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Yamada K, Soga F, Tokunaga S, Nagaoka H, Ozawa T, Kishi H, Takashima E, Sawasaki T. GATS tag system is compatible with biotin labelling methods for protein analysis. Sci Rep 2023; 13:10243. [PMID: 37353572 PMCID: PMC10290147 DOI: 10.1038/s41598-023-36858-y] [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: 11/09/2022] [Accepted: 06/11/2023] [Indexed: 06/25/2023] Open
Abstract
Polypeptide tags and biotin labelling technologies are widely used for protein analyses in biochemistry and cell biology. However, many peptide tag epitopes contain lysine residues (or amino acids) that are masked after biotinylation. Here, we propose the GATS tag system without a lysine residue and with high sensitivity and low non-specific binding using a rabbit monoclonal antibody against Plasmodium falciparum glycosylphosphatidylinositol (GPI)-anchored micronemal antigen (PfGAMA). From 14 monoclonal clones, an Ra3 clone was selected as it recognized an epitope-TLSVGVQNTF-without a lysine residue; this antibody and epitope tag set was called the GATS tag system. Surface plasmon resonance analysis showed that the tag system had a high affinity of 8.71 × 10-9 M. GATS tag indicated a very low background with remarkably high sensitivity and specificity in immunoblotting using the lysates of mammalian cells. It also showed a high sensitivity for immunoprecipitation and immunostaining of cultured human cells. The tag system was highly sensitive in both biotin labelling methods for proteins using NHS-Sulfo-biotin and BioID (proximity-dependent biotin identification) in the human cells, as opposed to a commercially available tag system having lysine residues, which showed reduced sensitivity. These results showed that the GATS tag system is suitable for methods such as BioID involving labelling lysine residues.
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Affiliation(s)
- Kohdai Yamada
- Division of Cell-Free Life Science, Proteo-Science Center, Ehime University, 3 Bunkyo-Cho, Matsuyama, Ehime, 790-8577, Japan
| | - Fumiya Soga
- Division of Cell-Free Life Science, Proteo-Science Center, Ehime University, 3 Bunkyo-Cho, Matsuyama, Ehime, 790-8577, Japan
| | - Soh Tokunaga
- Division of Cell-Free Life Science, Proteo-Science Center, Ehime University, 3 Bunkyo-Cho, Matsuyama, Ehime, 790-8577, Japan
| | - Hikaru Nagaoka
- Division of Malaria Research, Proteo-Science Center, 3 Bunkyo-Cho, Matsuyama, Ehime, 790-8577, Japan
| | - Tatsuhiko Ozawa
- Department of Immunology, Faculty of Medicine, Academic Assembly, Advanced Antibody Drug Development Center, University of Toyama, Toyama, 930-0194, Japan
| | - Hiroyuki Kishi
- Department of Immunology, Faculty of Medicine, Academic Assembly, Advanced Antibody Drug Development Center, University of Toyama, Toyama, 930-0194, Japan
| | - Eizo Takashima
- Division of Malaria Research, Proteo-Science Center, 3 Bunkyo-Cho, Matsuyama, Ehime, 790-8577, Japan
| | - Tatsuya Sawasaki
- Division of Cell-Free Life Science, Proteo-Science Center, Ehime University, 3 Bunkyo-Cho, Matsuyama, Ehime, 790-8577, Japan.
