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J. Biol. Chem., Vol. 280, Issue 37, 32356-32361, September 16, 2005
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From the Department of Anatomy, Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, FI-20700 Turku, Finland
Received for publication, December 17, 2004 , and in revised form, May 11, 2005.
| ABSTRACT |
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| INTRODUCTION |
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Recent studies have shown that Ras-related small GTPases of the Rab family control the endocytic, secretory, and recycling traffic of intracellular vesicles in mammalian cells (1114). Approximately 60 Rab proteins have been identified in the human genome. Each Rab protein localizes to a distinct cytoplasmic compartment where it regulates the steps of transport by the recruiting of specific effectors, which connect Rabs to either actin or microtubule-based motor proteins (1519). Rab proteins, like other small G proteins, control this machinery as molecular switches between GTP-bound (active) and GDP-bound (inactive) states. Their on/off regulatory function is restricted to the membrane compartment where they are localized. In this cycling, guanine nucleotide exchange factors replace GDP with GTP, thus activating Rabs, and act as a trigger to recruit effectors. GTPase-activating proteins, on the other hand, inactivate Rabs by inducing hydrolysis of GTP to GDP, release Rabs from the membrane into the cytosol and cause effectors to dissociate from Rabs (11, 12, 15).
Accumulating evidence suggests that Rab7 is a key regulator of the late steps of the endocytic pathway and also vacuolar fusion (2022). In the resorbing osteoclast, Rab7 was shown to be at the ruffled border (5, 10, 23, 24), whereas in the non-resorbing osteoclast, Rab7 localized around the nuclei where late endosomes and lysosomes accumulated. Moreover, down-regulation of Rab7 by antisense oligonucleotides prevented the formation of the ruffled border and consequently bone resorption (23).
However, the mechanism of how Rab7 regulates the ruffled border formation has remained obscure. Recently, four Rab7 effectors have been found by using the yeast two-hybrid system. One is Rab-interacting lysosomal protein (RILP)2 (25, 26), others are rabring7 (27), XAPC7 (28), and hVPS34/p150 (29). RILP has been shown to induce the recruitment of dynein-dynactin motor complexes to Rab7-containing late endosomes and lysosomes and to conduct these vesicles toward the minus end of microtubules surrounding the nucleus in cells with high expression of RILP (26). Moreover, RILP has also been reported as a Rab34 effector involved in the spatial positioning of the lysosomes in high RILP expression cells (30). Based on the fact that Rab7 controls the vesicular transport to the fusion zone of the ruffled border where the actin meshwork is present and underlines the membrane, and because we were unable to detect RILP in the cells,3 we hypothesized that other unknown effectors of Rab7 might exist in these specific cells. Thus, we chose a new strategy, the bacterial two-hybrid system, using a GTPase-deficient mutant Rab7Q67L as bait to screen a rat trabecular bone and bone marrow cDNA library. We identified a new Rab7-interacting protein, P21 Ras-related C3 botulinum toxin substrate 1 (Rac1), another small GTPase protein. Here we demonstrate further that Rac1 binds Rab7, and they colocalize in resorbing osteoclasts at the fusion zone of the ruffled border.
| MATERIALS AND METHODS |
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Osteoclast CultureAs described before (3, 4), osteoclasts were scraped from longitudinally cut long bones of 12-day-old rat pups and collected into
-essential medium with 20 mM Hepes, 10% heat-inactive fetal bovine serum, 100 IU/ml penicillin, and 100 µM/ml streptomycin. Subsequently, they were plated on bovine bone slices or on plastic coverslips. After a 30-min incubation at 37 °C in 5% CO2 and 95% air atmosphere for attachment, non-adherent cells were washed away, and attached cells were cultured further for 48 h in the same conditions.
