Loss of Compartmentalization Causes Misregulation of Lysine Biosynthesis in Peroxisome-Deficient Yeast Cells

Abstract

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...

A Peroxisomal Glutathione Transferase of Saccharomyces cerevisiae Is Functionally Related to Sulfur Amino Acid Metabolism

“…Besides the involvement in the ␤-oxidation of fatty acids (38), yeast peroxisomes participate in other cellular functions, such as lysine biosynthesis. In fact, Lys1 and Lys4 enzymes have been detected in S. cerevisiae peroxisomes (45) and probably Lys12 is also peroxisomal (8), whereas other enzymes of the pathway are cytosolic. Yeast cells negatively affected in peroxisome biogenesis upregulate lysine biosynthesis genes, although peroxisome-deficient S. cerevisiae cells are still able to synthesize lysine, probably through alternative reactions (8).…”

“…In fact, Lys1 and Lys4 enzymes have been detected in S. cerevisiae peroxisomes (45) and probably Lys12 is also peroxisomal (8), whereas other enzymes of the pathway are cytosolic. Yeast cells negatively affected in peroxisome biogenesis upregulate lysine biosynthesis genes, although peroxisome-deficient S. cerevisiae cells are still able to synthesize lysine, probably through alternative reactions (8). The cystathionine ␤-lyase Str3 is a second example of a peroxisomal S. cerevisiae enzyme involved in amino acid metabolism, in this case in the transulfuration pathway from cysteine to homocysteine (Fig.…”

Regulation of Amino Acid, Nucleotide, and Phosphate Metabolism in Saccharomyces cerevisiae

“…Finally, LYS gene expression is coordinately induced in cells lacking functional peroxisomes, suggesting that a-AAS is normally sequestered within this organelle (Breitling et al 2002). This latter finding raises the possibility that one or more steps of basal lysine biosynthesis may occur within peroxisomes, which would restrict a-AAS from entering the nucleus and preventing improper induction of Lys14-dependent gene expression.…”

“…The next two steps of the pathway from homocitrate to a-ketoadipate (LYS4 and LYS12), and the final three steps from a-aminoadipate to lysine (LYS2/LYS5, LYS9, and LYS1) are thought to take place in the mitochondria and cytosol, respectively (Xu et al 2006). Several mitochondrial carrier family members (Odc1, Odc2, and Ctp1) are implicated in the transport of AAA intermediates across the mitochondrial inner membrane (Table 5) (Breitling et al 2002;Palmieri et al 2006).…”

Coexpression Analysis of Human Genes Across Many Microarray Data Sets

“…Most existing studies that have analyzed multiple independently collected microarray data sets have focused on differential expression, comparing two or more similar data sets to look for genes that distinguish different sets of samples (Breitling et al 2002;Rhodes et al 2002;Yuen et al 2002;Choi et al 2003;Detours et al 2003;Ramaswamy et al 2003;Sorlie et al 2003;Xin et al 2003). Another type of comparison is exemplified by a study that examined the variability of expression for individual genes in several human and mouse data sets (Lee et al 2002).…”