Investigation of Proteomic and Phosphoproteomic Responses to Signaling Network Perturbations Reveals Functional Pathway Organizations in Yeast

Abstract

Summary: Governance of protein phosphorylation by kinases and phosphatases constitutes an essential regulatory network in eukaryotic cells. Network dysregulation leads to severe consequences and is often a key factor in disease pathogenesis. Previous studies revealed multiple roles for protein phosphorylation and pathway structures in cellular functions from different perspectives. We seek to understand the roles of kinases and phosphatases from a protein homeostasis point of view. Using a streamlined tandem mass tag (SL-TMT) strategy, we systematically measure proteomic and phosphoproteomic responses to perturbations of phosphorylation signaling networks in yeast deletion strains. Our results emphasize the requirement for protein normalization for more complete interpretation of phosphorylation data. Functional relationships between kinases and phosphatases were characterized at both proteome and phosphoproteome levels in three ways: (1) Gene Ontology enrichment analysis, (2) Δgene-Δgene correlation networks, and (3) molecule covariance networks. This resource illuminates kinase and phosphatase functions and pathway organizations. : Li et al. measure (phospho)proteomic responses to perturbations of phosphorylation signaling networks in 110 yeast deletion strains. The results emphasize that broad interpretation of phosphorylation data requires protein normalization. Kinase and phosphatase relationships are characterized at both proteome and phosphoproteome levels. Phosphorylation signaling pathway organizations are illuminated by network analyses. Keywords: streamlined tandem mass tag strategy, multi-notch MS3, proteomics, phosphoproteomics, protein kinases and phosphatases, protein regulation network, phosphorylation regulation network, phosphorylation signaling pathway organization