Article

• The EMBO Journal (2005) 24, 4271 - 4278
• doi:10.1038/sj.emboj.7600889

Published online: 24 November 2005

• Subject Categories:

  • Signal Transduction | Cellular Metabolism

Regulation of G₀ entry by the Pho80–Pho85 cyclin–CDK complex

Valeria Wanke^1,a, Ivo Pedruzzi^1,a, Elisabetta Cameroni^1,a, Frédérique Dubouloz¹ and Claudio De Virgilio¹

1. Department of Microbiology and Molecular Medicine, CMU, University of Geneva, Geneva, Switzerland

Correspondence to:

Claudio De Virgilio, Department of Microbiology & Molecular Medicine, CMU, University of Geneva, 1211 Geneva, Switzerland. Tel.: +41 22 379 54 95; Fax: +41 22 379 55 02; E-mail: Claudio.DeVirgilio@medecine.unige.ch

^aThese authors contributed equally to this work

Received 12 August 2005; Accepted 4 November 2005

• Keywords:

  • G₀,
  • nutrient starvation,
  • Pho80–Pho85 cyclin–CDK complex,
  • Rim15,
  • TORC1

Introduction

Eukaryotic signal transduction pathways convert extracellular cues such as growth factors, hormones, and/or nutrients to intracellular signals which, following proper integration, determine the decision between cell proliferation and entry into a nondividing resting state, termed quiescence (G₀). In the yeast Saccharomyces cerevisiae, the PKA and TORC1 signaling pathways, which positively regulate cell proliferation in response to nutrient availability, are key determinants of G₀ entry (Thevelein and de Winde, 1999; Gray et al, 2004; Martin and Hall, 2005). As a consequence, inactivation of either of these major pathways results in a G₀-like growth arrest phenotype, even in the presence of abundant nutrients. Recent evidence suggests that the signal flow through both pathways is integrated at various levels. For instance, TORC1 depletion was proposed to favor the formation of an inactive nuclear PKA/Bcy1 holoenzyme (Schmelzle et al, 2004). In addition, both PKA and TORC1 converge on common target proteins, such as the stress response transcription factors Msn2/4, as well as Rim15 (Schneper et al, 2004). Rim15 is a distinct member of the PAS kinase family, which functions as a key controller of many aspects of the G₀ program (including G₁ cell cycle arrest, glycogen and trehalose synthesis, and activation of Gis1- and/or Msn2/4-dependent transcription (e.g. of HSP26 and GRE1; Reinders et al, 1998; Pedruzzi et al, 2000, 2003; Cameroni et al, 2004).

Entry into a G₀-like state can also be triggered by phosphate starvation (Lillie and Pringle, 1980), albeit the corresponding regulatory mechanisms are largely unknown (Gray et al, 2004). The primary nutrient-signaling kinase that orchestrates the phosphate starvation response is Pho85, a CDK that associates with a family of 10 cyclins, each of which can potentially direct Pho85 to different target substrates (Carroll and O'Shea, 2002). The best-studied partner of Pho85 is the cyclin Pho80. It has previously been shown that the Pho80–Pho85 cyclin–CDK complex regulates the phosphate starvation response by controlling both the localization and activity of the transcription factor Pho4. Pho4, in turn, activates transcription of phosphate acquisition genes (Carroll and O'Shea, 2002). Interestingly, several studies indicate that Pho85 negatively controls the expression of an additional set of genes (including glycogen and trehalose synthesis, oxidoreductive stress, and protein folding genes) that are typically induced under glucose-limiting conditions prior to entry into G₀ (DeRisi et al, 1997; Timblin and Bergman, 1997; Ogawa et al, 2000; Carroll et al, 2001; Nishizawa et al, 2004). These findings suggest that proper execution of the G₀ program also includes integration of the Pho85-mediated phosphate signal.

The work presented here pinpoints Rim15 as a key target of the Pho85 signaling pathway. Results from physiologic, genetic and biochemical studies indicate that Rim15 is a Pho80–Pho85 kinase substrate and that the resulting phosphorylation of Rim15 favors its cytoplasmic retention via association with the 14-3-3 protein Bmh2. Our data further demonstrate that this regulation is important for proper control of G₀ entry in response to phosphate availability. Interestingly, inactivation of either Pho80–Pho85 or TORC1 leads to dephosphorylation of the 14-3-3 binding site in Rim15, suggesting that both signaling pathways converge on a single amino acid in Rim15 to regulate its nucleocytoplasmic distribution.

