In many organisms the coordinated synthesis of membrane lipids is controlled by feedback systems that regulate the transcription of target genes. However, a complete description of the transcriptional changes that accompany the remodeling of membrane phospholipids has not been reported. To identify metabolic signaling networks that coordinate phospholipid metabolism with gene expression, we profiled the sequential and temporal changes in genome-wide expression that accompany alterations in phospholipid metabolism induced by inositol supplementation in yeast. This analysis identified six distinct expression responses, which included phospholipid biosynthetic genes regulated by Opi1p, endoplasmic reticulum (ER) luminal protein folding chaperone and oxidoreductase genes regulated by the unfolded protein response pathway, lipid-remodeling genes regulated by Mga2p, as well as genes involved in ribosome biogenesis, cytosolic stress response, and purine and amino acid metabolism. We also report that the unfolded protein response pathway is rapidly inactivated by inositol supplementation and demonstrate that the response of the unfolded protein response pathway to inositol is separable from the response mediated by Opi1p. These data indicate that altering phospholipid metabolism produces signals that are relayed through numerous distinct ER-to-nucleus signaling pathways and, thereby, produce an integrated transcriptional response. We propose that these signals are generated in the ER by increased flux through the pathway of phosphatidylinositol synthesis.
The endoplasmic reticulum (ER)2 is a dynamic organelle that responds to environmental and developmental cues by regulating the levels of lipids and proteins required for the biogenesis and maintenance of membrane-bound compartments. It is the site of the synthesis and turnover of a major fraction of the lipid components that comprise the entire endomembrane system (1, 2), including phosphatidylinositol (PI), which is the precursor of the essential glycosylphosphatidylinositol lipids, sphingolipids, and phosphoinositides, as well as the soluble inositol polyphosphates (reviewed in Refs. 3-5). A variety of feedbackcontrol systems have been described in animals and fungi that allow cells to monitor and adjust membrane constituents to their proper stoichiometry. For example, the sterol regulatoryelement-binding protein-Scap pathway, which senses sterol levels in the ER, regulates the transcription of genes required for sterol biosynthesis (reviewed in Ref. 6), whereas the unfolded protein response (UPR) pathway, which senses ER secretory stress, regulates the expression of genes that are required for ER homeostasis (reviewed in Ref. 7). However, our understanding of how cells sense the ER membrane environment, then integrate and transmit these signals to the nucleus is incomplete.The model eukaryote, Saccharomyces cerevisiae, adjusts its membrane lipid composition according to the availability of the soluble phospholipid precursors, inositol and choline (8 -13). The additi...