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Vol. 17, Issue 3, 1306-1321, March 2006
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Department of Medical Genetics and Microbiology, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5S 1A8
Submitted June 1, 2005;
Revised December 13, 2005;
Accepted December 27, 2005
Monitoring Editor: David Drubin
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONACKNOWLEDGMENTSREFERENCES |
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONACKNOWLEDGMENTSREFERENCES |
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). Mutation of RVS161 or RVS167 causes a phenotype consistent with a role for the Rvs proteins in cortical actin cytoskeleton organization and endocytosis: loss of viability and unusual cell morphology in poor growth medium or salt-containing medium, delocalized actin distribution under suboptimal growth conditions, abnormal (random) budding in diploids, and defects in endocytosis and sporulation (Bauer et al., 1993). Ultrastructural studies have revealed that rvs mutants accumulate late secretory vesicles at sites of membrane and cell wall construction (Breton et al., 2001), suggesting an additional role for Rvs161p and Rvs167p in vesicle trafficking.
Rvs161p and Rvs167p are members of the BAR-domain family of proteins, which includes Bin1, Amphiphysin, and Rvs proteins (Sivadon et al., 1997). Amphiphysins are enriched in the mammalian brain and seem to function in synaptic vesicle endocytosis (for review, see Zhang and Zelhof, 2002). Bin1 is a splice isoform of amphiphysin 2 that has features of a tumor suppressor (Sakamuro et al., 1996). Proteins in this family are characterized by the presence of a conserved BAR domain, and it is through their BAR domains that Rvs161p interacts with Rvs167p (Navarro et al., 1997; Sivadon et al., 1997; Colwill et al., 1999). The crystal structure of the BAR domain of Drosophila amphiphysin has recently been solved (Peter et al., 2004). It is a crescent-shaped dimer, in which each monomer forms a coiled coil. The curved shape is only revealed upon dimerization of the two slightly kinked monomers, suggesting that the domain functions only as a dimer. The BAR domain binds preferentially to highly curved negatively charged membranes in vitro, and this property is thought to promote membrane deformation, leading to vesicle formation (Lee and Schekman, 2004; Peter et al., 2004). The central portion of Rvs167p consists of a region rich in glycine, proline, and alanine (the GPA region) and may play a role in Rvs regulation because it is phosphorylated in vivo (Friesen et al., 2003). At its carboxy terminus, Rvs167p, like the amphiphysins, has a Src homology 3 (SH3) domain (Figure 1A), a protein module well defined for binding proline-rich sequences (Pawson and Scott, 1997). Large-scale two-hybrid and phage-display screens have identified a number of proteins that bind to the SH3 domain of Rvs167p (Bon et al., 2000; Uetz et al., 2000; Drees et al., 2001; Ito et al., 2001; Tong et al., 2002); however, few of these interactions have been confirmed. Domain mapping of Rvs167p has revealed that the GPA region and the SH3 domain are largely dispensable for all Rvs167p functions tested (Navarro et al., 1997; Colwill et al., 1999). Thus, although the SH3 domain is conserved among amphiphysins, and several biologically important ligands have been seen to bind to the SH3 domain, its biological function remains unknown.
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Several lines of evidence support a model in which Rvs161p and Rvs167p function together. First, Rvs161p and Rvs167p interact with each other through their respective BAR domains in two-hybrid assays, and Rvs161p can be immunoprecipitated from cells overproducing tagged Rvs167p (Navarro et al., 1997; Colwill et al., 1999). Second, each RVS gene is required for the stability of its Rvs protein partner during vegetative growth in vivo (Lombardi and Riezman, 2001). Third, the phenotype of an rvs161
mutant seems identical to that of an rvs167 mutant in vegetative cells (Crouzet et al., 1991; Bauer et al., 1993; Sivadon et al., 1995), and the extragenic suppressors sur1, sur2, and sur4 (Desfarges et al., 1993), fen1, and ipt1 (Balguerie et al., 2002) and the multicopy suppressor SUR7 (Sivadon et al., 1997) are able to bypass the defects of either an rvs161 or rvs167 strain (Desfarges et al., 1993; Sivadon et al., 1997).
Nonetheless, evidence for distinct roles for the Rvs proteins has also been reported. The BAR domains of Rvs161p and Rvs167p cannot be functionally exchanged with each other, showing that, despite being structurally similar, this domain confers specificity to the activity of each Rvs protein (Sivadon et al., 1997). Rvs167p homodimerization has also been reported (Colwill et al., 1999; Bon et al., 2000; Lombardi and Riezman, 2001). Furthermore, the localization patterns of Rvs161p and Rvs167p do not completely overlap: Rvs167p is localized to cortical actin patches (Balguerie et al., 1999), whereas Rvs161p is reportedly mainly cytoplasmic with small dots distributed randomly within the cell cortex in unbudded cells and at the mother-bud neck during bud emergence and cytokinesis (Brizzio et al., 1998), although Rvs161p-green fluorescent protein has also been localized to small cortical patches during G1 (Balguerie et al., 2002). Finally, synthetic mating defects in combination with fus1 are seen with rvs161 but not rvs167, revealing a specific role for Rvs161p in cell fusion during mating (Brizzio et al., 1998).
