Cryptococcus neoformans is a fungal pathogen that causes meningitis in patients immunocompromised by AIDS, chemotherapy, organ transplantation, or high-dose steroids. Current antifungal drug therapies are limited and suffer from toxic side effects and drug resistance. Here, we defined the targets and mechanisms of antifungal action of the immunosuppressant rapamycin in C. neoformans. In the yeast Saccharomyces cerevisiae and in T cells, rapamycin forms complexes with the FKBP12 prolyl isomerase that block cell cycle progression by inhibiting the TOR kinases. We identified the gene encoding a C. neoformans TOR1 homolog. Using a novel two-hybrid screen for rapamycin-dependent TOR-binding proteins, we identified the C. neoformans FKBP12 homolog, encoded by the FRR1 gene. Disruption of the FKBP12 gene conferred rapamycin and FK506 resistance but had no effect on growth, differentiation, or virulence of C. neoformans. Two spontaneous mutations that confer rapamycin resistance alter conserved residues on TOR1 or FKBP12 that are required for FKBP12-rapamycin-TOR1 interactions or FKBP12 stability. Two other spontaneous mutations result from insertion of novel DNA sequences into the FKBP12 gene. Our observations reveal that the antifungal activities of rapamycin and FK506 are mediated via FKBP12 and TOR homologs and that a high proportion of spontaneous mutants in C. neoformans result from insertion of novel DNA sequences, and they suggest that nonimmunosuppressive rapamycin analogs have potential as antifungal agents.Cryptococcus neoformans is an opportunistic fungal pathogen that causes systemic mycosis in immunocompromised patients (20,45). Cryptococcosis in patients with AIDS is characterized by a poor response to therapy and a risk of recurrent disease requiring lifelong suppressive antifungal regimens. Current treatments include amphotericin B, flucytosine, and fluconazole. However, treatment failures and toxicity are common, and new antifungal agents are needed.C. neoformans is sensitive to the immunosuppressants rapamycin, FK506, and cyclosporine (CsA) (48, 49). These compounds are natural products with antifungal activity and are also potent immunosuppressants used to treat graft rejection in transplant recipients (7,38). Rapamycin is a macrolide originally discovered in a screen for antimicrobial activity against Candida albicans and later found to have potent immunosuppressive activity (62).Rapamycin, FK506, and CsA suppress the immune system by inhibiting signal transduction steps required for T-cell activation (for reviews, see references 19 and 59). The mechanisms of action of these compounds have been studied in lymphocytes and Sacharomyces cerevisiae (for reviews, see references 11, 18, 32, and 59). These hydrophobic compounds diffuse into the cell and bind intracellular receptors known as immunophilins. The immunophilins are ubiquitous and conserved from yeast to humans. FK506 and rapamycin bind the immunophilin FKBP12, whereas CsA binds cyclophilin A. Although the cyclophilin and FKBP proteins have no s...