Interaction of TOR and PKA Signaling in S. cerevisiae

Abstract

TOR and PKA signaling are the major growth-regulatory nutrient-sensing pathways in S. cerevisiae. A number of experimental findings demonstrated a close relationship between these pathways: Both are responsive to glucose availability. Both regulate ribosome production on the transcriptional level and repress autophagy and the cellular stress response. Sch9, a major downstream effector of TORC1 presumably shares its kinase consensus motif with PKA, and genetic rescue and synthetic defects between PKA and Sch9 have been known for a long time. Further, studies in the first decade of this century have suggested direct regulation of PKA by TORC1. Nonetheless, the contribution of a potential direct cross-talk vs. potential sharing of targets between the pathways has still not been completely resolved. What is more, other findings have in contrast highlighted an antagonistic relationship between the two pathways. In this review, I explore the association between TOR and PKA signaling, mainly by focusing on proteins that are commonly referred to as shared TOR and PKA targets. Most of these proteins are transcription factors which to a large part explain the major transcriptional responses elicited by TOR and PKA upon nutrient shifts. I examine the evidence that these proteins are indeed direct targets of both pathways and which aspects of their regulation are targeted by TOR and PKA. I further explore if they are phosphorylated on shared sites by PKA and Sch9 or when experimental findings point towards regulation via the PP2A^Sit4/PP2A branch downstream of TORC1. Finally, I critically review data suggesting direct cross-talk between the pathways and its potential mechanism.

Keywords: PKA; TOR; autophagy; cross-talk; kinase; nutrient sensing; ribosome production; signaling pathway interaction; stress response; substrate specificity.

Figure 1

Core components of the PKA pathway. In its inactive form, PKA exists as a tetramer of two regulatory subunits (Bcy1) and two catalytic subunits (Tpk1, Tpk2 or Tpk3). Binding of cAMP to Bcy1 leads to dissociation of the complex and activation of the catalytic subunits. Two main routes of activation of adenylate cyclase Cyr1 exist: via the G protein-coupled receptor Gpr1 and its G protein alpha subunit Gpa2 and via the small GTPases Ras1/2.

Figure 2

Model of the regulation of RP and RiBi genes via the transcriptional repressors Stb3, Tod6 and Dot6 downstream of TORC1 and PKA. In the absence of phosphorylation by Sch9 and PKA, the transcription factors Stb3, Tod6 and Dot6 bind specific promoter elements upstream of a subset of RP and RiBi genes, triggering their repression via the recruitment of histone deacetylase complex RPD3L. The promoter element bound by Stb3 in RP promoters is marked with a question mark as RP promoters generally do not contain RRPE sequences and the mode of interaction with these promoters is unclear. The thickness of arrows indicates a potentially stronger relative contribution of PKA than Sch9 on Dot6 phosphorylation and vice versa for Tod6 phosphorylation. Potential dephosphorylation of Tod6 by PP2A is omitted as direct evidence is lacking.

Figure 3

Model of the regulation of Pol III transcription factor Maf1. Maf1 is phosphorylated by Sch9 and PKA to prevent its nuclear localization. This is counteracted by dephosphorylation by PP2A. Unphosphorylated Maf1 translocates to the nucleus and binds Pol III in a manner that prevents association with the transcriptional activator Bfr1, and therefore impedes transcription initiation. Possibly, phosphorylation of Maf1 on sites other than the PKA and Sch9 sites, potentially by CK2, hinders Maf1 association with Pol III. The subcellular locations at which Maf1 phosphorylation and dephosphorylation take place are unknown and may differ from the ones shown).

Figure 4

PKA- and TORC1-regulated phosphorylation sites on Atg13. Sites reported by Stephan, 2009 are shown in red and by Fujioka, 2014 in blue. The position of the Atg17-interacting region is indicated by a green and the Atg1-interacting region as a yellow rectangle.

Figure 5

Model for signaling through Rim15. Rim15 is phosphorylated on T1062 by Sch9 and on T1075 by TORC1 and Pho80/85. Phosphorylation of these sites leads to cytoplasmic retention by Bmh1/2. Phosphorylation on five other sites by PKA inactivates Rim15 catalytic activity. This PKA-dependent phosphorylation may be limited to the cytoplasm due to association of PKA catalytic with regulatory subunits in the nucleus. Rim15 autophosphorylation may be required for its nuclear export. A form of Rim15 phosphorylated by both PKA and Sch9/TORC1/Pho80/85 is omitted for clarity. Phosphorylation of substrates by Rim15 is only shown in the nucleus for simplicity, while the true location has not yet been determined.

Figure 6

Model for the phospho-regulation of Msn2. Both the nuclear export signal (NES) and nuclear localization signal (NLS) are phosphorylated by PKA to promote Msn2 cytoplasmic localization. The NES is presumably dephosphorylated by PP2A^Cdc55 upon TORC1 inactivation. The NLS is additionally phosphorylated by Snf1 and dephosphorylated by PP1. The localization of phosphorylation sites by Rim15 and Yak1 on Msn2 are unknown. Nuclear-cytoplasmic localization as a consequence of NES and NLS phosphorylation is shown, but the subcellular compartment in which phosphorylation events take place is unknown. A speculative additional dephosphorylation of an unknown site in the zinc-finger domain (ZnF) by PP2A^Cdc55 is omitted.

Figure 7

Speculative mechanisms of interaction of PKA and TOR/Sch9 on shared targets. Top: Differential temporal (left) and subcellular (middle) activities of the pathways. Right: Phosphorylation of different sites by the two pathways. Bottom, left: Control of substrate phosphorylation by TOR via activation of Sch9 and inactivation of PP2A. PP2A may overcome weak, but not strong PKA activity. Right: Regulation of Sch9 via pathways additional to TOR. Activation by Pkh1/2 is shared with PKA. Substrates for which the mode of interaction may be relevant are proposed.