Rapamycin-modulated transcription defines the subset of nutrient-sensitive signaling pathways directly controlled by the Tor proteins

Abstract

The immunosuppressant rapamycin inhibits Tor1p and Tor2p (target of rapamycin proteins), ultimately resulting in cellular responses characteristic of nutrient deprivation through a mechanism involving translational arrest. We measured the immediate transcriptional response of yeast grown in rich media and treated with rapamycin to investigate the direct effects of Tor proteins on nutrient-sensitive signaling pathways. The results suggest that Tor proteins directly modulate the glucose activation and nitrogen discrimination pathways and the pathways that respond to the diauxic shift (including glycolysis and the citric acid cycle). Tor proteins do not directly modulate the general amino acid control, nitrogen starvation, or sporulation (in diploid cells) pathways. Poor nitrogen quality activates the nitrogen discrimination pathway, which is controlled by the complex of the transcriptional repressor Ure2p and activator Gln3p. Inhibiting Tor proteins with rapamycin increases the electrophoretic mobility of Ure2p. The work presented here illustrates the coordinated use of genome-based and biochemical approaches to delineate a cellular pathway modulated by the protein target of a small molecule.

The Target of Rapamycin Signaling Pathway Regulates mRNA Turnover in the YeastSaccharomyces cerevisiae

“…The fact that the majority of the mRNAs that we examined that are down-regulated at diauxic shift were destabilized strongly suggests that the regulation of mRNA turnover by TOR plays an important role in controlling yeast gene expression in response to nutrient limitation. Although the TOR signaling pathway has been demonstrated to regulate the transcription of specific genes, in particular genes for ribosomal proteins and proteins involved in nitrogen catabolite repression Hardwick et al, 1999;Powers and Walter, 1999), our observation that the CRY1 and GRC5 ribosomal protein mRNAs are destabilized illustrates that the regulation of both transcription and stability contribute to the overall changes in mRNA abundance seen when TOR signaling is blocked. Given the conservation of the TOR signaling pathway, the regulation of mRNA turnover may be an important mechanism in controlling the balance between cell growth and proliferation in multicellular eukaryotes as well.…”

“…Significant, widespread changes in mRNA abundance occur at diauxic shift and after TOR signaling has been blocked by rapamycin (DeRisi et al, 1997;Hardwick et al, 1999;Shamji et al, 2000). The fact that the majority of the mRNAs that we examined that are down-regulated at diauxic shift were destabilized strongly suggests that the regulation of mRNA turnover by TOR plays an important role in controlling yeast gene expression in response to nutrient limitation.…”

“…Second, rapamycin induced almost identical effects on mRNA turnover as those observed at diauxic shift. Finally, the observation that the rapamycin-resistant TOR1-1 allele or the deletion of FKBP reversed the rapamycin-induced changes in mRNA turnover directly indicates that mRNA turnover is regulated by the TOR signaling pathway.Significant, widespread changes in mRNA abundance occur at diauxic shift and after TOR signaling has been blocked by rapamycin (DeRisi et al, 1997;Hardwick et al, 1999;Shamji et al, 2000). The fact that the majority of the mRNAs that we examined that are down-regulated at diauxic shift were destabilized strongly suggests that the regulation of mRNA turnover by TOR plays an important role in controlling yeast gene expression in response to nutrient limitation.…”

Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise

“…Upregulated transcripts include SSY1, encoding a sensor of external amino acid concentration that also coordinates transcription of amino acid permease genes in response to nutrient deprivation; LST7, encoding a positive regulator of transport of amino acid permeases from the Golgi to the cell surface; and AGP3, encoding a low-affinity permease that might have a prominent role in amino acid transport induced by nitrogen starvation 23,24 . Other upregulated transcripts encode factors involved in the transport and catabolism of secondary nitrogen sources 25 , including the only known allantoate permeases, two putative allantoate permeases, five of six factors known to mediate allantoin degradation, a urea transport and degradation enzyme, and a sensor and transporter of ammonia. NMD inhibition was also associated with increased expression of crucial mediators of autophagy (bulk vacuolar degradation of cytosolic proteins to recycle amino acids in response to starvation) and sporulation.…”

Stress and mTORture signaling

“…Binding of FKBP12-rapamycin leads to the inhibition of mTOR function in a poorly understood manner, but might be caused by weakening/dissociation of the raptor-mTOR interaction Murakami et al, 2004). Transcriptional profiling of rapamycin treatment of yeast, Drosophila and mammalian cells shows that the drug affects expression of approximately 5% of all genes in the genome, indicating that TOR has a broad impact on cellular function (Hardwick et al, 1999;Peng et al, 2002;Guertin et al, 2006). mTOR exists in two functionally distinct complexes dubbed mTOR complex 1 (mTORC1) and mTORC2 ( Figure 1).…”