Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach
Small proteins play essential roles in bacterial physiology and virulence, however, automated algorithms for genome annotation are often not yet able to accurately predict the corresponding genes. The accuracy and reliability of genome annotations, particularly for small open reading frames (sORFs),...
Autores principales: | , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Public Library of Science
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8195425/ https://www.ncbi.nlm.nih.gov/pubmed/34061833 http://dx.doi.org/10.1371/journal.pgen.1009585 |
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author | Fuchs, Stephan Kucklick, Martin Lehmann, Erik Beckmann, Alexander Wilkens, Maya Kolte, Baban Mustafayeva, Ayten Ludwig, Tobias Diwo, Maurice Wissing, Josef Jänsch, Lothar Ahrens, Christian H. Ignatova, Zoya Engelmann, Susanne |
author_facet | Fuchs, Stephan Kucklick, Martin Lehmann, Erik Beckmann, Alexander Wilkens, Maya Kolte, Baban Mustafayeva, Ayten Ludwig, Tobias Diwo, Maurice Wissing, Josef Jänsch, Lothar Ahrens, Christian H. Ignatova, Zoya Engelmann, Susanne |
author_sort | Fuchs, Stephan |
collection | PubMed |
description | Small proteins play essential roles in bacterial physiology and virulence, however, automated algorithms for genome annotation are often not yet able to accurately predict the corresponding genes. The accuracy and reliability of genome annotations, particularly for small open reading frames (sORFs), can be significantly improved by integrating protein evidence from experimental approaches. Here we present a highly optimized and flexible bioinformatics workflow for bacterial proteogenomics covering all steps from (i) generation of protein databases, (ii) database searches and (iii) peptide-to-genome mapping to (iv) visualization of results. We used the workflow to identify high quality peptide spectrum matches (PSMs) for small proteins (≤ 100 aa, SP100) in Staphylococcus aureus Newman. Protein extracts from S. aureus were subjected to different experimental workflows for protein digestion and prefractionation and measured with highly sensitive mass spectrometers. In total, 175 proteins with up to 100 aa (SP100) were identified. Out of these 24 (ranging from 9 to 99 aa) were novel and not contained in the used genome annotation.144 SP100 are highly conserved and were found in at least 50% of the publicly available S. aureus genomes, while 127 are additionally conserved in other staphylococci. Almost half of the identified SP100 were basic, suggesting a role in binding to more acidic molecules such as nucleic acids or phospholipids. |
format | Online Article Text |
id | pubmed-8195425 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-81954252021-06-21 Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach Fuchs, Stephan Kucklick, Martin Lehmann, Erik Beckmann, Alexander Wilkens, Maya Kolte, Baban Mustafayeva, Ayten Ludwig, Tobias Diwo, Maurice Wissing, Josef Jänsch, Lothar Ahrens, Christian H. Ignatova, Zoya Engelmann, Susanne PLoS Genet Research Article Small proteins play essential roles in bacterial physiology and virulence, however, automated algorithms for genome annotation are often not yet able to accurately predict the corresponding genes. The accuracy and reliability of genome annotations, particularly for small open reading frames (sORFs), can be significantly improved by integrating protein evidence from experimental approaches. Here we present a highly optimized and flexible bioinformatics workflow for bacterial proteogenomics covering all steps from (i) generation of protein databases, (ii) database searches and (iii) peptide-to-genome mapping to (iv) visualization of results. We used the workflow to identify high quality peptide spectrum matches (PSMs) for small proteins (≤ 100 aa, SP100) in Staphylococcus aureus Newman. Protein extracts from S. aureus were subjected to different experimental workflows for protein digestion and prefractionation and measured with highly sensitive mass spectrometers. In total, 175 proteins with up to 100 aa (SP100) were identified. Out of these 24 (ranging from 9 to 99 aa) were novel and not contained in the used genome annotation.144 SP100 are highly conserved and were found in at least 50% of the publicly available S. aureus genomes, while 127 are additionally conserved in other staphylococci. Almost half of the identified SP100 were basic, suggesting a role in binding to more acidic molecules such as nucleic acids or phospholipids. Public Library of Science 2021-06-01 /pmc/articles/PMC8195425/ /pubmed/34061833 http://dx.doi.org/10.1371/journal.pgen.1009585 Text en © 2021 Fuchs et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Fuchs, Stephan Kucklick, Martin Lehmann, Erik Beckmann, Alexander Wilkens, Maya Kolte, Baban Mustafayeva, Ayten Ludwig, Tobias Diwo, Maurice Wissing, Josef Jänsch, Lothar Ahrens, Christian H. Ignatova, Zoya Engelmann, Susanne Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach |
title | Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach |
title_full | Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach |
title_fullStr | Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach |
title_full_unstemmed | Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach |
title_short | Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach |
title_sort | towards the characterization of the hidden world of small proteins in staphylococcus aureus, a proteogenomics approach |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8195425/ https://www.ncbi.nlm.nih.gov/pubmed/34061833 http://dx.doi.org/10.1371/journal.pgen.1009585 |
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