Global proteomics analysis of Saccharomyces WT versus PEX3 knockout cells

Peroxisomes are common eukaryotic cell organelles. So far, the inventory of the yeast peroxisomal proteome is still incomplete. To identify novel peroxisomal proteins, we compared yeast wild-type (WT) and PEX3 knockout cells, which lack functional peroxisomes by whole cell proteomics and transcriptomics. Cells were grown on acetate, a carbon source that involves peroxisomal enzymes of the glyoxylate cycle. Transcriptome analysis showed that, with the exception of transcripts of β-oxidation enzymes, the transcriptome of peroxisomal proteins was largely unchanged. In contrast, whole cell proteomics analysis revealed that peroxisome deficiency results in a reduction of the levels of peroxisomal membrane proteins. A set of non-peroxisomal membrane proteins showed a similar behavior. We therefore analyzed one of these proteins, the mitochondrial pyruvate carrier protein Mpc3, and show that Mpc3 has a dual localization on peroxisomes and mitochondria. In conclusion we present a novel approach to uncover new examples of dually localized membrane proteins.