Protein kinase activity of Rim15 is critical for its nuclear export

As part of our continued efforts to define in detail the molecular mechanism of Rim15 function, we asked whether the Rim15 kinase activity itself plays a role in its subcellular localization. To address this question, we analyzed the localization of kinase-inactive GFP-Rim15^K823Y and GFP-Rim15^C1176Y fusion proteins (see Materials and methods for further details) in rim15 cells. We found that GFP-Rim15^K823Y and GFP-Rim15^C1176Y, but not GFP-Rim15, accumulated in the nuclei of rapamycin-treated or glucose-limited rim15 cells (Figure 1A). Furthermore, when such rapamycin-treated or glucose-limited rim15 mutant cells were respectively re-supplied with nutrient-rich medium or released from the rapamycin block (both in the presence of the translation inhibitor cycloheximide), GFP-Rim15^K823Y and GFP-Rim15^C1176Y, but not GFP-Rim15, remained predominantly in the nucleus (data not shown). The simplest interpretation of these results is that the kinase activity of Rim15 is required for its efficient export from the nucleus. Moreover, from a collection of importin -related, nuclear-transport-receptor mutants tested, only the msn5 mutant showed both GFP-Rim15^C1176Y and GFP-Rim15^K823Y constitutively localized in the nucleus (Figure 1B). Thus, our data indicate that the kinase activity of Rim15 is needed for its efficient, Msn5-driven nuclear export and show that GFP-tagged kinase-inactive Rim15 variants are useful tools in the study of nutrient-regulated cytoplasmic retention and/or nuclear import of Rim15.

Figure 1.

Protein kinase-inactivating mutations permit the study of cytoplasmic retention and/or nuclear import of GFP-Rim15. (A) Localization of GFP-Rim15^K823Y, GFP-Rim15^C1176Y, and GFP-Rim15. Exponentially growing (EXP), rapamycin-treated (RAP), and diauxic (DS; OD₆₀₀=3.5) rim15 (IP31) cells expressing GFP-Rim15^K823Y (pFD1008), GFP-Rim15^C1176Y (pFD633), or GFP-Rim15 (pFD846) were visualized by fluorescence microscopy. (B) Localization of GFP-Rim15^K823Y (pFD1008), GFP-Rim15^C1176Y (pFD633), or GFP-Rim15 (pFD846) in exponentially growing wild-type (W303-1A) or msn5 (YBL029) cells. Notably, the msn5 mutant overexpressing GFP-Rim15 was very sick, which is consistent with the expectation that overproduction (from the ADH1 promoter) of nuclear GFP-Rim15 wild-type protein is detrimental to cell growth. Nevertheless, the overall very weak GFP-Rim15 signal observed in these cells was for the most part localized in the nuclei (WN, weak nuclear staining). N and C denote mainly nuclear and cytoplasmic localization of the GFP-fusion proteins, respectively.

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Cytoplasmic retention of GFP-Rim15 depends on its association with 14-3-3 proteins

Rim15 is a distant member of the NDR family of AGC kinases, which share the unique feature of harboring an insert of at least 30 amino acids between the protein kinase subdomains VII and VIII (Tamaskovic et al, 2003; Cameroni et al, 2004). Although the function of this insert segment is not well understood, at least in the case of NDR1, it is known to contain a nonconsensus nuclear localization signal (Tamaskovic et al, 2003). Interestingly, the corresponding kinase insert in Rim15 contains neither a consensus nor a nonconsensus NDR1 nuclear localization signal, but instead harbors (flanking amino-acid residue Thr¹⁰⁷⁵ [T1075]) the single high-stringency 14-3-3-binding motif in Rim15 (RSXpS/TXP; Figure 2A; Yaffe et al, 2001).

Figure 2.

Cytoplasmic retention of GFP-Rim15 depends on its association with 14-3-3 proteins. (A) Domain architecture of Rim15. The various domains of Rim15 include the N-terminal PAS, the C₂HC-type zinc-finger (ZnF), the central kinase catalytic domain (gray rectangles) with an insert of 188 amino acids between subdomains VII and VIII, and the C-terminal receiver (REC) domain. As predicted by the Scansite program (http://scansite.mit.edu) the single high-stringency, putative 14-3-3 protein-binding site in Rim15 (scoring in the top 0.165%) flanks amino-acid T1075. (B) Interaction between Rim15^KI and Bmh2. Bmh2-HA³ (pTB419) was immunoprecipitated from extracts prepared from wild-type cells (W303-1A) expressing either GST-Rim15^KI (pVW900) or GST-Rim15^KI-T1075A (pVW902). The input extracts (upper two panels) and the immunoprecipitates (lower panel) were analyzed via immunoblot analysis using anti-GST (upper and lower panels) or anti-HA antibodies (panel in the middle). (C) Localization of GFP-Rim15^C1176Y (pFD633), GFP-Rim15^{C1176Y/T1075A} (pVW1017), and GFP-Rim15^C1176Y/KI (pVW1068) in exponentially growing rim15 (IP31) cells. The numbers indicate the percentage of cells with clear nuclear staining of the GFP-fusion protein; >200 cells were counted. (D, E) Depletion of 14-3-3 proteins results in the nuclear accumulation of GFP-Rim15^C1176Y. GFP-Rim15^C1176Y (pFD633) expressing bmh1 bmh2 rim15 [pGAL1-BMH2] (CDV235) cells carrying either the control plasmid pLC921 (strain 1) or plasmid pCDV994 (expressing BMH2-HA³ from its own promoter; strain 2) were pregrown on SGal/Raf, transferred to SD medium, and grown exponentially (through repeated dilutions) for the times indicated. Bmh2-HA³ and Bmh2 levels (in strains 1 and 2) were analyzed prior (time zero) and following (24 or 48 h) the transfer of the cells from SGal/Raf to SD medium via immunoblot analysis using anti-HA (top panel) and anti-Bmh2 (lower panel) antibodies (D). GFP-Rim15^C1176Y was visualized 24 h following the transfer of the cells from SGal/Raf to SD medium (E). (F) Depletion of 14-3-3 proteins results in transcriptional activation of Rim15-dependent genes. GRE1 and HSP26 transcript levels were determined (via Northern blot analysis as described in Pedruzzi et al, 2000) at the times indicated following transfer of bmh1 bmh2 [pGAL1-BMH2] (SL1470) and bmh1 bmh2 rim15 [pGAL1-BMH2] (CDV235) cells from SGal/Raf to SD medium. Depletion of Bmh2 was monitored via immunoblot analysis using anti-Bmh2 antibodies (top panel).

