Comparison of the SDL dataset with other genome-wide screens. (A) Overlap between the “hub” SDL networks of CDC28 and the kinases SLT2, BCK1, ELM1, and PHO85. Data were obtained from Sharifpoor et al. (2012). (B) Overlap between the SDL screen and previously identified genes with a negative genetic relationship with CDC28. Data were obtained from BioGRID. (C and D) Overlap between the SDL screen and the SGA screen described in Zimmermann et al. (2011). (E) Overlap between the SDL screen and previously identified genes that cause dosage lethality of cdc28 mutants (data from BioGRID). SDL, synthetic dosage lethality; SGA, synthetic genetic array.

Analysis of the data reveals overrepresentation of genes involved in the cell cycle, DNA metabolism, and transcription. (A) GO Biological Process analysis of the genes that aggravate the cdc28-as1 phenotype (negative SDL interactions). GO analysis was performed using Metascape. (B) Network plot of the relationships among GO terms. Nodes represent enriched terms colored by its cluster ID. (C) The same network as presented in (B) but showing P values for the nodes. (D) Analysis of the negative SDL interactors using the GO Slim mapper tool of the SGD. (E) Analysis of the macromolecular complex components of the top 154 genes in the SDL network. Only those GO terms are shown for which at least five terms genes were identified. GO, gene ontology; ID, identifier; SDL, synthetic dosage lethality; SGD, Saccharomyces Genome Database.

The effect of overexpression of cyclins. (A) Overexpression of CLN2 and CLN3 causes SDL in cdc28-as1 mutants even under noninducing conditions. Cultures of cells transformed with plasmids containing the ORFs YEL074W (“Mock”), CLN2, or CLN3 were spotted on glucose-containing SC-URA plates supplemented with either DMSO or 1-NM-PP1, followed by incubation at 30° until colonies appeared. (B) Overexpression of CLN2 and CLN3 suppresses the growth defect of cdc28-4 mutants. Cultures of cells transformed with plasmids containing the control ORF YEL074W (“Mock”), CLN2, CLN3, or MSA1 were spotted on YPD or on YP-galactose and incubated at either 30° or 34° until colonies appeared. (C) cdc28-as1 strains transformed with plasmids harboring either the control ORF YEL074W (Mock) or CLN3 were grown to log phase and treated with 500 nM 1-NM-PP1, after which transcription was induced with galactose as described in the Materials and Methods. Subsequently, mRNA levels of CLN2, CLB6, ACT1, and CLN3 were determined by RT-qPCR. DMSO, dimethyl sulfoxide; ORF, open reading frame; RT-qPCR, quantitative reverse transcription polymerase chain reaction; SC-URA, synthetic complete-uracil; SDL, synthetic dosage lethality; WT, wild-type; YP, yeast extract peptone; YPD, YP and dextrose.

Overexpression of FIN1 in cdc28-as1 mutants induces mitotic spindle aberrancies. (A) No obvious differences in spindle misalignment between WT cells and cdc28-as1 mutants after overexpression of KAR9, SPC97, FIN1, or CIN8. TUB1-GFP-expressing WT cells and cdc28-as1 mutants were transformed with plasmids containing the indicated ORFs (Mock: YEL074W), after which cells were treated with 1-NM-PP1 and overexpression was induced by galactose as described in Materials and Methods. Spindle alignment in at least 100 M phase cells was imaged and quantified using fluorescence microscopy. (B) Overexpression of FIN1 in the cdc28-as1 mutant background results in aberrant spindle assembly. Cells were treated and imaged as in (A). At least 300 cells were analyzed per treatment and genotype. (C) Quantification of the data shown in (B). Error bars indicate SD. *P < 0.05. NS, not significant; WT, wild-type.

Genes that may promote dosage rescue of cdc28-as1 mutant cells. (A) Comparison of previously identified genes that mediate dosage suppression of cdc28 alleles with the ORFs that mediate dosage suppression identified by the synthetic dosage lethality (SDL) screen. The only ORF in common between these datasets was YBR160W, which encodes Cdc28. (B) Putative dosage suppressors identified by the SDL screen organized by their cellular functions.

The SDL dataset is enriched for proteins that are phosphorylated in a Cdc28-dependent manner. (A) Venn diagram depicting overlap between the SDL dataset and proteins that are phosphorylated in a Cdc28-dependent manner in vivo and in vitro, and which have previously been confirmed to be Cdc28 substrates. (B) Most proteins that have been found to be phosphorylated in a Cdc28-dependent manner in vivo cause dosage lethality when overexpressed in a cdc28-as1 mutant. The Venn diagram shows overlap between the SDL dataset and proteins that are phosphorylated in a Cdc28-dependent manner in vitro and in vivo. (C) The SDL dataset is enriched for known Cdc28 targets. The Venn diagram shows overlap between the SDL screen, proteins that have been found to be phosphorylated in a Cdc28-dependent manner in vivo, and previously confirmed Cdc28 substrates. (D and E) Overexpression of proteins phosphorylated on potential Cdc28 sites cause an SDL phenotype. The Venn diagrams show overlap between the SDL dataset, confirmed Cdc28 targets, and proteins that are known to be phosphorylated in vivo on either minimal Cdc28 sites (D) or on full Cdc28 consensus sites (E) in a Cdc28-dependent manner. (F–H) Domain structures of Nbp1 (F), Sak1 (G), and Epo1 (H), and location of sites known to be phosphorylated in vivo in a Cdc28-dependent manner. CDK, cyclin-dependent kinase; SDL, synthetic dosage lethality.