A genome-wide deletion mutant screen identifies pathways affected by nickel sulfate in Saccharomyces cerevisiae

Abstract

Background: The understanding of the biological function, regulation, and cellular interactions of the yeast genome and proteome, along with the high conservation in gene function found between yeast genes and their human homologues, has allowed for Saccharomyces cerevisiae to be used as a model organism to deduce biological processes in human cells. Here, we have completed a systematic screen of the entire set of 4,733 haploid S. cerevisiae gene deletion strains (the entire set of nonessential genes for this organism) to identify gene products that modulate cellular toxicity to nickel sulfate (NiSO(4)).

Results: We have identified 149 genes whose gene deletion causes sensitivity to NiSO(4) and 119 genes whose gene deletion confers resistance. Pathways analysis with proteins whose absence renders cells sensitive and resistant to nickel identified a wide range of cellular processes engaged in the toxicity of S. cerevisiae to NiSO(4). Functional categories overrepresented with proteins whose absence renders cells sensitive to NiSO(4) include homeostasis of protons, cation transport, transport ATPases, endocytosis, siderophore-iron transport, homeostasis of metal ions, and the diphthamide biosynthesis pathway. Functional categories overrepresented with proteins whose absence renders cells resistant to nickel include functioning and transport of the vacuole and lysosome, protein targeting, sorting, and translocation, intra-Golgi transport, regulation of C-compound and carbohydrate metabolism, transcriptional repression, and chromosome segregation/division. Interactome analysis mapped seven nickel toxicity modulating and ten nickel-resistance networks. Additionally, we studied the degree of sensitivity or resistance of the 111 nickel-sensitive and 72 -resistant strains whose gene deletion product has a similar protein in human cells.

Conclusion: We have undertaken a whole genome approach in order to further understand the mechanism(s) regulating the cell's toxicity to nickel compounds. We have used computational methods to integrate the data and generate global models of the yeast's cellular response to NiSO(4). The results of our study shed light on molecular pathways associated with the cellular response of eukaryotic cells to nickel compounds and provide potential implications for further understanding the toxic effects of nickel compounds to human cells.

Figure 1

S. cerevisiae genomic phenotypic screen with NiSO₄. (A) Representative plate of the YPD-agar plates containing no NiSO₄ (untreated), low (0.75), or high (1.25) concentration of NiSO₄ spotted with 96 S. cerevisiae gene deletion mutant strains used in the genomic phenotypic screen. Dark blue, purple, yellow, light blue and pink squares identify the NiSO₄-sensitive deletion strains fob1Δ, ydr338cΔ, trp4Δ, gga1Δ, and eaf1Δ, respectively. Red and green squares identify the NiSO₄-resistant deletion strains doa4Δ and ydr089wΔ, respectively. (B) Recompiled images of nickel-sensitive and resistant identified on the plate in A. doa4Δ and ydr089wΔ are examples of how Ni-resistant mutant strains were identified, whereas the colony of the control strain changed color from white to gray with increasing concentrations of NiSO₄, the resistant strains did not. The Ni-sensitive strains fob1Δ, ydr338cΔ, trp4Δ, gga1Δ, and eaf1Δ exhibited more of a growth defect compared to the control strain even under low (0.75 mM) NiSO₄ concentration.

Figure 2

Nickel toxicity modulating networks identified with proteins whose absence renders cells sensitive to NiSO₄. The yeast protein interactome consisting of 5,433 proteins, 14,656 protein-protein interactions, and 5,621 protein-DNA interactions was compiled using the program Cytoscape. Proteins corresponding to nickel sensitive gene deletion strains were mapped onto the interactome and then filtered to identify connected groups of proteins (N => 2). Straight lines indicate protein-protein interactions and arrows indicate DNA-protein interaction.

Figure 3

Nickel resistance networks identified with proteins whose absence renders cells resistant to NiSO₄. The yeast protein interactome consisting of 5,433 proteins, 14,656 protein-protein interactions, and 5,621 protein-DNA interactions was compiled using the program Cytoscape. Proteins corresponding to nickel resistant gene deletion strains were mapped onto the interactome and then filtered to identify connected groups of proteins (N => 2). Straight lines indicate protein-protein interactions and arrows indicate DNA-protein interaction.