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Several observations point to a role for the yeast 14-3-3 proteins Bmh1/2 in the nutrient-controlled nuclear exclusion of Rim15, possibly by a similar mechanism as previously described for the transcription factors Msn2/4 and the DYRK-family kinase Yak1 (Beck and Hall, 1999; Moriya et al, 2001). First, when fused to GST, the kinase insert of Rim15 (Rim15^KI) bound Bmh2-HA³ in co-immunoprecipitation (co-IP) experiments (Figure 2B). Importantly, this interaction was largely disrupted by introducing a T1075A mutation in Rim15^KI, which abolishes the presumed phosphothreonine (pT) residue critical for regulation of 14-3-3-protein–protein interactions (Yaffe et al, 2001). Second, while GFP-Rim15^C1176Y was rarely found in the nuclei of exponentially growing cells (i.e. in <1% of the cells), introduction of the T1075A mutation or deletion of the entire kinase insert in GFP-Rim15^C1176Y caused the corresponding fusion proteins to constitutively localize in the nuclei of 40 or 68% of the cells, respectively (Figure 2C). The slightly more robust constitutive nuclear localization of GFP-Rim15^C1176Y/KI suggests that additional domains in the kinase insert of Rim15 may participate in the cytoplasmic retention of Rim15 (see below). Third, the switch from galactose to glucose-rich medium of a strain in which the only source of Bmh protein was provided by BMH2 under the control of the GAL1 promoter resulted in the expected depletion of Bmh2 (Figure 2D), and was paralleled by the nuclear accumulation of GFP-Rim15^C1176Y (Figure 2E). In a strain carrying a genomic wild-type copy of RIM15, this nuclear localization resulted in the Rim15-dependent transcriptional activation of GRE1 and HSP26 (Figure 2F; notably, Bmh protein depletion caused a weak, transient activation of HSP26 even in the absence of Rim15, indicating that Bmh proteins regulate HSP26 transcription in part also via a Rim15-independent process). Interestingly, in this context, we found that 27 of the 76 genes that were reported to be induced following Bmh1/2 depletion (Ichimura et al, 2004), were also included in the set of genes that required Rim15 for induction at the diauxic shift (Cameroni et al, 2004). Taken together, our findings indicate that the association between Bmh1/2 proteins and the pT1075 14-3-3-binding site in Rim15 can account for the cytoplasmic retention of GFP-Rim15 in exponentially growing cells.

The Pho80–Pho85 cyclin–CDK complex phosphorylates T1075 in Rim15

The T1075 amino acid of Rim15 is not only a critical residue of the 14-3-3 binding site, but is also part of a proposed Pho85 consensus phophorylation sequence S/TPXI/L (Figure 2A; O'Neill et al, 1996). This suggested to us that Pho85 may phosphorylate T1075 in Rim15. In support of this assumption, we found that Pho85 physically interacted with Rim15 in co-IP experiments (Figure 3A), and that Pho85, but not kinase-inactive Pho85^E53A (Nishizawa et al, 1999), phosphorylated Rim15^KI in the presence of the cyclin Pho80 (see Materials and methods for identification of Pho80; Figure 3B). In addition, Pho80–Pho85-mediated phosphorylation was significantly reduced (to 46.0%6.6) by the introduction of the T1075A mutation in Rim15^KI (Figure 3B), indicating that T1075 is a Pho80–Pho85 target in vitro (notably, the residual phosphorylation level in Rim15^KI-T1075A suggests the presence of an additional site[s] in Rim15^KI that may be targeted in vitro by Pho80–Pho85). To assess whether Pho80–Pho85 indeed phosphorylates T1075 in Rim15 within cells, we raised antibodies that were highly specific for a pT1075-containing peptide, as indicated by their ability to recognize GST-Rim15, but not GST-Rim15^T1075A, or phosphatase-treated GST-Rim15 (Figure 3C). Using these specific anti-pT1075 antibodies, we found that phosphorylation of T1075 in Rim15-myc¹³ depends largely on the presence of Pho85 (Figure 3D). Thus, the T1075 residue in Rim15 is also a likely Pho80–Pho85 target in vivo. Taken together with our finding that loss of Pho85 or Pho80 (but not of Pcl1/Pcl2) resulted in the constitutive nuclear localization of GFP-Rim15^C1176Y in 71% and 58% of the cells, respectively (Figure 3E), our data suggest a model in which the Pho80–Pho85 kinase promotes the cytoplasmic retention of Rim15 in exponentially growing cells principally through phosphorylation of the T1075 residue of the 14-3-3 site in Rim15.

