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Originally published as Genetics Published Articles Ahead of Print on December 1, 2005.

Genetics, Vol. 172, 1369-1372, February 2006, Copyright © 2006
doi:10.1534/genetics.105.046110

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The Saccharomyces cerevisiae Phosphatase Activator RRD1 Is Required to Modulate Gene Expression in Response to Rapamycin Exposure

Julie Douville*, Jocelyn David*, Karine M. Lemieux{dagger}, Luc Gaudreau{dagger} and Dindial Ramotar*,1

{dagger} Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada and the * University of Montreal, Maisonneuve-Rosemont Hospital, Guy-Bernier Research Centre, Montreal, Quebec H1T 2M4, Canada

1 Corresponding author: University of Montreal, Maisonneuve-Rosemont Hospital, Guy-Bernier Research Centre, 5415 de l'Assomption, Montreal, Quebec H1T 2M4, Canada.
E-mail: dramotar.hmr{at}ssss.gouv.qc.ca

Manuscript received May 25, 2005. Accepted for publication November 12, 2005.


   ABSTRACT
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 ABSTRACT
ACKNOWLEDGEMENTS
 LITERATURE CITED
 
We show that mutants lacking either the phosphatase activator Rrd1 or the phosphatase Pph3 are resistant to rapamycin and that double mutants exhibit a synergistic response. This phenotype could be related to an inability of the mutants to degrade RNA polymerase II, leading to transcription of critical genes that sustain growth.

THE yPtpa1/Rrd1 protein shares 35% identity with the human phosphotyrosyl phosphatase activator, hPTPA, which has been proposed to function as a phosphatase activator (CAYLA et al. 1994; JANSSENS et al. 1998; RAMOTAR et al. 1998). Rrd1 interacts with Sit4, a catalytic subunit belonging to the PP2A Ser/Thr phosphatase family (DOUVILLE et al. 2004; ZHENG and JIANG 2005), and both proteins participate in the same genetic pathway to mediate resistance to 4-nitroquinoline-1-oxide and ultraviolet A (320–400 nm) light (DOUVILLE et al. 2004). The Rrd1–Sit4 complex may function to activate gene expression, as Sit4 is required for expression of several genes, e.g., SWI4 (FERNANDEZ-SARABIA et al. 1992).

rrd1{Delta} mutants are resistant to the immunosuppressant rapamycin, suggesting that Rrd1 plays a role in the cellular response to this drug (REMPOLA et al. 2000). In yeast, rapamycin binds to the peptidyl-prolyl isomerase Fpr1 and this complex inactivates the Tor1, -2 kinases (HEITMAN et al. 1991), leading to the activation of Sit4 via dissociation from an inhibitor protein Tap42 (DI COMO and ARNDT 1996; JIANG and BROACH 1999). The activated Sit4 dephosphorylates several targets, including the nutrient-responsive transcriptional activator Gln3 (which translocates to the nucleus to activate GLN1 and MEP2 expression) and the Ser/Thr kinase Npr1, which regulates the amino acid permeases (SCHMIDT et al. 1998). In general, rapamycin generates a profound modification in the transcriptional profile of yeast. While some genes, e.g., the diauxic shift genes CPA2 and PYC1, are upregulated by rapamycin exposure, others, such as the ribosomal protein genes including RPS26A, RPL30, and RPL9, are downregulated (HARDWICK et al. 1999; POWERS and WALTER 1999).

Here, we investigated the cellular response mechanism of rrd1{Delta} mutants to rapamycin. We first assessed whether rrd1{Delta} mutants respond to the initial challenge of rapamycin by examining Npr1 kinase phosphorylation status and MEP2 expression (SCHMELZLE et al. 2004). As shown in Figure 1, rapamycin quickly triggered Npr1 dephosphorylation, as well as MEP2 expression, in both the parent and the mutant, eliminating a role for Rrd1 in these early events. We next determined the effect of rapamycin on the growth rate of the rrd1{Delta} mutant. As shown in Figure 2A, the parent and rrd1{Delta} mutant grew at nearly the same rate in the absence of rapamycin, but growth was reduced when the strains were challenged with rapamycin. Interestingly, growth of the parent ceased by 9 hr, while the mutant continued to grow (Figure 2A) and divide (data not shown) in the presence of rapamycin. Thus, the mechanism by which rapamycin induces growth arrest appears to depend on Rrd1.


