Extended Data Fig. 6: Acute DNAJC15 depletion affects protein import capacity and OXPHOS function.
From: Stress adaptation of mitochondrial protein import by OMA1-mediated degradation of DNAJC15
The quantile box plot of all presented boxplots show median (center line), 25th and 75th percentiles, whiskers show minimum and maximum values after outlier removal (0.5 * IQR distance from median, outliers not shown). Two-sided Mann-Whitney U-test was performed (n = 5, biologically independent samples, including outliers). a, Boxplot visualizing the distribution of mitochondrial proteins (MitoCarta 3.0) compared to all identified proteins in the whole cell fraction in HeLa WT and DNAJC15−/− cells, treated with siRNA targeting TIMM17A or TIMM17B. b, MitoPathways enrichment analysis of the significant mitochondrial (according to MitoCarta 3.0) proteins, that are specifically affected in DNAJC15−/− treated with siRNA targeting TIMM17A (FDR < 0.05) (Fisher exact test, corrected by Benjamini Hochberg procedure, FDR < 0.02). c–f, Boxplot visualizing the distribution of significantly downregulated proteins in the mitochondrial fraction (log2FC < 0, FDR < 0.05) compared to all MitoCop or MitoCarta 3.0-annotated fractions. The distribution indicates the mean copies per cell, extracted from Morgenstern et al.31, in c, the protein length in d, the highest calculated MTS score in e and the length of the MTS with the highest MTS score in f, both extracted from the MTSviewer platform. g, Density plot visualizing the Ln half-life distribution of the mostly affected proteins (log2FC < -0.58) (n = 5, biologically independent samples). Half-life was extracted from Morgenstern et al.31. h–j, Quantification of the oxygen flux for Fig. 5a in h, Fig. 5d in i and Fig. 5e in j. Statistical significance in the log2 fold-changes in the oxygen flux between DNAJC15-depleted cells and WT cells was assessed using a paired two-sided t-test. Data are means ± SD (n = 5 for h, n = 4 for i and j, biologically independent samples). k, Statistical analysis of Fig. 5b, c of wild-type (WT) and siRNA-resistant DNAJC15Δ2 (JC15Δ2), or DNAJC15 (JC15) complemented HeLa cells after treatment with siRNA-mediated depletion of DNAJC15 (siJC15) compared to wild-type HeLa cells in phosphorylating and uncoupled conditions. Data are means ± s.d. (n = 4, biologically independent samples). P values were calculated using a two-sided unpaired t-test.
