Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs
Next generation sequencing (NGS) in combination with phage surface display (PSD) are powerful tools in the newly equipped molecular biology toolbox for the identification of specific target binding biomolecules. Application of PSD led to the discovery of manifold ligands in clinical and material res...
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doaj-2e3f44530c08466a9458abf990823f102020-11-28T00:05:16ZengMDPI AGViruses1999-49152020-11-01121360136010.3390/v12121360Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding MotifsRobert Braun0Nora Schönberger1Svenja Vinke2Franziska Lederer3Jörn Kalinowski4Katrin Pollmann5Department of Biotechnology, Helmholtz Institute Freiberg for Resource Technology, Helmholtz Center Dresden-Rossendorf, 01328 Dresden, GermanyDepartment of Biotechnology, Helmholtz Institute Freiberg for Resource Technology, Helmholtz Center Dresden-Rossendorf, 01328 Dresden, GermanyMicrobial Genomics and Biotechnology, CeBiTec–Center for Biotechnology, Bielefeld University, 33594 Bielefeld, GermanyDepartment of Biotechnology, Helmholtz Institute Freiberg for Resource Technology, Helmholtz Center Dresden-Rossendorf, 01328 Dresden, GermanyMicrobial Genomics and Biotechnology, CeBiTec–Center for Biotechnology, Bielefeld University, 33594 Bielefeld, GermanyDepartment of Biotechnology, Helmholtz Institute Freiberg for Resource Technology, Helmholtz Center Dresden-Rossendorf, 01328 Dresden, GermanyNext generation sequencing (NGS) in combination with phage surface display (PSD) are powerful tools in the newly equipped molecular biology toolbox for the identification of specific target binding biomolecules. Application of PSD led to the discovery of manifold ligands in clinical and material research. However, limitations of traditional phage display hinder the identification process. Growth-based library biases and target-unrelated peptides often result in the dominance of parasitic sequences and the collapse of library diversity. This study describes the effective enrichment of specific peptide motifs potentially binding to arsenic as proof-of-concept using the combination of PSD and NGS. Arsenic is an environmental toxin, which is applied in various semiconductors as gallium arsenide and selective recovery of this element is crucial for recycling and remediation. The development of biomolecules as specific arsenic-binding sorbents is a new approach for its recovery. Usage of NGS for all biopanning fractions allowed for evaluation of motif enrichment, in-depth insight into the selection process and the discrimination of biopanning artefacts, e.g., the amplification-induced library-wide reduction in hydrophobic amino acid proportion. Application of bioinformatics tools led to the identification of an SxHS and a carboxy-terminal QxQ motif, which are potentially involved in the binding of arsenic. To the best of our knowledge, this is the first report of PSD combined with NGS of all relevant biopanning fractions.https://www.mdpi.com/1999-4915/12/12/1360phage displaypeptidebiopanningtarget-unrelated peptidearsenicmotif |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Robert Braun Nora Schönberger Svenja Vinke Franziska Lederer Jörn Kalinowski Katrin Pollmann |
spellingShingle |
Robert Braun Nora Schönberger Svenja Vinke Franziska Lederer Jörn Kalinowski Katrin Pollmann Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs Viruses phage display peptide biopanning target-unrelated peptide arsenic motif |
author_facet |
Robert Braun Nora Schönberger Svenja Vinke Franziska Lederer Jörn Kalinowski Katrin Pollmann |
author_sort |
Robert Braun |
title |
Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs |
title_short |
Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs |
title_full |
Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs |
title_fullStr |
Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs |
title_full_unstemmed |
Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs |
title_sort |
application of next generation sequencing (ngs) in phage displayed peptide selection to support the identification of arsenic-binding motifs |
publisher |
MDPI AG |
series |
Viruses |
issn |
1999-4915 |
publishDate |
2020-11-01 |
description |
Next generation sequencing (NGS) in combination with phage surface display (PSD) are powerful tools in the newly equipped molecular biology toolbox for the identification of specific target binding biomolecules. Application of PSD led to the discovery of manifold ligands in clinical and material research. However, limitations of traditional phage display hinder the identification process. Growth-based library biases and target-unrelated peptides often result in the dominance of parasitic sequences and the collapse of library diversity. This study describes the effective enrichment of specific peptide motifs potentially binding to arsenic as proof-of-concept using the combination of PSD and NGS. Arsenic is an environmental toxin, which is applied in various semiconductors as gallium arsenide and selective recovery of this element is crucial for recycling and remediation. The development of biomolecules as specific arsenic-binding sorbents is a new approach for its recovery. Usage of NGS for all biopanning fractions allowed for evaluation of motif enrichment, in-depth insight into the selection process and the discrimination of biopanning artefacts, e.g., the amplification-induced library-wide reduction in hydrophobic amino acid proportion. Application of bioinformatics tools led to the identification of an SxHS and a carboxy-terminal QxQ motif, which are potentially involved in the binding of arsenic. To the best of our knowledge, this is the first report of PSD combined with NGS of all relevant biopanning fractions. |
topic |
phage display peptide biopanning target-unrelated peptide arsenic motif |
url |
https://www.mdpi.com/1999-4915/12/12/1360 |
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