Extended Data Fig. 4: Principal component analysis of proteome changes in response to iron depletion.
From: The metabolic growth limitations of petite cells lacking the mitochondrial genome
Wild-type (⍴+) and petite (⍴0) YSBN11 strains containing empty vector or plasmid-encoded ATP3-6 were cultured in iron-depleted SM medium (- iron) or SM medium containing 200 µg/L iron[III] chloride (+ iron). In the mid-exponential phase, cells were harvested, and proteins were extracted and trypsin-digested. Samples were analyzed by SWATH-MS and protein fold-changes were calculated in comparison to the iron-replete wild-type condition, and data was analyzed using principal component (PC) analysis. In PC1, proteomes were separated according to the petite (slow-growth) phenotype, with evolved petites (expressing ATP3-6) clustering with the wild-type. In PC2, iron-repleted yeast proteomes are separated from iron-depleted proteomes. Combined loadings of all proteins belonging to three GO term groups were plotted (red arrows), showing change of amino acid metabolism along PC1, and up-regulation of iron transport and down-regulation of iron-sulfur proteins (ISPs) along PC2. Data from n = 4 biological replicates per genotype.
