Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach.
Cast your vote
You can rate an item by clicking the amount of stars they wish to award to this item.
When enough users have cast their vote on this item, the average rating will also be shown.
Your vote was cast
Thank you for your feedback
Thank you for your feedback
Ahrens, Christian H
MetadataShow full item record
AbstractSmall 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.
CitationPLoS Genet. 2021 Jun 1;17(6):e1009585. doi: 10.1371/journal.pgen.1009585.
AffiliationHZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
The following license files are associated with this item:
- Creative Commons
- A workflow to identify novel proteins based on the direct mapping of peptide-spectrum-matches to genomic locations.
- Authors: Anders J, Petruschke H, Jehmlich N, Haange SB, von Bergen M, Stadler PF
- Issue date: 2021 May 26
- Optimized Proteomics Workflow for the Detection of Small Proteins.
- Authors: Bartel J, Varadarajan AR, Sura T, Ahrens CH, Maaß S, Becher D
- Issue date: 2020 Oct 2
- Genome sequence of Staphylococcus aureus strain Newman and comparative analysis of staphylococcal genomes: polymorphism and evolution of two major pathogenicity islands.
- Authors: Baba T, Bae T, Schneewind O, Takeuchi F, Hiramatsu K
- Issue date: 2008 Jan
- Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes.
- Authors: Guillot L, Delage L, Viari A, Vandenbrouck Y, Com E, Ritter A, Lavigne R, Marie D, Peterlongo P, Potin P, Pineau C
- Issue date: 2019 Jan 17