Quantitative Phosphoproteomic Analysis of T Cell Receptor Signaling Reveals System-Wide Modulation of Protein-Protein Interactions

Serine-threonine phosphorylation plays a role in regulating the interactions among proteins involved in T cell responses. Further Interactions The binding of antigen to the T cell receptor (TCR) complex triggers a cascade of responses that culminate in T cell activation. Key to the initial stages of this cascade is the phosphorylation of tyrosine residues in proteins proximal to the TCR, which enables the recruitment of other proteins that contain phosphotyrosine-binding domains. Given its importance to TCR signaling, tyrosine phosphorylation of target proteins has received considerable attention. To view protein phosphorylation from a larger perspective, Mayya et al. performed a system-level phosphoproteomics analysis of the events triggered by TCR activation in the human Jurkat T cell line. They found that the status of hundreds of phosphorylation sites was modulated in response to stimulation of the TCR. In addition to identifying previously unknown TCR-responsive phosphorylation events, this analysis also suggests a role for phosphorylated serine and threonine residues in modulating protein-protein interactions between many proteins involved in T cell responses. Protein phosphorylation events during T cell receptor (TCR) signaling control the formation of complexes among proteins proximal to the TCR, the activation of kinase cascades, and the activation of transcription factors; however, the mode and extent of the influence of phosphorylation in coordinating the diverse phenomena associated with T cell activation are unclear. Therefore, we used the human Jurkat T cell leukemia cell line as a model system and performed large-scale quantitative phosphoproteomic analyses of TCR signaling. We identified 10,665 unique phosphorylation sites, of which 696 showed TCR-responsive changes. In addition, we analyzed broad trends in phosphorylation data sets to uncover underlying mechanisms associated with T cell activation. We found that, upon stimulation of the TCR, phosphorylation events extensively targeted protein modules involved in all of the salient phenomena associated with T cell activation: patterning of surface proteins, endocytosis of the TCR, formation of the F-actin cup, inside-out activation of integrins, polarization of microtubules, production of cytokines, and alternative splicing of messenger RNA. Further, case-by-case analysis of TCR-responsive phosphorylation sites on proteins belonging to relevant functional modules together with network analysis allowed us to deduce that serine-threonine (S-T) phosphorylation modulated protein-protein interactions (PPIs) in a system-wide fashion. We also provide experimental support for this inference by showing that phosphorylation of tubulin on six distinct serine residues abrogated PPIs during the assembly of microtubules. We propose that modulation of PPIs by stimulus-dependent changes in S-T phosphorylation state is a widespread phenomenon applicable to many other signaling systems.