High-resolution chemical dissection of a model eukaryote reveals targets, pathways and gene functions

Abstract

Due to evolutionary conservation of biology, experimental knowledge captured from genetic studies in eukaryotic model organisms provides insight into human cellular pathways and ultimately physiology. Yeast chemogenomic profiling is a powerful approach for annotating cellular responses to small molecules. Using an optimized platform, we provide the relative sensitivities of the heterozygous and homozygous deletion collections for nearly 1800 biologically active compounds. The data quality enables unique insights into pathways that are sensitive and resistant to a given perturbation, as demonstrated with both known and novel compounds. We present examples of novel compounds that inhibit the therapeutically relevant fatty acid synthase and desaturase (Fas1p and Ole1p), and demonstrate how the individual profiles facilitate hypothesis-driven experiments to delineate compound mechanism of action. Importantly, the scale and diversity of tested compounds yields a dataset where the number of modulated pathways approaches saturation. This resource can be used to map novel biological connections, and also identify functions for unannotated genes. We validated hypotheses generated by global two-way hierarchical clustering of profiles for (i) novel compounds with a similar mechanism of action acting upon microtubules or vacuolar ATPases, and (ii) an un-annotated ORF, YIL060w, that plays a role in respiration in the mitochondria. Finally, we identify and characterize background mutations in the widely used yeast deletion collection which should improve the interpretation of past and future screens throughout the community. This comprehensive resource of cellular responses enables the expansion of our understanding of eukaryotic pathway biology.

Decatransin, a novel natural product inhibiting protein translocation at the Sec61/SecY translocon

“…The name also alludes to the cotransins, a group of heptadepsipeptide compounds without detectable molecular similarity that have previously been described as mammalian translocon inhibitors. The activity of decatransin on the yeast S. cerevisiae allowed for chemogenomic profiling to rapidly home in on the Sec61 complex as the potential fungal target: our high-resolution HIP and HOP platform (Hoepfner et al, 2014) identified all core subunits of the heptameric translocon complex. Essentially the same profile was obtained for a new yeast active heptadepsipeptide (compound 2) of the cotransin chemotype and for the original inhibitor HUN-7293 (compound 3).…”

“…HIP, HOP and microarray analysis were performed as described previously (Hoepfner et al, 2014). Sensitivity was computed as the median absolute deviation logarithmic (MADL) score for each compound and concentration combination.…”

“…Sensitivity was computed as the median absolute deviation logarithmic (MADL) score for each compound and concentration combination. z-scores are based on a robust parametric estimation of gene variability from .3000 different profilings and were computed as described in detail in previously (Hoepfner et al, 2014).…”

The Toxicity of a Novel Antifungal Compound Is Modulated by Endoplasmic Reticulum-Associated Protein Degradation Components

“…The effects of sr7575 on haploid yeast deletion strains were compared to profiles obtained from 1,824 different chemicals in a recently published large-scale chemogenomic screen (16). The compound CMB4166 had the highest Spearman correlation coefficient in this comparison (r ϭ 0.44) (Fig.…”

“…Most of the large chemogenomic data sets currently available have investigated nonessential gene deletions in haploid strains (10,16). Essential genes, representing about one-sixth of all Saccharomyces cerevisiae genes, are more difficult to study in haploid or heterozygous deletion strains, so an alternative approach is the use of DAmP (decreased abundance by mRNA perturbation) strains.…”