Sequence-based prediction of permissive stretches for internal protein tagging and knockdown
Abstract Background Internal tagging of proteins by inserting small functional peptides into surface accessible permissive sites has proven to be an indispensable tool for basic and applied science. Permissive sites are typically identified by transposon mutagenesis on a case-by-case basis, limiting...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2017-10-01
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| Series: | BMC Biology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12915-017-0440-0 |
| _version_ | 1818913078514810880 |
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| author | Sabine Oesterle Tania Michelle Roberts Lukas Andreas Widmer Harun Mustafa Sven Panke Sonja Billerbeck |
| author_facet | Sabine Oesterle Tania Michelle Roberts Lukas Andreas Widmer Harun Mustafa Sven Panke Sonja Billerbeck |
| author_sort | Sabine Oesterle |
| collection | DOAJ |
| description | Abstract Background Internal tagging of proteins by inserting small functional peptides into surface accessible permissive sites has proven to be an indispensable tool for basic and applied science. Permissive sites are typically identified by transposon mutagenesis on a case-by-case basis, limiting scalability and their exploitation as a system-wide protein engineering tool. Methods We developed an apporach for predicting permissive stretches (PSs) in proteins based on the identification of length-variable regions (regions containing indels) in homologous proteins. Results We verify that a protein's primary structure information alone is sufficient to identify PSs. Identified PSs are predicted to be predominantly surface accessible; hence, the position of inserted peptides is likely suitable for diverse applications. We demonstrate the viability of this approach by inserting a Tobacco etch virus protease recognition site (TEV-tag) into several PSs in a wide range of proteins, from small monomeric enzymes (adenylate kinase) to large multi-subunit molecular machines (ATP synthase) and verify their functionality after insertion. We apply this method to engineer conditional protein knockdowns directly in the Escherichia coli chromosome and generate a cell-free platform with enhanced nucleotide stability. Conclusions Functional internally tagged proteins can be rationally designed and directly chromosomally implemented. Critical for the successful design of protein knockdowns was the incorporation of surface accessibility and secondary structure predictions, as well as the design of an improved TEV-tag that enables efficient hydrolysis when inserted into the middle of a protein. This versatile and portable approach can likely be adapted for other applications, and broadly adopted. We provide guidelines for the design of internally tagged proteins in order to empower scientists with little or no protein engineering expertise to internally tag their target proteins. |
| first_indexed | 2024-12-19T23:24:46Z |
| format | Article |
| id | doaj.art-8f558c504023463dbcb27899e6c4bb8a |
| institution | Directory Open Access Journal |
| issn | 1741-7007 |
| language | English |
| last_indexed | 2024-12-19T23:24:46Z |
| publishDate | 2017-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Biology |
| spelling | doaj.art-8f558c504023463dbcb27899e6c4bb8a2022-12-21T20:01:53ZengBMCBMC Biology1741-70072017-10-0115111710.1186/s12915-017-0440-0Sequence-based prediction of permissive stretches for internal protein tagging and knockdownSabine Oesterle0Tania Michelle Roberts1Lukas Andreas Widmer2Harun Mustafa3Sven Panke4Sonja Billerbeck5Department of Biosystems Science and Engineering, ETH ZürichDepartment of Biosystems Science and Engineering, ETH ZürichDepartment of Biosystems Science and Engineering, ETH ZürichDepartment of Biosystems Science and Engineering, ETH ZürichDepartment of Biosystems Science and Engineering, ETH ZürichDepartment of Biosystems Science and Engineering, ETH ZürichAbstract Background Internal tagging of proteins by inserting small functional peptides into surface accessible permissive sites has proven to be an indispensable tool for basic and applied science. Permissive sites are typically identified by transposon mutagenesis on a case-by-case basis, limiting scalability and their exploitation as a system-wide protein engineering tool. Methods We developed an apporach for predicting permissive stretches (PSs) in proteins based on the identification of length-variable regions (regions containing indels) in homologous proteins. Results We verify that a protein's primary structure information alone is sufficient to identify PSs. Identified PSs are predicted to be predominantly surface accessible; hence, the position of inserted peptides is likely suitable for diverse applications. We demonstrate the viability of this approach by inserting a Tobacco etch virus protease recognition site (TEV-tag) into several PSs in a wide range of proteins, from small monomeric enzymes (adenylate kinase) to large multi-subunit molecular machines (ATP synthase) and verify their functionality after insertion. We apply this method to engineer conditional protein knockdowns directly in the Escherichia coli chromosome and generate a cell-free platform with enhanced nucleotide stability. Conclusions Functional internally tagged proteins can be rationally designed and directly chromosomally implemented. Critical for the successful design of protein knockdowns was the incorporation of surface accessibility and secondary structure predictions, as well as the design of an improved TEV-tag that enables efficient hydrolysis when inserted into the middle of a protein. This versatile and portable approach can likely be adapted for other applications, and broadly adopted. We provide guidelines for the design of internally tagged proteins in order to empower scientists with little or no protein engineering expertise to internally tag their target proteins.http://link.springer.com/article/10.1186/s12915-017-0440-0Permissive siteInternal protein taggingTEV proteaseProtein knockdownsCell-free biotechnology |
| spellingShingle | Sabine Oesterle Tania Michelle Roberts Lukas Andreas Widmer Harun Mustafa Sven Panke Sonja Billerbeck Sequence-based prediction of permissive stretches for internal protein tagging and knockdown BMC Biology Permissive site Internal protein tagging TEV protease Protein knockdowns Cell-free biotechnology |
| title | Sequence-based prediction of permissive stretches for internal protein tagging and knockdown |
| title_full | Sequence-based prediction of permissive stretches for internal protein tagging and knockdown |
| title_fullStr | Sequence-based prediction of permissive stretches for internal protein tagging and knockdown |
| title_full_unstemmed | Sequence-based prediction of permissive stretches for internal protein tagging and knockdown |
| title_short | Sequence-based prediction of permissive stretches for internal protein tagging and knockdown |
| title_sort | sequence based prediction of permissive stretches for internal protein tagging and knockdown |
| topic | Permissive site Internal protein tagging TEV protease Protein knockdowns Cell-free biotechnology |
| url | http://link.springer.com/article/10.1186/s12915-017-0440-0 |
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