Yeast Crf1p: An activator in need is an activator indeed

Abstract

Ribosome biogenesis is an energetically costly process, and tight regulation is required for stoichiometric balance between components. This requires coordination of RNA polymerases I, II, and III. Lack of nutrients or the presence of stress leads to downregulation of ribosome biogenesis, a process for which mechanistic target of rapamycin complex I (mTORC1) is key. mTORC1 activity is communicated by means of specific transcription factors, and in yeast, which is a primary model system in which transcriptional coordination has been delineated, transcription factors involved in regulation of ribosomal protein genes include Fhl1p and its cofactors, Ifh1p and Crf1p. Ifh1p is an activator, whereas Crf1p has been implicated in maintaining the repressed state upon mTORC1 inhibition. Computational analyses of evolutionary relationships have indicated that Ifh1p and Crf1p descend from a common ancestor. Here, we discuss recent evidence, which suggests that Crf1p also functions as an activator. We propose a model that consolidates available experimental evidence, which posits that Crf1p functions as an alternate activator to prevent the stronger activator Ifh1p from re-binding gene promoters upon mTORC1 inhibition. The correlation between retention of Crf1p in related yeast strains and duplication of ribosomal protein genes suggests that this backup activation may be important to ensure gene expression when Ifh1p is limiting. With ribosome biogenesis as a hallmark of cell growth, failure to control assembly of ribosomal components leads to several human pathologies. A comprehensive understanding of mechanisms underlying this process is therefore of the essence.

Keywords: CK2, casein kinase 2; Crf1, corepressor with forkhead like; Crf1p; FHA, forkhead-associated; FHB, forkhead-binding; FKBP, FK506 binding protein; Fhl1, forkhead like; Fpr1, FK506-sensitive proline rotamase; Gene regulation; Hmo1, high mobility group; Ifh1, interacts with forkhead like; Ifh1p; RASTR, ribosome assembly stress response; RP, ribosomal protein; Rap1, repressor/activator protein; RiBi, ribosome biogenesis; Ribosomal protein; Ribosome biogenesis; Sfp1, split finger protein; WGD, whole genome duplication; mTORC1; mTORC1, mechanistic target of rapamycin complex 1.

Graphical abstract

Fig. 1

Effectors and targets of mTORC1. An overview of events, which activate (green arrows) or inhibit (red lines) mTORC1. Examples of mTORC1 targets shown below. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 2

mTORC1 functions to control ribosome biogenesis. In the cytoplasm, active mTORC1 generally promotes translation, for example by direct phosphorylation of 4E-BP. Newly synthesized RPs translocate to the nucleolus for ribosome assembly. mTORC1 indirectly (via PKA and Yak1p) controls the subcellular localization of Crf1p, and it phosphorylates Maf1p to prevent its nuclear localization, thereby ensuring active Pol III transcription. Nuclear mTORC1 functions include direct binding of Tor kinase to both Pol I- and Pol III-transcribed rRNA genes and control of transcription factors associated with transcription by Pols I, II, and III. Inhibition of mTORC1 causes release of Ifh1p from RP genes and its sequestration within the nucleolar CURI complex, a process that also sequesters the RiBi proteins Utp22p and Rrp7p.

Fig. 3

Conservation of transcription factors. A. Phylogenetic tree of select ascomycetes. Species identified with solid lines diverged after the WGD event, and species identified with dashed lines diverged prior to the WGD. Adapted from . B. S. cerevisiae Ifh1p and Crf1p. Both proteins feature a conserved forkhead-binding (FHB) domain. Crf1p lacks N- and C-terminal extensions compared to Ifh1p. C. Alignment of Fhl1p, Ifh1p, and Utp22p from S. cerevisiae (blue), C. glabrata (orange), and K. lactis (red) using NCBI Blastp. Identity and coverage relative to the corresponding S. cerevisiae ortholog is indicated at the right. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 4

The dynamics of CURI complex formation may dictate dependence on Crf1p. When mTORC1 is active (left), Crf1p is predominantly cytoplasmic. Nuclear Crf1p may bind Fhl1p and promote transcription of RP genes if Ifh1p is limiting. Direct phosphorylation of Sfp1p by mTORC1 ensures its nuclear localization. The nucleolar UTP-C subcomplex composed of CKII, Utp22p, and Rrp7p processes pre-rRNA. On inhibition of mTORC1 (right), Sfp1p leaves the nucleus. Crf1p is phosphorylated and translocates to the nucleus. Ifh1p interacts directly with Utp22p, and both proteins become sequestered in the CURI complex. Alternatively, Ifh1p may become trapped within newly synthesized RP aggregates. Absence of Ifh1p is sufficient for repression of RP gene transcription. We propose that Crf1p may be required to maintain reduced RP gene expression under conditions where sequestration of Ifh1p is transient and re-binding of Ifh1p to RP genes is rapid.