Mol. Syst. Biol. 8, 571 (2012)

Large-scale studies investigating the relationship between one post-translational modification (PTM) and another in prokaryotes have been lacking. van Noort et al. evaluated cross-talk between phosphorylation and acetylation in Mycoplasma pneumoniae, a pathogen with a simple genome encoding only one protein phosphatase, two serine/threonine kinases and two lysine acetyltransferases (KATs). Using quantitative proteomics, the authors profiled phosphorylation and acetylation sites in wild-type bacteria and compared them to those found in bacteria deficient for the phosphatase, a kinase or a KAT. They reported that some of the phosphorylation sites showed inverted responses to deletion of a kinase compared to deletion of the phosphatase, whereas other sites were affected by deletion of both kinases, indicative of a dynamic regulatory network. Most of the modified proteins had multiple modifications, and over one-third of these showed coupling between phosphorylation and acetylation. Overall acetylation was detected as frequently as phosphorylation; knockout of one of the kinases or the phosphatase affected 81 acetylation sites, with the kinase mutations having opposing effects on levels of acetylation. Knockout of either KAT affected ∼20% of the phosphorylation sites. The authors also integrated data on protein-protein interactions, finding that modified sites are frequently located at interaction interfaces and raising the possibility that PTMs regulate oligomeric protein assemblies. Taken together, these data provide evidence for combinatorial activity of PTMs in protein interaction networks.