Synthetic lethality between toxic amino acids, retrograde target genes and chaperones in Saccharomyces cerevisiae

The toxicity of non-proteinogenic amino acids has been known for decades. Numerous reports describe their antimicrobial/anticancer potential. However, these molecules are often toxic to the host as well, therefore a synthetic lethality approach can be beneficial. Here we investigated the potential synthetic lethality between toxic amino acids, the retrograde pathway, and molecular chaperones. In Saccharomyces cerevisiae, mitochondrial retrograde (RTG) pathway activation induces transcription of RTG-target genes, which replenishes alpha- ketoglutarate and glutamate; both metabolites are required for arginine and lysine biosynthesis. We previously reported that tolerance of canavanine, a toxic arginine derivative, requires an intact RTG pathway, and low-dose canavanine exposure reduces the expression of RTG-target genes. At higher concentrations, canavanine causes protein misfolding. Here we show that in WT, low-dose thialysine exposure, a toxic lysine analog, has a similar effect as canavanine on RTG-target gene expression. To study if single amino acid deficiency and mild protein misfolding stress elicit a similar effect on RTG-target genes, we compared expression of heat shock protein (HSP) mutants grown without arginine or lysine to WT. Arginine deprivation induces RTG-target gene expression in sse2{Delta}, hsp78{Delta}, and mdj1{Delta}, but CIT2 and DLD3 are reduced in cpr7{Delta}. Lysine deprivation has the opposite effect on RTG-target gene expression in HSP mutants. Interestingly, exposure of HSP mutants to canavanine and thialysine reversed the trend of RTG-target gene expression in several cases. The RTG-target expression pattern in HSP mutants had a predictive value in canavanine sensitivity - the mutant with the lowest expression was the most sensitive - but this was not the case for thialysine. Some, but not all, mutants in RTG-target genes are sensitive to canavanine and thialysine; additional mutation in a certain HSP can exacerbate this sensitivity. Overall, we show that inhibiting molecular chaperones, RTG-target genes, or both can sensitize cells to low doses of toxic amino acids.