Figure 3.

The Pho80–Pho85 cyclin–CDK phosphorylates the T1075-containing 14-3-3-binding site in Rim15 and stimulates its cytoplasmic retention. (A) Interaction between Rim15 and Pho85. GST-Rim15 (pNB566; lanes 1–4) and GST (YCpIF2-GST; lane 5) were precipitated from extracts prepared from wild-type (KT1961) cells coexpressing HA²-Pho85 (pIP774; lanes 1 and 5), HA²-Tpk1 (pCDV503; lane 2), HA²-Tps1 (pAR502; lane 3), or Bud14-HA³ (pFD662; lane 4). Cell lysates (Input) and GST pull-down fractions were subjected to PAGE and immunoblots were probed using anti-GST or anti-HA antibodies as indicated. Tpk1 and Tps1 (both previously identified as Rim15-interacting proteins; Reinders et al, 1998) served as positive controls, while Bud14 served as a negative control. (B) In vitro phosphorylation of T1075 in Rim15. GST-Rim15^KI (pVW995), GST-Rim15^KI-T1075A (pVW997), and GST (pGEX3X), expressed and purified from bacteria, were used as in vitro substrates (see top panel for input blot) in protein kinase assays using equal amounts of GST-Pho80 and either HA²-Pho85 or protein kinase inactive HA²-Pho85^E53A. The protein input bands (top panel) and the phosphorylation levels of the Rim15^KI variants (lower panel) were quantified (see Materials and methods). The average ratio of [³²P]GST-Rim15^KI-T1075/GST-Rim15^KI-T1075 (from four independent experiments) is expressed in percent of the corresponding ratio for wild-type GST-Rim15^KI (set at 100% following the deduction of the background signal in the E53A lane) and is indicated below the relevant lane. (C) In vivo phosphorylation of T1075 in Rim15. GST-Rim15 (WT; pNB566) and GST-Rim15^T1075A (T1075A; pLC824) were purified from exponentially growing rim15 (IP31) cells and analyzed by immunoblotting (using either anti-GST antibodies or phospho-specific antibodies against Rim15-pT1075) following treatment with phosphatase inhibitors (PPI) alone or -phosphatase (-PPase)PPI. (D) Rim15-myc¹³ (pVW904) from exponentially growing rim15 (IP31) and pho85 rim15 (CDV201-3B) mutants were analyzed for phosphorylation of T1075 using Rim15-pT1075 phospho-specific antibodies. Equal amounts of the fusion proteins were verified by immunoblotting using anti-myc antibodies. (E) Localization of GFP-Rim15^C1176Y (pFD633) in exponentially growing rim15 (IP31), pcl1 pcl2 rim15 (CDV237-9D), pho85 rim15 (CDV201-3B), and pho80 rim15 (CDV237-7A) mutant cells. The numbers indicate the percentage of cells with clear nuclear staining of the GFP-fusion protein; >200 cells were counted.

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The Pho80–Pho85 cyclin–CDK complex antagonizes the Rim15-dependent G₀ program

To address the physiological importance of our findings, we next examined the role of Pho85, if any, in the Rim15-dependent G₀ phenotypes (Reinders et al, 1998; Pedruzzi et al, 2003). We observed that loss of Pho80 or Pho85 significantly enhanced GRE1-lacZ induction (Figure 4A) and trehalose synthesis (Figure 4B) particularly following glucose limitation. Notably, the corresponding higher induction levels, which in the case of pho85 mutant cells also correlated with a slightly enhanced G₀ survival (Figure 4C), depended to a large extent on the presence of Rim15 (Figure 4A–C). Similarly, glycogen hyperaccumulation in pho85 mutants (Timblin et al, 1996) was largely dependent on the presence of Rim15 (Figure 4D). Together with our data presented above, these genetic results suggest a model in which the Pho80–Pho85 cyclin–CDK complex antagonizes the Rim15-dependent G₀ program by regulating the nuclear exclusion of Rim15.

Figure 4.