In this study, we have used genetic analyses of RVS161 and RVS167 to ask whether Rvs161p and Rvs167p have separate functions in vivo and to characterize the roles of the Rvs proteins. Comprehensive synthetic lethal screens and biochemical studies have identified shared roles for Rvs161p and Rvs167p in cell polarity, cell integrity, cell wall synthesis, and vesicle trafficking, all processes that require proper formation and fusion of vesicles. Consistent with these biological roles, we found that purified Rvs161p-Rvs167p is able to bind to phospholipid vesicles, as is seen with its Drosophila and mammalian homologues. We have also devised specific genetic screens that uncovered a previously unappreciated role for Rvs167p in mating and an essential role for the Rvs167p SH3 domain in some strain backgrounds. We conclude that Rvs161p and Rvs167p function as an obligate heterodimer in vegetative cells and have partially overlapping roles during mating.
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MATERIALS AND METHODS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONACKNOWLEDGMENTSREFERENCES |
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) or were constructed using standard yeast genetic techniques (Sherman, 1991). Deletions of open reading frames (ORFs) were constructed by integrative transformation (Longtine et al., 1998). Standard methods and media were used for yeast growth and transformation (Guthrie and Fink, 1991). Supplemented minimal medium containing 2% dextrose (SD) or 2% galactose (SG) with appropriate amino acid supplements was used to select for plasmids. Salt-containing medium was made by adding NaCl to synthetic dextrose medium or YPD to a final concentration (wt/vol) as indicated. Sorbitol was added to minimal synthetic medium containing glucose or galactose to a final concentration of 1 M to maintain rvs167 slt2 mutants. Where indicated, 
-factor (obtained from the Louisiana State University Health Sciences Center Core Laboratory, New Orleans, LA) was added to log-phase cultures in YPD to a final concentration of 5 µM, and cells were incubated as indicated before harvesting. For spot assays, cultures grown to mid-log phase in SD were serially diluted 10-fold and spotted onto the appropriate plates.
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Plasmids
Plasmids are described in Table 2. Details of construction of all plasmids are available upon request. The ABP1PXXP (BA1732) plasmid was constructed with the use of PCR with Platinum Pfx (Invitrogen, Carlsbad, CA). Two PCR products were synthesized, using a plasmid containing ABP1 under the control of its own promoter as template. Each PCR product introduced an NheI site within the ABP1 coding sequence (the sequence of the primers is available upon request), one at each end of the proline-rich region. The 5'-PCR product was digested with NheI and BamHI and the 3'-PCR product was digested with NheI and ApaI. These were ligated into pRS315 (Sikorski and Hieter, 1989) that had been digested with BamHI and ApaI, giving pRS315-ABP1PXXP, which contained an in-frame deletion of amino acids 448–525. The integrity of all PCR products was confirmed by sequencing.
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Protein Immunoprecipitation and Western Blotting
Yeast strains were grown at 30°C to log phase, harvested, and lysed by vortexing with glass beads in lysis buffer as described previously (Tennyson et al., 1998). Where specified, -factor was added to 5 µM and the cultures treated as described in figure legends. For large-scale immunoprecipitation of Rvs167p-hemagglutinin (HA), log-phase cells were harvested in immunoprecipitation-lysis buffer (50 mM Tris-Cl, pH 7.4, 250 mM NaCl, 50 mM NaF, 0.1% NP-40, 40 mM 
-glycerophosphate, 5 mM EDTA, 1 mM dithiothreitol, 1 mM phenylmethylsulfonyl fluoride, 1 mM sodium orthovanadate, 0.1 mg/ml insulin, and protease inhibitor tablet without EDTA; Boehringer Mannheim, Laval, Quebec, Canada). Cells were lysed by vortexing in the presence of glass beads. One hundred milligrams of lysate was precleared with 300 µl of protein A-Sepharose for 1 h and then incubated with 200 µl of -HA antibodies coupled to protein A-Sepharose for 1 h. The beads were then washed in 3 x 5 ml lysis buffer and boiled in SDS sample buffer. For Western blotting of whole cell extract, the protein concentration of the lysates was measured using the Bradford assay (Bio-Rad, Mississauga, Ontario, Canada). Equivalent amounts of each sample were analyzed by SDS-PAGE and transferred to nitrocellulose using a dry transfer apparatus. Coimmunoprecipitations were done as described previously (Friesen et al., 2005). Immunoblotting was done with antibodies against Rvs161p (gift from H. Riezman, University of Geneva, Geneva, Switzerland), Rvs167p (Lee et al., 1998) and HA (12CA5). As a control, antibodies against Crn1p were used (Humphries et al., 2002). The protein signal was revealed using enhanced chemiluminescence (Amersham Biosciences, Little Chalfont, Buckinghamshire, United Kingdom).
Slt2p-HA was immunoprecipitated with monoclonal antibody 12CA5 (Wilson et al., 1984) from 100-ml cultures either grown at 24°C or grown at 24°C and transferred to 39°C for 2 h. Cells were collected by centrifugation, and lysates were prepared as described previously (Tennyson et al., 1998). Five milligrams of protein from the lysates were incubated with 1 µl of 12CA5 ascitic fluid for 1 h on ice and then rocked in the presence of protein A-Sepharose for 1 h at 4°C. Beads were collected by centrifugation and washed in lysis buffer four times.
