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Vol. 20, Issue 12, 2920-2931, June 15, 2009
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*Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235-1634; Laboratory of Cell Biochemistry and Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892; and Extremobiosphere Research Center, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka 237-0061, Japan
Submitted October 16, 2008;
Accepted April 16, 2009
Monitoring Editor: Akihiko Nakano
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONREFERENCES |
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, which correlates with an enhanced ability of Dnf P4-ATPases to functionally substitute for Drs2p. Loss of Kes1p also suppresses a drs2-ts allele in a strain deficient for Dnf P4-ATPases, suggesting that Kes1p antagonizes Drs2p activity in vivo. Indeed, Drs2-dependent phosphatidylserine translocase (flippase) activity is hyperactive in TGN membranes from kes1 cells and is potently attenuated by addition of recombinant Kes1p. Surprisingly, Drs2p also antagonizes Kes1p activity in vivo. Drs2p deficiency causes a markedly increased rate of cholesterol transport from the plasma membrane to the endoplasmic reticulum (ER) and redistribution of endogenous ergosterol to intracellular membranes, phenotypes that are Kes1p dependent. These data suggest a homeostatic feedback mechanism in which appropriately regulated flippase activity in the Golgi complex helps establish a plasma membrane phospholipid organization that resists sterol extraction by a sterol binding protein. |
INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONREFERENCES |
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). The mechanism for establishing and maintaining phospholipid asymmetry is uncertain; however, type IV P-type ATPases (P4-ATPases) seem to facilitate this process by flipping PS and PE to the cytosolic leaflet (Graham, 2004; van Meer et al., 2008). The budding yeast genome contains five P4-ATPase genes—DRS2, DNF1, DNF2, DNF3, and NEO1—whereas the human genome contains 14 members of this gene family (Graham, 2004). NEO1 is an essential gene and the other four members (DRS2 and the DNF genes) form an essential group with partially overlapping functions. Drs2p localizes to the trans-Golgi network (TGN) and is required for a flippase activity present in purified TGN membranes with specificity for PS and PE (Natarajan et al., 2004; Alder-Baerens et al., 2006). Dnf1p and Dnf2p seem to have a substrate preference for PE and PC and are primarily responsible for flippase activity in the yeast plasma membrane (Pomorski et al., 2003; Saito et al., 2004; Elvington et al., 2005). Most of the P4-ATPases interact with a noncatalytic subunit in the Cdc50p family. For example, Drs2p associates with Cdc50p, whereas Dnf1p and Dnf2p associate with Lem3p (also called Ros3p), and these interactions are required for export of the complexes out of the endoplasmic reticulum (ER) and the function of the P4-ATPase (Saito et al., 2004; Chen et al., 2006).
Another well-conserved feature of the eukaryotic plasma membrane is its high concentration of sterol relative to internal organelles. Even though different species produce unique sterols, for example cholesterol in mammals and ergosterol in fungi, the majority of unesterified cellular sterol is localized to the plasma membrane (Daum et al., 1998; Liscum and Munn, 1999). How sterols are concentrated in the plasma membrane is poorly understood. Surprisingly, sterols can move efficiently between the ER, the site of synthesis, and plasma membrane under conditions in which vesicle-mediated protein transport through the secretory pathway is blocked (Kaplan and Simoni, 1985; Li and Prinz, 2004; Baumann et al., 2005). Candidate proteins responsible for this nonvesicular, intracellular sterol transport include the oxysterol binding protein homologues (Osh proteins). These sterol binding proteins include seven members in Saccharomyces cerevisiae (Osh1p-Osh7p) and 16 human homologues (Beh et al., 2001). The structure of Osh4p/Kes1p (hereafter referred to as Kes1p) has been solved with sterol present in a deep, hydrophobic binding pocket that is similar to that present in other lipid transfer proteins (Im et al., 2005). Kes1p can transfer sterol between membranes in vitro and inactivation of Kes1p in a strain deficient for the other six Osh proteins perturbs nonvesicular sterol transport in vivo (Im et al., 2005; Raychaudhuri et al., 2006). However, whether Osh proteins mediate bulk sterol transport or function as signaling molecules in response to sterol binding is an important unresolved issue (Fairn and McMaster, 2008).
P4-ATPases and oxysterol binding proteins have also been implicated in vesicle-mediated protein transport (Graham, 2004; Mousley et al., 2007). DRS2 was recovered in a genetic screen for factors that function with ADP-ribosylation factor (ARF) in vesicle biogenesis from the Golgi (Chen et al., 1999). This screen also recovered CDC50 (Chen et al., 2006), which encodes a membrane protein that chaperones Drs2p from the ER to the TGN (Saito et al., 2004), the clathrin heavy chain gene (Chen and Graham, 1998), and an auxilin homologue required to uncoat clathrin-coated vesicles (Gall et al., 2000). As implicated from this screen, Drs2p function is required for a subset of ARF and clathrin-dependent pathways mediating protein transport from the TGN to the cell surface, as well as between the TGN and early endosome (Gall et al., 2002; Saito et al., 2004; Furuta et al., 2007; Liu et al., 2008). The Dnf P4-ATPases cannot compensate for the loss of Drs2p in the exocytic and early endosome transport pathways. However, functional overlap between Drs2p and Dnf1p is observed in the transport of proteins from the TGN to late endosomes and the vacuole (Hua et al., 2002).