The Pho80–Pho85 cyclin–CDK complex antagonizes induction of Rim15-dependent G₀ traits. (A, B) Induction of GRE1-lacZ expression (from integrative plasmid pIP490; A) and trehalose levels (B; for method see Pedruzzi et al, 2000) as wild-type (KT1961), rim15 (IP31), pho85 (IP48-3C), pho85 rim15 (CDV201-3B), pho80 (CDV237-10C), and pho80 rim15 (CDV237-7A) mutant cells were grown to stationary phase on YPD medium. (C) Stationary phase survival of wild-type (), rim15 (), pho85 (), and pho85 rim15 () mutant cells (for strains see [A, B]). (D) Glycogen levels in 4-day old batch cultures (visualized after exposure for 1 min to iodine vapor; for strains see [A, B]). (E) Both phosphate starvation and rapamycin treatment reduce the extent of phosphorylation of the T1075 residue in Rim15. Exponentially growing rim15 (IP31) cells expressing Rim15-myc¹³ (pVW904) were starved for phosphate (-P) or treated with rapamycin (+RAP) for the indicated times. Detection of fusion protein levels and pT1075 were as in Figure 3D. (F) Exponentially growing rim15 (IP31) cells expressing GFP-Rim15^C1176Y (pFD633; EXP) were treated for 45 min with rapamycin (+RAP), or submitted for 45 min to phosphate starvation in the absence (-P) or in the presence (-P/+RAP) of rapamycin and subsequently visualized by fluorescence microscopy. The numbers indicate the percentage of cells with clear nuclear staining of the GFP-fusion protein; >200 cells were counted.

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We also found that the levels of both Pho80 and Pho85 drop significantly in the late post-diauxic shift phase (data not shown), suggesting that the Pho80–Pho85 kinase modulates the Rim15-dependent G₀ program in response to phosphate levels as long as residual carbon sources are available. This conclusion is confirmed by the findings that phosphate starvation resulted in the dephosphorylation of Rim15-pT1075 (Figure 4E), nuclear accumulation of GFP-Rim15^C1176Y (Figure 4F), and, as recently published, Rim15 target gene expression (Swinnen et al, 2005). Thus, our physiologic, biochemical and genetic data are consistent with a model in which Rim15 represents a physiologically important Pho80–Pho85 cyclin–CDK target.

TORC1 also impinges on pT1075 in Rim15

We have previously shown that the nuclear accumulation of Rim15 is antagonized by the TORC1 pathway, and likely involves Rim15 hyper-phosphorylation (Pedruzzi et al, 2003). During our analyses of the various kinase-inactive Rim15 proteins, we observed that their electrophoretic mobility depended on the kinase activity of Rim15 itself and, therefore, likely reflects the autophosphorylation state of Rim15 (data not shown). A simple model could be that rapamycin-induced hyper-phosphorylation of Rim15 is a consequence, rather than the cause, of Rim15 nuclear import and may be due to the activation of Rim15 in the presumably low PKA nuclear environment (Griffioen and Thevelein, 2002; Pedruzzi et al, 2003).

How then does TORC1 regulate the nucleocytoplasmic distribution of Rim15? In this respect, we observed that rapamycin treatment caused rapid dephosphorylation of pT1075 in Rim15 (Figure 4E), indicating that TORC1, like Pho80–Pho85, regulates the cytoplasmic retention of Rim15 primarily by controlling the phosphorylation state of its 14-3-3-binding site. The fact that rapamycin treatment does not significantly change the expression pattern of genes controlled by the Pho80–Pho85-regulated Pho4 transcription factor (e.g. PHO5, PHO11, and PHO12; Hardwick et al, 1999) argues against TORC1 acting upstream of Pho80–Pho85. Thus, TORC1, rather than impinging on Pho80–Pho85, may instead inhibit the activity of a pT1075-targeting phosphatase(s) and/or activate an alternative T1075-targeting kinase (Figure 5). In this context, our previous findings indicated that the known TORC1 effectors, including the type 2A-related protein phosphatase Sit4 and possibly also the type 2A protein phosphatases Pph21 and Pph22 (Di Como and Arndt, 1996; Jiang and Broach, 1999), may not be required for rapamycin-induced nuclear accumulation of Rim15 (Pedruzzi et al, 2003). Thus, unless these protein phosphatases redundantly control Rim15 function, our data suggest the existence of an additional, yet unidentified TORC1 effector(s) that regulates the phosphorylation state of T1075 in Rim15. Lastly, we would like to point out that TORC1 and Pho80–Pho85 localize to the cytoplasm and nucleus, respectively (Kaffman et al, 1998; Harris and Lawrence, 2003), and these kinases may therefore act on different pools of Rim15 (Figure 5). Our observation that rapamycin treatment and phosphate starvation act synergistically to cause a more complete depletion of GFP-Rim15^C1176Y from the cytoplasm supports this model (Figures 1A and 4F).

Figure 5.

Model for the regulation of Rim15 by nutrient-sensory kinases. Cytoplasmic Rim15, anchored through its binding to 14-3-3 proteins, is kept inactivate through PKA-mediated phosphorylation (1). TORC1 inactivation results (either due to the activation of a phosphatase[s] and/or inactivation of a protein kinase) in dephosphorylation of pT1075 in Rim15 with concomitant abrogation of cytoplasmic retention of Rim15 by 14-3-3 proteins (2). Following its nuclear import (3), Rim15 presumably escapes from further PKA-mediated inhibition (4). Active Rim15 (drawn in black) induces the G₀ program, initiates an autophosphorylation process (illustrated with a circle around Rim15), and accelerates its Msn5-mediated nuclear export. The Pho80–Pho85 cyclin–CDK complex phosphorylates T1075 of Rim15 (5), thereby promoting (following export of Rim15; 6) the re-association between Rim15 and 14-3-3 proteins in the cytoplasm (7). The nutrient sensing protein kinases PKA, TOR (in TORC1), and Pho80-Pho85 sense glucose, nutrients (nitrogen), and phosphate (P_i), respectively (Wilson and Roach, 2002). See text for further details.

