Figure 2: Biotin starvation induces a retrograde-like proteome response and mitochondrial hyperacetylation.

(a) Proteome perturbations in response to biotin depletion. Signal intensities of identified proteins plotted against the corresponding normalized heavy/light ratio. Significant outliers in red (false discovery rate of P<0.0001) was determined using a Benjamini–Hochberg correction for multiple hypothesis testing. (b) Western blot of Mot3–GFP grown in the presence or absence of biotin and blotted with a GFP antibody. (c) Gene ontology annotation analyses of regulated proteins compared with their respective genome abundance. P values calculated separately for each GO term using Fisher’s exact test. (d) Relative biotin-dependent acetyl-CoA levels of WT yeast cells. (e) Venn diagram showing the overlap of quantified acetylation sites in the light-SILAC state from two independent experiments with either excess or depletion of biotin. (f) Box-plot analysis comparing the distribution of quantified proteins at the proteome and acetylome level of representative biotin excess or depletion experiments. The line across the box identifies the median sample value, the ends of the box are the 25th and 75th percentiles and whiskers represent minimum and maximum values. An unpaired t-test was performed to test difference between the mean log2 SILAC ratios. **P<0.01 (g) GO annotation of regulated acetylated proteins compared with their respective genome abundance from the biotin-depletion experiment. P values calculated separately for each GO term using Fisher’s exact test.