Kes1p is a negative regulator of vesicle budding in the TGN-early endosomal system, although the mechanistic basis of this repression is not known (Mousley et al., 2007). Loss of function kes1 alleles were recovered in screens for suppressors of the kre11 and sec14 protein trafficking mutants (Jiang et al., 1994; Fang et al., 1996). Kre11p is a component of the TRAPPII nucleotide exchange complex for the Rab proteins Ypt31p and Ypt32p, which regulate vesicle budding from the TGN and early endosomes (Chen et al., 2005; Morozova et al., 2006; Furuta et al., 2007). Sec14p is a yeast phosphatidylinositol/phosphatidylcholine (PI/PC) transfer protein required for exocytic vesicle budding from the TGN (Novick et al., 1980; Bankaitis et al., 1990). Sec14p down-regulates PC synthesis through the CDP-choline pathway (McGee et al., 1994) and also stimulates phosphoinositide synthesis (Rivas et al., 1999), perhaps by presenting substrate to PI 4-kinase (Schaaf et al., 2008). Thus, Sec14p helps generate a membrane composition that is permissive for vesicle budding. Disruption of KES1 can bypass the essential requirement for Sec14p by a mechanism that is downstream of the CDP-choline pathway for PC synthesis (Fang et al., 1996; Li et al., 2002). Kes1p is recruited to TGN membranes by PI 4-phosphate (PI4P) and may impart an inhibitory influence on vesicle budding by depressing PI4P levels or competing with other effectors for this lipid (Li et al., 2002; Fairn et al., 2007).
Here, we report that kes1 is also a suppressor of drs2 alleles, although kes1 cannot bypass the essential function of the DRS2/DNF family of P4-ATPases. Genetically, Kes1p seems to repress Dnf and Drs2p function at the TGN, and we provide biochemical evidence that Kes1p potently antagonizes Drs2p flippase activity in purified TGN membranes. Surprisingly, we also found that Kes1p is hyperactive in drs2 cells and causes a significant increase in the rate of sterol transport to intracellular membranes. Thus, Drs2p also antagonizes the influence of Kes1p on intracellular sterol transport. These observations imply that a system of checks and balances between a P4-ATPase and oxysterol binding protein controls vesicular and nonvesicular transport processes essential for membrane biogenesis.
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MATERIALS AND METHODS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONREFERENCES |
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Media and Strains
Yeast strains used in this study are listed in Supplemental Table 1 and were grown in standard rich medium (YPD) or synthetic defined (SD) minimal media containing the required nutritional supplements (Sherman, 1991). Yeast transformations were performed using a lithium acetate method (Gietz and Woods, 2006). KES1 was disrupted by polymerase chain reaction (PCR)-mediated replacement with HIS3 from Saccharomyces kluyveri by using primers forward (5'-TCG AAA AAT TTA TAA GAT TTA GTC TCA AGA ATT TCA AGT CCG GAT CCC CGG GTT AAT TAA-3') and reverse (5'-ATT AGT GCA ACG GTA ACA AGT TGT TAC TTT ATC GTT CTC CGA ATT CGA GCT CGT TTA AAC-3') primers with the pFA6a-His3MX6 template as described previously (Longtine et al., 1998). In other strains, KES1 was replaced with URA3 by transformation with pRE352 (Fang et al., 1996) digested with EcoRI and BamHI. The BY4741 kes1 drs2 strain was constructed using pZH523 (Hua et al., 2002) to disrupt DRS2 in the BY4741 kes1 strain background. For strains used for the cholesterol transport assays, UPC2 was replaced with upc2-1 by homologous recombination to allow these strains to take up exogenous cholesterol during aerobic growth (Raychaudhuri et al., 2006).
To test for growth inhibition, cells in early log phase were diluted to 0.1 OD/ml in rich media containing potential inhibitors at various concentrations, and growth was monitored using an enzyme-linked immunosorbent assay plate reader. The OD600 after 36 h in rich media without inhibitor was defined as 100% growth for a particular strain and used to normalize data with inhibitor (± SD; n = 6). Tests for growth at high-pressure was done as described previously (Abe and Minegishi, 2008).
Screen for Suppressors of drs2 and Cloning of KES1
Individual colonies of MAT
and MATa drs2 strains (SEY6210 drs2::TRP1 and SEY6211 drs2::LEU2) were streaked on rich media and incubated at the nonpermissive growth temperature (20 or 17°C) to select for spontaneous bypass suppressors. Cold-resistant (CR) suppressor strains were backcrossed to parental strains to define recessive and dominant suppressor alleles. Recessive suppressor mutants were intercrossed to define two complementation groups suppressor of drs2 knockout (SDK) 1 and SDK2. To clone SDK1, strain BMY1001 (drs2 sdk1-1) was transformed with a genomic library (Goodson et al., 1996) and 
50,000 Leu+ transformants were replica plated and incubated at 17°C for 5–7 d to screen for cold-sensitive colonies. The genomic library plasmids pBMP1 and pBMP2 were rescued from two cold-sensitive (cs) colonies and were identical in restriction digestion pattern. pBMP1 restored cs growth to BMY1001 upon retransformation and DNA sequencing indicated that it carried an 8.6-kbp fragment of chromosome XVI containing KES1.
Microscopy and Immunological Methods
Imaging of cells expressing green fluorescent protein (GFP) fusion proteins and stained with filipin was done as described previously (Beh and Rine, 2004; Liu et al., 2007). Samples for electron microscopy were prepared as described previously (Chen et al., 1999). Sections (50–100 nm) were observed on a CM12 electron microscope (Philips, Eindhoven, The Netherlands). Vesicles (100 nm in diameter) were counted in 50 cell sections for each strain. Error bars are SD (n = 2). Metabolic labeling, immunoprecipitation (Graham, 2001), and immunoblotting (Chen et al., 1999) were performed as described previously. An Odyssey infrared fluorescence detector (LI-COR, Lincoln, NE) was used to quantify Western blots and Coomassie-stained gels.
