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

Abstract

BackgroundThe 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 (NiSO4).ResultsWe have identified 149 genes whose gene deletion causes sensitivity to NiSO4 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 NiSO4. Functional categories overrepresented with proteins whose absence renders cells sensitive to NiSO4 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.ConclusionWe 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 NiSO4. 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.

Transition metal homeostasis: from yeast to human disease

“…Among the many experiments where S. cerevisiae has proved to be a useful model organism are then many high throughput studies that have aided in the identification of genes and gene products with novel implications in transition metal metabolism (for examples see Pagani et al 2007;Jo et al 2008;Arita et al 2009;Shakoury-Elizeh et al 2010;Takumi et al 2010;Bleackley et al 2011). The contribution of yeast based studies and the identification of homologous systems in humans will continue to facilitate advances in the diagnosis and treatment of diseases involving transition metals while also contributing to the general understanding of how cells maintain the balance of metals as essential nutrients versus toxic entities.…”

Evolution in changing environments : heavy metal adaptation in experimental yeast populations as a case study

“…Ni may also enter the cell via iron transporters, because it was found to interfere with iron uptake (Chen et al 2005). Additionally, several studies point towards a role for the vacuolar H + -ATPase in sequestering Ni into the vacuole, possibly as a histidine conjugate (Joho et al 1995;Nishimura et al 1998;Arita et al 2009). Because Ni interferes with Zrc1p-dependent Zn transport, it is also possible that Ni is transported into the vacuole by this protein.…”

“…stop codon or frameshift mutations), while the effect of all other mutations is predicted to be deleterious based on changes in sequence similarity to a set of homologous protein sequences (PROVEAN score < -2.5 in all cases (Choi et al 2012); Table S3.2). Null mutants of several of these genes have previously been reported to exhibit increased resistance to the metals that we used (Δsmf1/Δfet4: + Cd resistance (Ruotolo et al 2008), Δvip1/Δbul1/Δvtc4: + Ni resistance (Ruotolo et al 2008;Arita et al 2009)) or have increased overall performance in rich nutrient media similar to the medium that we used (Δwhi2 (Qian et al 2012)). …”

“…For example, many different genes are involved in metal homeostasis (Jin et al 2008;Ruotolo et al 2008;Arita et al 2009), and as such there are numerous ways in which a cell can potentially adapt to changes in external metal concentration. Mutations with subtly different effects on metal homeostasis may be favored most strongly at concentrations that are only slightly different, which increases the scope for reranking GxE.…”

“…In response to the constant high Ni treatment, mutations in VTC4 and WHI2 were found in combination multiple times. Mutations in WHI2 have previously been reported to decrease Ni tolerance in isolation (Arita et al 2009), raising the possibility that they were selected specifically in the background of mutations in VTC4, which would similarly suggest contingency/epistasis. Finally, in response to high Ni we either found mutations in VTC4 and WHI2 in combination, or in BUL1 in isolation.…”