Figure 1
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  		FIGURE 1.— rrd1{Delta} mutant exhibits a normal response to the early events of rapamycin exposure. (A) Rapamycin-induced dephosphorylation of the Npr1 kinase in the parent and rrd1{Delta} mutant. Exponentially growing wild-type (WT, SEY6210) (MAT{alpha}, leu2-3 112, ura3-52, his3-{Delta}200, trp1-{Delta}901, lys2-801, suc2-{Delta}9, Mel–) and the rrd1{Delta} mutant bearing the plasmid pHA-NPR1 (kindly provided by Michael Hall, Basel, Switzerland) expressing a HA-Npr1 fusion protein were treated without and with rapamycin (Sigma, St. Louis) (50 and 200 ng/ml for 15 min) and the phosphorylation status of the HA–Npr1 kinase was determined by Western blot using an anti-HA monoclonal antibody (Santa Cruz). Samples without rapamycin were treated with a drug vehicle (90% ethanol, 10% Tween 20). (B) Rapamycin-induced expression of the MEP2 gene in the parent and the rrd1{Delta} mutant. Cells were treated as in A and total RNA was probed for expression of the MEP2 and ACT1 genes. The data are representative of three independent experiments. RAP, rapamycin.

 

Figure 2
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  		FIGURE 2.— Growth of the parent and the mutants rrd1{Delta}, pph3{Delta}, and rrd1{Delta} pph3{Delta} in the absence or presence of rapamycin. (A and B) Exponential-phase cells, wild-type strain (SEY6210), and the indicated isogenic mutants growing in YPD medium were diluted to an optical density of 600 nm (OD600) of 0.2 in fresh YPD medium with the drug vehicle and with rapamycin (50 or 100 ng/ml). Growth of the cultures was monitored by measuring the OD600 at the indicated time. The data are the average of three independent experiments. RAP, rapamycin.

 
A genomewide screen revealed that the Pph3 catalytic subunit of the PP2A family is involved in rapamycin resistance (CHAN et al. 2000). We therefore tested whether Rrd1 might function via Pph3. As expected, growth of the parent ceased within 9 hr, while the rrd1{Delta} and pph3{Delta} single mutants continued growing in the presence of rapamycin (Figure 2B). Importantly, the rrd1{Delta} pph3{Delta} double mutant showed a synergistic response (Figure 2B), suggesting that Rrd1 and Pph3 act separately to mediate rapamycin-induced growth arrest. Whether Rrd1 acts via another member of the PP2A family, such as Pph21 and Pph22, is not known (STARK 1996).

We next tested whether Rrd1 could influence expression of genes known to be regulated in response to rapamycin (HARDWICK et al. 1999). Expression of the CPA2 and PYC1 genes was induced in the parent strain, but not in the rrd1{Delta} mutant (Figure 3A), suggesting that Rrd1 is required to mediate rapamycin-induced gene expression. Since rapamycin is also known to trigger the downregulation of some genes, e.g., RPS26A and RPL9A, we tested whether Rrd1 is involved in this process. The RPS26A gene was nearly completely downregulated in the parent strain, but remained partially expressed in the rrd1{Delta} mutant upon rapamycin exposure (Figure 3B). Since RPL9A is downregulated in both strains, it appears that a subset of rapamycin-responsive genes is under the control of Rrd1. In fact, Rrd1 is required to support activator-dependent in vitro transcription of a well-characterized reporter E4 (WU et al. 1996; data not shown), consistent with Rrd1 involvement in gene expression.


Figure 3
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  		FIGURE 3.— Northern blot analysis of rapamycin-responsive genes in the parent and the mutants rrd1{Delta}, pph3{Delta}, and rrd1{Delta} pph3{Delta} . (A) Rapamycin-induced expression of the CPA2 and PYC1 genes is Rrd1 dependent. Exponentially growing cells in YPD medium were treated with a drug vehicle and with rapamycin (200 ng/ml) for 30 min before extracting total RNA. Samples of this RNA were analyzed by Northern blot for the expression of the CPA2 and PYC1 genes. (B) Rapamycin-induced downregulation of the ribosomal gene RSP26A is partially dependent on Rrd1. Cells were cultured as described in A, except that they were treated for 2 hr. Total RNA was probed for expression of the RSP26A and RPL9A genes. For A and B, the actin gene ACT1 was used as a control for total RNA loaded on the gel. The data are representative of three independent experiments. RAP, rapamycin; Wt, wild-type strain (SEY6210).

