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Selection of green fluorescent proteins by in vitro compartmentalization using microbead-display libraries. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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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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Kojima T. Ultra-high-throughput analysis of functional biomolecules using in vitro selection and bioinformatics. Biosci Biotechnol Biochem 2020; 84:1767-1774. [PMID: 32441212 DOI: 10.1080/09168451.2020.1768823] [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: 10/24/2022]
Abstract
Functional analysis of biomolecules, including nucleic acids and proteins, is important for understanding biological mechanisms in living cells such as gene expression and metabolism. To analyze diverse biomolecular functions, large-scale screening systems for biomolecules have been developed for various applications such as to improve enzyme activity and identify target binding molecules. One of these systems, the Bead Display system, utilizes emulsion technology and is a powerful tool for rapidly screening functional nucleic acids or proteins in vitro. Furthermore, an analytical pipeline that consists of genomic systematic evolution of ligands by exponential enrichment (gSELEX)-Seq, gene expression analysis, and bioinformatics was shown to be a robust platform for comprehensively identifying genes regulated by a transcription factor. This review provides an overview of the biomolecular screening methods developed to date.
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Affiliation(s)
- Takaaki Kojima
- Graduate School of Bioagricultural Sciences, Nagoya University , Nagoya, Japan
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Kojima T, Hata J, Oka H, Hayashi K, Hitomi K, Nakano H. Spatial arrangement of proteins using scCro-tag: application for an in situ enzymatic microbead assay. Biosci Biotechnol Biochem 2018; 82:1911-1921. [PMID: 30067465 DOI: 10.1080/09168451.2018.1501265] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In natural systems, various metabolic reactions are often spatially organized to increase enzyme activity and specificity. Thus, by spatially arranging enzyme molecules in synthetic systems to imitate these natural systems, it is possible to promote a high rate of enzymatic turnover. In this present study, a normal and mutant form of the scCro DNA-binding protein were shown to bind orthogonally to specific recognition sequences under appropriate conditions. Furthermore, these DNA-binding tags were used to establish an enzyme assay system based on the spatial arrangement of transglutaminase and its substrate at the molecular level. Together, the results of the present study suggest that the scCro-tag may be a powerful tool to facilitate the synthetic spatial arrangement of proteins on a DNA ligand.
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Affiliation(s)
- Takaaki Kojima
- a Graduate School of Bioagricultural Sciences , Nagoya University , Nagoya , Japan
| | - Jumpei Hata
- a Graduate School of Bioagricultural Sciences , Nagoya University , Nagoya , Japan
| | - Hiroya Oka
- a Graduate School of Bioagricultural Sciences , Nagoya University , Nagoya , Japan
| | - Kenta Hayashi
- a Graduate School of Bioagricultural Sciences , Nagoya University , Nagoya , Japan
| | - Kiyotaka Hitomi
- b Graduate School of Pharmaceutical Sciences , Nagoya University , Nagoya , Japan
| | - Hideo Nakano
- a Graduate School of Bioagricultural Sciences , Nagoya University , Nagoya , Japan
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Kojima T, Mizoguchi T, Ota E, Hata J, Homma K, Zhu B, Hitomi K, Nakano H. Immobilization of proteins onto microbeads using a DNA binding tag for enzymatic assays. J Biosci Bioeng 2016; 121:147-53. [DOI: 10.1016/j.jbiosc.2015.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 06/02/2015] [Accepted: 06/10/2015] [Indexed: 12/16/2022]
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Ultra-high-throughput screening of an in vitro-synthesized horseradish peroxidase displayed on microbeads using cell sorter. PLoS One 2015; 10:e0127479. [PMID: 25993095 PMCID: PMC4439038 DOI: 10.1371/journal.pone.0127479] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 04/14/2015] [Indexed: 11/30/2022] Open
Abstract
The C1a isoenzyme of horseradish peroxidase (HRP) is an industrially important heme-containing enzyme that utilizes hydrogen peroxide to oxidize a wide variety of inorganic and organic compounds for practical applications, including synthesis of fine chemicals, medical diagnostics, and bioremediation. To develop a ultra-high-throughput screening system for HRP, we successfully produced active HRP in an Escherichia coli cell-free protein synthesis system, by adding disulfide bond isomerase DsbC and optimizing the concentrations of hemin and calcium ions and the temperature. The biosynthesized HRP was fused with a single-chain Cro (scCro) DNA-binding tag at its N-terminal and C-terminal sites. The addition of the scCro-tag at both ends increased the solubility of the protein. Next, HRP and its fusion proteins were successfully synthesized in a water droplet emulsion by using hexadecane as the oil phase and SunSoft No. 818SK as the surfactant. HRP fusion proteins were displayed on microbeads attached with double-stranded DNA (containing the scCro binding sequence) via scCro-DNA interactions. The activities of the immobilized HRP fusion proteins were detected with a tyramide-based fluorogenic assay using flow cytometry. Moreover, a model microbead library containing wild type hrp (WT) and inactive mutant (MUT) genes was screened using fluorescence-activated cell-sorting, thus efficiently enriching the WT gene from the 1:100 (WT:MUT) library. The technique described here could serve as a novel platform for the ultra-high-throughput discovery of more useful HRP mutants and other heme-containing peroxidases.