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A final point remaining to be addressed is our previous finding that nuclear exclusion of Rim15 also requires the yeast PKB/Akt homolog Sch9. Analysis of the kinase insert sequence of Rim15 reveals three sites (S1004, S1044, and T1096), each of which is very similar to the consensus site phosphorylated by PKB/Akt (RXRXXS/T; Alessi et al, 1996) and conforms to a low-stringency 14-3-3-binding site (Yaffe et al, 2001). Given the dimeric nature of 14-3-3 proteins, it is possible that the kinase insert of Rim15 may engage in binding both monomeric subunits within a single 14-3-3 protein dimer, as previously shown to be the case for other proteins (Yaffe, 2002). Since our preliminary data indicate that Sch9 can phosphorylate Rim15^KIin vitro, it will be of interest to determine whether Sch9 phosphorylates an additional 14-3-3 site in Rim15^KI, which may act in concert with the 14-3-3-binding site flanking amino-acid residue T1075 to mediate tandem 14-3-3 binding.

In conclusion, we have identified a new regulatory mechanism by which the availability of phosphate modulates the G₀ program in yeast. We propose that the PAS kinase Rim15, in addition to integrating carbon and/or nitrogen source signals via the PKA, TORC1, and Sch9 nutrient-sensory kinases (Pedruzzi et al, 2003), also integrates information on the availability of phosphate via the Pho80-Pho85 cyclin–CDK complex to properly orchestrate the G₀ program, a key developmental process in eukaryotic cells.

Yeast strains, media and genetic techniques

The rim15 strains IP31 and CDV115 and their corresponding wild-type strains KT1960/1 and W303-1A, respectively, have been described earlier (Thomas and Rothstein, 1989; Pedruzzi et al, 2003). The msn5 strain YBL029, which is isogenic to PAY20 and W303-1A (Blondel et al, 1999), was a kind gift of Dr M Peter. Polymerase chain reaction (PCR)-based gene deletions (pcl1kanMX2, pcl2kanMX2, pho80kanMX2, pho85kanMX2, and rim15kanMX2 transformed into KT1960 and/or KT1961) were carried out as described (Longtine et al, 1998). The corresponding single mutants (all in same isogenic background) were used to construct IP48-3C (pho85), CDV201-3B (pho85 rim15), CDV237-10C (pho80), CDV237-7A (pho80 rim15), and CDV237-9D (pcl1 pcl2 rim15) by a series of repeated combinatorial mating and sporulation of the resulting diploids. Gene deletions were confirmed by PCR with gene-specific primers. PCR-based deletion of RIM15 (using a rim15kanMX2 cassette) in strain SL1470 (bmh1 bmh2 [pGAL1-BMH2]; described in Gelperin et al, 1995) yielded strain CDV235. The isogenic strains BY236 (wild type), BY714 (pcl1 pcl2 pcl5 pcl9 clg1), BY708 (pcl1 pcl2 pcl5 pcl9), BY637 (pcl1 pcl2 pcl5 clg1), BY634 (pcl1 plc2), and BY490 (pho80) have been previously described (Measday et al, 1997). Strains were grown at 30°C in standard rich medium with 2% glucose (YPD) or synthetic medium with 2% glucose (SD), 4% galactose (SGal), or 2% raffinose (SRaf) as carbon source (Burke et al, 2000). High- and no-phosphate media were described earlier (Kaffman et al, 1998). Rapamycin was added to the media at a final concentration of 2 g ml^-1. Standard yeast genetic manipulations were used (Burke et al, 2000). DNA was stained with 4,6-diamidino-2-phenylindole (DAPI), which was added to the cultures (4 h prior to fluorescence microscopy) at a concentration of 1 g ml^-1.

