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Plant Cell. 2006 Mar; 18(3): 715–730.
PMCID: PMC1383645

Vacuolar H+-ATPase Activity Is Required for Endocytic and Secretory Trafficking in Arabidopsis[W]


In eukaryotic cells, compartments of the highly dynamic endomembrane system are acidified to varying degrees by the activity of vacuolar H+-ATPases (V-ATPases). In the Arabidopsis thaliana genome, most V-ATPase subunits are encoded by small gene families, thus offering potential for a multitude of enzyme complexes with different kinetic properties and localizations. We have determined the subcellular localization of the three Arabidopsis isoforms of the membrane-integral V-ATPase subunit VHA-a. Colocalization experiments as well as immunogold labeling showed that VHA-a1 is preferentially found in the trans-Golgi network (TGN), the main sorting compartment of the secretory pathway. Uptake experiments with the endocytic tracer FM4-64 revealed rapid colocalization with VHA-a1, indicating that the TGN may act as an early endosomal compartment. Concanamycin A, a specific V-ATPase inhibitor, blocks the endocytic transport of FM4-64 to the tonoplast, causes the accumulation of FM4-64 together with newly synthesized plasma membrane proteins, and interferes with the formation of brefeldin A compartments. Furthermore, nascent cell plates are rapidly stained by FM4-64, indicating that endocytosed material is redirected into the secretory flow after reaching the TGN. Together, our results suggest the convergence of the early endocytic and secretory trafficking pathways in the TGN.


Organelles along the endocytic and secretory pathways have characteristic luminal pH values suited to their biochemical functions. The maintenance and regulation of these acidic microenvironments is achieved by the activity of vacuolar H+-ATPases (V-ATPases), a class of primary electrogenic proton pumps found in all eukaryotes. V-ATPases are multisubunit enzyme complexes composed of the cytosolic ATP-hydrolyzing V1 subcomplex (subunits A to H) and the membrane-bound proton-translocating V0 subcomplex (subunits a, c, c′, c″, d, and e) (Nishi and Forgac, 2002; Nelson, 2003).

In plants, the most prominent role of the V-ATPase is to maintain ion and metabolite homeostasis by energizing secondary active transport across the tonoplast (Sze et al., 1999; Kluge et al., 2003). Although V-ATPases have also been found throughout the endomembrane system, including the endoplasmic reticulum, Golgi, and provacuoles (Chanson and Taiz, 1985; Ali and Akazawa, 1986; Herman et al., 1994; Oberbeck et al., 1994), the functions of the plant V-ATPase in secretory and endocytic trafficking are not well defined. In tobacco (Nicotiana tabacum) cells, inhibition of the V-ATPase interferes with secretion and leads to missorting of vacuolar proteins, suggesting that the functionality of a nonvacuolar compartment depends on V-ATPase function (Matsuoka et al., 1997). Analysis of V-ATPase null mutants of Arabidopsis thaliana has recently shown that the V-ATPase is essential for Golgi function during the development of the male gametophyte and during embryogenesis (Dettmer et al., 2005; Strompen et al., 2005). Therefore, it seems possible that the growth inhibition observed in plants with reduced V-ATPase activity (Schumacher et al., 1999; Padmanaban et al., 2004) is caused by a defect in vesicle trafficking rather than by reduced turgor pressure attributable to a lack of osmolyte transport into the vacuole.

In Arabidopsis, as in many higher eukaryotes, most subunits are encoded by small gene families (Sze et al., 2002), thus offering an enormous potential for different V-ATPase isoforms. The choice of subunits may determine not only the intrinsic activity of the pump or its ability to respond to regulatory signals but also its targeting to different intracellular locations. In yeast, subunit a is the only subunit encoded by two genes, VPH1 (for Vacuolar acidification–defective1) and STV1 (for Similar to VPH1) (Manolson et al., 1992, 1994). Whereas Vph1p resides at the tonoplast, Stv1p cycles continuously between a late Golgi compartment and prevacuolar endosomes (Manolson et al., 1994; Kawasaki-Nishi et al., 2001a). The membrane-integral subunit a consists of a hydrophilic N-terminal domain and a hydrophobic C-terminal domain with several predicted membrane-spanning domains (Manolson et al., 1992; Leng et al., 1999). Whereas the cytosolic N-terminal domain interacts with several subunits of the V1 subcomplex and might be part of the peripheral stator (Landolt-Marticorena et al., 2000), the C-terminal domain is involved in proton translocation and assembly of the V-ATPase complex (Leng et al., 1998; Kawasaki-Nishi et al., 2001b).

A dynamic equilibrium between the fully assembled V-ATPase complex and the free subcomplexes V1 and V0 exists in many organisms and is known to be regulated by extracellular conditions in yeast and insects (Kane, 2000). Interestingly, it has been shown that the dissociation of V-ATPase complexes in response to glucose withdrawal differs between Vph1p-containing complexes at the vacuole and Stv1p-containing complexes at the late Golgi/early endosome (Kawasaki-Nishi et al., 2001c). Moreover, recent work has established precedence for acidification-independent functions of the V0 subcomplex during homotypic vacuole fusion in yeast (Peters et al., 2001; Bayer et al., 2003) and synaptic vesicle fusion in Drosophila (Hiesinger et al., 2005). Although the presence of free V1 and V0 complexes has been demonstrated in plants (Li and Sze, 1999), it remains to be determined how V1V0 assembly is regulated and whether V0 has functions independent of acidification in plants. To address these questions, it is first necessary to better understand the function of subunit a in plants and to gain insight into the roles of its isoforms.