Construction of a Rat Trabecular Bone Marrow cDNA LibraryTrabecular bone with marrow cells was taken from long bones of 12-day-old rat pups into
-essential medium. The mRNA from the sedimented cells was isolated using the Quickprep micro mRNA purification kit (Amersham Biosciences). A cDNA library was constructed with the BacterioMatch two-hybrid system XR cDNA library construction kit, according to the protocols provided by the manufacturer (Stratagene). Briefly, the first strand cDNA was primed with oligo(dT) and synthesized with reverse transcriptase. Double-stranded cDNAs were cloned into pTRG target plasmid opened with EcoRI and XhoI and transformed into XL1-blue MRF' Kan library pack competent cells (Stratagene). The library plasmids were isolated using the plasmid maxi kit (Qiagen).
Plasmid ConstructsThe coding region of rat Rab7, Rab9, Rac1, Rac2, Cdc42, and C-terminal Rac1 were obtained by PCR amplification with specific primers designed according to the sequences from the gene data bank from trabecular bone marrow cDNA. The reading frame of Rab7 (GenBankTM accession number AF 286535) and Rab9 (GenBankTM accession number AF325692 [GenBank] ) were subcloned into SalI/NotI sites in pGEX-4T-1 plasmid (Amersham Biosciences). The complete reading frame of Rac1 and C-terminal Rac1 (GenBankTM accession number AY 491395), Rac2 (GenBankTM accession number XM_345854), and Cdc42 (GenBankTM accession number NM_171994 [GenBank] ) reading frame were subcloned into SalI/XhoI sites in pQE 80L series vectors (Qiagen). The constitutively active GTP-bound form of Rab7, Rab7Q67L, and the GDP-bound form of Rab7, Rab7T22N, were made from Rab7 in pGEX-4T-1 construct using the Stratagene QuikChange site-directed mutagenesis kit. Rab7Q67L was further subcloned into NotI/XhoI sites in the pBT bait plasmid in which a flexible linker was inserted in front of the start codon of Rab7. All constructs were confirmed by sequencing.
Bacterial Two-hybrid ScreeningThe bacterial two-hybrid system was used to clone the trabecular bone marrow proteins that interact with the full-length constantly GTP-bound form of Rab7. Rat Rab7 was inserted in a frame into pBT bait vector containing full-length bacterial phage
repressor protein (
CI) with the N-terminal DNA-binding domain. A rat trabecular bone marrow-derived cDNA library in the pTRG target plasmid fused to the N-terminal domain of the
-subunit of RNA polymerase was screened by using Rab7Q67L as a bait protein in BacterioMatch two-hybrid reporter strain. The interactions were evaluated based on the promoter activation of transcription of two reporter genes, an ampicillin-resistant gene and a
-galactosidase gene in the BacterioMatch two-hybrid system reporter strain. In the first round of selection, surviving colonies were selected on plates with carbenicillin, kanamycin, chloramphenicol, and tetracycline. The second round was
-galactosidase gene expression assay using X-gal substrate. Finally, the interactions were confirmed by individual recotransformation with the bait and rescued target plasmids and evaluating reporter gene expression.
In Vitro Binding Histidine6-tagged Proteins with GST-tagged Rabs His6-tagged Rac1, either full-length or the C-terminal 149 amino acid residues, Rac2, CDC42, and RhoB were purified from bacterial lysates on nickel-nitrilotriacetic acid-agarose columns (Qiagen). Eluates, 35 mg/ml protein, were used without further purification. GST-fused Rab7, Rab7Q67L, Rab7T22N and Rab9 were bound onto glutathione-Sepharose beads directly from bacterial lysates in binding buffer consisting of 50 mM Tris-HCl, 150 mM NaCl, 5 mM MgCl2, and 0.1% Triton X-100, pH 7.4. The beads were washed free of unbound protein. One µg of bound Rab was used in one experimental point in binding buffer containing 100 µM GTP (or GDP for Rab7T22N). His-tagged protein was added in excess, and the beads were incubated for 3 h at 4 °C. After three washings with binding buffer, the bound proteins were separated on SDS-PAGE. Bound His-tagged proteins were detected by monoclonal antibody against His6, and visualized bands were detected by horseradish peroxidase-conjugated anti-mouse secondary antibody with the ECL system (Amersham Biosciences).
