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Proteomes 2016, 4(1), 8; doi:10.3390/proteomes4010008

A Staphylococcus aureus Proteome Overview: Shared and Specific Proteins and Protein Complexes from Representative Strains of All Three Clades

1
Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
2
Institut für Mikrobiologie Ernst-Moritz-Arndt-Universität Greifswald, Friedrich-Ludwig-Jahn-Straße 15, D-17487 Greifswald, Germany
3
Structural and Computational Biology, European Molecular Biology Laboratory, Mayerhofstr. 1, D-69126 Heidelberg, Germany
4
FG13 Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institut (RKI); Burgstr. 37; D-38855 Wernigerode, Germany
These authors contributed equally to this work.
*
Author to whom correspondence should be addressed.
Academic Editors: Michael Hecker and Katharina Riedel
Received: 24 September 2015 / Revised: 31 January 2016 / Accepted: 5 February 2016 / Published: 19 February 2016
(This article belongs to the Special Issue Microbial Proteomics)
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Abstract

Staphylococcus aureus is an important model organism and pathogen. This S. aureus proteome overview details shared and specific proteins and selected virulence-relevant protein complexes from representative strains of all three major clades. To determine the strain distribution and major clades we used a refined strain comparison combining ribosomal RNA, MLST markers, and looking at highly-conserved regions shared between strains. This analysis shows three sub-clades (A–C) for S. aureus. As calculations are complex and strain annotation is quite time consuming we compare here key representatives of each clade with each other: model strains COL, USA300, Newman, and HG001 (clade A), model strain N315 and Mu50 (clade B) and ED133 and MRSA252 (clade C). We look at these individual proteomes and compare them to a background of 64 S. aureus strains. There are overall 13,284 S. aureus proteins not part of the core proteome which are involved in different strain-specific or more general complexes requiring detailed annotation and new experimental data to be accurately delineated. By comparison of the eight representative strains, we identify strain-specific proteins (e.g., 18 in COL, 105 in N315 and 44 in Newman) that characterize each strain and analyze pathogenicity islands if they contain such strain-specific proteins. We identify strain-specific protein repertoires involved in virulence, in cell wall metabolism, and phosphorylation. Finally we compare and analyze protein complexes conserved and well-characterized among S. aureus (a total of 103 complexes), as well as predict and analyze several individual protein complexes, including structure modeling in the three clades. View Full-Text
Keywords: Staphylococcus aureus; proteome; protein complexes; model strain Staphylococcus aureus; proteome; protein complexes; model strain
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Liang, C.; Schaack, D.; Srivastava, M.; Gupta, S.K.; Sarukhanyan, E.; Giese, A.; Pagels, M.; Romanov, N.; Pané-Farré, J.; Fuchs, S.; Dandekar, T. A Staphylococcus aureus Proteome Overview: Shared and Specific Proteins and Protein Complexes from Representative Strains of All Three Clades. Proteomes 2016, 4, 8.

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