Expression and Purification of Rvs167p and Rvs161p from Insect Cells
A BamHI fragment containing full-length RVS161 was subcloned into pAC-HLT (BD Biosciences PharMingen, San Diego, CA) that had been digested with BglII to generate a His-tagged Rvs161p fusion product. A BamHI fragment containing full-length RVS167 was subcloned into pAC-GHLT (BD Biosciences PharMingen) that had been digested with BglII to generate a glutathione S-transferase (GST)-His-tagged Rvs167p fusion product as described previously (Friesen et al., 2003). Recombinant baculoviruses containing RVS161 and RVS167 were isolated from Sf9 insect cells and coinfected into Hi5 cells as recommended by the manufacturer (Invitrogen). Approximately 48 h after infection, cells were harvested, washed, and lysed in insect cell lysis buffer (50 mM Tris-HCl, 20% glycerol, 50 mM NaCl, 0.5 mM EDTA, and 10 mM -mercaptoethanol). Cell extracts were incubated with glutathione-Sepharose beads (Amersham Biosciences) for 1 h at 4°C. Beads were washed 4 times in 10 volumes of lysis buffer, and GST-His-Rvs167p and associated His-Rvs161p were eluted with lysis buffer containing 100 mM glutathione.
Synthetic Lethality Screens and Complementation Assays
We used the synthetic genetic array (SGA) method to systematically identify mutant backgrounds in which RVS167 or RVS161 is required for viability or wild-type growth at 30°C (Tong et al., 2001, 2004). All interactions were confirmed by tetrad dissection. Nonoverlapping interactions between the RVS161 and RVS167 screens were tested against both rvs deletions. Because the frequency of false negatives in SGA analysis can be as high as 40% (Tong et al., 2004), we also tested candidate genes encoding members of a protein complex for interactions with our query genes if genes encoding two or more members of the protein complex were identified to have synthetic interactions (e.g., members of the prefoldin complex). The data for the RVS161 and RVS167 screens have been published previously (Tong et al., 2004).
Complementation of the sla1 abp1 strain was assayed using the plasmid shuffle method. The sla1 abp1 strain containing the URA3-based plasmid pRS316-ABP1 was transformed with the LEU2-based plasmid pRS315-ABP1 or pRS315-ABP1-PXXP. Double transformants were pregrown on SD-Leu, and then cells that had lost the URA3 plasmid were selected on 5-fluoroorotic acid (5-FOA) and assayed by spot dilution on YPD at 37°C and YPD + 3 mM caffeine at 35°C.
Synthetic Mating Defects Screen and Mating Assays
SGA screens were done to construct MATa double mutants that had rvs161 marked with URA3 (rvs161::URA3 xxx::kan) (see above; Tong et al., 2001). To identify genes that were important for mating in the absence of RVS161, the 
5000 viable MATa rvs161::URA3 xxx::kan mutants were crossed to a MAT strain in which the RVS161 ORF had been replaced with the gene encoding nourseothricin resistance (rvs161::Nat) by replica pinning onto YPD plates. The cells were allowed to mate for 6 h at 30°C and then replica pinned onto YPD plates containing nourseothricin (Nat) and G418 to select for diploid cells. Strains that had apparent synthetic mating defects in combination with rvs161 were retested in limited plate matings with rvs161 essentially as described previously (Brizzio et al., 1998). In brief, cells of each mating type were patched on top of each other on YPD plates. The plates were incubated at 30°C and replica plated after 2, 3, and 4 h to YPD + G418 + Nat to select for diploids. Likewise, limited mating assays of other strains were done by crossing a MAT rvs167::Nat strain with MATa rvs167::URA3 fus1::kan, rvs167::URA3 fus2::kan, rvs167::URA3 prm9::kan, and rvs167::URA3 fig2::kan strains; a MAT sla1::Nat strain with MATa sla1::URA3 fus1::kan, sla1::URA3 fus2::kan, sla1::URA3 prm9::kan, and sla1::URA3 fig2::kan strains; and a MAT end3::Nat strain with MATa end3::URA3 fus1::kan, end3::URA3 fus2::kan, end3::URA3 prm9::kan, and end3::URA3 fig2::kan strains.
Fluorescence Microscopy
Ten milliliters of cells were grown to mid-log phase in YPD, fixed in 4% formaldehyde for 1.5 h with shaking, and then washed two times with phosphate-buffered saline (PBS), resuspended in 100 µl of PBS, and stored at 4°C. Thirty-six microliters of fixed cells were incubated with 4 µl of rhodamine-phalloidin (Invitrogen), 0.5 µl of 10% Triton X-100, and 4 µl of 1 mg/ml Fluorescent Brightener (also known as Calcofluor White; Sigma-Aldrich, St. Louis, MO) for 1.5 h in the dark with occasional gentle vortexing. Cells were washed three times in PBS, visualized using VectaShield mounting medium containing 4,6-diamidino-2-phenylindole (DAPI) (Vector Laboratories, Burlingame, CA), and viewed through fluorescein isothiocyanate and rhodamine filters. Photographs were taken with a Micromax 1300y high-speed digital camera (Princeton Instruments, Trenton, NJ) mounted on a Leica DM-LB microscope. Images from the camera were analyzed with MetaVue software (Universal Imaging, Media, PA).
Overexpression of MNN9 and CCW12 in an rvs167 slt2 Strain
Strains BY1891 (slt2) and BY2506 (rvs167 slt2) were transformed with pGAL-ORFs or empty vector, and BY2506 was kept alive on selective synthetic medium plus glucose and 1 M sorbitol at 30°C. Cells were then replica plated onto synthetic selective media plus 2% galactose and 1 M sorbitol, to induce expression of the pGAL-ORF. Ten-fold serial dilutions were made onto SD and SG containing 1 M sorbitol, and plates were incubated at 30°C to assess the growth of the cells.