Pharmacological studies using the specific, membrane-permeable inhibitors bafilomycin A and concanamycin A (ConcA) have established that V-ATPase activity is crucial for many aspects of the mammalian secretory and endocytic pathways, including the dissociation of receptor–ligand complexes (Forgac, 1999), the recruitment of proteins involved in vesicle formation (Aniento et al., 1996; Maranda et al., 2001), and transport between different endosomal compartments (Clague et al., 1994; van Weert et al., 1995; Tawfeek and Abou-Samra, 2004). Genetic evidence supports the results obtained with V-ATPase inhibitors: in vph1Δ/stv1Δ and other V-ATPase null mutants of yeast, transport of the endocytic tracer FM4-64 to the vacuole is delayed (Perzov et al., 2002; Iwaki et al., 2004), and reduced expression of the Dictyostelium gene encoding subunit a slowed phagocytosis and prolonged endosomal transit time (Liu et al., 2002).

Endocytic cycling of plasma membrane proteins has been shown to be important for plant cell polarity and behavior (Geldner et al., 2003; Meckel et al., 2004). However, structural and operational descriptions of plant endosomal compartments still need to be reconciled (Geldner, 2004; Samaj et al., 2005), and the role of the V-ATPase in endocytic trafficking in plants is largely unaddressed.

To determine whether organelle-specific V-ATPase isoforms exist in higher plants and to gain further insight into the functions of the Arabidopsis V-ATPase in the endocytic and secretory pathways, we analyzed the subcellular localization of the three Arabidopsis isoforms of subunit a (VHA-a). Here, we provide evidence that VHA-a1 is localized in an early endosomal compartment, which we identified by immunogold labeling as well as by colocalization experiments as the trans-Golgi network (TGN). Our analysis shows that ConcA leads to the accumulation of endocytosed material together with newly synthesized plasma membrane proteins, suggesting that, in Arabidopsis, trafficking pathways to and from the plasma membrane converge in the TGN.


Arabidopsis VHA-a Isoforms Are Differentially Localized

To determine the subcellular localization of the three Arabidopsis VHA-a isoforms VHA-a1 (At2g28520), VHA-a2 (At2g21410), and VHA-a3 (At4g39080), we constructed translational fusions between their genomic sequences and the reporter gene green fluorescent protein (GFP). The genomic DNA fragments included promoter regions of 1.3 kb (VHA-a1), 3.2 kb (VHA-a2), and 4.1 kb (VHA-a3), and GFP was fused to the last exon. Based on the prediction of six transmembrane-spanning domains for all Arabidopsis VHA-a isoforms (Schwacke et al., 2003), a cytosolic location of GFP is assumed. Homozygous lines with a single T-DNA insertion site were established, and RT-PCR was used to identify lines in which the expression level of the transgene was comparable to that of the endogenous gene (see Supplemental Figure 1A online). Furthermore, we performed coimmunoprecipitations of VHA-a1–GFP and VHA-A to demonstrate that at least a substantial fraction of V-ATPase complexes contain VHA-a1–GFP (see Supplemental Figure 1B online). The fact that VHA-a1–GFP is integrated into the V-ATPase holocomplex suggests that it is functional, because the integration of a nonfunctional subunit into the complex likely would have had dominant negative effects. However, all lines expressing VHA-a1–GFP were indistinguishable from the wild type.

In seedlings, expression of the GFP fusion proteins was detectable in all cells (see Supplemental Figure 2 online), and their localization in cells of the root elongation zone was examined by confocal laser scanning microscopy (CLSM). A mobile, punctate staining pattern was observed in seedlings of all lines expressing VHA-a1–GFP (Figure 1A), whereas seedlings expressing VHA-a2–GFP (Figure 1B) or VHA-a3–GFP (see Supplemental Figure 2L online) displayed fluorescence preferentially at the tonoplast. To exclude the possibility that the observed localization of VHA-a1 was an artifact caused by the fusion of GFP to its C terminus, we constructed a chimeric protein consisting of the N-terminal part of VHA-a1 (amino acids 1 to 228) and the C terminus of VHA-a2 (amino acids 233 to 820) fused to GFP. In transgenic seedlings expressing VHA-a1a2–GFP, a similar pattern as for VHA-a1–GFP was observed (Figure 1C); therefore, we assume that the C-terminal GFP fusion does not cause the mislocalization of VHA-a1. This result further indicates that the first 228 amino acids of the cytosolic N-terminal domain contain the targeting information necessary for the specific localization of VHA-a1.

Figure 1.
Subcellular Localization of VHA-a–GFP Fusion Proteins Expressed in Roots of Seedlings.

