
- Laurens Lindenburg
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
| | - Tuomas Huovinen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
| | - Kayleigh van de Wiel
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
| | - Michael Herger
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
- AstraZeneca Medimmune Cambridge, Antibody Discovery and Protein Engineering, Cambridge, UK
| | - Michael R Snaith
- AstraZeneca Medimmune Cambridge, Antibody Discovery and Protein Engineering, Cambridge, UK
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
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Ohta R, Demachi-Okamura A, Akatsuka Y, Fujiwara H, Kuzushima K. Improving TCR affinity on 293T cells. J Immunol Methods 2018; 466:1-8. [PMID: 30468736 DOI: 10.1016/j.jim.2018.11.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/16/2018] [Accepted: 11/19/2018] [Indexed: 12/17/2022]
Abstract
This study presents an efficient method to improve TCR affinity, comprising 1) CDR-directed saturation mutation of TCR cDNA, 2) transient TCR display on CD3-expressing HEK293T (CD3-293T) cells by simple plasmid transfection, 3) staining with HLA-tetramers, and 4) multi-round sorting of cells with CD8-independent tetramer binding on a flow cytometer. Using these procedures, we successfully identified mutant TCRs with enhanced binding from an HLA-A*24:02-restricted, human telomerase reverse transcriptase (hTERT)-specific TCR. Two such clones, 2A7A and 2D162, harboring mutations in CDR1 and CDR2 of TCRβ, respectively, were isolated with both showing sequential four amino acid substitutions. When expressed on CD3-293T cells along with wild-type TCRα, the TCR molecules of these mutants as well as their combinatory mutation, bound to HLA-A24/hTERT-tetramers more strongly than the wild-type TCRs, without binding to control tetramers. Besides, in order to facilitate a functional study of TCR, we established an artificial T cell line, designated as CD8I-J2, which expresses a human CD8 and IFN-γ producing cassette by modifying Jurkat-derived J.RT3-T3.5 cells. CD8I-J2 cells expressing wild-type or affinity-enhanced hTERT-specific TCRs were analyzed for their recognition of serially diluted cognate peptide on HLA-A*24:02-transduced T2 cells. CD8I-J2 cells expressing each mutant TCR recognized the hTERT peptide at lower concentrations than wild-type TCR. The hierarchy of peptide recognition is concordant with tetramer binding on CD3-293T cells and none of these mutant TCRs were cross-reactive with irrelevant peptides reported to be present on HLA-A*24:02 molecules as far as tested. These methods might thus be useful for obtaining high affinity mutants from other TCRs of interest.
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Affiliation(s)
- Rieko Ohta
- Division of Immune Response, Aichi, Cancer Center Research Institute, Nagoya 464-8681, Japan
| | - Ayako Demachi-Okamura
- Division of Immune Response, Aichi, Cancer Center Research Institute, Nagoya 464-8681, Japan
| | - Yoshiki Akatsuka
- Division of Immune Response, Aichi, Cancer Center Research Institute, Nagoya 464-8681, Japan; Department of Hematology, Fujita Health University, Aichi 470-1192, Japan
| | - Hiroshi Fujiwara
- Department of Hematology, Clinical Immunology and Infectious Disease, Ehime University Graduate School of Medicine, Ehime, 791-0295, Japan
| | - Kiyotaka Kuzushima
- Division of Immune Response, Aichi, Cancer Center Research Institute, Nagoya 464-8681, Japan; Division of Cellular Oncology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan.
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11
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12
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Copp JN, Mowday AM, Williams EM, Guise CP, Ashoorzadeh A, Sharrock AV, Flanagan JU, Smaill JB, Patterson AV, Ackerley DF. Engineering a Multifunctional Nitroreductase for Improved Activation of Prodrugs and PET Probes for Cancer Gene Therapy. Cell Chem Biol 2017; 24:391-403. [DOI: 10.1016/j.chembiol.2017.02.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 12/31/2016] [Accepted: 02/01/2017] [Indexed: 12/20/2022]
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13
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Zeng F, Zhang Y, Zhang Z, Malik AA, Lin Y. Multiple-site fragment deletion, insertion and substitution mutagenesis by modified overlap extension PCR. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1279033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Fanli Zeng
- College of Life Sciences, Agricultural University of Hebei, Baoding, P.R. China
- Biophysics Unit, Department of Biochemistry and Molecular Biology, Medical School, and Center of Biophysics, Autonomous University of Barcelona, Barcelona, Spain
| | - Yujie Zhang
- College of Life Sciences, Agricultural University of Hebei, Baoding, P.R. China
| | - Ze Zhang
- College of Life Sciences, Agricultural University of Hebei, Baoding, P.R. China
| | - Asrar Ahmad Malik
- Biophysics Unit, Department of Biochemistry and Molecular Biology, Medical School, and Center of Biophysics, Autonomous University of Barcelona, Barcelona, Spain
| | - Yibin Lin
- Biophysics Unit, Department of Biochemistry and Molecular Biology, Medical School, and Center of Biophysics, Autonomous University of Barcelona, Barcelona, Spain
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, The University of Texas Houston Medical School, Houston, TX, USA
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14
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Carrico ZM, Strobel KL, Atreya ME, Clark DS, Francis MB. Simultaneous selection and counter-selection for the directed evolution of proteases in E. coli using a cytoplasmic anchoring strategy. Biotechnol Bioeng 2015; 113:1187-93. [PMID: 26666461 DOI: 10.1002/bit.25904] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 11/20/2015] [Accepted: 12/07/2015] [Indexed: 11/10/2022]
Abstract
With the goal of generating new enzymes that can cleave custom sequences, this article describes a selection strategy for evolving proteases with desirable characteristics. Positive selection and counter-selection are combined to select for and against specified cleavage sequences simultaneously. Cleavage of the positive selection sequence permits E. coli growth, and cleavage of the counter-selection sequence slows growth. Growth occurs when cleavage of the positive selection sequence releases β-lactamase into the periplasm where it can confer antibiotic resistance. The counter-selection traps β-lactamase in the cytoplasm, preventing antibiotic resistance and growth. Thus, proteases with a preference for the positive selection sequence relative to the counter-selection sequence grow more rapidly. This system was used to select a tobacco etch virus (TEV) protease mutant with new substrate compatibility. Biotechnol. Bioeng. 2016;113: 1187-1193. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Zachary M Carrico
- Department of Chemistry, University of California, Berkeley, California, 94720.
