Cyclophilin A is conserved from yeast to humans and mediates the ability of cyclosporine to perturb signal transduction cascades via inhibition of calcineurin. Cyclophilin A also catalyzes cis-trans peptidyl-prolyl isomerization during protein folding or conformational changes; however, cyclophilin A is not essential in yeast or human cells, and the true biological functions of this highly conserved enzyme have remained enigmatic. In Saccharomyces cerevisiae, cyclophilin A becomes essential in cells compromised for the nuclear prolyl-isomerase Ess1, and cyclophilin A physically interacts with two nuclear histone deacetylase complexes, Sin3-Rpd3 and Set3C, which both control meiosis. Here we show that cyclophilin A is localized to the nucleus in yeast cells and governs the meiotic gene program to promote efficient sporulation. The prolyl-isomerase activity of cyclophilin A is required for this meiotic function. We document that cyclophilin A physically associates with the Set3C histone deacetylase and analyze in detail the structure of this protein-protein complex. Genetic studies support a model in which cyclophilin A controls meiosis via Set3C and an additional target. Our findings reveal a novel nuclear role for cyclophilin A in governing the transcriptional program required for the vegetative to meiotic developmental switch in budding yeast.Cyclophilin A was originally identified as the intracellular receptor of the immunosuppressive drug cyclosporine (Cs), and the two molecules form a complex that binds to and inhibits the protein phosphatase calcineurin, preventing T-cell activation in mammals (36,52,53). Although cyclophilin A is highly conserved from yeast to humans, establishing the normal biological functions of this nonessential protein has proven elusive. Cyclophilin A is the founding member of a class of ubiquitous and highly conserved enzymes collectively known as peptidyl-prolyl cis-trans isomerases, or prolyl-isomerases, which catalyze cis-trans isomerization of the peptide bonds preceding proline residues. The prolyl-isomerase group spans three structurally unrelated protein families: the cyclophilins, FKBPs (for FK506 binding proteins), and parvulins (34,40,69,81). All three families are present in the budding yeast Saccharomyces cerevisiae, which expresses eight different cyclophilins (Cpr1 to Cpr8), four FKBPs (Fpr1 to Fpr4), and a single parvulin (Ess1), which is the only essential prolyl-isomerase in this organism (20,37,39). Cellular roles have been established for several prolylisomerases in both mammals and yeast. In mammals, cyclophilin A associates with the human immunodeficiency virus type 1 Gag polyprotein and is incorporated into virion particles, where it is required for human immunodeficiency virus type 1 infectivity (7,9,28,84). Cyclophilin A also binds to and regulates the tyrosine kinase Itk in T lymphocytes (11,55). FKBP12regulates the activity of the ryanodine receptor, a calcium release channel in the sarcoplasmic reticulum (61,85,86), and both FKBP12 and cyclophilin A intera...