Rapid and cost-effective epitope mapping using PURE ribosome display coupled with next-generation sequencing and bioinformatics
A novel, efficient and cost-effective approach for epitope identification of an antibody has been developed using a ribosome display platform. This platform, known as PURE ribosome display, utilizes an Escherichia coli-based reconstituted cell-free protein synthesis system (PURE system). It stabiliz...
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| Published in | Journal of bioscience and bioengineering Vol. 137; no. 4; pp. 321 - 328 |
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| Main Authors | , , , |
| Format | Journal Article |
| Language | English |
| Published |
Japan
Elsevier B.V
01.04.2024
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| Subjects | |
| Online Access | Get full text |
| ISSN | 1389-1723 1347-4421 1347-4421 |
| DOI | 10.1016/j.jbiosc.2024.01.008 |
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| Abstract | A novel, efficient and cost-effective approach for epitope identification of an antibody has been developed using a ribosome display platform. This platform, known as PURE ribosome display, utilizes an Escherichia coli-based reconstituted cell-free protein synthesis system (PURE system). It stabilizes the mRNA-ribosome-peptide complex via a ribosome-arrest peptide sequence. This system was complemented by next-generation sequencing (NGS) and an algorithm for analyzing binding epitopes. To showcase the effectiveness of this method, selection conditions were refined using the anti-PA tag monoclonal antibody with the PA tag peptide as a model. Subsequently, a random peptide library was constructed using 10 NNK triplet oligonucleotides via the PURE ribosome display. The resulting random peptide library-ribosome-mRNA complex was selected using a commercially available anti-HA (YPYDVPDYA) tag monoclonal antibody, followed by NGS and bioinformatic analysis. Our approach successfully identified the DVPDY sequence as an epitope within the hemagglutinin amino acid sequence, which was then experimentally validated. This platform provided a valuable tool for investigating continuous epitopes in antibodies. |
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| AbstractList | A novel, efficient and cost-effective approach for epitope identification of an antibody has been developed using a ribosome display platform. This platform, known as PURE ribosome display, utilizes an Escherichia coli-based reconstituted cell-free protein synthesis system (PURE system). It stabilizes the mRNA-ribosome-peptide complex via a ribosome-arrest peptide sequence. This system was complemented by next-generation sequencing (NGS) and an algorithm for analyzing binding epitopes. To showcase the effectiveness of this method, selection conditions were refined using the anti-PA tag monoclonal antibody with the PA tag peptide as a model. Subsequently, a random peptide library was constructed using 10 NNK triplet oligonucleotides via the PURE ribosome display. The resulting random peptide library-ribosome-mRNA complex was selected using a commercially available anti-HA (YPYDVPDYA) tag monoclonal antibody, followed by NGS and bioinformatic analysis. Our approach successfully identified the DVPDY sequence as an epitope within the hemagglutinin amino acid sequence, which was then experimentally validated. This platform provided a valuable tool for investigating continuous epitopes in antibodies. A novel, efficient and cost-effective approach for epitope identification of an antibody has been developed using a ribosome display platform. This platform, known as PURE ribosome display, utilizes an Escherichia coli-based reconstituted cell-free protein synthesis system (PURE system). It stabilizes the mRNA-ribosome-peptide complex via a ribosome-arrest peptide sequence. This system was complemented by next-generation sequencing (NGS) and an algorithm for analyzing binding epitopes. To showcase the effectiveness of this method, selection conditions were refined using the anti-PA tag monoclonal antibody with the PA tag peptide as a model. Subsequently, a random peptide library was constructed using 10 NNK triplet oligonucleotides via the PURE ribosome display. The resulting random peptide library-ribosome-mRNA complex was selected using a commercially available anti-HA (YPYDVPDYA) tag monoclonal antibody, followed by NGS and bioinformatic analysis. Our approach successfully identified the DVPDY sequence as an epitope within the hemagglutinin amino acid sequence, which was then experimentally validated. This platform provided a valuable tool for investigating continuous epitopes in antibodies.A novel, efficient and cost-effective approach for epitope identification of an antibody has been developed using a ribosome display platform. This platform, known as PURE ribosome display, utilizes an Escherichia coli-based reconstituted cell-free protein synthesis system (PURE system). It stabilizes the mRNA-ribosome-peptide complex via a ribosome-arrest peptide sequence. This system was complemented by next-generation sequencing (NGS) and an algorithm for analyzing binding epitopes. To showcase the effectiveness of this method, selection conditions were refined using the anti-PA tag monoclonal antibody with the PA tag peptide as a model. Subsequently, a random peptide library was constructed using 10 NNK triplet oligonucleotides via the PURE ribosome display. The resulting random peptide library-ribosome-mRNA complex was selected using a commercially available anti-HA (YPYDVPDYA) tag monoclonal antibody, followed by NGS and bioinformatic analysis. Our approach successfully identified the DVPDY sequence as an epitope within the hemagglutinin amino acid sequence, which was then experimentally validated. This platform provided a valuable tool for investigating continuous epitopes in antibodies. |
| Author | Ojima-Kato, Teruyo Nakano, Hideo Jia, Beixi Kojima, Takaaki |
| Author_xml | – sequence: 1 givenname: Beixi orcidid: 0000-0001-8758-398X surname: Jia fullname: Jia, Beixi organization: Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan – sequence: 2 givenname: Teruyo surname: Ojima-Kato fullname: Ojima-Kato, Teruyo organization: Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan – sequence: 3 givenname: Takaaki surname: Kojima fullname: Kojima, Takaaki organization: Department of Agrobiological Resources, Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya 468-8502, Japan – sequence: 4 givenname: Hideo orcidid: 0000-0001-6133-9794 surname: Nakano fullname: Nakano, Hideo email: hnakano@agr.nagoya-u.ac.jp organization: Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan |
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| Cites_doi | 10.1038/nprot.2007.160 10.1038/s41598-017-14277-0 10.1016/0092-8674(84)90412-4 10.1007/978-1-61779-379-0_14 10.3389/fimmu.2013.00302 10.1016/S0092-8674(02)00649-9 10.1007/978-1-4939-7841-0_2 10.1016/j.jbiosc.2016.12.004 10.1097/00000441-200207000-00004 10.1002/biot.202100358 10.1016/j.jmb.2005.06.073 10.1371/journal.pone.0163962 10.1038/s41598-022-17494-4 10.1016/0022-2836(82)90546-0 10.1021/acsomega.6b00015 10.1073/pnas.94.10.4937 10.1146/annurev.iy.01.040183.000511 10.1016/j.pep.2014.01.009 10.1002/cbic.202200303 10.1016/j.molcel.2006.03.033 10.1016/S0378-1119(98)00538-1 10.1016/j.jbc.2023.104676 10.1039/D2SC05709C 10.1093/protein/gzi038 10.1016/S0022-1759(97)00083-5 10.1038/90802 10.1016/S0300-483X(96)03599-8 10.1007/978-1-4939-7841-0_1 10.1093/jb/mvp027 |
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| Keywords | Epitope mapping Anti-HA tag antibody Python program Cell-free protein synthesis Ribosome display |
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| SubjectTerms | algorithms Anti-HA tag antibody bioinformatics Cell-free protein synthesis cost effectiveness Epitope mapping epitopes hemagglutinins monoclonal antibodies oligonucleotides peptide libraries Python program Ribosome display ribosomes |
| Title | Rapid and cost-effective epitope mapping using PURE ribosome display coupled with next-generation sequencing and bioinformatics |
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