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Fogeron ML, Lecoq L, Cole L, Harbers M, Böckmann A. Easy Synthesis of Complex Biomolecular Assemblies: Wheat Germ Cell-Free Protein Expression in Structural Biology. Front Mol Biosci 2021; 8:639587. [PMID: 33842544 PMCID: PMC8027086 DOI: 10.3389/fmolb.2021.639587] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/20/2021] [Indexed: 12/18/2022] Open
Abstract
Cell-free protein synthesis (CFPS) systems are gaining more importance as universal tools for basic research, applied sciences, and product development with new technologies emerging for their application. Huge progress was made in the field of synthetic biology using CFPS to develop new proteins for technical applications and therapy. Out of the available CFPS systems, wheat germ cell-free protein synthesis (WG-CFPS) merges the highest yields with the use of a eukaryotic ribosome, making it an excellent approach for the synthesis of complex eukaryotic proteins including, for example, protein complexes and membrane proteins. Separating the translation reaction from other cellular processes, CFPS offers a flexible means to adapt translation reactions to protein needs. There is a large demand for such potent, easy-to-use, rapid protein expression systems, which are optimally serving protein requirements to drive biochemical and structural biology research. We summarize here a general workflow for a wheat germ system providing examples from the literature, as well as applications used for our own studies in structural biology. With this review, we want to highlight the tremendous potential of the rapidly evolving and highly versatile CFPS systems, making them more widely used as common tools to recombinantly prepare particularly challenging recombinant eukaryotic proteins.
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Affiliation(s)
- Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Laura Cole
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Matthias Harbers
- CellFree Sciences, Yokohama, Japan
- RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
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Mahmoudi Gomari M, Saraygord-Afshari N, Farsimadan M, Rostami N, Aghamiri S, Farajollahi MM. Opportunities and challenges of the tag-assisted protein purification techniques: Applications in the pharmaceutical industry. Biotechnol Adv 2020; 45:107653. [PMID: 33157154 DOI: 10.1016/j.biotechadv.2020.107653] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 10/22/2020] [Accepted: 10/29/2020] [Indexed: 01/16/2023]
Abstract
Tag-assisted protein purification is a method of choice for both academic researches and large-scale industrial demands. Application of the purification tags in the protein production process can help to save time and cost, but the design and application of tagged fusion proteins are challenging. An appropriate tagging strategy must provide sufficient expression yield and high purity for the final protein products while preserving their native structure and function. Thanks to the recent advances in the bioinformatics and emergence of high-throughput techniques (e.g. SEREX), many new tags are introduced to the market. A variety of interfering and non-interfering tags have currently broadened their application scope beyond the traditional use as a simple purification tool. They can take part in many biochemical and analytical features and act as solubility and protein expression enhancers, probe tracker for online visualization, detectors of post-translational modifications, and carrier-driven tags. Given the variability and growing number of the purification tags, here we reviewed the protein- and peptide-structured purification tags used in the affinity, ion-exchange, reverse phase, and immobilized metal ion affinity chromatographies. We highlighted the demand for purification tags in the pharmaceutical industry and discussed the impact of self-cleavable tags, aggregating tags, and nanotechnology on both the column-based and column-free purification techniques.
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Affiliation(s)
- Mohammad Mahmoudi Gomari
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Neda Saraygord-Afshari
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran.
| | - Marziye Farsimadan
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran
| | - Neda Rostami
- Department of Chemical Engineering, Faculty of Engineering, Arak University, Iran
| | - Shahin Aghamiri
- Student research committee, Department of medical biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad M Farajollahi
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
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CF-PA 2Vtech: a cell-free human protein array technology for antibody validation against human proteins. Sci Rep 2019; 9:19349. [PMID: 31852950 PMCID: PMC6920144 DOI: 10.1038/s41598-019-55785-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 12/02/2019] [Indexed: 12/16/2022] Open
Abstract
Antibodies are widely used for the detection of specific molecules such as peptides, proteins, and chemical compounds. The specificity of an antibody is therefore its most important feature. However, it is very difficult to confirm antibody specificity. Recently, we made a human protein array consisting of 19,712 kinds of recombinant human proteins produced by a wheat cell-free protein production system. Here, we demonstrate a novel protein array technology for antibody validation (CF-PA2Vtech). Full-length human cDNAs were fused to N-terminal FLAG-GST and then synthesized by the wheat cell-free system. To construct a 20 K human protein array, about 10 to 14 kinds of human proteins were mixed and captured in each well by glutathione-conjugated magnetic beads in 12 plates or one plate with 384- or 1536-well format, respectively, using a strong magnetic device. Using this protein array plate, commercially available anti-HA or anti-PD-1 antibody reacted to 13 or three human proteins, respectively. The cross-reactivity of these proteins was also confirmed by immunoblotting. These proteins have a similar epitope, and alanine mutations of these epitope candidates dissolved the reactivity. These results indicated that CF-PA2Vtech is very useful for validation of antibodies against human protein.