Phospholipid Translocase Assays
The methods for purifying TGN membranes and assaying Drs2p- and ATP-dependent 7-nitro-2-1,3-benzoxadiazol-4-yl (NBD)-PS translocase activities have been described previously (Natarajan and Graham, 2006). Briefly, equal volumes of purified TGN membranes (0.5 mg/ml), NBD phospholipid (10 µM), and an ATP regenerating system (without ATP) were mixed on ice and then shifted to 37°C to initiate the assay. After 2 h of incubation at 37°C with no ATP, the samples were split and 3 µl of 100 mM ATP or buffer H (10 mM HEPES, pH 7.5, and 150 mM NaCl) was added per 100 µl of sample. The kes1 membrane samples were split again and received 1 µl of Kes1p or buffer H per 100 µl of sample. The samples were incubated an additional 2 h at 37°C. Aliquots of membranes were removed at 0, 2 (before ATP addition), and 4 h of incubation and NBD-PS in the cytosolic leaflet was extracted onto fatty-acid free BSA and quantified. The difference in the percentage of NBD-PS in the cytosolic leaflet of wild-type (WT) TGN membranes incubated with or without ATP at the 4-h time point was defined as 100% NBD-PS flippase activity and was used to normalize data for other conditions assayed. Assays were performed in duplicate and averages from at least three independent experiments (± SD) are reported. Quantification of ergosterol in kes1 TGN membranes was done as described previously (Hanover et al., 2005).
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RESULTS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONREFERENCES |
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Cold-sensitive Growth strains can only grow over a temperature range of 21–40°C. To explore the mechanism underlying this extreme cs growth defect, we carried out a selection for spontaneous extragenic suppressors that allowed growth of drs2 at 17°C. Complementation tests indicated that the recessive drs2 suppressor mutants fell into two complementation groups, which we named SDK1 and SDK2. The SDK1 and SDK2 groups are composed of 12 and four recessive extragenic bypass suppressors of drs2, respectively. Figure 1A shows the 30 and 17°C growth phenotypes of representative drs2 sdk1 and drs2 sdk2 mutants relative to parental drs2 and WT strains. Surprisingly, the drs2 sdk1 double mutant formed larger colonies than even the WT strain at 17°C (Figure 1B).
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sdk1-1 sdk1-1 cells (Figure 1B). Among the five open reading frames in pBMP1, KES1 was the most likely candidate for the sdk1-complementing gene and as expected, a KES1 subclone complemented the cold-resistant phenotype of drs2 sdk1-1 (Figure 1B). Several of the kes1 alleles isolated in the sec14 suppressor screen contained nonsense mutations, leading to the expression of truncated, nonfunctional proteins (Fang et al., 1996; Li et al., 2002). We examined the expression of Kes1p in the drs2 sdk mutants by Western blotting and found that seven of the 12 sdk1 alleles failed to express full-length Kes1p, suggesting that they also carry nonsense mutations (Supplemental Figure 1). These data indicate that sdk1 strains carry mutations in KES1 (i.e., SDK1 and KES1 are the same gene) and that loss of function kes1 mutations suppresses drs2 cs growth. Kes1p is one of seven oxysterol binding protein homologues in yeast. None of the other six members were able to restore a cs growth phenotype to either drs2 sdk1-1 or drs2 sdk2, even when overexpressed from multicopy plasmids (data not shown). We have not yet succeeded in cloning SDK2; so, this report focuses on SDK1/KES1.
Mutations in three genes (CKI1, PCT1, and CPT1) encoding enzymes of the CDP-choline pathway involved in phosphatidylcholine biosynthesis can bypass the essential requirement of SEC14. However, we found that disruption of CKI1 in the drs2 background failed to suppress cs growth of drs2 (Figure 1C). Hence, inactivation of phosphatidylcholine biosynthesis via the CDP-choline pathway does not exert bypass suppression of drs2. Deletion of SAC1, a phosphoinositide phosphatase, increases PI4P levels and suppresses sec14-ts (Rivas et al., 1999). SAC1 deletion suppressed the cold sensitivity of drs2 at 20°C but not at 17°C (Figure 1C). However, the sac1 single mutant also failed to grow at 17°C and so the lack of drs2 suppression at this temperature may not be significant.
A high percentage of Saccharomyces mutants that cannot grow at low temperature, including drs2, also fail to grow at high hydrostatic pressure (Abe and Minegishi, 2008). This strong positive correlation suggests that the mutants have a defect in membrane order and fluidity. To determine whether kes1 would also suppress the high-pressure growth defect of drs2 at 30°C, we measured the growth of WT, drs2, kes1, and drs2 kes1 strains at atmospheric pressure (0.1 MPa) and high pressure (25 MPa; 250 kg/cm2) in liquid medium over a 10-h period. Under these conditions, drs2 grew slower than WT or kes1 cells at 0.1 MPa, and this growth defect was exacerbated at 25 MPa. At both pressure conditions, the drs2 kes1 cells showed improved growth, indicating that the drs2 high-pressure sensitivity was at least partially suppressed by kes1 (Figure 1D).
kes1 Suppression of drs2 Requires DNF P4-ATPase Genes
Drs2p is part of an essential group of P4-ATPases that also includes Dnf1p, Dnf2p, and Dnf3p (Hua et al., 2002). In the absence of Dnf P4-ATPases (dnf1,2,3 cells), Drs2p can support growth of yeast over the full temperature range by itself, but the drs2 dnf1,2,3 quadruple mutant is dead at any temperature (Hua et al., 2002). To determine whether kes1 could bypass the essential requirement for DRS2/DNF function, or whether the mechanism of suppression required the presence of Dnf ATPases, we tested whether deletion of KES1 would rescue viability of a drs2 dnf1,2,3 strain. A strain was generated that carries null alleles of all four members of the DRS2/DNF group by first introducing a wild-type copy of DRS2 on a URA3-based plasmid (pURA3-DRS2) (Hua et al., 2002). This quadruple mutant strain (drs2 dnf1,2,3) could not lose pURA3-DRS2 and grow on 5-fluoro-orotic acid (5-FOA) (Figure 2A), a compound that kills cells retaining URA3-based plasmids. In contrast, WT and drs2 cells were able to lose the pURA3-DRS2 plasmid and form colonies on 5-FOA plates. Importantly, the drs2 dnf1,2,3 kes1 strain failed to grow on the 5-FOA plate (Figure 2A). Therefore, kes1 suppression of drs2 requires one or more Dnf P4-ATPase.