VHA-a1–GFP Is Localized in the TGN

The fungal toxin brefeldin A (BFA) inhibits certain ADP-ribosylation factor–guanine-nucleotide exchange factors (ARF-GEFs) and is widely used as a vesicle trafficking inhibitor (Peyroche et al., 1999; Robineau et al., 2000; Nebenfuhr et al., 2002). After BFA treatment, both VHA-a1–GFP and VHA-a1a2–GFP signals rapidly aggregated and were found throughout the vesicle agglomerations known as BFA compartments (Figures 1D and 1F) together with the endocytic tracer FM4-64 (Figure 1E). Early endosomal compartments accumulate in the core of BFA compartments (Geldner et al., 2001), whereas trans-Golgi markers tend to be found more in the periphery of BFA compartments (Wee et al., 1998; Grebe et al., 2003). The presence of VHA-a1–GFP in BFA compartments suggests that it is localized either in endosomes or in a trans-Golgi compartment; therefore, we performed colocalization experiments with appropriate marker proteins fused to monomeric red fluorescent protein (mRFP) (Campbell et al., 2002). In Arabidopsis, the plant-unique Rab5 homolog ARA6 and the Rab5 homolog ARA7 are localized on two distinct but partially overlapping populations of endosomes (Ueda et al., 2001, 2004). In transgenic T1 seedlings coexpressing VHA-a1–GFP and ARA7-mRFP (Ueda et al., 2004), little overlap was detected (Figures 1G to 1I). Quantification of CLSM images revealed that <20% of the pixels with signal intensities above the chosen threshold overlapped between the red and green channels, and line scans confirmed that the intensity maxima did not colocalize (see Supplemental Figure 4A online). SYP41 (Tlg2a) is a member of the Qa SNARE group localized at the TGN in a complex with At VTI12, At VPS45, and SYP61 (Bassham et al., 2000; Sanderfoot et al., 2001). A fusion of SYP41 with GFP colocalizes with SYP61 but not with Golgi and prevacuolar compartment markers (Uemura et al., 2004). SYP41-mRFP had not been described previously; therefore, we confirmed that it showed the same localization as SYP41-GFP in transiently expressing protoplasts (see Supplemental Figures 3A to 3C online), indicating that the presence of mRFP did not affect the targeting of SYP41. In transgenic T1 seedlings coexpressing VHA-a1–GFP and SYP41-mRFP (Figures 1J to 1L), the punctate staining patterns were almost identical, indicating colocalization of the two proteins. Quantification of CLSM images revealed that >80% of the pixels with signal intensities above the chosen threshold overlapped between the red and green channels, and line scans confirmed that the intensity maxima did colocalize (see Supplemental Figure 4B online).

Immunogold electron microscopy was performed to confirm the colocalization results. In ultrathin cryosections of root tissue from VHA-a1–GFP seedlings incubated with a GFP antibody, gold particles specifically labeled tubulovesicular membranes in the vicinity of the trans site of Golgi stacks (Figures 2A, 2D, 2E, and 2G) that we interpret to be the TGN. Both the density of gold particles and their distance from the Golgi stack showed some variation; however, ultrastructural analysis (Figures 2C and 2F) showed that the extension of the TGN and its position relative to the Golgi stack are similarly variable. Labeling of the TGN was observed in seedlings in which transgene expression matched the level of the endogenous gene and in seedlings that overexpressed VHA-a1–GFP. Unfortunately, colabeling with a SYP41 antibody (Bassham et al., 2000) was not possible because of a lack of specific SYP41 signals. Labeling of the TGN was also observed in cells expressing the chimeric VHA-a1a2–GFP (Figure 2I), confirming that the targeting information resides in the N-terminal domain of VHA-a1. In cells expressing the trans-Golgi marker N-ST-YFP (Grebe et al., 2003), gold particles were located at the trans-most Golgi cisternae (Figure 2J) and in cells with high expression levels, also often in the TGN. No labeling above background was detected in wild-type cells (Figure 2L).

Figure 2.
Immunogold Localization of VHA-a1–GFP and TGN Morphology.

To provide further evidence that the observed localization of VHA-a1–GFP reflects the localization of the endogenous protein, we analyzed the distribution of the V-ATPase in wild-type root cells. Immunogold labeling using an antibody against VHA-E (Betz and Dietz, 1991) resulted in the expected labeling of the tonoplast (Figure 2B), but labeling in the TGN was also observed (Figure 2H). In tuff embryos lacking VHA-E1 (Strompen et al., 2005), the VHA-E antibody did not yield staining above background, thus confirming the specificity of the observed signals at the TGN and the tonoplast (Figure 2M).

Our results show that, in Arabidopsis root cells, the TGN and the tonoplast are the endomembranes with the highest V-ATPase density and provide evidence that VHA-a1–GFP reflects the preferential localization of the endogenous protein in the TGN.

Rapid Colocalization of VHA-a1–GFP with FM4-64

After BFA treatment, VHA-a1–GFP was found to colocalize with FM4-64, raising the possibility that it resides in an endosomal compartment. Although concerns have been raised (Bolte et al., 2004), FM4-64 is now widely accepted as a reliable tracer for endocytic trafficking (Geldner et al., 2003; Grebe et al., 2003; Meckel et al., 2004; Samaj et al., 2005); therefore, we used FM4-64 to determine the position of VHA-a1–GFP in the endocytic pathway.

The uptake of FM4-64 into Arabidopsis root tip cells can be blocked either by cold pretreatment or by treatment with wortmannin (data not shown); thus, it can be assumed that FM4-64 is internalized exclusively via endocytosis and follows the endocytic pathway from the plasma membrane to the tonoplast. Colocalization of FM4-64 and GFP was observed in root cells expressing VHA-a1–GFP after uptake for 6 min (Figures 3A to 3C; see Supplemental Figure 4C online). In fact, the first detectable intracellular FM4-64 fluorescence observed after only 2 min coincided with VHA-a1–GFP-labeled compartments. In agreement with this observation, the first intracellular FM4-64 fluorescence was often found adjacent to or overlapping with N-ST-YFP signals (Figures 3D to 3F). Uptake experiments were also performed with T1 seedlings expressing ARA6-GFP (Grebe et al., 2003) or ARA7-GFP (Ueda et al., 2001). No colocalization of FM4-64 with ARA7-GFP (Figures 3G to 3I) or ARA6-GFP (Figures 3J to 3L) was observed after 6 min. After 15 min, partial overlap was detected with ARA7-GFP but not with ARA6-GFP (data not shown). Together, these results indicate that VHA-a1–GFP resides in an early endosomal compartment distinct from the endosomes marked by either ARA6-GFP or ARA7-GFP.

