The yeast peroxisomal proteome at absolute quantitative scale

Peroxisomes are dynamic organelles vital for lipid metabolism and redox homeostasis. In Saccharomyces cerevisiae , the expression of peroxisomal proteins is tightly regulated in response to metabolic conditions. Here, we provide the first absolute quantification of the yeast peroxisomal proteome under peroxisome-inducing (oleate) and fermentative (glucose) conditions using a label-free mass spectrometry approach. We determined protein copy numbers for ~ 4500 proteins, including 99 peroxisomal and peroxisome-associated proteins. Our data reveal that the overall peroxisomal proteome is approximately threefold more abundant in oleate-grown cells, constituting 2.8% (2.01 × 10 6 protein copies) of the total proteome compared to 0.8% (6.67 × 10 5 protein copies) in glucose. Considering only peroxisomal core proteins, i.e., proteins exclusively or predominantly localized in peroxisomes, total copy numbers for peroxisomal proteins were even ninefold higher on oleate (0.9%, 6.29 × 10 5 protein copies) compared to glucose (0.1%, 7.78 × 10 4 protein copies), reflecting the necessity for peroxisomal functions such as fatty acid beta-oxidation. Enzymes of the beta-oxidation and glyoxylate cycle showed up to > 500-fold higher abundance in oleate. In contrast, core components of the peroxisomal protein import machinery (e.g., Pex5, Pex14) exhibited only moderate changes (~ 2- to 8-fold). In addition to metabolic enzymes and components of the peroxisomal protein import pathways, we provide copy number data for proteins involved in cellular stress response, peroxisome proliferation, division and organization, peroxisome-associated membrane contact sites, and metabolite transporter. Taken together, our dataset offers a quantitative framework of peroxisomal remodeling under different metabolic conditions and highlights the organelle’s adaptive flexibility, providing a valuable resource for future studies on peroxisome biology.