A global protein kinase and phosphatase interaction network in yeast

Abstract

The interactions of protein kinases and phosphatases with their regulatory subunits and substrates underpin cellular regulation. We identified a kinase and phosphatase interaction (KPI) network of 1844 interactions in budding yeast by mass spectrometric analysis of protein complexes. The KPI network contained many dense local regions of interactions that suggested new functions. Notably, the cell cycle phosphatase Cdc14 associated with multiple kinases that revealed roles for Cdc14 in mitogen-activated protein kinase signaling, the DNA damage response, and metabolism, whereas interactions of the target of rapamycin complex 1 (TORC1) uncovered new effector kinases in nitrogen and carbon metabolism. An extensive backbone of kinase-kinase interactions cross-connects the proteome and may serve to coordinate diverse cellular responses.

Fig. 1

Cdc14 phosphatase network. (A) Hierarchical two-dimensional clustering of bait interaction profiles in the KPI dataset. See fig. S9 for full clustergram. Networks for indicated clusters and other kinases are shown in fig. S19. (B) Cdc14-Net1-Sir2 (RENT) interaction network. Kinases are in orange, phosphatases in blue, kinase-associated proteins in yellow, and other proteins in gray. Red connecting lines indicate KPI interactions, gray lines LTP interactions, and gray dashed lines HTP-HC interactions. Line thickness indicates peptide count of interaction; node size is proportional to total number of interactions in the KPI dataset. Bold dashed circle indicates RENT complex and known associated proteins. RAM, regulation of Ace2p activity and cellular morphogenesis. (C) Sensitivity of a GAL1-CDC14 strain to 0.03% methyl methanesulfonate (MMS) when induced by 0.02% galactose (see fig. S20 for expression titration) and a cdc14-3 strain to 200 mM hydroxyurea (HU) at 33°C. (D) Sensitivity of a GAL1-CDC14 strain to either rapamycin (5 ng/ml) or glycerol medium when induced by 0.05% galactose. Resistance of a cdc14-3 strain to rapamycin (20 ng/ml) and sensitivity to 2-deoxyglucose (DG, 100 μg/ml) at 33°C. (E) Sensitivity of a GAL1-CDC14 strain to 1 M sorbitol when induced by 0.05% galactose. Sensitivity of a cdc14-3 strain to calcofluor white (CFW, 18 μg/ ml) at 33°C. (F) Representative tetrads bearing combinations of slt2Δ, bck1Δ, cdc15-2, and mob1-77 alleles. Double-mutant spore clones are circled in yellow; pbs2Δ and tor1Δ served as negative controls.

Fig. 2

TORC1 kinase network. (A) Partial network of new TORC1-associated kinases. (B) Overexpression of GAL1-FMP48 inhibits growth on glycerol and confers rapamycin resistance. (C) Overexpression of GAL1-FMP48 causes abnormal mitochondrial morphology as visualized with an Ilv3^GFP mitochondrial matrix fusion protein (GFP, green fluorescent protein). DIC, differential interference contrast. (D) Genome-wide expression profiles of GAL1-FMP48 and GAL1-MKS1 strains induced with 0.2% galactose. RTG-responsive (orange), mitochondrial (red), stress-responsive (green), and Gln3/Gcn4-responsive (blue) genes are marked. (E) Fmp48^FLAG or Sch9^FLAG complexes were immunopurified from cells grown in the presence or absence of rapamycin (200 ng/ml) for 30 min, then incubated with [³³P]-γ-ATP, and radiolabeled species were resolved by SDS–polyacrylamide gel electrophoresis. Nonregulated Sch9-associated activity served as a negative control. (F) Immunopurified Nnk1^FLAG complexes were incubated with [³³P]-γ-ATP, then denatured, and radiolabeled Gdh2 species were repurified with antibody to hemagglutinin (HA). (G) A gdh2Δ strain is rapamycin resistant when glutamate is the sole nitrogen source. (H) Expression of GAL1-NNK1 in 2% galactose confers sensitivity to rapamycin (5 ng/ml). (I) Expression of GAL1-NNK1 in 2% galactose for 1 hour causes nuclear accumulation of Gln3^GFP. (J) Expression of GAL1-NNK1 in 0.2% galactose for 1.5 hours specifically induces Gln3 target genes. Color bar indicates fold increase (red) or decrease (green) relative to empty vector control.

Fig. 3

A kinase-kinase (K-K) network connects the proteome. (A) Combined K-K interaction network derived from the KPI, LTP, and HTP-HC datasets. Interactions from known kinase regulatory subunits and paralogs were collapsed into single nodes (table S8). The reduced network contains 156 interactions between 75 kinases, 66 of which contain documented phosphorylation sites (table S9). Colors indicate fraction of GO Super-Slim biological processes assigned by interaction partners of each kinase (2). (B) Nodes in the combined K-K network were deleted in decreasing degree order. Characteristic path length and largest residual connected component were normalized to initial values. K-K networks derived from KPI and LTP+HTP-HC datasets were used as controls. (C) Clustering of GO Slim biological processes associated with kinase interaction partners. Full clustergram is shown in fig. S17. (D) Multifunctionality of kinase associations. Ratio indicates number of GO Slim biological processes per kinase normalized to all processes (2).