Figure 3.
Rapid Colocalization of VHA-a1–GFP with FM4-64.

ConcA Affects Endocytic Trafficking

The results presented to this point suggest that VHA-a1–GFP labels a compartment that may be part of both the endocytic and the secretory pathways. To determine whether V-ATPase activity is necessary for the biological functions of this compartment, we next analyzed the effects of the V-ATPase inhibitor ConcA (Drose et al., 1993; Huss et al., 2002) on endocytic trafficking. To determine whether ConcA blocks the transport of FM4-64 to the tonoplast, we first analyzed the time course of FM4-64 trafficking in untreated root tip cells. After 1 h, FM4-64 staining distinct from that of the VHA-a1–GFP-labeled compartment was observed (Figures 4A to 4C), which can be interpreted as a later endosomal compartment through which the dye has to pass on its way to the tonoplast. Staining of the tonoplast was clearly detectable after 2 h (Figures 4D to 4F). Pretreatment with ConcA for 1 h and subsequent staining with FM4-64 revealed that the internalization of the dye is at least not strongly affected. However, after 2 h, neither FM4-64 signals clearly distinct from VHA-a1–GFP nor staining of the tonoplast was observed (Figures 4G to 4I). Weak tonoplast staining was seen only after prolonged incubation (Figures 4J to 4L). Comparable results were obtained using Arabidopsis suspension cultured cells, which were either untreated or pretreated with ConcA for 1 h, stained with FM4-64 at 4°C for 30 min, and washed before incubation in inhibitor-free medium or in ConcA medium (see Supplemental Figure 5 online).

Figure 4.
ConcA Blocks FM4-64 Transport to the Tonoplast.

Based on the results that VHA-a1–GFP is localized in the first compartment stained after FM4-64 uptake and that ConcA interferes with transport from this compartment to the vacuole, we conclude that ConcA inhibits transport from an early to a later endosomal compartment.

ConcA Affects Golgi Morphology and Interferes with BFA Action

ConcA not only blocked FM4-64 transport, it also affected the appearance of the VHA-a1–GFP staining pattern. Compared with untreated cells, diffuse and enlarged intracellular fluorescence signals (Figures 4E and 4G) were observed. Ultrastructural images of high-pressure frozen and freeze-substituted ConcA-treated root cells showed changes in Golgi morphology and aggregations of swollen vesicles, as described previously for tobacco BY2 cells (Robinson et al., 2004) and lily (Lillium longiflorum) pollen tubes (Dettmer et al., 2005). The effects of ConcA include bending of Golgi cisternae, swelling of their ends (Figure 5A), fragmentation of Golgi stacks, and the accumulation of large vesicles (Figures 5B to 5D). Immunogold labeling using GFP antibodies confirmed the presence of VHA-a1–GFP in ConcA-induced vesicle aggregates, indicating that they are derived from the TGN (Figure 5G).

Figure 5.
ConcA Induces Changes of TGN and Golgi Stack Morphology and Interferes with BFA Action.

Having shown that V-ATPase activity is necessary for endocytic trafficking and that VHA-a1–GFP is present in BFA compartments, we next asked whether V-ATPase function is also necessary for the formation of BFA compartments. The ultrastructure of a typical BFA compartment is shown in Figure 5E, and immunogold labeling using GFP antibodies confirmed that VHA-a1–GFP is evenly distributed in BFA compartments (Figure 5H). When seedlings were pretreated with ConcA for 1 h before BFA treatment, the typical large BFA compartments were never observed by CLSM. Electron microscopy images show a mixture of ConcA-like (Figure 5F) and small BFA-like aggregations. The observed effects of BFA and ConcA on VHA-a1–GFP were reversible by incubation of seedlings without inhibitors for 3 h (data not shown). Together, these results show that the TGN is a core component of BFA compartments and that V-ATPase function is required for their formation.

Endocytic and Secretory Trafficking Merge in the TGN

The TGN is the main sorting station of the secretory pathway; therefore, ConcA should interfere not only with endocytic trafficking but also with secretory trafficking. Root cells of seedlings expressing the plasma membrane steroid receptor BRI1 (Friedrichsen et al., 2000; Kinoshita et al., 2005) fused to GFP show detectable intracellular fluorescence (Russinova et al., 2004). The majority of intracellular BRI1-GFP signals were costained with FM4-64 in <10 min (Figure 6B), suggesting that they could be derived from TGN-localized molecules. After ConcA treatment, many cells showed increased intracellular BRI1-GFP fluorescence in irregular patches (Figure 6C). The BRI1-GFP patches were only partly stained by FM4-64 (Figure 6D), suggesting that ConcA may cause the accumulation of BRI1-GFP not only in the TGN but also either in Golgi stacks, if ConcA causes the accumulation of newly synthesized plasma membrane proteins, or in a later endosomal compartment, if ConcA interferes with the recycling of internalized plasma membrane proteins. To determine whether the intracellular BRI1-GFP fluorescence was caused by internalized or newly synthesized molecules, protein synthesis was inhibited with cycloheximide (CHX). In both untreated (Figure 6E) and ConcA-treated (Figure 6G) seedlings, intracellular fluorescence was strongly reduced by CHX treatment, indicating that a substantial fraction of the intracellular BRI1-GFP signal is derived from secretory cargo. The intracellular signals remaining after CHX treatment did not show rapid colocalization with FM4-64 (Figures 6F and 6H), suggesting that they might be derived from later endosomal compartments. After ConcA treatment, these compartments seem to be associated with but still separated from the FM4-64–stained membranes (Figure 6H). Our findings suggest that after ConcA treatment, secretory and endocytic cargos accumulate together in TGN-derived structures.