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Okochi M, Kuboyama M, Tanaka M, Honda H. Design of a dual-function peptide probe as a binder of angiotensin II and an inducer of silver nanoparticle aggregation for use in label-free colorimetric assays. Talanta 2015; 142:235-9. [PMID: 26003717 DOI: 10.1016/j.talanta.2015.04.054] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 04/17/2015] [Indexed: 01/21/2023]
Abstract
Label-free colorimetric assays using metallic nanoparticles have received much recent attention, for their application in simple and sensitive methods for detection of biomolecules. Short peptide probes that can bind to analyte biomolecules are attractive ligands in molecular nanotechnology; however, identification of biological recognition motifs is usually based on trial-and-error experiments. Herein, a peptide probe was screened for colorimetric detection of angiotensin II (Ang II) using a mechanism for non-crosslinking aggregation of silver nanoparticles (AgNPs). The dual-function peptides, which bind to the analyte and induce AgNP aggregation, were identified using a two-step strategy: (1) screening of an Ang II-binding peptide from an Ang II receptor sequence library, using SPOT technology, which enable peptides synthesis on cellulose membranes via an Fmoc method and (2) selection of peptide probes that effectively induce aggregation of AgNPs using a photolinker modified peptide array. Using the identified peptide probe, KGKNKRRR, aggregation of AgNPs was detected by observation of a pink color in the absence of Ang II, whereas AgNPs remained dispersed in the presence of Ang II (yellow). The color changes were not observed in the presence of other hormone molecules. Ang II could be detected within 15 min, with a detection limit of 10 µM, by measuring the ratio of absorbance at 400 nm and 568 nm; the signal could also be observed with the naked eye. These data suggest that the peptide identified here could be used as a probe for simple and rapid colorimetric detection of Ang II. This strategy for the identification of functional peptides shows promise for the development of colorimetric detection of various diagnostically important biomolecules.
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Affiliation(s)
- Mina Okochi
- Department of Biotechnology, School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan; Department of Chemical Engineering, Graduate School of Science and Engineering, Tokyo Institute of Technology, 2-12-1-S1-24, O-okayama, Meguro-ku, Tokyo 152-8552, Japan.
| | - Masashi Kuboyama
- Department of Biotechnology, School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Masayoshi Tanaka
- Department of Chemical Engineering, Graduate School of Science and Engineering, Tokyo Institute of Technology, 2-12-1-S1-24, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Hiroyuki Honda
- Department of Biotechnology, School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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Kojima T, Zhu B, Nakano H. Construction of a DNA Library on Microbeads Using Whole Genome Amplification. Methods Mol Biol 2015; 1347:87-100. [PMID: 26374311 DOI: 10.1007/978-1-4939-2990-0_6] [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: 06/05/2023]
Abstract
A polymerase chain reaction (PCR) in water droplets with water-in-oil emulsion (emulsion PCR) facilitates parallel amplification of a single-molecule template. The amplified DNA can be immobilized onto microbeads bound to primer DNA. The product, termed a "bead library", has various applications such as next-generation sequencing (NGS) and the directed evolution of various functional biomolecules. Here, we describe a method for genomic library construction on microbeads using emulsion PCR.
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Affiliation(s)
- Takaaki Kojima
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Bo Zhu
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Hideo Nakano
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.
