Fpr1, a primary target of rapamycin, functions as a transcription factor for ribosomal protein genes cooperatively with Hmo1 in Saccharomyces cerevisiae.

Author summary In eukaryotic cells, ribosome production requires the activity of all three RNA polymerases plus vast amounts of energy and resources. Therefore, ribosome production is regulated strictly and in a coordinated manner in response to specific environmental conditions. Fpr1 forms a complex with the immunosuppressive agent rapamycin, and this binary complex inhibits TORC1, a central player in coordinated ribosome production. Fpr1 is known to play a crucial role in drug efficacy, but its involvement in ribosomal biogenesis under physiological conditions remains unclear.FPR1mutation has been shown to cause synthetic lethality with mutation ofHMO1, a widely recognised transcriptional regulator of ribosomal component genes. A previous study demonstrated that the growth defect ofhmo1 Delta fpr1 Delta cells could be suppressed by increasing the copy number ofRPL25, an essential RPG, which suggested that decrease ofRPL25expression caused the growth defect. Here, we found that Fpr1 specifically binds to the promoters of RPGs, includingRPL25, in a Rap1-dependent manner, and promotes Fhl1/Ifh1 binding to certain RPG promoters. Mutation analyses of Fpr1 revealed that transcriptional regulation by Fpr1 is a physiological process that is unrelated to its non-physiological function in interacting with TORC1. We conclude that Fpr1 is a transcriptional regulator of RPGs. Fpr1 (FK506-sensitiveprolinerotamase 1), a protein of the FKBP12 (FK506-bindingprotein 12 kDa) family inSaccharomyces cerevisiae, is a primary target for the immunosuppressive agents FK506 and rapamycin. Fpr1 inhibits calcineurin and TORC1 (targetofrapamycincomplex 1) when bound to FK506 and rapamycin, respectively. Although Fpr1 is recognised to play a crucial role in the efficacy of these drugs, its physiological functions remain unclear. In ahmo1 Delta (highmobility group family 1-deleted) yeast strain, deletion ofFPR1induced severe growth defects, which could be alleviated by increasing the copy number ofRPL25(ribosomeprotein of thelarge subunit 25), suggesting thatRPL25expression was affected inhmo1 Delta fpr1 Delta cells. In the current study, extensive chromatin immunoprecipitation (ChIP) and ChIP-sequencing analyses revealed that Fpr1 associates specifically with the upstream activating sequences of nearly all RPG (ribosomalproteingene) promoters, presumably in a manner dependent on Rap1 (repressor/activator site bindingprotein 1). Intriguingly, Fpr1 promotes the binding of Fhl1/Ifh1 (forkhead-like 1/interacts withforkhead 1), two key regulators of RPG transcription, to certain RPG promoters independently of and/or cooperatively with Hmo1. Furthermore, mutation analyses of Fpr1 indicated that for transcriptional function on RPG promoters, Fpr1 requires its N-terminal domain and the binding surface for rapamycin, but not peptidyl-prolyl isomerase activity. Notably, Fpr1 orthologues from other species also inhibit TORC1 when bound to rapamycin, but do not regulate transcription in yeast, which suggests that these two functions of Fpr1 are independent of each other.