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to suppress different combinations of drs2 and dnf alleles (Figure 2B). Growth defects of a drs2 dnf1 strain at 30 and 17°C were efficiently suppressed by kes1, indicating that DNF2, DNF3, or both can support kes1 suppression. A strain expressing only DNF2 was weakly suppressed, whereas a strain carrying only DNF1 exhibited a WT level of suppression. We were unable to recover a drs2 dnf1,2 kes1 strain expressing only DNF3. However, the strain with wild-type DNF2 and DNF3 was suppressed better than the strain carrying only DNF2, indicating some influence from DNF3. Therefore, we conclude that all three Dnf ATPases contribute to the suppression of drs2 by kes1. We also tested whether kes1 could suppress a temperature-sensitive (ts) for function allele of drs2 in the absence of the Dnf ATPases. Disruption of KES1 restored a wild-type growth rate at 37C to a drs2-ts dnf1,2,3 strain (Figure 2C), and so loss of Kes1p can improve the function of a crippled Drs2p.
Kes1p Attenuates Drs2p Flippase Activity at the TGN
The ability of kes1 to suppress drs2-ts in the dnf1,2,3 background suggests that Kes1p antagonizes Drs2p activity at the Golgi complex. To test this possibility biochemically, TGN membranes were purified from WT, drs2, kes1, and drs2 kes1 cells to assay for phospholipid translocase (flippase) activity. Equal amounts of protein from each TGN preparation were first probed for Kes1p by immunoblot to determine whether Kes1p copurifies with these membranes (data for WT membranes is shown in Figure 3A). Relative to the recombinant Kes1p standard, the TGN membranes from WT and drs2 cells carry 2 ng (40 fmol) of Kes1p per 3 µg of total protein. From similar quantitative immunoblots, the WT and kes1 membranes contain 0.6 ng of Drs2p (4 fmol) per 3 µg of total protein.
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membranes displayed significantly greater NBD-PS flippase activity than WT membranes. This flippase activity was eliminated in the drs2 membrane sample and was substantially reduced in drs2 kes1 membranes (Figure 3B). Thus, Drs2p was primarily responsible for the enhanced NBD-PS flippase activity in kes1 membranes. The Dnf P4-ATPases may have contributed the small increase in drs2 kes1 NBD-PS flippase activity relative to drs2 membranes, although these data are not statistically different.
It was formally possible that the enhanced NBD-PS flippase activity in kes1 membranes was an indirect effect of the chronic Kes1p deficiency. Therefore, we tested whether adding back recombinant Kes1p to the mutant membranes would repress the Drs2-dependent flippase activity. Addition of recombinant Kes1p to the kes1 TGN membranes attenuated NBD-PS flippase activity to wild-type levels (Figure 3B). Remarkably, the half-maximal inhibitory concentration was in the range of 1 to 10 pg of Kes1p per 17 µg of total Golgi protein (0.02–0.2 pM Kes1p). For comparison, the WT membrane preparation contained 10 ng of endogenous Kes1p and addition of up to 1 µg of recombinant Kes1p to the kes1 membranes conferred no additional inhibition of NBD-PS flippase activity (unpublished observation). We considered the possibility that the recombinant Kes1p was attenuating Drs2p activity by extracting ergosterol from the TGN membrane. However, the kes1 TGN membranes used for these assays contained 60 ± 15 µg of ergosterol per milligram of protein. At 0.1 ng of Kes1p, the Kes1p to ergosterol stoichiometry would be 1:10,000; so, it is unlikely that this concentration of Kes1p would significantly alter the ergosterol content of the TGN membrane.
The NBD-PS flippase activity shown in Figure 3B was determined after 2 h of incubation with ATP, at which time all the NBD-PS probe in the kes1 samples was flipped to the cytosolic leaflet, and so the flippase assay was saturated. To better assess the influence of Kes1p on the kinetics of NBD-PS translocation, we measured the amount of NBD-PS flipped in 15 min of incubation with ATP (Figure 3C). After initial incorporation of the NBD-PS probe in the cytosolic leaflet, WT and kes1 TGN membranes were incubated for 4 h without ATP to allow spontaneous redistribution of 40% of the probe to the lumenal leaflet (NBD-PS that is resistant to back-extraction with fatty-acid free BSA). ATP was then added and the membranes were incubated at 37C for 15 min before back-extraction of the probe with BSA. Again, nearly all of the NBD-PS was flipped to the cytosolic leaflet of the kes1 membranes in 15 min. Under these conditions, we estimate that 345 NBD-PS molecules were flipped per Drs2p molecule per minute in the kes1 membranes, relative to 160 NBD-PS molecules flipped/Drs2p/min in WT membranes.
Drs2p Antagonizes the Influence of Kes1p on Sterol Trafficking and Subcellular Distribution
Because Kes1p binds ergosterol and is implicated the intracellular transport of this sterol, we examined the relationship of drs2 suppression by kes1 to ergosterol metabolism and localization. We found that drs2 cells are hypersensitive to mevastatin (Figure 4A) an inhibitor of 3-hydroxy–3-methylglutaryl-CoA reductase, the rate-limiting enzyme of ergosterol synthesis. kes1 cells are slightly hypersensitive to mevastatin, but the drs2 kes1 strain exhibits WT resistance. Perturbation of TGN function in drs2 cells also alters the trafficking, function, or both of cell wall biosynthetic enzymes. This causes hypersensitivity of drs2 to CW, a chitin-binding compound that can interfere with cell wall assembly. By contrast to the mevastatin hypersensitivity, kes1 does not suppress the CW hypersensitivity of drs2 (Figure 4A). kes1 also completely suppressed the hypersensitivity of drs2 to nystatin (Figure 4B), a polyene antifungal compound that binds ergosterol in the plasma membrane.
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is synthetically lethal with erg6, a gene encoding the (24)-sterol C-methyltransferase that converts zymosterol to fucosterol in the ergosterol biosynthetic pathway (Kishimoto et al., 2005). Viability of a drs2 erg6 strain can be sustained with WT DRS2 carried on a URA3 plasmid (pURA3-DRS2). This strain cannot lose pURA3-DRS2 and therefore failed to form colonies on media containing 5-FOA, whereas the other single and double mutants grew well (Figure 4C). However, a drs2 erg6 kes1 strain readily lost the pURA3-DRS2 plasmid and grew robustly on 5-FOA. Thus, kes1 suppresses the synthetic lethality between drs2 and erg6. The data shown in Figure 4, A–C, suggests that drs2 cells might have a defect in ergosterol synthesis. However, a normal concentration of ergosterol in drs2 cells has been reported previously (Fei et al., 2008), and we have confirmed this result (data not shown).
