Host protein phosphorylation during "Shigella flexneri" infection : a phosphoproteomic based systems biology approach

Abstract

The enteroinvasive bacterium Shigella flexneri triggers its uptake into epithelial cells by injecting several effector proteins via its type three secretion system (TTSS) and interferes with various host cell processes at later stages of infection. In this study, we systematically addressed the impact of S. flexneri infection on the host signaling network by quantitative phosphoproteomics. We were able to identify several hundreds of proteins undergoing a change in their phosphorylation state during the first two hours of infection. Using bioinformatic tools, we could demonstrate that many phosphoproteins are related to the cytoskeleton, signal transduction, cell cycle, and transcription regulation. The temporal phosphorylation patterns were addressed by fuzzy c-means clustering, revealing six temporally distinct phosphorylation profiles as well as kinases potentially responsible for these phosphorylations. In particular, we found a cluster of ataxia telangiectasia mutated (ATM) substrates, related to genotoxic stress, that became phosphorylated at a late stage of infection. We identified mTOR as the most overrepresented signaling pathway and could demonstrate that both, mTORC1 and mTORC2, become activated during S. flexneri infection. To identify phosphoproteins commonly regulated during bacterial infection, we compared our dataset to a published phosphoproteome of cells infected with Salmonella typhimurium. This analysis revealed a large subset of co-regulated phosphoproteins, indicating that both pathogens interfere with similar cellular signaling cascades. Furthermore, we addressed the impact of the S. flexneri effector protein OspF on the host phosphorylation network. OspF is known to inactivate the MAPKs p38 and ERK. The phosphorylation of several hundred proteins was affected in an OspF-dependent manner, demonstrating the massive impact a single bacterial effector can have on the host signaling network. In a second project we addressed the activation mechanism of AKT and mTOR during S. flexneri infection by studying the effector IpgD. IpgD is a phosphoinositide 4-phosphatase generating PI5P from PI(4,5)P2 leading to activation of AKT. We could demonstrate that the effector protein IpgD is sufficient to induce mTOR activation by the use of a protein delivery tool based on the TTSS of Yersinia enterocolitica. Interestingly, AKT activation was independent of canonical PI3K activity shortly after IpgD translocation, whereas at later timepoints AKT activation was PI3K-dependent. These data suggest two distinct IpgD-dependent AKT activation mechanisms. Finally, we could show that the Inositol polyphosphate multikinase IPMK contributes to AKT phosphorylation during infection.