SCRAPPY - a single cell rapid assay of proteome perturbation in yeast uncovers a joint role of aromatic amino acids and oxidative stress in the toxicity of lipophilic nucleoside analogs

Assaying cellular responses to antimicrobial molecules is a path to understanding modes of action of potential drugs. This is often achieved via transcriptomics and proteomics, but simple and inexpensive methods for rapid characterization are lacking. To bridge this gap, we assayed changes in the abundance of a panel of 64 "sentinel" proteins fused to GFP in the yeast Saccharomyces cerevisiae using flow cytometry. This method produced expected patterns for classical antifungals and allowed inference of common mechanisms between known and novel compounds. Single-cell data also revealed diverging responses in mitochondrial protein abundance in response to thiazolidine antifungals, and perturbations of the cell cycle caused by various compounds. Finally, the method provided insight into the unknown mode of action of alkylated nucleosides, which can be used against fungi residing on works of art. These substances elevate levels of proteins involved in the biosynthesis of aromatic amino acids (AAA), as well as in oxidative stress. Furthermore, deficiencies of Trp and Tyr biosynthesis increased the efficacy of these compounds, while antioxidants reduced it. Most surprisingly, antioxidant effectiveness relied on AAA biosynthesis. Thus, our approach and its possible modifications for other microbes provides an easy and reliable platform for revealing modes of action of novel compounds.