To determine whether drs2 perturbs ergosterol subcellular distribution, we stained cells with filipin, a fluorescent polyene antifungal compound that also binds ergosterol. Filipin primarily stained the plasma membrane of WT cells (Figure 4D), where most cellular ergosterol is localized. In contrast, substantial intracellular filipin staining was observed with drs2 cells (Figure 4D). kes1 cells also exhibited more intracellular filipin staining than WT cells. However, filipin primarily stained the plasma membrane of drs2 kes1 cells (Figure 4D). In this case, we observed cosuppression because the drs2 kes1 double mutant seemed more similar to WT than either single mutant.
Previous studies indicated that inactivation of Kes1p/Osh4p perturbs transport of sterols from the plasma membrane to the ER (Raychaudhuri et al., 2006). The toxicity of Kes1p to drs2 and the enhanced intracellular filipin staining in this mutant suggested the possibility that Kes1p is hyperactive in transporting sterol from the drs2 plasma membrane to internal organelles. To test this hypothesis, we compared the rate of esterification for exogenously supplied radiolabeled cholesterol in WT, drs2, kes1, and drs2 kes1 cells. Esterification of cholesterol requires its transport from the plasma membrane, where it is taken up, to the ER, where the acyl-CoA:cholesterol acyltransferases (ACATs) are localized. S. cerevisiae will not normally take up exogenous sterol in aerobic conditions. Therefore, we introduced an altered allele of a transcription factor (upc2-1) into our strains to permit aerobic sterol uptake (Raychaudhuri et al., 2006). After incubation with [14C]cholesterol, the cells were harvested at the times indicated in Figure 5, and the amount of free cholesterol and cholesteryl ester were measured. The drs2 cells transported cholesterol from the plasma membrane to the ER 5 to 6 times faster than WT cells at 30°C, and three times faster than WT at 20C (Figure 5, cholesteryl ester). The drs2 cells also took up significantly more cholesterol (free) than WT cells. In contrast, the drs2 kes1 cells took up cholesterol and transported it to the ER at rates indistinguishable from the WT cells. Therefore, Kes1p was required for the markedly enhanced rate of cholesterol transport in drs2 cells.
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cells (Pomorski et al., 2003; Chen et al., 2006) and we tested whether kes1 would suppress this defect. PS and PE, which are normally restricted to the inner, cytosolic leaflet, are aberrantly exposed on the outer leaflet of drs2 cells. This loss of asymmetry makes drs2 hypersensitive to papuamide B and Ro, antifungal compounds that permeabilize cells exposing PS or PE, respectively. Disruption of membrane integrity can also make cells hypersensitive to membrane permeating agents; so, sensitivity to low concentrations of SDS was also examined to control for general effects of the mutations on membrane integrity. kes1 partially suppressed the SDS, papuamide B, and Ro sensitivity of drs2, but the double mutant remained significantly more sensitive to papuamide B and Ro than WT cells (Figure 6). We conclude that loss of Kes1p improves the plasma membrane integrity of drs2 cells, presumably by restoring sterol content, but it does not restore the normal asymmetric distribution of PS and PE. Surprisingly, kes1 was also hypersensitive to papuamide B and Ro, yet resistant to SDS, indicating a partial loss of membrane asymmetry. This observation suggests that hyperactivity of P4-ATPases may also disrupt normal plasma membrane organization.
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Does Not Suppress drs2 Defects in Protein Trafficking between the TGN, Plasma Membrane, and Early Endosomes suggested that the protein trafficking defects of drs2 would also be suppressed by kes1. Therefore, we examined the ability of kes1 to suppress trafficking defects in several distinct pathways caused by drs2. Loss of Drs2p function perturbs formation of one class of exocytic vesicles that rely on actin cables for efficient transport to the bud plasma membrane (Gall et al., 2002). The sla2 mutation interferes with actin assembly and causes an accumulation of an average of 10 post-Golgi transport vesicles per cell section in electron micrographs. However, sla2 drs2 cells have only an average of one to two vesicles per cell section, comparable with WT cells, indicating that drs2 is epistatic to sla2 for the vesicle accumulation phenotype and is essential for budding these vesicles at 30°C (Figure 7A; Gall et al., 2002). Surprisingly, kes1 did not suppress the drs2 defect in budding in these post-Golgi exocytic vesicles because the sla2 drs2 kes1 cells contained about the same low number of vesicles as sla2 drs2 cells (Figure 7A).
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plasma membrane early endosome TGN loop. In wild-type cells, Snc1-GFP primarily localized to the bud plasma membrane, whereas in drs2 Snc1-GFP was mislocalized to internal punctate structures (Figure 7B; Hua et al., 2002), reflecting a defect in the early endosome to TGN transport step (Saito et al., 2004). We found no difference in the localization of Snc1-GFP to intracellular punctate structures in drs2 and drs2 kes1 cells (Figure 7B). We also found no evidence for kes1 suppression of the drs2 defect in AP-1–dependent trafficking of chitin synthase between the TGN and early endosome (Supplemental Figure 2).
kes1 Suppresses drs2 Defects in TGN to Vacuole Protein Transport
The protein trafficking steps examined above are disrupted at high temperatures (30–37°C) as well as low temperatures in drs2 cells. In contrast, transport of carboxypeptidase Y (CPY) from the Golgi to the vacuole is kinetically delayed in drs2 cells at low temperatures but is normal at 30°C (Chen et al., 1999). We tested whether kes1 would suppress this cold-sensitive defect in CPY transport kinetics by using pulse-chase analyses. CPY is initially synthesized in the ER as a 67-kDa p1 precursor form that is further modified in the Golgi to the 69 kDa p2 precursor. p2 CPY is then sorted from secretory cargo at the TGN, transported to the late endosome and on to the vacuole where it is processed to the 61-kDa mature form (mCPY) (Stevens et al., 1982). WT, drs2, kes1, and drs2 kes1 strains were labeled with 35S-amino acids and chased at 30 and 15°C for the times indicated in Figure 8A. At 30°C, no significant difference was found for CPY maturation kinetics in these four strains. In contrast, drs2 cells exhibited a threefold kinetic delay in CPY transport at 15C relative to WT and kes1 cells (Figure 8A). This cold-sensitive CPY transport defect was completely suppressed in the drs2 kes1 cells.
