Integrative Omics reveals changes in the cellular landscape of yeast without peroxisomes

Peroxisomes are organelles that are crucial for cellular metabolism. However, these organelles play also important roles in non-metabolic processes, such as signalling. To uncover the consequences of peroxisome deficiency, we compared two extremes, namely Saccharomyces cerevisiae wild-type and pex3 cells, which lack functional peroxisomes, employing transcriptomics and quantitative proteomics technology. Cells were grown on acetate, a carbon source that involves peroxisomal enzymes of the glyoxylate cycle and does not repress peroxisomal proteins. Transcripts of peroxisomal {beta}-oxidation genes and the corresponding proteins were enhanced in pex3 cells. Peroxisome-deficiency also caused reduced levels of membrane bound peroxins, while the soluble receptors Pex5 and Pex7 were enhanced at the protein level. In addition, we observed alterations in non-peroxisomal transcripts and proteins, especially mitochondrial proteins involved in respiration or import processes. Our results not only reveal the impact of the absence of peroxisomes in yeast, but also represent a rich resource of candidate genes/proteins that are relevant in peroxisome biology. SummaryOmics comparison of wild-type and peroxisome-deficient (pex3) yeast cells uncovered processes that are affected by loss of peroxisomes. {beta}-oxidation enzymes were upregulated, whereas most peroxins were decreased. Also, several non-peroxisomal transcripts/proteins were significantly altered. Our data represent a rich source of candidate genes connected to peroxisome biology.