PMC:7321036 / 23168-26120
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7321036","sourcedb":"PMC","sourceid":"7321036","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7321036","text":"To study global changes in kinase signaling and their effect on host protein phosphorylation, regulated phosphorylation sites were grouped in five clusters based on their dynamics using a data-driven clustering approach (Figure 4 A; STAR Methods). For each of the groups, an enrichment analysis was performed for functions and pathways (Figure 4A; Table S3). The dynamics of these changes can be linked to the viral life cycle: entry (0–2 h), replication (4–12 h), and egress (24 h). Clusters 1 and 2 include phosphorylation sites that are, on average, upregulated during infection. Cluster 1 sites tended to be upregulated within 2 h (i.e., linked to viral entry) and were enriched in mRNA processing, cell cycle, apoptosis, and proteins involved in HIV infection. Cluster 2 included apoptosis proteins with later onset of phosphorylation, associated with replication and/or egress. Phosphorylation sites in clusters 3 and 4 were downregulated and enriched in RNA-processing functions. Sites within cluster 5 possessed a dynamic response to infection, with immediate downregulation followed by a rise during the middle and renewed downregulation at late time points. This cluster was enriched for DNA replication and the cell cycle, among others. These observations are corroborated by standard Gene Ontology (GO) enrichment analyses of biological processes regulated by phosphorylation (Figure S1G; Table S3; STAR Methods).\nFigure 4 Signaling Changes in Host Cells in Response to SARS-CoV-2 Infection\n(A) Clusters of significantly changing PHs (abs(log2FC) \u003e 1 and adjusted p \u003c 0.05) across the time course of infection with non-redundant enriched Reactome pathway terms (adjusted p value [q] \u003c 0.01) for each cluster. Horizontal red lines below each pathway term correspond to phosphorylated proteins belonging to the pathway, and a black-bordered rectangle is indicative of a significantly enriched term.\n(B) Kinases depicting a strong change in activity upon infection (abs(log10(p)) \u003e 2.5) in at least one time point, with predicted activity in at least 5 of 6 time points.\n(C) Schematic representation of interaction between host kinases and SARS-CoV-2 viral proteins from Gordon et al. (2020). Substrate PHs for each kinase are color-coded as blue (down) and red (up) based on the direction of change during infection. Only PHs corresponding to the kinase activity direction are shown.\n(D) Correlation of kinase activity profiles of each time point with other biological conditions with at least one significantly changing kinase (abs(log10(p)) \u003e 2.5) and having significant correlation with at least one time-point (false discovery rate [FDR] \u003c 5%).\n(E) Overall phosphorylation change (−log10(p)) of a protein complex, estimated as the change in phosphorylation on member proteins. Only non-redundant protein complexes with a significant change in phosphorylation (abs(log10(p)) \u003e 2.5) in at least one time point are shown.\nSee also Figure 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