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cells at 15°C (p1 and p2 CPY were not completely resolved by SDS-PAGE), indicating a partial defect in a terminal mannosylation event catalyzed within late Golgi compartments (Chen et al., 1999). This cold-sensitive glycosylation defect was also completely suppressed by kes1. We also examined the transport kinetics of carboxypeptidase S (CPS), another vacuolar protein that seems to follow the same route to the vacuole as CPY (Costaguta et al., 2001). The drs2 cells also showed a cs, 3-fold kinetic defect in the transport of CPS to the vacuole that was suppressed by kes1 (data not shown).
Drs2p and Dnf P4-ATPases have a redundant function in the transport of CPY and alkaline phosphatase (ALP) to the vacuole (Hua et al., 2002). In contrast to CPY and CPS, ALP seems to be transported directly from the Golgi to the vacuole without passing through an endosomal intermediate. ALP vacuolar transport is weakly perturbed by drs2, but a strong defect is observed in drs2 dnf1 double mutants. To test for kes1 suppression of this transport defect, we examined the localization of ALP-GFP in WT, drs2 dnf1, and drs2 dnf1 kes1 cells. ALP-GFP was mislocalized to punctate structures outside the vacuolar membrane in drs2 dnf1 (Figure 8B, arrowheads). In contrast, ALP-GFP was properly targeted to the drs2 dnf1 kes1 vacuolar membrane (Figure 8B).
The steady-state levels of CPY and ALP precursor forms, which are normally transient and hard to detect by Western blot of WT cell lysates, were readily apparent in the drs2 dnf1 cells because of the trafficking defect. The accumulation of these precursors was completely suppressed in drs2 dnf1 kes1 cells (Figure 8C), indicating that kes1 suppressed the trafficking defect. The Gga1p and Gga2p clathrin adaptors are also implicated in the CPY and CPS transport pathway (Costaguta et al., 2001). By comparison, gga1 gga2 showed a similar accumulation of p2 CPY as drs2 dnf1, but this accumulation of the precursor was not suppressed in a gga1 gga2 kes1 strain. Thus, kes1 cells retain their dependence on GGAs for CPY transport but become less discriminate for the P4-ATPase requirement.
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DISCUSSION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONREFERENCES |
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cells and uncover a mutually antagonistic relationship between Drs2p and Kes1p. Genetic data indicate that Kes1p is hyperactive in drs2 and inhibits growth of these cells at low temperature, most likely through inhibition of Dnf P4-ATPases at the Golgi and their function in TGN-to-late endosome protein transport. Kes1p hyperactivity in drs2 cells also causes a substantial increase in the flux of exogenously applied sterol from the plasma membrane to sites of esterification and an alteration in the distribution of endogenous ergosterol. Kes1p also represses Drs2p function as deletion of KES1 can suppress a drs2-ts allele and causes hyperactivity of Drs2p-dependent flippase activity in purified TGN membranes. Remarkably, flippase activity is attenuated in vitro by addition of picomolar concentrations of recombinant Kes1p to kes1 TGN membranes. We suggest that mutual repression between Kes1p and Drs2p provides a critical homeostatic mechanism for controlling the intracellular trafficking of both protein and sterol.
The recovery of kes1 in a screen for suppressors of drs2 cold-sensitive growth further emphasizes the importance of Drs2p to protein trafficking in the TGN/early endosome system and provides the first genetic link between drs2 and sec14. In addition to kes1, other sec14 suppressors include mutations in genes controlling the CDP-choline pathway for PC synthesis and SAC1, encoding a phosphoinositide phosphatase. Cold-sensitive growth of drs2 is not suppressed by a CDP-choline pathway mutation, but it is partially suppressed by sac1. Therefore, the mechanism of drs2 suppression by kes1 is independent of PC biosynthesis. Stt4p, a plasma membrane PI 4-kinase, synthesizes most of the PI4P that accumulates in sac1 mutants. Accumulation of PI4P at non-TGN sites causes partial mislocalization of Kes1p from the TGN, thereby relieving its repressive effect on this organelle (Li et al., 2002). This influence on Kes1p seems to account to the suppression of sec14-ts by sac1 and may also explain the suppression of drs2 by sac1.
We had suggested previously that the inability of drs2 cells to grow at temperatures below 23°C was caused by a failure of the Dnf P4-ATPases to support an essential Drs2p function at the colder temperatures (Hua et al., 2002). The current studies support this hypothesis, because suppression of drs2 growth defects by kes1 requires the presence of Dnf P4-ATPases. Importantly, kes1 cannot suppress drs2 defects in protein transport pathways that have a strict requirement for Drs2p. These include the formation of one exocytic vesicle class, and the AP-1/clathrin and Rcy1 pathways mediating transport between the TGN and early endosomes (Gall et al., 2002; Liu et al., 2008). In contrast, drs2 defects in ALP and CPY transport from the TGN to the vacuole, pathways supported by either Drs2p or Dnf P4-ATPases (Hua et al., 2002), are suppressed by kes1. The TGN is the likely point of suppression because Kes1p and Drs2p normally localize to the TGN, and this is presumably the last common site in the ALP and CPY transport pathways before these proteins arrive at the vacuole. Therefore, we suggest that removal of Kes1p improves Dnf function in the TGN so these P4-ATPases can better compensate for the loss of Drs2p.
