Intricate regulation of ribosome biogenesis genes in response to mTORC1 signaling

Abstract

SummaryGenes encoding ribosomal proteins are repressed in response to inhibition of mTORC1. In Saccharomyces cerevisiae, this involves dissociation of the activator Ifh1p in a process that depends on Utp22p, a protein that also functions in pre-rRNA processing. Ifh1p has a paralog, Crf1p, which can mediate mTORC1 inhibition by acting as a repressor. Ifh1p and Crf1p derive from a common ancestor, which may have acted as both an activator and a repressor. We report here that UTP22 and RRP7, which encodes another pre-rRNA processing factor, are controlled by mTORC1; both gene promoters are bound by Ifh1p, which dissociates on mTORC1 inhibition. Notably, Crf1p acts as an activator as evidenced by reduced expression in a crf1Δ strain. By contrast, Crf1p is required to repress expression of HMO1, which encodes a cofactor involved in communicating mTORC1 activity to target genes. Our data therefore indicate that Crf1p exhibits the dual repressor/activator functions of the Ifh1p-Crf1p ancestor.

Yeast Crf1p: An activator in need is an activator indeed

“…Regulation of HMO1 appears to be more complex. Rapamycin treatment does not lead to reduced HMO1 mRNA abundance in a W303-derived crf 1Δ strain, except under conditions of prolonged (>1h) exposure [105] . It is also notable that HMO1 mRNA abundance is not reduced as efficiently as RP genes (<50%) when wild-type cells are treated with rapamycin.…”

“…This experiment also showed that repression of Category I and II RP genes in response to rapamycin treatment is compromised when Crf1p entirely replaces Ifh1p [37] , consistent with absence of the N- and C-terminal protein domains in Crf1p, which have been implicated in removing Ifhl1p from RP gene promoters. Furthermore, we have recently reported that endogenous Crf1p also promotes expression of select Category I and II RP genes during balanced growth as evidenced by reduced mRNA accumulation in a crf 1Δ strain [105] . Taken together, these observations suggest that Crf1p functions as an activator.…”

“…Addition of rapamycin represses transcription, and it causes the release of Ifh1p, similar to what occurs on RP genes, and the dissociation of Ifh1p is followed by accumulation of Crf1p. In the W303-derived crf 1Δ strain, UTP22 and RRP7 mRNA abundance decreases on mTORC1 inhibition, indicating that Crf1p is dispensable for regulation [105] . While this observation may seem unremarkable in that it recapitulates the regulation seen for RP genes, it is notable because it reveals a regulatory mechanism, which is unlike that reported for other RiBi genes.…”

“…Notably, the requirement for Crf1p is not conserved among S. cerevisiae strains. The inference that Crf1p functions as a repressor in controlling of RP gene expression was based on experiments with S. cerevisiae strain TB50; by contrast, RP gene expression declines in strain W303 after mTORC1 inhibition irrespective of the presence of Crf1p [37] , [90] , [91] , [105] , [106] . These differences were inferred to derive from multiple differences, as opposed to a single gene, as suggested by the behavior of haploid segregants resulting from crosses between W303 and TB50 [106] .…”

“…Amongst the very few non-RP gene targets of Fhl1p-Ifh1p are HMO1, UTP22 and RRP7 . Fhl1p, Ifh1p, and Hmo1p bind these gene promoters under nutrient-replete conditions [35] , [60] , [87] , [90] , [105] . Addition of rapamycin represses transcription, and it causes the release of Ifh1p, similar to what occurs on RP genes, and the dissociation of Ifh1p is followed by accumulation of Crf1p.…”