Indirect Immunofluorescence MicroscopyOsteoclasts were grown on bone slices or on coverslips, washed with PBS, and permeabilized with 0.01% saponin in 80 mM Pipes, pH 6.8, 5 mM EGTA, 1 mM MgCl2 for 5 min at room temperature. The cells were then fixed in 3% paraformaldehyde in PBS for 20 min and quenched with 50 mM NH4Cl for 10 min. The cells were then washed in 2% bovine serum albumin with 0.01% saponin in PBS for 5 min to block nonspecific binding. Primary antibodies in 0.2% bovine serum albumin with 0.01% saponin in PBS buffer were incubated with the permeabilized cells for 1 h at room temperature. After washing three times with the same buffer, the cells were incubated with Alexa Fluor 488-, TRITC- and Alexa Fluor 647-conjugated secondary antibodies in 0.2% bovine serum albumin with 0.01% saponin in PBS buffer 1 h at room temperature. Nuclei were stained with Hoechst 33258; cells were washed and then mounted with 80% glycerol in PBS. Confocal laser scanning microscopy was performed to obtain and analyze the immunofluorescence images with a Leica TCS-SP unit equipped with argon-krypton lasers (Leica Microsystems Heidelberg GmbH) and a x63 oil immersion lens.
| RESULTS |
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-galactosidase. Approximately 2 x 106 transformants were screened. The first screening was performed in four antibiotic plates, including chloramphenicol, kanamycin, tetracycline, and carbenicillin, which led to isolation of 2,800 colonies that activated the upstream Ampr reporter gene. Here we used carbenicillin instead of ampicillin to reduce the background, because carbenicillin is a more stable analog of ampicillin. Of the above, 104 colonies turned strongly blue on X-gal plates containing also chloramphenicol, kanamycin, and tetracycline, which meant that the bait-target interaction had been strong enough to trigger the downstream reporter gene, too. Finally, the interactions were confirmed by cotransformation of the bait and the rescued target plasmid pairs individually back into the reporter strain. Only the target plasmids that survived on the four antibiotics plates were selected to be studied further. We finally obtained a limited number of colonies for further studies. One of the strong positive colonies contained a 658-bp long insert, consisting of a 445-bp open-reading frame, a stop codon, and a 213-bp 3'-untranslated region, and a poly(A) tail. A search in the Ensembl rat genome data bank produced 100% sequence match on the p11 band of chromosome 12 (ENSRNOG00000001068 and predicted transcript: ENSRNOT00000001417). The gene on this site codes for Rac1, which is a member of the Rho family small GTPase proteins. Thus, we had isolated the C-terminal 149 residues moiety of Rac1 with the two-hybrid method. To get the full reading frame, we designed a primer pair based on the predicted sequence and PCR-amplified the full-length reading frame and the 3'-untranslated region. We then cloned and sequenced it and deposited the sequence in the GenBankTM (accession number AY491395 [GenBank] ) (Fig. 1). Comparison with the Rac1 transcript from the rat genome data bank of EMBL, the Rac1 cDNA of mouse (GenBankTM accession number BC003828 [GenBank] ), and human (GenBankTM accession number BC004247 [GenBank] ) in the gene data bank revealed a more than 30-base-pair completely conserved sequence starting with the translation start codon. Rat and mouse sequences showed 97% similarity, whereas between rat and human it was 90% in the coding region. At the protein level, Rac1 sequences of rat and mouse are identical, only one amino acid is different in man at position 135, which is isoleucine instead of threonine.