Plasmids

Full-length Rim15, Rim15^K823Y, Rim15^C1176Y, Rim15^{C1176Y/T1075A}, and Rim15^C1176Y/KI (in which the kinase insert domain encompassing amino acids 952–1138 is deleted; KI) were expressed as GFP-tagged versions under the control of the constitutive ADH1 promoter from low copy number plasmids pFD846, pFD1008, pFD633, pVW1017, and pVW1068, respectively. In addition, full-length Rim15 and Rim15^T1075A were expressed as GST-tagged versions under the control of the GAL1 promoter from the high copy number plasmids pNB566 and pLC824, respectively. Finally, full-length Rim15 was also expressed as myc¹³-tagged version under the control of the TDH3 promoter from high copy number plasmids pVW904. Plasmids expressing epitope-tagged variants of full-length Rim15 were constructed with the QuickChange Site-Directed Mutagenesis Kit (Stratagene) using appropriate primers that introduced the K823Y-, C1176Y-, and/or T1075A-encoding mutations in the corresponding parent plasmids (pFD846 and pNB566). To express a GST-tagged version of the kinase insert of Rim15 (Rim15^KI) under the control of the tetO7 promoter, an NotI–SalI fragment, containing the 672 nucleotides downstream of and including the GST start codon (Reinders et al, 1998), and a PCR-generated SalI–PstI fragment, encoding amino-acid residues 944 to 1149 of Rim15, were coligated with NotI–PstI-cut pCM184 (Garí et al, 1997), thus creating pVW900 (tetO7-GST-RIM15^KI). Plasmid pVW902 (tetO7-GST-RIM15^KI-T1075A) was obtained by site-directed mutagenesis (see above) of RIM15^KI in pVW900 using appropriate primers that introduced the T1075A-encoding mutation. For expression of GST-Rim15^KI in Escherichia coli (BL21; Stratagene), a PCR-generated BamHI–EcoRI fragment, encoding amino-acid residues 944 to 1149 of Rim15, was ligated into BamHI–EcoRI-digested pGEX3X (Amersham) to yield pVW995 (P_tac-GST-RIM15^KI). Plasmid pVW997 (P_tac-GST-RIM15^KI-T1075A) was obtained by site-directed mutagenesis (see above) of RIM15^KI in pVW995 using appropriate primers that introduced the T1075A-encoding mutation. Bmh2-HA³ was expressed under the control of its own promoter from either a high-copy number plasmid (pTB419), which was kindly provided by Dr M Hall (Beck and Hall, 1999), or a low copy number plasmid (pCDV994) that was created by cloning the BamHI–HindIII-digested, BMH2-HA³ carrying fragment of pTB419 at the BamHI–HindIII sites of pLC921, a YCplac33 (Gietz and Sugino, 1988) version that carries the natMX4 cassette-containing EcoRI–HindIII fragment of pAG25 (Goldstein and McCusker, 1999) in its polylinker region. Full-length Tpk1, Tps1 and Pho85 were expressed as HA²-tagged versions under the control of the GAL1 promoter from plasmids pCDV503 (GAL1-HA²-TPK1), pAR502 (GAL1-HA²-TPS1) and pIP774 (GAL1-HA²-PHO85), respectively. Full-length Bud14 was expressed as HA³-tagged version under its own promoter from plasmid pFD662 (BUD14-HA³). In addition, full-length Pho85 was also expressed as a HA²-tagged version under the control of the tetO7 promoter from plasmid pVW883 (tetO7-HA²-PHO85). Plasmid pVW884 (tetO7-HA²-PHO85^E53A) was obtained by site-directed mutagenesis (see above) of PHO85 in pVW883 using appropriate primers to introduce the kinase-inactivating E53A-encoding mutation. The integrative pLS9-GRE1-lacZ plasmid (pIP490) was constructed by cloning a PCR-generated EcoRI fragment, containing the 778 nucleotides upstream of the GRE1 start codon, into the EcoRI site of pLS9 (Sarokin and Carlson, 1986). Plasmids YCpIF2-GST and p2466, which allow expression of GST-Pho80 under the control of the CUP1 promoter, have been described earlier (Reinders et al, 1998; Tan et al, 2003).

Kinase-inactivating K823Y and C1176Y mutations in Rim15

The K823Y substitution replaces the invariant lysine in kinase subdomain II of Rim15 with tyrosine and results in an ATP-binding deficient version of Rim15 (Vidan and Mitchell, 1997; Reinders et al, 1998). During detailed analyses of our original GFP-Rim15 clone (pFD633; Pedruzzi et al, 2003), we discovered that it acquired a fortuitous point mutation (G3527A) that changes the cysteine residue at position 1176 to a tyrosine (C1176Y), located immediately downstream of the almost invariant glycine of the kinase catalytic sub-domain IX (Hanks et al, 1988). Subsequent experiments indeed revealed that the C1176Y mutation results in inactivation of the Rim15 protein kinase activity (data not shown). Consistent with our previous results, GFP-Rim15^C1176Y accumulates in the nuclei of glucose-limited and rapamycin-treated rim15 cells (Figure 1A; Pedruzzi et al, 2003). However, the presence of a functional (genomic or plasmid-expressed) Rim15 kinase efficiently prevents the observed nuclear accumulation of Rim15 (data not shown). While these new findings do not affect our previous conclusions (Pedruzzi et al, 2003), they provide a basis for the present study of cytoplasmic retention and/or nuclear import of GFP-Rim15.

Identification of the Pho80 cyclin

We expected that loss of the Pho85 partner cyclins, either alone or in combination, should phenocopy the loss of Pho85 with respect to hyper-induction of Rim15-dependent genes. Indeed, we found that loss of the cyclin Pho80 (in strain BY490), but none of various combinations of other cyclin mutations (including pcl1 pcl2 pcl5 pcl9 clg1 [BY714], pcl1 pcl2 pcl5 pcl9 [BY708], pcl1 pcl2 pcl5 clg1 [BY637], and pcl1 plc2 [BY634]), resulted in hyperactivation of HSP26, SSA3, and GRE1 transcription when assayed during the early diauxic shift phase (data not shown).

