Expression of PEX5 proteins fused to a bulky C-terminal tag promotes a decrease in peroxisome number. SV40T-MEFs were cotransfected with plasmids encoding mitochondria-targeted EGFP (mt-EGFP; green color; marker for transfected cells) and either HsPEX5(S), HsPEX5(S)-FLAG, EGFP-HsPEX5(S), HsPEX5(S)-EGFP, HsPEX5(L), HsPEX5(L)-EGFP, HsPEX5(L)-KR, or mouse (Mus musculus, Mm) PEX5(L)-EGFP. One day later, the cells were fixed, counterstained with DAPI, and processed for immunofluorescence with anti-ABCD3 antibodies followed by TxRed- or Alexa Fluor 488-conjugated secondary antibodies. The number of peroxisomes in each transfected cell was counted and cataloged as more than 50 (>50 ), between 1 and 50 (1–50), or none (0). (A) Images of cells co-expressing mt-EGFP and PEX5(S)-EGFP with >50 (left panels), 1–50 (middle panels), or 0 (right panels) remaining peroxisomes are shown (these images depict representative examples of all phenotypes observed). Scale bar: 10 µm. (B) The percentage of transfected cells displaying each phenotype is plotted. The values above each bar represent the number of transfected cells analyzed per condition. A compilation of the results of at least 3 independent experiments (see Fig. S21) is shown. The “>50 peroxisomes” values from the “HsPEX5(S)” and “HsPEX5(L)” subpanels were statistically compared with the value from the corresponding control (−) condition (* p < 0.05; ** p < 0.01).