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

Abstract

Fpr1 (FK506-sensitive proline rotamase 1), a protein of the FKBP12 (FK506-binding protein 12 kDa) family in Saccharomyces cerevisiae, is a primary target for the immunosuppressive agents FK506 and rapamycin. Fpr1 inhibits calcineurin and TORC1 (target of rapamycin complex 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 a hmo1Δ (high mobility group family 1-deleted) yeast strain, deletion of FPR1 induced severe growth defects, which could be alleviated by increasing the copy number of RPL25 (ribosome protein of the large subunit 25), suggesting that RPL25 expression was affected in hmo1Δfpr1Δ 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 (ribosomal protein gene) promoters, presumably in a manner dependent on Rap1 (repressor/activator site binding protein 1). Intriguingly, Fpr1 promotes the binding of Fhl1/Ifh1 (forkhead-like 1/interacts with forkhead 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.

Toward the discovery of biological functions associated with the mechanosensor Mtl1p of Saccharomyces cerevisiae via integrative multi-OMICs analysis

“…5 ). FPR1 is a protein of the FKBP12 family in S. cerevisiae, which is a primary target for rapamycin 99 . Addition of rapamycin results in the formation of the FPR1-rapamycin complex required for TORC1 inhibition 100 .…”

Transcriptional control of ribosome biogenesis in yeast: links to growth and stress signals

“…We thus argue that the most parsimonious explanation of these data is that loss of Hmo1 may destabilize or alter Fhl1 and Ifh1 binding in such a way that reduces or abrogates their chromatin immunoprecipitation (ChIP) signal while only modestly affecting their ability to activate transcription. Curiously, the proline isomerase and rapamycin target protein Fpr1 (FK506-sensitive proline rotamase 1), which binds to the majority of RPG promoters ( Figure 1C ), often co-incident with Rap1 [ 28 ], also appears to stabilize Fhl1/Ifh1 binding. Fpr1 is discussed in more detail below.…”

“…As alluded to above, the yeast FKBP12 prolyl isomerase Fpr1 [ 67 ], which also mediates the rapamycin-induced inhibition of TORC1 and interacts physically and genetically with Hmo1, has been identified recently as a novel TF at RPGs [ 28 ]. Fpr1 is robustly detected by ChIP at the promoters of most RPGs (95%; thus, not exclusively at those bound by Hmo1) and at very few (∼10) other genes.…”

“…The effect of fpr1 Δ on RPG transcription is less than one might expect given its widespread binding, with only four RPGs showing a significant decrease in steady-state mRNA levels, compared to the ∼50 genes affected by hmo1 Δ [ 28 ]. Interestingly, an fpr1 Δ hmo1 Δ double mutant displays a number of additive or synergistic decreases in transcription of specific RPGs, consistent with its severe slow-growth phenotype (or lethality; [ 67 ]).…”

“…Fpr1, on the other hand, contains no known DNA-binding motif and its high degree of specificity for RPG promoters remains unexplained. Though Rap1 binding may be necessary for association of Fpr1 at RPG promoters [ 28 ], it cannot be sufficient given the large number of non-RPG promoters that bind Rap1 but not Fpr1. One is thus left with the impression that the majority of RPG TFs rely upon small networks of cooperative interactions (protein–protein and/or protein–DNA) to achieve specificity.…”