To characterize the metabolic role of peroxisomes in yeast cells under physiological conditions, we performed a comprehensive meta-analysis of published microarray data. Previous studies of yeast peroxisomes have mainly been focused on the function of peroxisomes under extreme conditions, such as growth on oleate or methanol as the sole carbon source, and may therefore not be representative of the normal physiological role of yeast peroxisomes. Surprisingly, our analysis of the microarray data reveals that the only pathway responding to peroxisome deficiency in mid-log phase is lysine biosynthesis, whereas classical peroxisomal pathways such as beta-oxidation are unaffected. We show that the upregulation of lysine biosynthesis genes in peroxisome-deficient yeasts shares many characteristics with the physiological response to lysine starvation. We provide data that suggest that this is the result of a "pathological" stimulation of the Lys14p transcriptional activator by the pathway intermediate aminoadipate semialdehyde. Mistargeting of the peroxisomal lysine pathway to the cytosol increases the active concentration of aminoadipate semialdehyde, which is no longer contained in the peroxisome and can now activate Lys14p at much lower levels than in wild-type yeasts. This is the first well-documented example of pathway misregulation in response to peroxisome deficiency and will be useful in understanding the phenotypic details of human peroxisome-deficient patients (Zellweger syndrome).Peroxisomes are single-membrane-bounded organelles present in most eukaryotic cells, with the exception of Plasmodium, Giardia, Trichomonas, Entamoeba, and related species. Peroxisomes typically contain the enzymes of fatty acid betaoxidation and catalase, which converts the hydrogen peroxide formed by fatty acyl-coenzyme A (CoA) oxidase to water and oxygen. Several other oxidases, e.g., monoamine oxidase, urate oxidase, hydroxyacid oxidase, methanol oxidase, and acetylspermidine oxidase, are also present in peroxisomes of some species and benefit from the same detoxification mechanism. In addition to these oxidative reactions, peroxisomes may contain many other biosynthetic pathways. Enzymes of these supplemental pathways are usually absent or localized in nonperoxisomal compartments in most eukaryotes, and their peroxisomal localization is a specialization of relatively few species. Examples of facultative peroxisomal pathways are glycolysis and purine salvage (in the peroxisomes of kinetoplastids, such as Trypanosoma and Leishmania [23]), isoprenoid biosynthesis (in vertebrates [1]), ether phospholipid biosynthesis (in kinetoplastids and animals [15,33]), and the glyoxylate cycle, which channels the products of beta-oxidation into gluconeogenesis in plants, yeasts, and Caenorhabditis elegans (7).Peroxisome-deficient mutants of most organisms are viable (with the possible exception of kinetoplastids), but a lack of functional peroxisomes can lead to severe pathologies in multicellular organisms (3,5,8,16,20,24). In all organisms ex...