Actin Binding Assay
Actin filament binding assays was performed as described previously (Goode et al., 1999). Purified Rvs167-GPA-SH3p-His (2.5 µM; Friesen et al., 2003) or Crn1p (2.5 µM; Humphries et al., 2002) was added to preassembled yeast actin filaments (5 µM) and incubated for 15 min at 25°C. The reactions were centrifuged at 90,000 rpm for 15 min in a TLA100.3 rotor, and the supernatants and pellets were analyzed by SDS-PAGE and Coomassie blue staining.
Liposome Sedimentation Assays
Purified GST-Rvs167p-Rvs161p was subjected to centrifugation at 140,000 x g for 30 min to remove insoluble material. Soluble Rvs167p-Rvs161p heterodimer (7 nM) was incubated with 0.8 mg/ml liposomes from total bovine brain lipids (Avanti Polar Lipids, Alabaster, AL; prepared as described by Peter et al., 2004) or buffer for 30 min at 25°C and then centrifuged at 140,000 x g for 20 min as described previously (Peter et al., 2004). After centrifugation, supernatants were removed immediately and pellets were resuspended in an equal volume of buffer. Samples of pellet and supernatant were analyzed by PAGE and Western blot with -Rvs167p antibodies.
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RESULTS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONACKNOWLEDGMENTSREFERENCES |
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). Drosophila amphiphysin and other mammalian amphiphysins form homodimers; however, heterodimers have been observed for some members of the BAR domain family, for example, rat amphiphysin 1 and 2 (Wigge et al., 1997). A search of the SMART database (Letunic et al., 2004) reveals that Rvs161p and Rvs167p are the only BAR domain-containing proteins in S. cerevisiae. Thus, if dimerization is required for BAR-domain activity, the Rvs proteins must act as either an obligate heterodimer or they must homodimerize. Several laboratories have detected a two-hybrid interaction between the BAR domains of Rvs161p and Rvs167p (Navarro et al., 1997; Colwill et al., 1999; Lombardi and Riezman, 2001; Figure 1A), and Rvs161p has been found to coimmunoprecipitate with overproduced Rvs167p (Navarro et al., 1997). To test whether Rvs proteins expressed from their endogenous loci interact and to assay for other proteins that interact with Rvs167p at a stoichiometric level, we used an immunoaffinity purification procedure to isolate Rvs167p–HA complexes from yeast extracts (Figure 1B). By Coomassie blue staining, the only protein that immunoprecipitated with Rvs167p-HA was a protein of 30 kDa. Mass spectrometric analysis of peptides derived from the 30-kDa band indicated that the protein was Rvs161p (our unpublished data). The similar recovery of Rvs161p and Rvs167p in the Rvs167p-HA immune complexes suggests that Rvs161p-167p may form a stoichiometric complex in vivo.
In both rvs161 and rvs167 mutants, the Rvs protein levels are reduced because of reduced stability of one Rvs protein in the absence of the other (Lombardi and Riezman, 2001). This suggests that the interaction between Rvs161p and Rvs167p is required for their stability. Based on our finding that Rvs161p and Rvs167p interact in vivo, we thought that their interaction might function to stabilize each component of the complex in a heterologous system. Consistent with the requirement for an Rvs161p–167p interaction, we found that proteins encoded by either His-RVS161 or GST-His-RVS167 was largely insoluble when expressed (separately) in insect cells (Friesen et al., 2003; our unpublished data), and His-Rvs161p and GST-Rvs167p were insoluble when produced (separately) in Escherichia coli (our unpublished data), suggesting that the protein products may not fold properly in the absence of their partner (Colwill et al., 1999; Maxwell et al., 1999). To test whether the interaction between the Rvs proteins might allow production of a stable protein complex, we coinfected insect cells with baculoviral vectors that expressed both GST-His-RVS167 and His-RVS161. Cell lysates from coinfected cells were bound to glutathione-Sepharose columns, and both Rvs167p and Rvs161p were detected in the column eluates (Figure 1C). Thus, when coexpressed, Rvs167p and Rvs161p were able to form a soluble protein complex. These biochemical data are consistent with the hypothesis that Rvs167p and Rvs161p must function together in vivo.
Several laboratories have reported a two-hybrid interaction between the BAR domain of Rvs167p and full-length Rvs167p (Colwill et al., 1999; Bon et al., 2000; Lombardi and Riezman, 2001). However, a two-hybrid assay does not address whether homodimerization of Rvs167p occurs in vivo. We tested for Rvs167p homodimerization in a coimmunoprecipitation assay using a diploid strain expressing two alleles of RVS167, one encoding an HA-tagged version of Rvs167p and the other encoding an untagged Rvs167p protein. We found that Rvs167p did not coimmunoprecipitate with Rvs167p-HA, showing that homodimerization of Rvs167p does not occur in log-phase cells (Figure 1D, top). To confirm that the epitope-tagged Rvs167p was functional (i.e., able to bind Rvs161p), we showed that Rvs167p could immunoprecipitate an Rvs161p-myc fusion protein (Figure 1D, bottom). These data suggest that previous two-hybrid interactions between the BAR domain of Rvs167p and full-length Rvs167p may have been indirect or an artifact of BAR domain overproduction. In support of this, Bon et al. (2000) saw a two-hybrid interaction between Rvs167p and Rvs167p when both genes were on high-copy plasmids but not when they were on low-copy plasmids.