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Lane MD, Seelig B. Advances in the directed evolution of proteins. Curr Opin Chem Biol 2014; 22:129-36. [PMID: 25309990 DOI: 10.1016/j.cbpa.2014.09.013] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 09/13/2014] [Indexed: 12/21/2022]
Abstract
Natural evolution has produced a great diversity of proteins that can be harnessed for numerous applications in biotechnology and pharmaceutical science. Commonly, specific applications require proteins to be tailored by protein engineering. Directed evolution is a type of protein engineering that yields proteins with the desired properties under well-defined conditions and in a practical time frame. While directed evolution has been employed for decades, recent creative developments enable the generation of proteins with previously inaccessible properties. Novel selection strategies, faster techniques, the inclusion of unnatural amino acids or modifications, and the symbiosis of rational design approaches and directed evolution continue to advance protein engineering.
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Affiliation(s)
- Michael D Lane
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA; BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Burckhard Seelig
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA; BioTechnology Institute, University of Minnesota, St. Paul, MN, USA.
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Ninomiya R, Zhu B, Kojima T, Iwasaki Y, Nakano H. Role of disulfide bond isomerase DsbC, calcium ions, and hemin in cell-free protein synthesis of active manganese peroxidase isolated from Phanerochaete chrysosporium. J Biosci Bioeng 2014; 117:652-7. [DOI: 10.1016/j.jbiosc.2013.11.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 10/23/2013] [Accepted: 11/01/2013] [Indexed: 11/27/2022]
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Diamante L, Gatti-Lafranconi P, Schaerli Y, Hollfelder F. In vitro affinity screening of protein and peptide binders by megavalent bead surface display. Protein Eng Des Sel 2013; 26:713-24. [PMID: 23980186 PMCID: PMC3785251 DOI: 10.1093/protein/gzt039] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 06/30/2013] [Accepted: 07/02/2013] [Indexed: 11/12/2022] Open
Abstract
The advent of protein display systems has provided access to tailor-made protein binders by directed evolution. We introduce a new in vitro display system, bead surface display (BeSD), in which a gene is mounted on a bead via strong non-covalent (streptavidin/biotin) interactions and the corresponding protein is displayed via a covalent thioether bond on the DNA. In contrast to previous monovalent or low-copy bead display systems, multiple copies of the DNA and the protein or peptide of interest are displayed in defined quantities (up to 10(6) of each), so that flow cytometry can be used to obtain a measure of binding affinity. The utility of the BeSD in directed evolution is validated by library selections of randomized peptide sequences for binding to the anti-hemagglutinin (HA) antibody that proceed with enrichments in excess of 10(3) and lead to the isolation of high-affinity HA-tags within one round of flow cytometric screening. On-bead K(d) measurements suggest that the selected tags have affinities in the low nanomolar range. In contrast to other display systems (such as ribosome, mRNA and phage display) that are limited to affinity panning selections, BeSD possesses the ability to screen and rank binders by their affinity in vitro, a feature that hitherto has been exclusive to in vivo multivalent cell display systems (such as yeast display).
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Affiliation(s)
| | | | | | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, UK
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Kojima T, Ohuchi S, Ito Y, Nakano H. High-throughput screening method for promoter activity using bead display and a ligase ribozyme. J Biosci Bioeng 2012; 114:671-6. [PMID: 22835855 DOI: 10.1016/j.jbiosc.2012.06.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 06/10/2012] [Accepted: 06/20/2012] [Indexed: 10/28/2022]
Abstract
In this report, we describe the development of a novel in vitro high-throughput system for detecting and screening promoter activity; the method employs emulsified reactions and a ligase ribozyme. In our study, a promoter DNA fragment containing the ribozyme gene was immobilized on a bead by using emulsion PCR, followed by in vitro transcription of the immobilized DNA in water-in-oil emulsions. Owing to the self-ligation activity of the ribozyme, it was co-transcriptionally linked to the active promoter immobilized on the beads. The bead complex containing the active promoter sequence was then labeled by reverse transcription with a fluorescently labeled primer. Employing flow cytometry, the fluorescence intensity corresponding to the strength of each promoter was observed, indicating the applicability of the system for promoter evaluation. Moreover, two rounds of screening with T7 RNA polymerase using a cell sorter enriched the T7 promoter fragment by 70 folds from a 1:100 mixture of T7 promoter and SP6 promoter fragments, suggesting that this system can be used to screen promoters.
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Affiliation(s)
- Takaaki Kojima
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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