Functional exploration of a deep Mycobacterium tuberculosis phosphoproteome

ABSTRACT Phosphosignaling provides the major conduit for bacterial adaptation. The two component systems (TCSs) have long been viewed as the canonical phosphosignaling systems in bacteria, but increasingly, O- phosphorylation mediated by Ser/Thr kinases is recognized as a relevant bacterial phosphosignaling mechanism as well. We now show that in fact, Mycobacterium tuberculosis (Mtb) has an expansive, distributed, and cooperative O-phosphorylation system of a size and complexity that is typically only associated with eukaryotes. By using a comprehensive STPK loss- and gain-of-function mutant panel and quantitative mass spectrometry, we show that >70% of Mtb proteins are phosphorylated on Ser/Thr/Tyr, identify thousands of individual Ser/Thr kinase substrates, and show that the Ser/Thr kinases collectively control the expression of ~30% of Mtb genes. Here, we will test a new and extensive regulatory connection between the Ser/Thr kinases and the His kinases of the TCSs and test the role of O-phosphorylation on the regulation of transcription factors. As a result of our exhaustive analysis of Mtb phosphorylation, we also obtained the first evidence of Arg phosphorylation in Mtb- the first bacterial Arg phosphoproteome outside of gram-positive bacteria. We will identify the relevant phosphoenzymes and test the idea that pArg functions as a degradation tag for ClpP- mediated proteolysis.