Figure 6.
ConcA Induces Intracellular BRI1-GFP Accumulation.

Nascent Cell Plates Are Rapidly Stained by FM4-64

Because it could be argued that the observed coaccumulation of endocytic and secretory cargos in the TGN is based on an artificial fusion of the TGN and endosomes caused by ConcA, we next addressed the question of whether early convergence of endocytic and secretory trafficking can be demonstrated in undisturbed cells. Transport to the plane of division is assumed to be the default pathway for Golgi-derived vesicles in dividing cells. It has been shown previously that FM4-64 enters the secretory pathway and stains cell plates in dividing Fucus and BY2 cells (Belanger and Quatrano, 2000; Bolte et al., 2004), but to date rapid entry into the secretory pathway has only been described in pollen tubes (Parton et al., 2001). Based on the results presented here, developing cell plates in Arabidopsis root tips should be rapidly stained by FM4-64 if the dye is redirected into the secretory vesicle flow after reaching the TGN. Indeed, in seedlings expressing VHA-a1–GFP, staining of cell plates was observed within 5 to 10 min after FM4-64 staining of the TGN was detected (Figure 7A). Three-dimensional reconstruction of Z scans showed that cell plates stained by FM4-64 were not yet connected with the cortical plasma membrane (Figure 7B). These findings strongly suggest that early endocytic and secretory trafficking converge in the TGN of Arabidopsis root tip cells.

Figure 7.
Nascent Cell Plates Are Rapidly Stained by FM4-64.


Differential Localization of V-ATPase Isoforms in a Higher Plant

Organelle-specific isoforms of V-ATPase subunits have been best characterized in yeast, but specific sorting of isoforms of subunit a has also been reported in mouse osteoclasts (Toyomura et al., 2000) and in Torpedo neurons (Morel et al., 2003), in which specific isoforms are associated with the plasma membrane. We show here that organelle-specific distribution also exists in plants. As isoform-specific antibodies against VHA-a are not available, we used stable transgenic seedlings expressing GFP fusion proteins of the VHA-a isoforms to determine their subcellular localization. In contrast with the tonoplast-localized GFP fusion proteins of VHA-a2 and VHA-a3, VHA-a1 showed a distinct punctate staining pattern. GFP fusion proteins do not necessarily reflect the localization of the endogenous protein, as targeting signals might be obstructed by the presence of GFP or overexpression might interfere with correct targeting. Therefore, we used material in which the expression of VHA-a1 and VHA-a1–GFP was comparable and constructed a chimeric protein to demonstrate that the observed localization of VHA-a1 is caused neither by GFP nor by overexpression and to conclude that VHA-a1–GFP reflects the localization of the endogenous protein.

Colocalization as well as immunogold labeling experiments showed that VHA-a1–GFP was preferentially localized in the TGN, whereas VHA-a2–GFP and VHA-a3–GFP were detected at the tonoplast. None of the three Arabidopsis VHA-a isoforms showed a specific endoplasmic reticulum localization (Kluge et al., 2004). As in the case of Stv1p, the targeting information resides in the N-terminal cytosolic domain of VHA-a1; however, obvious sequence similarities that might reveal potential targeting signals do not exist, and it remains to be determined how the specific localization is achieved. Moreover, it has been shown in yeast that the isoforms confer different stability and different kinetic properties to the V-ATPase (Kawasaki-Nishi et al., 2001a), and it will be of interest to determine in which way complexes containing VHA-a1 are adapted to the requirements of the TGN. Interestingly, it has been shown that the V-ATPases found in Golgi- or tonoplast-enriched tobacco membrane fractions show different sensitivities to the V-ATPase inhibitors ConcA and bafilomycin A (Matsuoka et al., 1997). Moreover, mutations in subunit a reduced inhibition by bafilomycin A (Wang et al., 2005); therefore, it seems possible that the sensitivity toward different inhibitors is influenced by the presence of different isoforms of subunit a.

V-ATPases have previously been detected both biochemically (Chanson and Taiz, 1985; Ali and Akazawa, 1986) and histochemically (Zhang et al., 1996; Kluge et al., 2004) in the plant Golgi apparatus, and the analysis of Arabidopsis mutants has shown that the V-ATPase is necessary for the structural integrity of Golgi stacks (Dettmer et al., 2005; Strompen et al., 2005). The fact that immunogold labeling of VHA-a1–GFP and VHA-E did not yield significant signals along Golgi stacks might simply reflect the fact that the pump density in the Golgi cisternae is below the detection limit. Mathematical modeling predicts that a small number of pumps would be sufficient to acidify certain compartments (Grabe and Oster, 2001); therefore, it seems possible that VHA-a1 is found throughout the secretory and endocytic pathways at levels below the detection limit.

Position of the TGN in the Plant Endosomal System

We used the styryl dye FM4-64, which is widely accepted as an endocytic tracer (Samaj et al., 2005), to determine the position of VHA-a1–GFP relative to the known markers of the endocytic pathway. To our surprise, we found that the first intracellular FM4-64 signals coincided with the TGN labeled by VHA-a1–GFP. The TGN has been defined as the clathrin-coated tubular network contained within the matrix of a Golgi stack (Staehelin and Moore, 1995), and the sorting of cargo destined either for vacuolar or secretory trafficking takes place in the TGN (Liu et al., 2002). However, there is evidence that the TGN may also be part of endocytic trafficking. Early ultrastructural work established the partially coated reticulum (Pesacreta and Lucas, 1985), a structure closely associated or identical with the TGN (Hillmer et al., 1988; Staehelin and Moore, 1995), as an early endosomal compartment (Tanchak et al., 1988). Endocytic cycling of plasma membrane proteins has been shown to be important for plant cell polarity and behavior (Geldner et al., 2003; Meckel et al., 2004), but structural and operational descriptions of plant endosomal compartments still need to be reconciled.