 
Since Rrd1 interacts with Sit4 and this complex has been shown to dephosphorylate the target proteins Sap185 and Gln3 (CRESPO et al. 2002; FELLNER et al. 2003), it is reasonable to assume that Rrd1 could affect gene expression by modulating the phosphorylation status of the C-terminal domain (CTD) of the Rpb1 subunit of RNA polymerase II upon rapamycin exposure. As such, the parent strain, the isogenic single mutants rrd1{Delta} and pph3{Delta}, and the double mutant rrd1{Delta} pph3{Delta} were assessed for the phosphorylation status of Rpb1. As shown in Figure 4A, the high-molecular-weight bands (~150–200 kDa), corresponding to a heterogeneous population of Rpb1 polypeptides, disappeared when the parent strain was treated with rapamycin. Interestingly, a polypeptide band of ~70 kDa was intensified following the drug treatment (Figure 4A), suggesting that Rpb1 is not dephosphorylated, but proteolytically processed. It is noteworthy that rapamycin treatment caused degradation of both the phosphorylated and the nonphosphorylated form of Rpb1 (data not shown). When a similar experiment was conducted with the rrd1{Delta} mutant, the phenomenon was significantly reduced, and more dramatically in the rrd1{Delta} pph3{Delta} double mutant (Figure 4A), but not in the gln3{Delta} mutant, which also displays rapamycin resistance (data not shown) (CARDENAS et al. 1999; POWERS and WALTER 1999). These data are consistent with a model whereby both Rrd1 and Pph3 contribute separately to the molecular process that acts independently of the Gln3 signaling pathway to trigger degradation of Rpb1 upon rapamycin exposure. We note that the timing of Rpb1 degradation coincided with the reported kinetics of downregulation of the ribosomal protein genes that occurred within 60 min following rapamycin treatment (CARDENAS et al. 1999; POWERS and WALTER 1999). At least, >50% of Rpb1 was converted to the 70-kDa form after 75 min of rapamycin treatment (Figure 4B). Thus, the downregulation of the ribosomal protein genes triggered by rapamycin could be a consequence of increased degradation of Rpb1 in the parent strain.


Figure 4
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  		FIGURE 4.— Rapamycin exposure triggers degradation of RNA polymerase II large subunit Rpb1. (A) Rrd1 and Pph3 are required for rapamycin-induced degradation of Rpb1. Exponentially growing cells, wild type, and the indicated mutant strains were treated with a drug vehicle or with rapamycin (200 ng/ml) for 2 hr. Total protein extracts were derived from these samples and analyzed for the Rpb1 protein by Western blot using the H14 antibody (Covance), which recognizes phospho-Ser5 of the CTD of Rpb1. (B) Time-course analysis of Rpb1 degradation in the wild-type strain exposed to rapamycin. Exponentially growing wild-type cells were treated with a fixed concentration of rapamycin (200 ng/ml) and samples were taken at the indicated time points. Samples were processed for Western blot as in A. The data are representative of three independent experiments. RAP, rapamycin.

 
The rationale underlying the potential degradation of Rpb1 during rapamycin treatment may be the necessity of the cell to drastically reduce its metabolism. Since rapamycin mimics starvation conditions, drug-treated cells will adapt to a specific energy-saving response involving the downregulation of several physiological processes, including transcription. In this context, destruction of an important fraction of Rpb1 would be an efficient mechanism to prevent unnecessary initiation of gene transcription. Although the half-life of Rpb1 (<75 min) correlates with the timing of the downregulation of the ribosomal protein genes triggered by rapamycin, the cell growth ceased only at a much later time, presumably due to the additional time required to dilute and turn over all the Rpb1 and various other molecules (CARDENAS et al. 1999). Thus, preventing the destruction of Rpb1, as in the case of rrd1{Delta} mutants and the even more pronounced case of rrd1{Delta} pph3{Delta} double mutants, is expected to permit continuous expression of critical genes required to promote growth in the presence of rapamycin.

The only other protein documented to be degraded in response to rapamycin is the translation initiation factor eIF-4G (BERSET et al. 1998). eIF-4G is degraded within 2–3 hr in response to rapamycin treatment, while other initiation factors, such as eIF-4E associated with eIF-4G, remain unaffected (BERSET et al. 1998). The degradation of eIF-4G requires a functional Tor1–kinase signaling pathway (BERSET et al. 1998). Since the time frame during which Rpb1 is degraded coincides with that of eIF-4G, it is likely that Rpb1 degradation is also via the Tor1 pathway. If so, Rrd1 might execute a function downstream of the Tor1 pathway that culminates in the activated expression of a protease (e.g., those induced by rapamycin such as Lap3, Lap 4, Pep4, and Pbr1) that could degrade key proteins involved in translation and transcription (MEWES et al. 1999). Clearly, additional experiments are needed to unravel the exact molecular function by which Rrd1 controls rapamycin resistance.


   ACKNOWLEDGEMENTS
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 ABSTRACT
 ACKNOWLEDGEMENTS
LITERATURE CITED
 
This study was supported by a grant to D.R. from the Canadian Institutes of Health Research. During the tenure of this work D.R. was supported by a career scientist award from the National Cancer Institute of Canada, and currently by a senior fellowship from the Fonds de la Recherche en Sante du Quebec.


   LITERATURE CITED
TOP
 ABSTRACT
 ACKNOWLEDGEMENTS
 LITERATURE CITED
 

BERSET, C., H. TRACHSEL and M. ALTMANN, 1998 The TOR (target of rapamycin) signal transduction pathway regulates the stability of translation initiation factor eIF4G in the yeast Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 95: 4264–4269.[Abstract/Free Full Text]

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Communicating editor: B. J. ANDREWS




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