We also tested whether Rvs161p could homodimerize. Because Rvs161p and Rvs167p are the only BAR-domain-containing proteins in yeast and because Rvs161p is required for fusion during mating and Rvs167p is not (Brizzio et al., 1998), we were especially interested in whether Rvs161p would form homodimers in cells during the mating response. To test for Rvs161p homodimerization, we constructed a strain expressing RVS161-myc from its endogenous locus and transformed it with a plasmid containing an untagged version of RVS161. As a negative control, we used an untagged strain containing the RVS161 plasmid. We immunoprecipitated Rvs161p-myc with anti-myc antibodies and assayed for the presence of Rvs161p. As a positive control, we assayed for coimmunoprecipitation of Rvs167p. Although Rvs167p efficiently coimmunoprecipitated with Rvs161p-myc, Rvs161p did not immunoprecipitate with Rvs161p-myc, either in log-phase cells or in cells treated with factor (Figure 1E). Together, these data show that Rvs161p is the predominant protein partner for Rvs167p in vivo and that these proteins do not form homodimers. These data strongly suggest that the Rvs161p-Rvs167p heterodimer is the functional unit of the Rvs proteins in vivo.
RVS161 and RVS167 Are Genetically Identical as Revealed by Analysis of Synthetic Lethality
To test whether the heterodimer of Rvs161p and Rvs167p accounts for all the cellular functions of the Rvs proteins, we looked at whether one Rvs protein had a function in the absence of its Rvs partner. We predicted that if Rvs161p and Rvs167p function only as a heterodimer, deletion of one RVS gene would be genetically identical to deletion of the other. To test this, and to explore the biological roles of Rvs161p and Rvs167p, we screened for genes that had synthetic genetic interactions with RVS161 and RVS167 by using SGA analysis. Double mutant strains that failed to grow, or that grew more slowly than wild type, identified candidate genetic backgrounds in which RVS was required. All the interactions with either RVS167 or RVS161 were confirmed by tetrad analysis in crosses with both rvs161 and with rvs167 mutants. The complete data set from these screens has been published previously (Tong et al., 2004).
We found 49 strains whose deletion caused death or synthetic growth defects in combination with deletion of RVS167 (Figure 2A). All of these mutant strains (and no others) also showed synthetic lethal or synthetic growth defects with a deletion of RVS161. Genes that are required in the absence of RVS161 and RVS167 were organized into categories according to their roles as defined by the Yeast Proteome Database (https://proteome.incyte.com/control/tools/proteome), the Saccharomyces Genome Database (http://www.yeastgenome.org), and published reports (Figure 2A). As expected from the phenotypes of rvs deletion mutants (Crouzet et al., 1991; Sivadon et al., 1995, 1997; Lee et al., 1998; Breton et al., 2001; Lombardi et al., 2001; Balguerie et al., 2002), the RVS interactions were enriched for genes with roles in cell polarity, cell wall synthesis, cell wall integrity, and vesicle trafficking.
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The Pattern of Identical Synthetic Genetic Interactions with RVS161 and RVS167 Is Not Because of Destabilization of the Rvs Partner
Because each Rvs protein is required for the solubility and stability of its Rvs partner in vivo (Lombardi and Riezman, 2001; Figure 1C), it was possible that the identical SGA profiles for RVS161 and RVS167 reflected the decreased protein levels of the remaining Rvs protein. We next asked whether increasing the cellular concentration of Rvs167p to wild-type levels in the rvs161 double mutants (which we refer to as rvs161 xxx strains) could suppress their growth defect. Expression of RVS167 from the MET25 promoter restores Rvs167p protein to wild-type levels in the rvs161 RVS167+ strain (Figure 2B). We predicted that if the rvs161 xxx mutant strains were slow growing because Rvs167p was destabilized, heterologous expression of RVS167 should rescue the growth defects of the double mutants. We compared the ability of empty vector, p416-MET-RVS167 and p316-RVS161 (RVS161 under the control of its own promoter) to complement the growth defects of 20 slow-growing rvs161 xxx mutants grown on medium containing 3% salt, which provides more stringent conditions to detect the subtle growth defects of some of the double mutants. We found that restoring levels of Rvs167p by expressing RVS167 failed to rescue the growth defects of these strains (Figure 2C). Weak suppression of the rvs161 xxx slow growth phenotype by RVS167 was detected in the sum1, skt5, and ybr255w double mutants, but in all cases the RVS161 plasmid complemented the growth defect of the rvs161 xxx strains much more efficiently than the RVS167 plasmid (Figure 2C; our unpublished data). These data show that restoring Rvs167p protein to wild-type levels is not sufficient to restore wild-type growth in strains in which RVS161 is needed. Thus, the decreased protein levels of the Rvs partner are not sufficient to explain the overlap of the genetic profiles of strains deleted for RVS167 or RVS161.
