Yeast cells were grown in glucose-limited chemostat cultures and forced to switch to a new carbon source, the fatty acid oleate. Alterations in gene expression were monitored using DNA microarrays combined with bioinformatics tools, among which was included the recently developed algorithm REDUCE. Immediately after the switch to oleate, a transient and very specific stress response was observed, followed by the up-regulation of genes encoding peroxisomal enzymes required for fatty acid metabolism. The stress response included up-regulation of genes coding for enzymes to keep thioredoxin and glutathione reduced, as well as enzymes required for the detoxification of reactive oxygen species. Among the genes coding for various isoenzymes involved in these processes, only a specific subset was expressed. Not the general stress transcription factors Msn2 and Msn4, but rather the specific factor Yap1p seemed to be the main regulator of the stress response. We ascribe the initiation of the oxidative stress response to a combination of poor redox flux and fatty acid-induced uncoupling of the respiratory chain during the metabolic reprogramming phase.
INTRODUCTIONAerobic life is associated with the production of reactive oxygen species (ROS) by various metabolic processes. ROS can modify lipids, proteins, and nucleic acids and can particularly cause mutations in DNA, which might contribute to tumor formation. Normally, ROS production is kept at bay by a variety of detoxifying enzymes, some of which derive their reducing power from glutathione (GSH) or thioredoxins (TRXs) (Hohmann and Mager, 1997;Jamieson and Storz, 1997;Grant et al., 1998). However, in certain pathological conditions caused by tissue damage or during treatment with certain pharmaceuticals, this protection fails, probably due to a compromised redox state: [NAD(P)H/ NAD(P)]. Although the mitochondrial respiratory chain is an important source of ROS, peroxisomal metabolism is another contributor in this respect. For instance, in rodents, application of hypolipidemic drugs resulted in enlargement of the peroxisome compartment, and long-term treatment even caused cancer (Lock et al., 1989;Reddy and Mannaerts, 1994).Peroxisomes house a number of oxidative enzymes producing ROS, such as H 2 O 2 , which is formed during the -oxidation of fatty acids (Beevers, 1969;Van den Bosch et al., 1992). In the classic view, the raison d'etre of the organelle is to provide a boundary to keep ROS confined within a compartment where they can be quickly detoxified. Several considerations indicate that this concept may be too simple (Tabak et al., 1999). H 2 O 2 can easily permeate through membranes and loss of peroxisomal catalase remains without symptoms. Is this due to the fact that other detoxifying enzymes come to the rescue? There are indeed suggestions that peroxisomes harbor additional GSH or thioredoxin-dependent detoxifying enzymes (Jeong et al., 1999;Lee et al., 1999b), but it may also be that cytosolic enzymes are recruited. An opportunity to study the role of perox...