The molecular characterization of plant endosomes has relied to date on the analysis of the unique plant Rab GTPase, ARA6, and the Arabidopsis homolog of mammalian Rab5, ARA7 (Ueda et al., 2001). Transiently expressed ARA6 and ARA7 reside on distinct but partially overlapping populations of punctate structures, which have been shown by FM4-64 staining to represent endosomes (Ueda et al., 2004). In our hands, FM4-64 staining of the TGN occurred significantly faster than staining of either ARA6- or ARA7-positive compartments. The appearance of ARA7-positive endosomes is altered in cells lacking the ARF-GEF protein GNOM (Geldner et al., 2003), suggesting that GNOM-dependent recycling of plasma membrane proteins takes place in this compartment. If ARA7 indeed resides in a compartment equivalent to the recycling endosome (Ueda et al., 2004), this would only be stained after passage of FM4-64 through early or sorting endosomes. However, we cannot exclude the possibility that FM4-64 passes through ARA7 endosomes without accumulating to detectable levels before reaching the TGN, where it first becomes visible. The exact position of ARA7 in the endocytic pathway is still a matter of debate, as it has also been reported to be localized in the prevacuolar compartment (Lee et al., 2004) and to affect vacuolar trafficking (Kotzer et al., 2004). Assuming that endosomal maturation takes place, it will be of great interest to determine the relationship between the TGN and the endosomal compartments marked by the presence of Rab5-related proteins.

BFA has been instrumental in demonstrating the constitutive cycling of plant proteins between the plasma membrane and endosomal compartments (Geldner et al., 2001), but it has been a matter of debate whether the BFA-induced vesicle agglomerations observed in Arabidopsis root cells are entirely Golgi-derived or, at least in part, endosomal (Wee et al., 1998; Nebenfuhr et al., 2002; Geldner et al., 2003; Grebe et al., 2003). We have shown here that the TGN is incorporated into BFA compartments, but our results also show that both views are not necessarily contradictory. However, our results indicate that costaining of intracellular signals with FM4-64 is not sufficient to demonstrate the cycling of plasma membrane proteins (Russinova et al., 2004). In the case of BRI1-GFP, intracellular fluorescence was greatly diminished after CHX treatment, indicating that it was largely derived from newly synthesized molecules in the TGN.

Whether endocytic and secretory cargos indeed merge in the TGN or the TGN has specialized subdomains that would allow the separation of both cargo types remains to be determined. For this purpose, it will be necessary to develop tools that can distinguish between newly synthesized and recycling plasma membrane proteins to be able to reliably trace the latter on their way into the cell.

V-ATPase Is Required for Secretory and Endocytic Trafficking

We have shown that ConcA leads to dramatic changes in Golgi and TGN morphology; therefore, the observed effects on secretory trafficking and vacuolar trafficking in tobacco cells (Matsuoka et al., 1997) are not surprising. Although we have provided only pharmacological evidence, our results are consistent with findings from other eukaryotes, and we have observed very similar effects on Golgi morphology in V-ATPase null mutants of Arabidopsis (Dettmer et al., 2005; Strompen et al., 2005).

How does V-ATPase inhibition lead to the observed effects on TGN and Golgi, and how does it interfere with BFA action? Similar effects on Golgi morphology have been described after treatment with the ionophore monensin, but in that case swelling and vacuolation can be ascribed to the osmotic water uptake caused by the exchange of cytoplasmic K+ or Na+ for luminal H+ (Mollenhauer et al., 1990). Interestingly, it has been shown that membrane recruitment of components of the vesicle budding machinery, including ARFs, ARF-GEFs, and coat proteins, can depend on luminal acidification (Zeuzem et al., 1992; Aniento et al., 1996; Maranda et al., 2001). However, further studies of the role of the V-ATPase in the plant endomembrane system will also have to consider acidification-independent functions of V0, as they have recently been described (Peters et al., 2001; Hiesinger et al., 2005). ConcA interferes with both endocytic and secretory trafficking and leads to the accumulation of cargo from both pathways in the ConcA-induced vesicle aggregates. Therefore, it could be argued that the proposed convergence of the two pathways is caused by the fusion of two otherwise independent compartments. However, the fact that nascent cell plates are heavily stained within 15 min after FM4-64 uptake provides strong evidence that the early convergence of endocytic and secretory trafficking is not an artifact caused by ConcA treatment.


We have determined the subcellular localization of the Arabidopsis VHA-a isoforms and have shown that the V-ATPase in the TGN is essential for endocytic and secretory trafficking. We propose that the TGN serves as a junction between early endocytic and secretory trafficking, and our results predict that the sorting of newly synthesized and internalized plasma membrane proteins may occur in the same compartment.


Plant Materials and Growth Conditions

All plants used were Arabidopsis thaliana ecotype Col-0. Seedlings used for microscopy were grown on Murashige and Skoog (MS) medium + 1% sucrose at 22°C, with cycles of 16 h of light and 8 h of dark for 3 to 5 d.