| | - Kathryn L Strobel
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California
| | - Meera E Atreya
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California
| | - Matthew B Francis
- Department of Chemistry, University of California, Berkeley, California, 94720
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15
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Acevedo-Rocha CG, Reetz MT, Nov Y. Economical analysis of saturation mutagenesis experiments. Sci Rep 2015; 5:10654. [PMID: 26190439 PMCID: PMC4507136 DOI: 10.1038/srep10654] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/20/2015] [Indexed: 11/15/2022] Open
Abstract
Saturation mutagenesis is a powerful technique for engineering proteins, metabolic pathways and genomes. In spite of its numerous applications, creating high-quality saturation mutagenesis libraries remains a challenge, as various experimental parameters influence in a complex manner the resulting diversity. We explore from the economical perspective various aspects of saturation mutagenesis library preparation: We introduce a cheaper and faster control for assessing library quality based on liquid media; analyze the role of primer purity and supplier in libraries with and without redundancy; compare library quality, yield, randomization efficiency, and annealing bias using traditional and emergent randomization schemes based on mixtures of mutagenic primers; and establish a methodology for choosing the most cost-effective randomization scheme given the screening costs and other experimental parameters. We show that by carefully considering these parameters, laboratory expenses can be significantly reduced.
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Affiliation(s)
- Carlos G Acevedo-Rocha
- 1] Department of Organic Synthesis, Max-Planck-Institut für Kohlenforschung, Mulheim, 45470, Germany [2] Department of Chemistry, Philipps-Universität Marburg, 35032, Germany [3] Prokaryotic Small RNA Biology Group, Max-Planck-Institut für terrestrische Mikrobiologie, Marburg, 35043, Germany [4] Landes-Offensive zur Entwicklung Wissenschafltich-ökonomischer Exzellenz (LOEWE) Centre for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, 35032, Germany
| | - Manfred T Reetz
- 1] Department of Organic Synthesis, Max-Planck-Institut für Kohlenforschung, Mulheim, 45470, Germany [2] Department of Chemistry, Philipps-Universität Marburg, 35032, Germany
| | - Yuval Nov
- Department of Statistics, University of Haifa, Haifa, 31905, Israel
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16
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Hu F, Zhao Y, Qi X, Cui H, Gao Y, Gao H, Liu C, Wang Y, Zhang Y, Li K, Wang X, Wang Y. Soluble expression and enzymatic activity evaluation of protease from reticuloendotheliosis virus. Protein Expr Purif 2015; 114:64-70. [PMID: 26102339 DOI: 10.1016/j.pep.2015.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 05/11/2015] [Accepted: 06/17/2015] [Indexed: 11/26/2022]
Abstract
The protease (PR) encoded by most retroviruses is deeply involved in the lifecycle and infection process of retroviruses by possessing the specificity necessary to correctly cleave the viral polyproteins and host cell proteins. However, as an important representative of avian retroviruses, the enzymatic properties of PR from reticuloendotheliosis virus (REV) have not been clearly documented. The recombinant PR, its mutant fused with a His-tag, and its substrate p18-p30 fused with a GST-tag were expressed in the Escherichia coli system as soluble enzymes. The soluble PR and p18-p30 were purified using Ni-NTA His Bind Resin and Glutathione Sepharose 4B, respectively. The enzymatic activity of PR was analyzed using the substrate of p18-p30. The expressed prokaryotic protease has enzyme activity that is dependent on such conditions as temperature, pH, and ions, and its activity can be inhibited by caspase inhibitor and the divalent metal ions Ca(2+) and Ni(2+). In addition, the key role of the residue Thr (amino acids 28) for the enzymatic activity of PR was identified. Furthermore, the caspase inhibitor Z-VAD-FMK was confirmed to inhibit the PR enzymatic activity of REV. For the first time, the PR of REV was expressed in the soluble form, and the optimal enzymatic reaction system in vitro was developed and preliminarily used. This study provides essential tools and information for further understanding the infection mechanism of REV and for the development of antiviral drugs treating retroviruses.
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Affiliation(s)
- Feng Hu
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, China.
| | - Yan Zhao
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, China.
| | - Xiaole Qi
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, China.
| | - Hongyu Cui
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, China.
| | - Yulong Gao
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, China.
| | - Honglei Gao
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, China.
| | - Changjun Liu
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, China.
| | - Yongqiang Wang
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, China.
| | - Yanping Zhang
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, China.
| | - Kai Li
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, China.
| | - Xiaomei Wang
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou 225009, China.
| | - Yunfeng Wang
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, China; National Engineering Research Center of Veterinary Biologics, Harbin, China.
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17
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Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
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Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
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