Supplementary Figure 1: Δgene target strain characteristics and respiration culture optimization.

(a) Proteins encoded by the individual genes knocked out of the 174 yeast strains investigated in this study, shown in the context of biological pathways. APS, adenosine-5’-phosphosulfate; CII–CV, oxidative phosphorylation complexes II–V; ER, endoplasmic reticulum; EMC, ER membrane complex; ERMES, ER-mitochondria encounter structure; ETF, electron transfer flavoprotein complex; MAM, mitochondria-associated membrane; MECA, mitochondria-ER-cortex anchor; MICOS, mitochondrial contact site and cristae organizing system; MIM, mitochondrial inner membrane; MOM, mitochondrial outer membrane; mtDNA, mitochondrial DNA; mtRibosome, mitochondrial ribosome; NAD, nicotinamide adenine dinucleotide; PDH, pyruvate dehydrogenase; TCA, tricarboxylic acid cycle; vCLAMP, vacuole and mitochondria patch. The pie charts show the total number of characterized and uncharacterized genes profiled (top); the total number of profiled genes that have human homologs (upper middle); of these genes with human homologs, the number of profiled genes that are also associated with disease (lower middle); and of the uncharacterized genes profiled, the number of genes that have human homologs (bottom). (b) Density of yeast cultures in the respiratory growth condition (mean, n = 3) plotted in strain rank order (left) or against fermentation culture density (mean, n = 3) (right). (c) Optical density at 600 nm (OD₆₀₀) of yeast cultures (media with 3% [w/v] glycerol and 0.1% [w/v] glucose) indicating time points at which yeast were harvested during fermentation (F1–F3) or respiration (R4–R8). Time point R6 (25 h) was selected for the respiration culture condition of the larger study. (d) Whole-proteome plot of protein abundances at time points R5 and R8. (e) Pairwise whole proteome plot comparisons (as in d) across all eight time points (lower left) and linear regression analysis of each comparison (r², Pearson correlation coefficients) (upper right).