Plasmid Constructs and Plant Transformation

For VHA-a1 (At2g28520), a 10,421-bp ClaI fragment was isolated from BAC clone T17D12 and ligated into pBluescript II-KS+ (pBSII-KS+). A total of 1547 bp of the VHA-a1 3′ end was amplified by PCR from BAC T17D12, using the primers VHA-a1.XcmI.FOR and VHA-a1.KpnI-SpeI.REV (see Supplemental Table 1 online), and subcloned into pCR2.1-TOPO (Invitrogen). The subcloned PCR product was digested with Kpn2I-SpeI, and the resulting 414-bp fragment was ligated to the Kpn2I-SpeI–digested BAC fragment in pBSII-KS+. The genomic sequence, including a 1335-bp promoter and a 4670-bp coding sequence, was isolated via KpnI from pBSII-KS+ and ligated into pGTkan. pGTkan is a derivate of pPZP212 (Hajdukiewicz et al., 1994) containing the GFP5(S65T) coding sequence and the pea (Pisum sativum) rbcs terminator.

For VHA-a2 (At2g21410), a 7218-bp fragment of BAC clone F3K23 digested with KpnI was ligated into pBSII-KS+. A total of 1792 bp of the VHA-a2 3′ end was amplified from BAC F3K23, using the primers VHA-a2-XbaI.FOR and VHA-a2-KpnI.REV, and subcloned into pCR2.1-TOPO. The subcloned PCR product was digested with XbaI and ligated to the XbaI-digested KpnI fragment in pBSII-KS+. The genomic sequence, including a 3195-bp promoter and a 5436-bp coding sequence, of which 1775 bp was amplified by PCR, was isolated from pBSII-KS+ by partial digestion with KpnI and ligated into pGTkan.

For VHA-a3 (At4g39080), a 10,407-bp SacI fragment of BAC clone F19H22 was ligated into pBSII-KS+. A total of 2126 bp of the VHA-a3 3′ end was amplified from BAC clone F19H22, using the primers VHA-a3-PstI.FOR and VHA-a3-KpnI.REV, and subcloned into pCR2.1-TOPO. The subcloned PCR product was digested with KpnI-PstI and ligated to the Kpn-PstI–digested SacI fragment in pBSII-KS+. The genomic sequence, comprising a 4146-bp promoter and a 5237-bp coding sequence, of which 2105 bp was amplified by PCR, was isolated from the pBSII-KS+ vector with SacI-KpnI and ligated into the pGTkan vector.

To exchange the VHA-a1 with the VHA-a2 3′ end, the genomic sequence of VHA-a1 in pBSII-KS+ was digested with BamHI, blunted using Accuprime Pfx DNA polymerase (Invitrogen), and finally cut with SpeI. This removes a 3498-bp fragment from the 3′ end. From the BAC clone F3K23, a 4083-bp PCR fragment was amplified with the primers a2-a1.for and a2-KpnISpeI.REV. The PCR product was cut with SpeI and phosphorylated with T4 PNK (Invitrogen) to allow blunt/SpeI ligation into pBSII-KS+ containing the 5′ end of VHA-a1. The 7428-bp chimeric fragment was isolated via partial KpnI digestion and ligated into pGTkan. PCR amplifications were performed with Accuprime Pfx DNA polymerase (Invitrogen), and primers were purchased from Invitrogen or Metabion. All PCR-amplified fragments were controlled by sequencing performed by GATC.

The resulting binary plasmids were introduced into Agrobacterium tumefaciens strain GV3101:pMP90 and selected on 5 μg/mL rifampicin, 10 μg/mL gentamycin, and 100 μg/mL spectinomycin. Col-0 plants were transformed using standard procedures, and transgenic plants were selected on MS medium + 1% sucrose plates containing 50 μg/mL kanamycin.

Transient Expression of Arabidopsis Suspension Cultured Protoplasts

Polyethylene glycol–mediated transformation of Arabidopsis cell suspension protoplasts for transient coexpression of GFP- and RFP-fused proteins was performed with modifications to the protocol as described by Negrutiu et al. (1987).


Total RNA was extracted from 5-d-old light-grown seedlings using the RNeasy plant mini kit (Qiagen) and used as a template for cDNA synthesis with Moloney murine leukemia virus reverse transcriptase (Fermentas) according to the manufacturer's instructions. The abundance of VHA-a1 and VHA-a1–GFP transcript levels was compared by PCR.


For total protein extracts, 4-d-old etiolated seedlings were ground in liquid nitrogen and resuspended in extraction buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 0.5% Triton X-100, and 1× Complete protease inhibitor mix [Roche]). After incubation on ice for 30 min and centrifugation (300g, 4 min, 4°C), 0.8 mg of the supernatant was preincubated with 50 μL of protein A–agarose (Roche) (1 h, 4°C). After centrifugation, an aliquot of the supernatant was prepared for protein gel blot analysis (S1). The cleared supernatant was incubated with 1 μL of anti-GFP (Molecular Probes) or 1 μL of anti-hemagglutinin (Santa Cruz Biotechnology) antibody (1 h, 4°C). One hundred microliters of fresh protein A–agarose was added, and the incubation was continued for 3 h. The protein A beads were pelleted by centrifugation, and the supernatant was prepared for protein gel blot analysis (S2). The pellet was washed with 500 μL of 50 mM Tris-HCl, 150 mM NaCl, pH 7.5, and 10 mM NH4HCO3, pH 8, followed by boiling in 30 μL of sample buffer. Equal volumes of supernatant before (S1) and after (S2) precipitation were compared with the pellet fraction by protein gel blot analysis. We used the monoclonal antibody against V1 subunit VHA-A (Ward et al., 1992), horseradish peroxidase–conjugated rabbit α-mouse IgG antibodies, and the SuperSignal West Pico chemiluminescent (Pierce Perbio) for detection.