Reduced Stability of Each Rvs Protein in the Absence of its Partner in Pheromone-treated Cells
As noted above, previous studies showed that the levels of Rvs167p protein are reduced in an rvs161 mutant during log phase, and, similarly, the levels of Rvs161p are strongly reduced in an rvs167 mutant (Lombardi et al., 2001). The instability of the Rvs proteins in the absence of their partner is consistent with the model that they function together during vegetative growth. However, distinct phenotypes for rvs mutants have been reported during the mating response, and it is unclear whether the Rvs proteins function as a heterodimer during mating (Brizzio et al., 1998). We hypothesized that if Rvs167p has a role in mating, then Rvs161p protein levels might remain low in an rvs167 strain exposed to mating pheromone, despite the rapid induction of RVS161 expression in response to factor (Brizzio et al., 1998). To test this, we used Western blots to look at the protein levels of Rvs161p and Rvs167p from extracts of cells treated with pheromone. Rvs161p protein levels were greatly decreased in extracts from rvs167 mutants in log phase compared with levels in wild-type cells (Figure 3A, compare lanes 2 and 6). On treatment with factor, Rvs161p was detected at much lower levels in the rvs167 strain than in wild-type cells, even after incubation for 2 h in pheromone-containing medium (Figure 3A, lanes 7–9). In an analogous assay, we examined the protein levels of Rvs167p in rvs161 extracts after exposure to pheromone. Rvs167p protein levels were strongly reduced in log-phase rvs161 cells compared with wild-type cells and remained reduced during treatment with factor (Figure 3B). These data reveal a requirement for the Rvs partner for the stability of the Rvs proteins during pheromone exposure, suggesting that the Rvs161p-Rvs167p heterodimer may function during mating.
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Identification of Mutations That Lead to Synthetic Mating Defects in Combination with Deletion of RVS161 and RVS167
Our finding that stability of Rvs161p depends on Rvs167p during pheromone response suggests a function for both Rvs161p and Rvs167p during mating. However, only RVS161, but not RVS167, has been shown to be important for mating (Brizzio et al., 1998). The mating defects of a strain deleted for RVS161 alone are subtle but are exacerbated in combination with a deletion of FUS1 (Brizzio et al., 1998). We were therefore interested in identifying additional genetic backgrounds in which the mating defect of the rvs161 strain was exacerbated, to test whether a role for RVS167 in mating could be uncovered in these backgrounds. We used SGA to create double mutants of rvs161 in combination with the 5000 yeast gene deletions. These rvs161 xxx mutants were then screened in limited mating assays for synthetic mating defects in crosses with an rvs161 mating partner using SGA (see Materials and Methods). We identified a number of genes that seemed to be required for mating in the absence of RVS161 (our unpublished data). We arbitrarily chose three genes, each of which has a role in cell fusion during mating: PRM9, AXL1, and FIG2. PRM9 encodes a pheromone-regulated membrane protein (Heiman and Walter, 2000), and its mutant phenotype has not yet been characterized. AXL1 encodes a protease required for cell fusion during mating (Elia and Marsh, 1998) and is required for axial budding (Fujita et al., 1994). FIG2 is involved in agglutination during mating (Zhang et al., 2002). We next tested whether some of these genes were required for mating in the absence of RVS167 using limited mating assays. We also included crosses with fus1 and fus2 mutants as positive and negative controls, because a strain with a deletion of RVS161 has mating defects in combination with fus1 but not fus2 (Brizzio et al., 1998), and mnn4, another positive control, which had no defect in combination with rvs161 or rvs167. All of these mutants showed no mating defect in an RVS+ background when crossed to rvs161 or rvs167 strains (Figure 4A, left). In an rvs161 background, a synthetic mating defect was seen in fus1, prm9, axl1, and fig2, but not in fus2 or in mnn4 (Figure 4A, right). In the rvs167 background, no mating defect was seen in fus1, fus2, axl1, or in mnn4 strains, although the axl1 strain seemed to be delayed in mating (Figure 4A, right). But rvs167 prm9 and rvs167 fig2 strains had a mating defect similar to that seen in an rvs161 background. All these results were confirmed in quantitative mating assays (our unpublished data). We also found that the rvs161 and rvs167 double mutants (with fus1, fus2, prm9, and fig2) were able to form shmoos with >50% wild-type efficiency, indicating that their pheromone signaling pathway was functional, consistent with the defect in cell fusion previously reported in rvs161 strains. In summary, we found that rvs161 has synthetic mating defects with fus1 and axl1 that are not seen with rvs167. Both rvs161 and rvs167 have defects in combination with deletions in prm9 and fig2.
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Because we had found that Rvs161p levels were significantly decreased during exposure to mating pheromone in an rvs167 strain (Figure 3A), one possibility was that the mating defect was because of destabilized Rvs161p and not absence of Rvs167p. To test this possibility, we assayed rvs167 cells transformed with a high copy plasmid containing RVS161 under its own promoter in a limited mating assay. As a positive control, we also tested rvs167 cells with a plasmid containing RVS167. In this experiment, RVS167 but not high copy RVS161 was able to complement the mating defect of the rvs167 xxx mutants (Figure 4B). This suggests that the mating defect in rvs167 cells is not because of reduced stability of Rvs161p.
The BAR domain of Rvs167p is largely able to complement all the defects of an rvs167 strain during log-phase growth, but we were interested in whether the SH3 domain or the phosphorylation sites within the GPA region of Rvs167p were needed for mating. Rvs167p is hyperphosphorylated during the mating response (Lee et al., 1998; Friesen et al., 2003). We tested the rvs167 xxx mutants for complementation using a plasmid that encodes Rvs167p with a mutant SH3 domain (Rvs167p-P473L). This Rvs167p SH3 mutant protein does not interact with the proline-rich region of Abp1 in a two-hybrid assay, but it does bind other proteins that interact with Rvs167p outside the SH3 domain, indicating that this mutant specifically disrupts the function of the SH3 domain (Colwill et al., 1999). We also tested for complementation using a plasmid with RVS167 encoding a protein with alanine substitutions at all four of the residues that are phosphorylated in vivo (Rvs167p-4A; Friesen et al., 2003). The rvs167 xxx mutants were complemented equally efficiently by wild-type RVS167 and by RVS167-P473L and by RVS167-4A (Figure 4B). This indicates that neither an intact SH3 domain nor phosphorylation of Rvs167p is required for Rvs167p function during mating.