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Brown ZP, Takagi J. Advances in domain and subunit localization technology for electron microscopy. Biophys Rev 2019; 11:149-155. [PMID: 30834502 DOI: 10.1007/s12551-019-00513-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 02/20/2019] [Indexed: 12/26/2022] Open
Abstract
The award of the 2017 Nobel Prize in chemistry, 'for developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution', was recognition that this method, and electron microscopy more generally, represent powerful techniques in the scientific armamentarium for atomic level structural assessment. Technical advances in equipment, software, and sample preparation, have allowed for high-resolution structural determination of a range of complex biological machinery such that the position of individual atoms within these mega-structures can be determined. However, not all targets are amenable to attaining such high-resolution structures and some may only be resolved at so-called intermediate resolutions. In these cases, other tools are needed to correctly characterize the domain or subunit orientation and architecture. In this review, we will outline various methods that can provide additional information to help understand the macro-level organization of proteins/biomolecular complexes when high-resolution structural description is not available. In particular, we will discuss the recent development and use of a novel protein purification approach, known as the the PA tag/NZ-1 antibody system, which provides numberous beneficial properties, when used in electron microscopy experimentation.
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Affiliation(s)
- Zuben P Brown
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
| | - Junichi Takagi
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
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Brown ZP, Takagi J. The PA Tag: A Versatile Peptide Tagging System in the Era of Integrative Structural Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1105:59-76. [PMID: 30617824 DOI: 10.1007/978-981-13-2200-6_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
We have recently developed a novel protein tagging system based on the high affinity interaction between an antibody NZ-1 and its antigen PA peptide, a dodecapeptide that forms a β-turn in the binding pocket of NZ-1. This unique conformation allows for the PA peptide to be inserted into turn-forming loops within a folded protein domain and the system has been variously used in general applications including protein purification, Western blotting and flow cytometry, or in more specialized applications such as reporting protein conformational change, and identifying subunits of macromolecular complexes with electron microscopy. Thus the small and "portable" nature of the PA tag system offers a versatile and powerful tool that can be implemented in various aspects of integrative structural biology.
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Affiliation(s)
- Zuben P Brown
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Junichi Takagi
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Suita, Osaka, Japan.
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Okumura M, Ozawa T, Hamana H, Norimatsu Y, Tsuda R, Kobayashi E, Shinoda K, Taki H, Tobe K, Imura J, Sugiyama E, Kishi H, Muraguchi A. Autoantibodies reactive to PEP08 are clinically related with morbidity and severity of interstitial lung disease in connective tissue diseases. Eur J Immunol 2018; 48:1717-1727. [DOI: 10.1002/eji.201747381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 05/15/2018] [Accepted: 07/05/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Maiko Okumura
- Department of Immunology; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
- The First Department of Internal Medicine; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
| | - Tatsuhiko Ozawa
- Department of Immunology; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
| | - Hiroshi Hamana
- Department of Immunology; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
| | - Yu Norimatsu
- Department of Immunology; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
- School of Medicine Program of Medicine; Hiroshima University; Minami Hiroshima Japan
| | - Reina Tsuda
- Department of Immunology; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
- The First Department of Internal Medicine; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
| | - Eiji Kobayashi
- Department of Immunology; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
| | - Koichiro Shinoda
- The First Department of Internal Medicine; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
| | - Hirofumi Taki
- The First Department of Internal Medicine; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
| | - Kazuyuki Tobe
- The First Department of Internal Medicine; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
| | - Johji Imura
- Department of Diagnostic Pathology; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
| | - Eiji Sugiyama
- Department of Clinical Immunology and Rheumatology; Hiroshima University Hospital; Minami Hiroshima Japan
| | - Hiroyuki Kishi
- Department of Immunology; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
| | - Atsushi Muraguchi
- Department of Immunology; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
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