title: AStaphylococcus aureusProteome Overview: Shared and Specific Proteins and Protein Complexes from Representative Strains of All Three Clades.
abstract: Staphylococcus aureusis an important model organism and pathogen. ThisS. aureusproteome 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) forS. 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 64S. aureusstrains. There are overall 13,284S. aureusproteins 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 amongS. aureus(a total of 103 complexes), as well as predict and analyze several individual protein complexes, including structure modeling in the three clades.
authors.affiliation: Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany. liang@biozentrum.uni-wuerzburg.de.
authors.forename: Chunguang
authors.initials: C
authors.lastname: Liang
authors.affiliation: Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany. dominik.schaack@uni-wuerzburg.de.
authors.forename: Dominik
authors.initials: D
authors.lastname: Schaack
authors.affiliation: Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany. mugdha.srivastava@uni-wuerzburg.de.
authors.forename: Mugdha
authors.initials: M
authors.lastname: Srivastava
authors.affiliation: Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany. shishir.gupta@uni-wuerzburg.de.
authors.forename: Shishir K
authors.initials: SK
authors.lastname: Gupta
authors.affiliation: Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany. edita.sarukhanyan@uni-wuerzburg.de.
authors.forename: Edita
authors.initials: E
authors.lastname: Sarukhanyan
authors.affiliation: Institut für Mikrobiologie Ernst-Moritz-Arndt-Universität Greifswald, Friedrich-Ludwig-Jahn-Straße 15, D-17487 Greifswald, Germany. anne.giese@uni-greifswald.de.
authors.forename: Anne
authors.initials: A
authors.lastname: Giese
authors.affiliation: Institut für Mikrobiologie Ernst-Moritz-Arndt-Universität Greifswald, Friedrich-Ludwig-Jahn-Straße 15, D-17487 Greifswald, Germany. pagelsm@uni-greifswald.de.
authors.forename: Martin
authors.initials: M
authors.lastname: Pagels
authors.affiliation: Structural and Computational Biology, European Molecular Biology Laboratory, Mayerhofstr. 1, D-69126 Heidelberg, Germany. natalie.romanov@embl.de.
authors.forename: Natalie
authors.initials: N
authors.lastname: Romanov
authors.affiliation: Institut für Mikrobiologie Ernst-Moritz-Arndt-Universität Greifswald, Friedrich-Ludwig-Jahn-Straße 15, D-17487 Greifswald, Germany. janpf@uni-greifswald.de.
authors.forename: Jan
authors.initials: J
authors.lastname: Pané-Farré
authors.affiliation: FG13 Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institut (RKI); Burgstr. 37; D-38855 Wernigerode, Germany. FuchsS@rki.de.
authors.forename: Stephan
authors.initials: S
authors.lastname: Fuchs
authors.affiliation: Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany. dandekar@biozentrum.uni-wuerzburg.de.|Structural and Computational Biology, European Molecular Biology Laboratory, Mayerhofstr. 1, D-69126 Heidelberg, Germany. dandekar@biozentrum.uni-wuerzburg.de.
authors.forename: Thomas
authors.initials: T
authors.lastname: Dandekar
keywords: Staphylococcus aureus; model strain; protein complexes; proteome