RAFT1/FRAP/mTOR is a key regulator of cell growth and division and the mammalian target of rapamycin, an immunosuppressive and anticancer drug. Rapamycin deprivation and nutrient deprivation have similar effects on the activity of S6 kinase 1 (S6K1) and 4E-BP1, two downstream effectors of RAFT1, but the relationship between nutrient-and rapamycin-sensitive pathways is unknown. Using transcriptional profiling, we show that, in human BJAB B-lymphoma cells and murine CTLL-2 T lymphocytes, rapamycin treatment affects the expression of many genes involved in nutrient and protein metabolism. The rapamycin-induced transcriptional profile is distinct from those induced by glucose, glutamine, or leucine deprivation but is most similar to that induced by amino acid deprivation. In particular, rapamycin treatment and amino acid deprivation up-regulate genes involved in nutrient catabolism and energy production and down-regulate genes participating in lipid and nucleotide synthesis and in protein synthesis, turnover, and folding. Surprisingly, however, rapamycin had effects opposite from those of amino acid starvation on the expression of a large group of genes involved in the synthesis, transport, and use of amino acids. Supported by measurements of nutrient use, the data suggest that RAFT1 is an energy and nutrient sensor and that rapamycin mimics a signal generated by the starvation of amino acids but that the signal is unlikely to be the absence of amino acids themselves. These observations underscore the importance of metabolism in controlling lymphocyte proliferation and offer a novel explanation for immunosuppression by rapamycin.Rapamycin is an immunosuppressive drug used to prevent the rejection of transplanted organs and a promising anticancer agent (18,26,27,32). Studies of its mechanism of action have led to the discovery of the TOR pathway, an evolutionarily conserved signaling network that plays critical roles in eukaryotic cell growth and cell cycle progression. In mammalian cells, the complex of rapamycin with its receptor, FKBP12, binds directly to the central component of the pathway, a large protein kinase called RAFT1/FRAP/mTOR (5, 33, 34). Exactly how the rapamycin-FKBP12 complex perturbs the function of RAFT1 is not well understood. Work in yeast, Drosophila, and mammals suggests that the TOR proteins participate in nutrient-sensitive signaling. Treatment of yeast and Drosophila larvae with rapamycin causes a starvation-like phenotype (2,7,17,39), and in mammalian cells, extracellular amino acids regulate the activity of two translational regulators downstream of RAFT1, S6 kinase 1 (S6K1), and 4E-BP1 (15). Recent studies indicate that the levels of ATP and phosphatidic acid may regulate the TOR pathway in mammalian cells (11,13), but the connection to nutrient signaling is not clear.Available evidence indicates that the TOR pathway is ubiquitously expressed in mammalian cell types, and it is not known why rapamycin causes immunosuppression in human beings and other mammals without significantly affecti...