We were interested in whether the mating defects in rvs167 cells were characteristic of all endocytosis mutants. Brizzio et al. (1998) assayed several mutants defective in endocytosis for defects in mating and found that end3-1, end4-1, end6-1, and end7-1 behaved like wild type, suggesting that endocytosis did not play a role in cell fusion. However, it was possible that these defects could only be uncovered in certain specific genetic backgrounds, as we had seen for rvs167. We tested two well-characterized endocytosis mutants, end3 (Raths et al., 1993) and sla1 (Warren et al., 2002), along with rvs161 and rvs167, for mating in the absence of FUS1, FUS2, PRM9, and FIG2 (Figure 4C). As described above (Figure 4, A and B), rvs161 had a mating defect in the absence of FUS1, and rvs161 and rvs167 had mating defects in the absence of PRM9 and FIG2 (Figure 4C). In contrast, the sla1 strain and the end3 strain were able to mate in the absence of PRM9 and FIG2 (Figure 4C). Mating of the end3 strain was not as efficient as mating in the other strains, possibly because the end3 strain is slow growing by itself. Thus, in these assays, RVS167 has a role in mating that is partially distinct from that of RVS161 but is not found in other endocytosis mutants.
Synthetic Defects in Actin Organization and Chitin Distribution in Double Mutants
Identification of synthetic lethal interactions or synergistic growth defects provides support for a functional interaction between gene products (Bender and Pringle, 1991, Tong et al., 2004). Furthermore, the subtle defects in the organization and polarity of cortical actin structures of null mutations in cytoskeleton protein genes, and the large number of synthetic lethal interactions among these genes reveal their multiple overlapping functions (Ayscough and Drubin, 1996; Goode and Rodal, 2001). However, the cellular basis for the synthetic lethality is not always clear, and we decided to characterize the phenotypes of a subset of the mutants identified in our SGA analysis to determine whether polarity was defective in the double mutant strains. We first decided to examine the actin cytoskeleton. The rvs161 and rvs167 strains have partial defects in the polarization of their cortical actin cytoskeleton, suggesting their function in this process must be partially redundant with other cytoskeleton proteins (Sivadon et al., 1995; Lee et al., 1998; Balguerie et al., 1999). In a subset of the viable rvs167 xxx mutants with synthetic growth defects and in the corresponding single mutants, we visualized filamentous actin using rhodamine-phalloidin staining (Figure 5A). Quantification of cells showing a defect in actin polarization revealed that rvs167 cells had a partially depolarized actin cytoskeleton (Figure 5A, left), as reported previously. In some of the rvs167 xxx mutants, the defects in actin organization were no worse than in the single mutants. However, in the myo5 rvs167 and yke2 rvs167 double mutants cortical actin patches were seen randomly distributed over the periphery of both mother and daughter cell at all stages of the cell cycle (Figure 5A). This suggests that in these mutants the synergistic growth defect may be because of a depolarized actin cytoskeleton.
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xxx mutants were also examined for another phenotype that is often associated with perturbation of the actin cytoskeleton: cell wall defects. Mutations affecting actin can cause cell wall defects as indicated by depolarized chitin deposition (Novick and Botstein, 1985; Yang et al., 1997). We looked at cells stained with Calcofluor White to visualize the chitin deposited in the cell wall in bud scars and with DAPI to monitor position in the cell cycle. As reported previously (Bauer et al., 1993), the rvs167 mutant contained slightly diffuse chitin distributed over the entire mother cell surface (Figure 5B). Of the six rvs167 xxx strains tested, rvs167 myo5, rvs167 sla1, rvs167 vps21, and rvs167 yke2 showed a more diffuse chitin localization and weaker staining of bud scars than either of the single mutants (Figure 5B, quantification shown on the left). Interestingly, deletion of the genes with roles in endocytosis, MYO5 (Geli and Riezman, 1996), SLA1 (Warren et al., 2002), and VPS21 (Singer-Krüger et al., 1994), in combination with deletion of RVS167, resulted in cell wall defects. Thus, although rvs167 mutants have only partial defects in their actin cytoskeleton and cell wall, one or both of these defects were made more severe in several of the double mutants tested. Together, these data show that the growth defects of rvs167 double mutants may be caused by synergistic defects in cell wall structure and in the organization of the actin cytoskeleton.
