Fig. 6: UBE2D1/2/3 regulates the turnover of several peroxins (PEX) and UBE2D1/2/3 knockdown increases PEX protein levels post-transcriptionally. | Nature Communications

Fig. 6: UBE2D1/2/3 regulates the turnover of several peroxins (PEX) and UBE2D1/2/3 knockdown increases PEX protein levels post-transcriptionally.

From: An adaptive stress response that confers cellular resilience to decreased ubiquitination

Fig. 6: UBE2D1/2/3 regulates the turnover of several peroxins (PEX) and UBE2D1/2/3 knockdown increases PEX protein levels post-transcriptionally.The alternative text for this image may have been generated using AI.

a PEX protein upregulation by RNAi for individual or related E2s. Cumulative Log2FC of PEX protein abundance induced by E2 RNAi versus control NT RNAi, arising independently from mRNA changes. UBE2D1/2/3 RNAi upregulates many PEX proteins, suggesting that UBE2D1/2/3 has a key role in PEX turnover. See also Supplementary Fig. 11. b PEX3 and PEX11 are among the PEXs more commonly upregulated upon E2 knockdown whereas others (such as PEX5 and PEX7) are not modulated. c UBE2D1/2/3 RNAi upregulates PEX proteins (P < 0.05 and Log2FC > 0.2) without significant and/or consistent mRNA changes. N = 4 (NT siRNAs) and N = 3 (UBE2D1/2/3 siRNAs) biological replicates/group, mean ±SD (P-values were obtained with unpaired two-tailed t tests for TMT data and with non-parametric ANOVA for RNA-seq data). d Modulation of the peroxisomal proteome by UBE2D1/2/3 siRNAs. The x-axis displays the Log2FC of UBE2D1/2/3 RNAi versus control NT RNAi whereas the y-axis reports the significance, -Log10(P value). UBE2D1/2/3 siRNAs upregulate several peroxins (PEX) and other peroxisomal proteins. e UBE2D1/2/3 knockdown increases PEX3-FLAG and PEX11A-FLAG protein levels, which correspond to PEXs that are upregulated by UBE2D1/2/3 RNAi in TMT studies (a–c). Conversely, PEX5-FLAG, PEX11B-FLAG, and PEX13-FLAG are not regulated by UBE2D1/2/3 RNAi, consistent with TMT studies (a–c). N = 4 biological replicates/group with mean ± SD and P values indicated (*P < 0.05 and **P < 0.01, obtained with unpaired two-tailed t tests). f Immunoprecipitation of PEX-FLAG proteins from cells treated with UBE2D1/2/3 RNAi (siUBE2D) and control NT RNAi (siNT). Anti-ubiquitin immunoblotting is used to determine the ubiquitination status of FLAG-tagged PEXs. Compared to control NT siRNAs (gray), knockdown of UBE2D1/2/3 (blue) reduces the ubiquitination of several FLAG-tagged peroxins, although this is significant only for PEX5-FLAG and PEX13-FLAG; n = 3 biological replicates/group, mean ± SEM, *P < 0.05 (unpaired two-tailed t-tests). Source data are provided in the Source data file.

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