The ability of kes1 to restore growth of drs2 cells at low temperature best correlates with the restoration of a wild-type rate of CPY and CPS transport from the Golgi to the vacuole at low temperature. The TGN late endosome vacuole route followed by these proteins is the only protein trafficking pathway we have found that is normal in drs2 cells at permissive growth temperatures (Chen et al., 1999) and defective at nonpermissive growth temperatures. This trafficking defect may be caused by a cs perturbation of a GGA/clathrin pathway. The GGA and AP-1 clathrin adaptors seem to mediate parallel pathways emanating from the TGN that deliver cargo to the late and early endosome, respectively (Black and Pelham, 2000; Costaguta et al., 2001; Hirst et al., 2001). Mutations in either pathway do not perturb growth of yeast; however, simultaneous loss of both pathways severely abrogates growth (Costaguta et al., 2001; Hirst et al., 2001). We had shown previously that drs2 cells exhibit a constitutive loss of the AP-1 pathway and that drs2 gga1 gga2 triple mutants are severely compromised for growth (Liu et al., 2008). Here, we propose that the cold-sensitive defect in growth of drs2 cells is caused by a temperature-conditional defect in the GGA/clathrin pathway elicited only at low temperatures, combined with a constitutive defect in AP-1/clathrin function.
Why is Dnf function and the GGA/clathrin pathway perturbed at low temperature in drs2 cells, and how does loss of Kes1p suppress this defect? Important clues came from the analysis of ergosterol distribution and sterol trafficking in drs2 and drs2 kes1 cells. Relative to wild type, drs2 cells display reduced filipin staining of the plasma membrane and an altered sensitivity to nystatin, but no change in bulk ergosterol levels. These phenotypes are temperature independent and are suppressed by kes1, suggesting that loss of Drs2p causes redistribution of ergosterol from the plasma membrane to internal membranes by a Kes1p-dependent mechanism. In fact, we found that drs2 cells exhibit a five- to sixfold increase in the rate of exogenously applied cholesterol esterification. This result implies an increased rate of transport from the plasma membrane to the ER, where the ACATs are localized. Elimination of Kes1p restored a wild-type rate of esterification in spite of the presence of six other Osh proteins in the drs2 kes1 cells. Thus, it seems that Kes1p is the only oxysterol binding protein homologue that is hyperactive in drs2 cells. These data support the proposed sterol transport function for Kes1p (Raychaudhuri et al., 2006), although we cannot rule out the possibility that Kes1p regulates the activity of other proteins that directly mediate nonvesicular sterol transport. As a consequence of the altered sterol transport in drs2, we suggest that either an increased concentration of sterol in the Golgi membrane, or an increased occupancy of Kes1p with sterol, inhibits the activity of P4-ATPases in the Golgi. In the case of drs2 cells, it is likely the combination of diminished membrane fluidity at low temperature and the repressive effect of Kes1p on Dnf P4-ATPases that disrupts protein transport in the CPY/GGA pathway. The observation that drs2 cells are high-pressure sensitive as well as cold-sensitive for growth suggests a lipid packing defect may contribute to this loss of membrane fluidity.
The molecular basis for hyperactivity of Kes1p in drs2 cells is not known. One possibility is that drs2 cells accumulate a sterol that is a potent activator of Kes1p. In support of this model, drs2 and cdc50 (noncatalytic subunit) mutations exhibit a strong synthetic lethal relationship with erg mutations (Kishimoto et al., 2005) that disrupt late steps in ergosterol synthesis (for example erg6) and accumulate ergosterol precursors. The synthetic lethality between erg6 and drs2 is completely suppressed by kes1, indicating that Kes1p, but not other Osh proteins, is extremely toxic to drs2 cells producing sterols with an altered structure. cdc50 is synthetically lethal with erg6, erg2, erg3, and erg5 (Kishimoto et al., 2005), whose products catalyze in series the conversion of zymosterol to ergosta-5-7-22-24(28)-tetraenol, the final intermediate to ergosterol. Accumulation of one or more of the intermediates in this pathway may stimulate the repressive activity of Kes1p at the Golgi. Consistently, cells depleted for Cdc50p and Erg3p massively accumulate Golgi and/or endosomal structures, reminiscent of strains deficient for Drs2 and Dnf P4-ATPases (Hua et al., 2002; Kishimoto et al., 2005).
However, it is also possible that Kes1p hyperactivity is a function of membrane disorganization rather than its sterol ligand. For example, Drs2p may help establish a plasma membrane structure with high-affinity for ergosterol, and therefore a low escape potential for this sterol, relative to the ER or Golgi (see Maxfield and Menon, 2006 and Lange and Steck, 2008 for discussion of cholesterol escape potential). Consistent with this possibility, loss of plasma membrane asymmetry in erythrocytes and fibroblasts has been shown to increase the escape potential of cholesterol from the plasma membrane (Lange et al., 2007). In yeast, a membrane structure with low ergosterol escape potential may be established during budding of exocytic vesicles from the TGN as these vesicles are reported to have a concentration of ergosterol similar to the plasma membrane (300 µg ergosterol/mg protein; Daum et al., 1998), much higher than what we find in TGN membranes (50–60 µg ergosterol/mg protein). This membrane organization may restrict the ability of Kes1p to bind and extract sterol from exocytic vesicles or the plasma membrane and redistribute it to internal membranes. In addition, ergosterol biosynthetic intermediates may have a reduced affinity for plasma membrane lipids, allowing a more efficient extraction from the plasma membrane (Li and Prinz, 2004; Lange and Steck, 2008). Thus, drs2 and erg perturbations may additively increase occupancy of Kes1p with sterol, thereby increasing its inhibitory effect on the remaining P4-ATPases. It does not seem to be the asymmetric distribution of PS and PE to the inner leaflet that is the critical structural feature of the plasma membrane needed to retain ergosterol. dnf1,2,3 cells exhibit a similar loss of PE and PS asymmetry as drs2, and yet the plasma membrane of these cells stains normally with filipin. The neo1-ts mutant also stains normally with filipin (unpublished observations). Thus, Drs2p is the only P4-ATPase whose loss impacts sterol transport or localization, suggesting a unique and undefined influence of Drs2p on membrane organization and/or Kes1p activity.