The Cell Integrity Pathway Is Activated in rvs Mutants
The Slt2p kinase becomes phosphorylated on T190 and Y192 upon activation of the Slt2p MAP kinase pathway during periods in which yeast cells are undergoing polarized cell growth, namely, during bud formation and in response to mating pheromone and in response to environmental conditions such as cell wall damage and heat stress (Zarzov et al., 1996; de Nobel et al., 2000). Based on the observations that rvs161 and rvs167 mutants have defects in their cell wall (Figure 5B) and synthetic lethal interactions with genes that encode components of the Slt2p pathway (Figure 2A; Breton et al., 2001), we hypothesized that rvs mutants may have a constitutively activated Slt2p pathway. We used anti-phospho-p42/p44 MAP kinase antibody, which specifically recognizes the phosphorylated (activated) form of Slt2p (Verna et al., 1997; de Nobel et al., 2000), to examine activation of the Slt2p pathway in wild-type and rvs161 and rvs167 cells. Because we were unable to detect endogenous Slt2p using this antibody (our unpublished data), we transformed cells with a high-copy plasmid encoding HA-tagged Slt2p and immunoprecipitated Slt2p-HA from these cells using anti-HA antibodies, for detection with the anti-phospho-p42/p44 MAP kinase antibody (Madden et al., 1997). We immunoprecipitated Slt2p-HA using anti-HA antiserum from wild-type, rvs161, and rvs167 cells grown at 24°C. As a positive control for Slt2p activation, we also activated the Slt2p pathway in a wild-type strain by incubating the cells at 39°C for 2 h (Kamada et al., 1995). No proteins were recognized by the anti-phospho-p42/44 antibody in immunoprecipitates from a wild-type strain with untagged Slt2p (Figure 6A, top). In wild-type cells grown at 24°C, only a small amount of phosphorylated Slt2-HA was detected by the anti-phospho-p42/p44, whereas incubation of cells at 39°C resulted in the accumulation of a larger amount of phosphorylated Slt2p (Figure 6A, top, lanes 2 and 3). Consistent with the hypothesis that Slt2p is constitutively activated in the absence of Rvs161p and Rvs167p, rvs161 and rvs167 mutants grown at 24°C displayed a higher level of phosphorylated Slt2p than the wild-type strain grown at 24°C (Figure 6A, lanes 4 and 5 respectively). Immunoblot analysis using an anti-HA antibody confirmed that similar amounts of Slt2p were present in every lane (Figure 6A, bottom).
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). Slt2p activates the transcription factors Rlm1p and SBF, a heterodimer composed of Swi4p and Swi6p (Andrews and Herskowitz, 1989), leading to expression of specific subsets of genes (Madden et al., 1997; Watanabe et al., 1997; Jung and Levin, 1999; Baetz et al., 2001). Thus, one possible explanation for the requirement for the Slt2p pathway components in rvs mutants is that genes whose expression is Slt2p-dependent are essential in the absence of Rvs161p and Rvs167p. Consistent with this hypothesis, we had identified two genes whose transcription is known to be dependent on Slt2p, CCW12 and CHS3 (Jung and Levin, 1999; Baetz et al., 2001), in our screen for genes that had synergistic growth defects in combination with deletions of rvs161 and rvs167 (Figure 2A).
We hypothesized that overproduction of transcriptional targets of Slt2p might rescue the synthetic lethality of the slt2 rvs167 mutant. The double mutant strain is unable to grow on galactose-containing medium, even in the presence of the osmotic stabilizer sorbitol, but we could keep it alive on glucose-containing medium containing 1 M sorbitol (Figure 6B; Breton et al., 2001). We transformed an slt2 strain and an rvs167 slt2 strain with overexpression plasmids containing the various genes involved in cell wall maintenance that had come out of our synthetic lethality screen and looked for suppression on galactose. Overexpression of two of the genes, MNN9 and CCW12, but not vector alone, could partially suppress the lethality of an rvs167 slt2 strain (Figure 6B). These data suggest that the essential role of the Slt2p–MAP kinase pathway in the absence of RVS167 may be to activate transcription of genes involved in cell wall maintenance, presumably through the transcription factor Swi4p.
The SH3 Domain of Rvs167p Does Not Bind Actin But Is Required in the Absence of SLA1
The SH3 domain of Rvs167p interacts with many actin cytoskeleton proteins in two-hybrid studies, including Abp1p, Las17p, and actin (Amberg et al., 1995; Lila and Drubin, 1997; Wendland et al., 1998; Colwill et al., 1999; Bon et al., 2000; Landgraf et al., 2004). A biological role for the SH3 domain remains unclear because it is not required to complement any rvs167 defects; the BAR domain of Rvs167p is largely sufficient to rescue all rvs167 phenotypes (Colwill et al., 1999). One possible role for the SH3 domain is to bind actin. An interaction between the carboxy-terminal region of Rvs167p and actin has been demonstrated in two-hybrid assays, but it is unclear whether this interaction is direct or whether it is mediated through interactions with other actin-binding proteins (Amberg et al., 1995; Lombardi and Riezman, 2001). To test the carboxy-terminal portion of Rvs167p for binding to actin, we asked whether purified GPA-SH3 domain could bind actin in vitro. GPA-SH3 domain was added to preassembled F-actin, and binding was tested in a high-speed cosedimentation assay. Background levels of GPA-SH3 pelleting (20%) were observed in reactions that contained GPA-SH3 alone (Figure 7A, lanes 3 and 4). No increase in GPA-SH3 pelleting was detected in reactions containing F-actin (Figure 7A, lanes 9 and 10). In contrast, despite similar background levels of pelleting, the majority of Crn1p, which was used in this assay as a positive control for F-actin binding (Goode et al., 1999) was detected in the pellet fractions in reactions containing F-actin (Figure 7A, lanes 7 and 8). These data suggest that previous two-hybrid interactions between actin and the carboxy terminus of Rvs167p are indirect (Lila and Drubin, 1997; Lombardi et al., 2001). It is possible, however, that the SH3 domain of Rvs167p has no role in the absence of the BAR domain and depends on interactions between Rvs161p and Rvs167p.