Fluorescent Markers

The coding sequence for SYP41-mRFP was amplified by PCR from a plasmid for transient expression (provided by T. Ueda) and cloned into the binary plant transformation vector pPZP312 carrying the 35S promoter and the rbcs terminator. pPZP312 is a derivative of the pPZP vectors carrying BASTA resistance under the control of the 5′ mas promoter and the 3′ mas terminator.

Transgenic plants expressing VHA-a1–GFP were transformed using standard procedures, and T1 seedlings were generated expressing ARA7-mRFP (Takano et al., 2005) or SYP41-mRFP and VHA-a1–GFP. The coding sequence of ARA7-GFP (Ueda et al., 2001) was excised from pBSII-KS+ and cloned into the binary vector pBINPLUS, and the resulting construct was transformed into wild-type plants using standard procedures. N-ST-YFP and ARA6-GFP have been described (Grebe et al., 2003).

Inhibitor Treatments and FM4-64 Staining

Three- to four-day-old seedlings were incubated in 1 mL of liquid medium (half-strength MS medium + 0.5% sucrose, pH 5.8) containing 50 μM BFA, 2 μM ConcA, or 50 μM CHX or combinations of these inhibitors. Endocytosis and colocalization studies were performed with 4 μM FM4-64. The seedlings were incubated with inhibitors and dye at room temperature for the indicated times. For time-dependent colocalization experiments, seedlings expressing VHA-a1–GFP, N-ST-YFP, ARA6-GFP, or ARA7-GFP were incubated for 3 min in medium containing FM4-64, then the seedlings were transferred to a microscope slide and imaged via CLSM. The following stock solutions were used: 50 mM BFA in DMSO:ethanol (1:1), 10 mM ConcA in DMSO, 20 mM wortmannin in DMSO, 50 mM CHX in DMSO, and 10 mM FM4-64 in DMSO. Control treatments were performed with equal amounts of the respective solvents.

Fluorescence Microscopy

Fluorescence microscopy was performed using a Leica TCS SP2 confocal laser-scanning microscope. All CLSM images were obtained using the Leica Confocal software and a 63× water-immersion objective. The excitation wavelength was 488 nm; emission was detected for GFP between 500 and 530 nm, for RFP between 565 and 600 nm, and for FM4-64 between 620 and 680 nm. Images were processed using Adobe Photoshop. Quantification of colocalization was performed by assessing the intensities of individual pixels within the images using the colocalization function of Metamorph Offline software (Universal Imaging).

Transmission Electron Microscopy

Immunogold labeling was performed on ultrathin thawed Tokuyasu cryosections of formaldehyde-fixed (8%, 3 h) and sucrose-infiltrated (2.1 M) root tips using rabbit anti-GFP serum (1:25; Abcam) or rabbit anti-VHA-E serum (1:500) (Betz and Dietz, 1991) and silver-enhanced (HQ Silver, 6 min; Nanoprobes) goat (Fab′) anti-rabbit IgG coupled to Nanogold (No. 2004; Nanoprobes). In parallel, GFP-labeled NST-GFP–expressing root cells were also labeled with a silver-enhanced (HQ Silver, 5 min) Quantum dot marker (goat [Fab′]2 anti-rabbit-IgG coupled to Qdot525 [1:20]; No. 1144-1; Tebu-lab). For structural analysis, root tips were either chemically fixed with 2.5% glutaraldehyde, 1% aqueous uranyl acetate, and 1% osmium tetroxide, dehydrated, and embedded in Epon or high-pressure frozen (Bal-Tec HPM 010; Balzers) in hexadecane (Merck Sharp and Dohme), freeze-substituted (72 h, −90°C; 8 h, −60°C; 8 h, −35°C; 4 h, 0°C) in acetone containing 2% osmium tetroxide and 0.5% uranyl acetate, washed at 0°C, and embedded in Epon.

Accession Numbers

Arabidopsis Genome Initiative numbers for the genes discussed in this article are as follows: VHA-a1, At2g28520; VHA-a2, At2g21410; VHA-a3, At4g39080.

Supplemental Data

The following materials are available in the online version of this article.

  • Supplemental Figure 1. VHA-a1–GFP Expression Levels and Integration into the V-ATPase Complex.
  • Supplemental Figure 2. Ubiquitous Expression of VHA-a Isoforms.
  • Supplemental Figure 3. Colocalization of SYP41-GFP and SYP41-mRFP.
  • Supplemental Figure 4. Line Scan Analysis of Colocalization.
  • Supplemental Figure 5. Transport of FM4-64 to the Tonoplast in Suspension Cells.
  • Supplemental Table 1. Sequences of Primers.

Supplementary Material

[Supplemental Data]


We thank Felicity de Courcy, Claudia Oecking, Gerd Jürgens, and Niko Geldner for critical reading of the manuscript. We thank Pankash Dhonukshe (Center for Plant Molecular Biology), Junpei Takano, Takashi Ueda (University of Tokyo), Masa Sato (Kyoto University), and Tomohiro Uemura (RIKEN) for sharing mRFP-tagged markers and Markus Grebe (Umea Plant Science Center) for providing GFP marker lines. We are grateful to Zhao-Xin Wang and Dagmar Ripper for excellent technical assistance. This work was supported by the Deutsche Forschungsgemeinschaft (SFB 446: A20, Z2).


The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantcell.org) is: Karin Schumacher (ed.negnibeut-inu@rehcamuhcs.nirak).

[W]Online version contains Web-only data.

Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.105.037978.


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