The role of Drs2-related P4-ATPases in establishing a membrane structure that resists sterol extraction seems to be conserved through evolution and is medically relevant. The human disease progressive familial intrahepatic cholestasis (type I) is caused by mutations in the Atp8b1 P4-ATPase (also called FIC1) (Bull et al., 1998), which has 41% amino acid sequence identity to Drs2p. A mouse model for Atp8b1 deficiency has been developed, and studies of these mice led to the proposal that loss of PS asymmetry at the bile canalicular membrane makes this membrane more sensitive to damage by the detergent effects of the excreted bile (Paulusma et al., 2006; Cai et al., 2009). Normally, cholesterol excretion into bile requires the action of the Abcg5/8 transporter, such that an Abcg8(–/–)-deficient mouse has a very low cholesterol output into bile. Surprisingly, mice deficient for both Atp8b1 and Abcg8 excrete wild-type levels of cholesterol into bile (Groen et al., 2008). The Abcg5/8-independent excretion of bile in Atp8b1-deficient mice suggests that the disorganized structure of the bile canalicular membrane fails to retain cholesterol leading to its nonspecific extraction into the bile.
Elimination of Kes1p also suppresses the high-temperature growth defect caused by a drs2-ts allele in the absence of the Dnf P4-ATPases. This observation suggested that Kes1p represses the activity of Drs2p. In support of this possibility, we found a substantial increase in Drs2-dependent flippase activity in TGN membranes purified from kes1 cells. Addition of recombinant Kes1p to these membranes attenuated Drs2p activity back to wild-type levels. Remarkably, the half-maximal inhibitory effect of Kes1 was attained at a stoichiometry of 1–10 Kes1p molecules per 1000 Drs2p molecules. A 1000-fold increase in Kes1p concentration had no further inhibitory effect on flippase activity. Thus, the inhibitory influence of Kes1p on Drs2 activity is unlikely to be mediated by a direct protein-protein interaction between Kes1p and Drs2p. Consistently we have not been able to detect a direct interaction between Drs2p and Kes1p (unpublished observations). Inhibitory concentrations of Kes1p are also too low to significantly alter the ergosterol concentration of the TGN membrane preparation. It also seems unlikely that these low levels of Kes1p could effectively compete with other effectors for PI4P binding, which has been proposed to explain the negative influence of Kes1p on vesicle budding from the TGN (Li et al., 2002).
The potency of the Kes1p attenuation of flippase activity suggests it is acting through an enzymatic intermediate, perhaps comparable with the signal transducing function of oxysterol binding protein (OSBP), a mammalian homologue of Kes1p. When bound to cholesterol, OSBP forms a complex with protein phosphatase 2A and a tyrosine phosphatase that attenuates signaling through the extracellular signal-regulated kinase (ERK) pathway. In response to 25-hydroxycholesterol binding, the OSBP phosphatase complex dissociates and OSBP translocates onto the Golgi (Wang et al., 2005). Thus, it is possible that Kes1p attenuates Drs2p activity by regulating protein phosphorylation at the TGN. The Dnf P4-ATPases seem to be regulated by FPK1 and FPK2 protein kinases (Nakano et al., 2008) although it is not known whether Drs2p is regulated by these or other protein kinases. Alternatively, Kes1p may regulate the activity of PI 4-kinases or 4-phosphatases that could secondarily influence flippase activity. Deletion of KES1 has been shown to increase PI4P levels or availability at the TGN and suppresses growth defects caused by pik1ts (Li et al., 2002; Fairn et al., 2007). The in vitro assay for Drs2p activity in purified TGN membranes should be amenable to testing these potential regulatory mechanisms of Kes1p.
Drs2p plays a critical role in vesicle budding from the TGN and early endosomes by a mechanism that is independent of coat recruitment. We proposed previously that the physical displacement of phospholipid from the lumenal to cytosolic leaflet by Drs2p induces curvature in the membrane that is captured and molded by coat proteins into vesicles (Chen et al., 1999; Graham, 2004; Liu et al., 2008). It is logical that an appropriately balanced and coordinated activity between Drs2p and the vesicle budding machinery would be essential for the orderly segregation of protein and lipids into different transport pathways. Kes1p is well suited to regulate the activity of P4-ATPases in generating membrane curvature because it contains an ArfGAP lipid packing sensor (ALPS) domain that binds highly curved membranes (Drin et al., 2007). The ALPS domain forms a lid over the sterol-binding pocket of Kes1p, suggesting that lipid packing density and/or membrane curvature may influence sterol binding to Kes1p.
We speculate that Drs2p imparts a degree of curvature to the TGN membrane that has an ideal set point for vesicle formation and for establishing sterol rich raft-like membrane structures for export to the plasma membrane. As Drs2p flippase activity drives membrane curvature beyond this set point, Kes1p would sense the stress on the membrane and inhibit Drs2p activity until the membrane relaxes and inhibition is relieved. This model is consistent the observed mode of Kes1p inhibition of Drs2p flippase activity: Kes1p potently prevents hyperactivity of Drs2p but will not inhibit Drs2p activity below a basal level, even at very high concentrations of Kes1p. The membrane structure at this set point would also restrict the ability of sterol transfer proteins to extract ergosterol from the membrane. The set point model would explain why drs2 (reduced TGN flippase activity) and kes1 (enhanced TGN flippase activity) single mutants both display reduced filipin staining of the plasma membrane, whereas the double mutant seems more similar to wild-type cells. Although many aspects of this model remain to be tested, it provides a conceptual framework for understanding why a system of checks and balances between a P4-ATPase and an oxysterol binding protein may have evolved.
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ACKNOWLEDGMENTS |
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Footnotes |
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Address correspondence to: Todd R. Graham (tr.graham{at}vanderbilt.edu)
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0.0223 compared with kes1
