Fig. 4: Leu supplementation reduces the degradation of endogenous OMM proteins and increases mitochondrial protein content.
a, The experimental paradigm of proteomic profiling of whole worms and mitochondria of worms supplemented with dH2O, 20 mM Leu, CHX and Leu + CHX for 3 h. Four independent biological replicates were analysed for each condition. b, The percentage of proteins increased or decreased in the whole-worm proteome, MitoCarta 3.0 proteins and OMM proteins for each comparison indicated. c, The log2 fold change of the whole-worm proteome, MitoCarta 3.0 proteins and OMM proteins comparing Leu + CHX with CHX treatment. Two-tailed Mann–Whitney U test between whole-worm proteins and other protein groups. d, Volcano plot showing changes of OMM proteins upon Leu + CHX treatment compared with CHX treatment. P values were determined by an unpaired two-tailed t-test. OMM proteins show the tendency to be more abundant in Leu-treated worms in the presence of CHX. e, Volcano plot showing changes of whole worm and MitoCarta 3.0 proteins upon Leu + CHX treatment compared with CHX treatment. P values were determined by an unpaired two-tailed t-test. Mitochondrial proteins show the tendency to be more abundant in Leu-treated worms in the presence of CHX. f, The experimental paradigm of proteomic profiling of HEK293 whole cells and mitochondria of cells supplemented with dH2O, Leu, CHX and Leu + CHX for 3 h. Four independent biological replicates were analysed for each condition. g, The percentage of proteins increased or decreased in the whole cell proteome, MitoCarta 3.0 proteins and OMM proteins in each comparison indicated. h, The log2 fold change of the whole cell proteome, MitoCarta 3.0 proteins and OMM proteins comparing Leu + CHX with CHX treatment. Two-tailed Mann–Whitney U test between whole cell proteins and other protein groups. i, A volcano plot showing changes of OMM proteins upon Leu + CHX treatment compared with CHX treatment. P values were determined by an unpaired two-tailed t-test. OMM proteins show the tendency to be more abundant in Leu-treated cells in the presence of CHX. j, A volcano plot showing the changes in whole cell and MitoCarta 3.0 proteins upon Leu + CHX treatment compared with CHX treatment. P values were determined by an unpaired two-tailed t-test. Mitochondrial proteins show the tendency to be more abundant in Leu-treated cells in the presence of CHX. k, Enriched GO terms (P < 0.001 and FDR < 0.2 cut-off) for upregulated proteins from the worm mitochondrial proteome in the Leu + CHX condition compared with the CHX condition. l, Enriched GO terms (P < 0.001 and FDR <0.2 cut-off) for upregulated proteins from the HEK293 cell mitochondrial proteome in the Leu + CHX condition compared with the CHX condition. A full list of significantly enriched GO terms is presented in Supplementary Table 3 for worm and HEK293 cells.