GST pull-down, immunoprecipitation, immunoblot analyses, and phospho-specific antibodies

To perform coprecipitation experiments between Rim15 and Pho85, strain KT1960 was cotransformed with pNB566 or YCpIF2-GST (expressing GST-Rim15 or GST under the GAL1 promoter, respectively) and either pIP774, pCDV503, pAR502, or pFD662, which express HA²-Pho85, HA²-Tpk1, HA²-Tps1, or Bud14-HA³, respectively. Induction of GAL1-driven expression and cell lysis were essentially performed as described (Lenssen et al, 2005). GST and GST-tagged Rim15 were purified from clarified extracts using glutathione sepharose 4B beads (Amersham Biosciences). Bound proteins were eluted with sample buffer (5 min, 95°C) and subjected to standard immunoblot analysis for detection of coprecipitated HA²-Pho85, HA²-Tpk1 and HA²-Tps1. For co-IP experiments between Bmh2 and Rim15^KI or Rim15^KI-T1075, strain W303-1A was cotransformed with pTB419 expressing Bmh2-HA³ under the control of its own promoter and pVW900 or pVW902, which express GST-Rim15^KI or GST-Rim15^KI-T1075A, respectively, under the control of the tetO7 promoter. To allow expression of the tetO7-controlled genes, cells were grown for at least six generations in exponential growth phase (OD₆₀₀<1.0) in the absence of doxycycline. Subsequently, cells were lysed (see above) and HA-tagged Bmh2 proteins were purified from clarified extracts with the protein G-agarose IP kit (Roche Diagnostics GmbH) following the manufacturer's instructions using monoclonal mouse anti-HA antibodies (HA.11; Covance). Bound proteins were eluted (as above) and subjected to standard immunoblot analysis for detection of co-precipitated GST-Rim15^KI and GST-Rim15^KI-T1075A. Dephosphorylation of GST-Rim15 (purified from whole-cell extracts; see above) was carried out by a 30-min incubation at 30°C with 1 U of -phosphatase (Biolabs, NewEngland). In control reactions, phosphatase inhibitors (10 mM NaF, 10 mM Na-orthovanadate, 10 mM p-NO₂-phenylphosphate, 10 mM -glycerophosphate, and 10 mM Na-pyrophosphate) were added. Antibodies against Rim15 phosphorylated on T1075 were raised against a phosphorylated synthetic peptide (S-R-S-S-pT-P-P-L-A-N-P-T; where pT represents phosphothreonine 1075 of Rim15), adsorbed with the unphosphorylated form of the peptide, and affinity-purified with the phosphorylated peptide by Eurogentec.

Protein kinase assays and quantification of substrate phosphorylation

To assay in vitro phosphorylation of Rim15 by Pho85, HA²-Pho85 (pVW883) and HA²-Pho85^E53A (pVW884), fusion proteins were expressed in (following growth for at least six generations in exponential growth phase in the absence of doxycycline) and purified from rim15 pho85 (CDV201-3B) cells. Following this, cells were disrupted by vortexing in lysis buffer (50 mM Tris–HCl, pH 7.5, 0.15 M NaCl, 0.5 mM EDTA, 0.1% NP-40, 10% glycerol, 1 mM PMSF, 1 mM DTT, one tablet of Complete Protease Inhibitor Cocktail [CPIC; Roche Diagnostics GmbH] per 50 ml, and phosphatase inhibitors [see above] in the presence of acid-washed glass beads. HA-tagged Pho85 and Pho85^E53A proteins were purified as outlined above for the HA-tagged Bmh2 protein. Kinase assays were performed with HA²-Pho85- and HA²-Pho85^E53A-bound beads at 30°C for 30 min in kinase buffer (50 mM Tris–HCl, pH 7.5, 20 mM MgCl₂, 1 mM DTT, 1 mM ATP, one tablet of CPIC per 50 ml, and 10 Ci -ATP) containing 50 ng of GST-Pho80 (purified from rim15 pho85 (CDV201-3B) cells; see also Tan et al, 2003) and the indicated Rim15-derived substrates (purified from E. coli). Reactions were stopped by adding SDS-gel loading buffer and boiling for 5 min and then subjected to SDS–PAGE. Gels were dried and exposed to X-ray film. Substrate phosphorylation levels were quantified using a PhosphorImager (Cyclone Phosphor System; PerkinElmer) and analysed with OptiQuant Image Analysis software (Packard). Digital images of immunoblots were acquired with a CanoScan LiDE scanner (Canon) and Photoshop 7.0 (Adobe) and densitometric analysis of protein bands was done with OptiQuant Image Analysis software.

We thank Drs B Andrews, J Cannon, M Hall, and S Lemmon for providing yeast strains, plasmids, and/or anti-Bmh2 antibodies, R Bisig for technical assistance, and Drs C Georgopoulos and R Loewith for critical reading of the manuscript. CDV is supported by the Swiss National Science Foundation grant 631-062731.00 and the Canton of Geneva.

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