Figure S4.
Analysis of electron transport chain (ETC) component peptide counts, mitochondrial ribosome expression, mitoTracker CMXRos staining and mitochondrial abundance and DNA coverage in haploinsufficient RP mutants. (A) Raw peptide counts from all three replicates were combined to analyze the ETC components, differentiating between those encoded by nuclear genes (red) and those encoded by mitochondrial genes (blue). Although coverage of mitochondrially encoded ETC components was lower, nuclear-encoded components showed a nearly diagonal pattern, indicating minimal deviation from expected levels. The y-axes of all four graphs display peptide reads from heterozygous ribosomal protein mutants, while the x-axes correspond to stage-matched wild-type controls. (B) Overall, RNA expression, TE, and protein level changes of all mitochondrial RP genes were plotted in RP haploinsufficient mutants. Y-axes show mitochondrial ribosomal proteins that belong to large or small subunits (top and bottom plots, respectively) and x-axes show log2 fold changes that were predicted by EdgeR for RNA and TE, and by DEP for proteins. For statistical analysis, ROAST multivariate gene expression analysis was conducted (Wu et al., 2010). (C) Staining specificity was assessed through co-localization studies using a C. elegans strain with a CRISPR-engineered knock-in of cox-4 gene tagged with GFP (cox-4::GFP), serving as a marker for mitochondrial inner membranes. These co-localization analyses were conducted using a Leica Stellaris Confocal System equipped with a 63× objective. A representative image is shown with MitoTracker CMXRos staining (left), COX::GFP (middle) and merged images (right). Yellow color indicates co-localization of the staining with the mitochondrial inner membrane marker, COX-4. (D) Body length and width were assessed for stage-matched rps-10(0)/+ and wild-type controls used in oxygen consumption experiments depicted in Fig. 5 C. (E) Mitochondrial genome coverage was charted for heterozygous C. elegans mutants and stage-matched wild-type controls. The x-axes represent mitochondrial genome positions, and the y-axes show mitochondrial genome coverage normalized to the nuclear genome. Orange lines indicate heterozygous mutant animals, and blue lines represent stage-matched wild-type controls at the L4 stage. Source data are available for this figure: SourceData FS4 C.

Analysis of electron transport chain (ETC) component peptide counts, mitochondrial ribosome expression, mitoTracker CMXRos staining and mitochondrial abundance and DNA coverage in haploinsufficient RP mutants. (A) Raw peptide counts from all three replicates were combined to analyze the ETC components, differentiating between those encoded by nuclear genes (red) and those encoded by mitochondrial genes (blue). Although coverage of mitochondrially encoded ETC components was lower, nuclear-encoded components showed a nearly diagonal pattern, indicating minimal deviation from expected levels. The y-axes of all four graphs display peptide reads from heterozygous ribosomal protein mutants, while the x-axes correspond to stage-matched wild-type controls. (B) Overall, RNA expression, TE, and protein level changes of all mitochondrial RP genes were plotted in RP haploinsufficient mutants. Y-axes show mitochondrial ribosomal proteins that belong to large or small subunits (top and bottom plots, respectively) and x-axes show log2 fold changes that were predicted by EdgeR for RNA and TE, and by DEP for proteins. For statistical analysis, ROAST multivariate gene expression analysis was conducted (Wu et al., 2010). (C) Staining specificity was assessed through co-localization studies using a C. elegans strain with a CRISPR-engineered knock-in of cox-4 gene tagged with GFP (cox-4::GFP), serving as a marker for mitochondrial inner membranes. These co-localization analyses were conducted using a Leica Stellaris Confocal System equipped with a 63× objective. A representative image is shown with MitoTracker CMXRos staining (left), COX::GFP (middle) and merged images (right). Yellow color indicates co-localization of the staining with the mitochondrial inner membrane marker, COX-4. (D) Body length and width were assessed for stage-matched rps-10(0)/+ and wild-type controls used in oxygen consumption experiments depicted in Fig. 5 C. (E) Mitochondrial genome coverage was charted for heterozygous C. elegans mutants and stage-matched wild-type controls. The x-axes represent mitochondrial genome positions, and the y-axes show mitochondrial genome coverage normalized to the nuclear genome. Orange lines indicate heterozygous mutant animals, and blue lines represent stage-matched wild-type controls at the L4 stage. Source data are available for this figure: SourceData FS4 C.

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