Extended Data Fig. 1: Log2 fold change in transcription of genes related to peroxisomes between a strain with engineered TFs (constitutively expressed and constitutively active version of Adr1, Oaf1, and Pip2) and WT.

From the GO: 0007031 term related to peroxisome organization, only the TFs that were constitutively expressed had more than a log2-fold change greater than 0.5. The remaining genes all fall within a log2 fold change of -0.36 and 0.41, indicating relatively small changes to transcription levels for genes involved in peroxisome organization. In comparison, other oleate-induction transcriptomics results report log2 fold changes greater than 5 for other genes, even for some membrane proteins. Thus, these TF-induced transcription changes are minimal compared to other studies. From the GO: 0005777 term related to peroxisomes, the genes with the highest increase in transcription were all beta-oxidation of fatty acid genes located in the peroxisome matrix and PEX11, involved in peroxisome fission. The proteins involved in beta-oxidation of fatty acids are unlikely to also control peroxisome morphology and proliferation. Pex11p has important roles controlling peroxisome fission and therefore morphology¹⁸. The genes most downregulated in the TFs compared to WT are: OPT2, CIT2, PNC1, PXP2, and MLS1. These genes encode proteins that localize to the peroxisome matrix but have no reported relationship to peroxisome proliferation, morphology, or oleate induction. Excluding these genes, the rest of the genes in this category, including all PEX genes (Supplementary Table 1) fall between a log2 fold of -0.506 and 0.530, indicating the rest of the genes in this category have relatively small changes in transcription. The GO: 000425 and 0030242 terms related to peroxisome pexophagy showed small downregulations in transcription for most of the genes. Overall, the data show small transcription increases to many genes and decreases in transcription to most pexophagy-related genes.