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

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.

Comparative Proteomic and Morphological Change Analyses of Staphylococcus aureus During Resuscitation From Prolonged Freezing

“…However, it should be noted that the results obtained using this representative strain cannot be relevant for all the common variants of S. aureus . Because strain-specific protein repertoires are involved in many biological processes ( Liang et al, 2016 ), it seems unlikely that there is only one resuscitation mechanism for freezing survived cells. Moreover, the present proteomics analysis was performed using cells directly exposed to freezing but not in a frozen food sample.…”

Modeling of stringent-response reflects nutrient stress induced growth impairment and essential amino acids in different Staphylococcus aureus mutants

“…Thus, all this information was used to verify the nodes and types of interactions, making sure the network comprises all the central genes, products, metabolic intermediates and enzymes as well as their interactions for stringent response and amino acid metabolism. The model represents the strain HG001 but the interactions of this model are valid and well conserved for all related strains of clade A according to 19 .…”

The Shared and Specific Genes and a Comparative Genomics Analysis within Three Hanseniaspora Strains

“…Among the analyses of shared and specific genes, a total of 3223 (Supplementary file 3) gene families were obtained. They were divided into single-copy orthologue families, multiple-copy orthologue families, unique families, and other orthologue families (Table 1) [24]. The numbers of shared genes (single-copy and multiple-copy genes) in K. apiculata 34-9, H. uvarum DSM 2768, and H. vineae T02/19AF were calculated to be 2108, 2056, and 2242, respectively (Supplementary file 4).…”