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),...

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Autores principales:	Stephan Fuchs, Martin Kucklick, Erik Lehmann, Alexander Beckmann, Maya Wilkens, Baban Kolte, Ayten Mustafayeva, Tobias Ludwig, Maurice Diwo, Josef Wissing, Lothar Jänsch, Christian H Ahrens, Zoya Ignatova, Susanne Engelmann
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Genetics QH426-470
Acceso en línea:	https://doaj.org/article/00f37bb424e54b35991ac9f080fef8f5
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spelling	oai:doaj.org-article:00f37bb424e54b35991ac9f080fef8f52021-12-02T20:02:43ZTowards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach.1553-73901553-740410.1371/journal.pgen.1009585https://doaj.org/article/00f37bb424e54b35991ac9f080fef8f52021-06-01T00:00:00Zhttps://doi.org/10.1371/journal.pgen.1009585https://doaj.org/toc/1553-7390https://doaj.org/toc/1553-7404Small 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.Stephan FuchsMartin KucklickErik LehmannAlexander BeckmannMaya WilkensBaban KolteAyten MustafayevaTobias LudwigMaurice DiwoJosef WissingLothar JänschChristian H AhrensZoya IgnatovaSusanne EngelmannPublic Library of Science (PLoS)articleGeneticsQH426-470ENPLoS Genetics, Vol 17, Iss 6, p e1009585 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Genetics QH426-470
spellingShingle	Genetics QH426-470 Stephan Fuchs Martin Kucklick Erik Lehmann Alexander Beckmann Maya Wilkens Baban Kolte Ayten Mustafayeva Tobias Ludwig Maurice Diwo Josef Wissing Lothar Jänsch Christian H Ahrens Zoya Ignatova Susanne Engelmann Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach.
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	article
author	Stephan Fuchs Martin Kucklick Erik Lehmann Alexander Beckmann Maya Wilkens Baban Kolte Ayten Mustafayeva Tobias Ludwig Maurice Diwo Josef Wissing Lothar Jänsch Christian H Ahrens Zoya Ignatova Susanne Engelmann
author_facet	Stephan Fuchs Martin Kucklick Erik Lehmann Alexander Beckmann Maya Wilkens Baban Kolte Ayten Mustafayeva Tobias Ludwig Maurice Diwo Josef Wissing Lothar Jänsch Christian H Ahrens Zoya Ignatova Susanne Engelmann
author_sort	Stephan Fuchs
title	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_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_sort	towards the characterization of the hidden world of small proteins in staphylococcus aureus, a proteogenomics approach.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/00f37bb424e54b35991ac9f080fef8f5
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Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach.

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