coli-specific … The annotation and validation of all the implied prokaryotic interaction data and protein complexes is nontrivial. One important way to achieve this is to make them accessible by a Wiki, for instance, the “SubtiWiki” or the “WikiPathways”. These Wikis

provide a knowledgebase for the Gram-positive model bacterium Bacillus subtilis [19], Inhibitors,research,lifescience,medical or pathways in general [20]. The SubtiWiki includes the companion databases SubtiPathways [21] and SubtInteract with graphical presentations of metabolism, its regulation, as well as protein–protein interactions and complexes, and is highly recommended as an exemplary resource to study systems biology of protein complexes in bacteria. Moreover, protein modifications have to be charted. They influence protein complex formation, and removing or adding a protein modification allows corresponding protein complexes to change with time. An important mechanism is phosphorylation. Interacting proteins may specifically bind to these protein

modifications or only bind if these modifications are absent. Thus, Van Noort et al. [22] Inhibitors,research,lifescience,medical compared this mechanism with other posttranscriptional regulatory mechanisms in M. pneumoniae. This organism is particularly suited for such studies because it encodes only two protein kinases and one protein phosphatase. This fact allows an elegant identification of the protein-specific Inhibitors,research,lifescience,medical effects on the phosphorylation network using specific deletion mutants. Van Noort and co-workers also considered changes in protein abundance and lysine acetylation [22]. Introduction of the mutations did not alter the transcriptional response, but deletion of the two putative N-acetyltransferases affected protein phosphorylation, which demonstrates Inhibitors,research,lifescience,medical the cross-talk between the two posttranslational modification systems. Phosphoproteome studies were also reported for B. subtilis. Jers et al. [23] identified nine previously unknown tyrosine-phosphorylated proteins in B. subtilis, and the majority of these were at least in vitro PtkA substrates. 2.2. Metabolic Adaptation and Protein Complexes For growth, intracellular model pathogens

rely on different metabolic Inhibitors,research,lifescience,medical resources and exploit suitable protein complexes for Digestive enzyme their utilization and thus regulate metabolism accordingly. Therefore, comparing the wild-type S. aureus strain 8325 and the isogenic deletion mutants (either lacking the eukaryotic-like protein serine/threonine kinase PknB or the phosphatase Stp, [24]) remarkable differences were found. Those differences were in nucleotide metabolism and cell wall precursor metabolites, such as peptidoglycan and cell wall teichoic acid biosynthesis in S. aureus. This phosphatase and the kinase are also antagonistic players in central metabolism, affecting enolase, triose phosphate isomerase, fructose biphosphate aldolase, Tyrphostin B42 order pyruvate dehydrogenase, phosphate acetyl transferase, and others. Similarly, S. aureus pathogenicity potential depends on the iron status of the host [25].