The chemical genomic portrait of yeast: uncovering a phenotype for all genes

Abstract

Genetics aims to understand the relation between genotype and phenotype. However, because complete deletion of most yeast genes ( approximately 80%) has no obvious phenotypic consequence in rich medium, it is difficult to study their functions. To uncover phenotypes for this nonessential fraction of the genome, we performed 1144 chemical genomic assays on the yeast whole-genome heterozygous and homozygous deletion collections and quantified the growth fitness of each deletion strain in the presence of chemical or environmental stress conditions. We found that 97% of gene deletions exhibited a measurable growth phenotype, suggesting that nearly all genes are essential for optimal growth in at least one condition.

Fig. 1

Fraction of genome required for optimal growth under experimental conditions. (A) Percent of gene deletion strains that exhibit significant sensitivity in at least one treatment as a function of number of experiments performed, ordered by date. We used a significance threshold (z score P < 1 × 10^-5 and P < 1 × 10^-6 for homozygous and heterozygous experiments, respectively) that limited the FDR of genes exhibiting any phenotype to ~0.1 (figs. S2 and S3). Treatment experiments measure the growth of the deletion strains in a drug or altered environmental conditions; control experiments measure growth of the same deletion strains in no-drug rich medium (8). The percent of strains exhibiting a phenotype begins at the percentage previously observed in rich medium (3% for heterozygotes and 34% for homozygotes). (B) Percentage of yeast genes with a phenotype under particular conditions: 19% are essential genes, 15% exhibited a growth defect as homozygous deletions in rich medium, and 63% exhibited a phenotype as either homozygous or heterozygous deletions under particular conditions in this study.

Fig. 2

Genes required for optimal growth in multiple conditions. (A) The percent of deletion strains inhibited by the given percent of unique conditions at P < 0.01 (z score). Most strains are perturbed by multiple distinct conditions. Genes whose deletion strains showed sensitivity to at least 20% of the unique small molecules are defined as MDR genes. (B) Enriched functions of the homozygous MDR genes. Shown are the important GO biological processes, molecular functions, and cellular components, the hypergeometric enrichment P value, and the locations of the processes in the cell. AP, adaptor protein; ESCRT, endosomal sorting complex required for transport.

Fig. 3

Gene clusters with similar co-fitness profiles and similar biological functions, extracted from twoway hierarchical clustering on the complete data set (using all genes and all experiments). Each cell in the matrix is a sensitivity score of the deletion strain in the experiment: yellow indicates that the strain was sensitive; blue indicates resistance. Essential genes are marked with asterisks, and open reading frames (ORFs) that overlap a dubious ORF are in parentheses. (A) CCT complex genes, mediators of cytoskeletal assembly, cluster as heterozygous deletion strains primarily because of sensitivity to the cytoskeletal disrupting agents latrunculin and benomyl. (B) Genes of the proteasome core complex cluster in the heterozygous deletion assays because of sensitivity to three structurally similar compounds that target the lipid synthesis pathway. (C) Peroxisomal genes clustered as homozygous deletions because of sensitivity to hydrogen peroxide, high pH, and oxidative stress-inducing conditions.