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Rac1 Colocalizes with Rab7 in Rat Osteoclasts and Fibroblast-like CellsTo visualize subcellular localization of endogenous Rab7 and Rac1, we used indirect immunofluorescence staining and laser confocal microscopy. In non-resorbing osteoclasts, we found that Rab7-positive vesicles were distributed around the nuclei. As also in other cells, Rab7 colocalized with the late endosomal/lysosomal marker LAMP2 (data not shown, see Ref. 23), whereas Rac1 displayed a rather uniform distribution in the cytoplasm. We found that Rab7 colocalized with Rac1 in some but not all vesicles around the nuclei of osteoclasts where late endosomes and lysosomes were located (data not shown). Next, we examined the location of these two proteins in resorbing osteoclasts on bone. As has been shown previously (10, 23, 24), Rab7 was redistributed to the fusion zone of the ruffled border just inside the sealing zone (actin ring) (10, 23, 35). We also found a large amount of Rac1 present at same area, clearly colocalizing with Rab7 (Fig. 3, AF). In the same rat osteoclast culture on the bovine bone slice, we also saw Rab7 clearly colocalizing with Rac1 in numerous vesicles of fibroblast like cells (Fig. 3, GI).
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| DISCUSSION |
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Most Rab proteins have been reported to recruit effectors to specific membrane compartments in their GTP-bound form. The Rab proteins recruit the tethering, docking, and fusion factors and assemble them as a complex to control the membrane docking and fusion events (11, 12, 13). Some effectors of Rab proteins indirectly attach actin or microtubule-related motor proteins, and thus they control vesicular trafficking. Cantalupo et al. (25) and Jordens et al. (26) found an effector of Rab7, RILP, which controls lysosomal transport by inducing the recruitment of dynein-dynactin motors to the minus ends of microtubules. RILP has also been reported as the Rab34 effector involved in the lysosomal spatial positioning in high RILP expression cells (30). However, the interaction between RILP and motor proteins may be indirect. We examined the endogenous RILP in resorbing osteoclasts, but we could not find Rab7 colocalized with RILP (antibody kindly provided by Dr. J. Neefjes).
The absence of RILP-Rab7 in osteoclast prompted us to look for more Rab7-interacting proteins/effectors. The two-hybrid system is generally used for this purpose. We chose the relatively new bacterial two-hybrid system for the following reasons. The yeast two-hybrid system has been used by many others, and we judged that its potential for Rab7 may be exhausted. Yeast has its own Vps small GTP-binding proteins that might confound the finding of further effectors. Cantalupo et al. (25) have reported that prenylation of Rab7 in yeast can cause a strong background in yeast, so they deleted the last three (prenylable) amino acid residues from the bait sequence, although those might be important in effector recognition. In bacteria, there is no Rab-like protein remaining; there is no prenylation, and full-length Rab7 can be used as bait.
Making a cDNA library for the target constructs from rat osteoclasts would have been a major effort, considering the scarcity of these cells. Therefore, we have chosen newborn rat bone marrow, which is a rich source of osteoclasts. For the bait construct, the full-length Rab7 was chosen with a mutation in its GTP-binding region. The Q67L mutation renders the protein unable to hydrolyze GTP, keeping it in a constantly activated state (25, 26).
To our satisfaction, we found new Rab7-interacting peptide sequences with the bacterial two-hybrid assay, one of them was Rac1, which is subject of this paper. The direct protein-protein interaction between Rab7 and Rac1 was also proven by GST-fused protein pull-down experiments. Apparently, the interaction is specific for Rac1, because other Rho GTPases such as RhoB, Rac2, or CDC42 have no affinity to Rab7 in these pull-down assays.
Rab7 and Rac1 also colocalize in osteoclasts. Fluorescent images show punctate staining of this colocalization, which indicates that they stain the same intracellular vesicles. The overlap is far from 100%; this also corroborates with the notion that Rab7 does not need Rac1 for the full-length of transport. Another, possibly far reaching, observation is that the partial colocalization of Rab7 and Rac1 is not confined to resorbing osteoclasts, it can be seen in other cell types, i.e. the phenomenon is general. In these cells, the costained structures are mostly perinuclear, where the late endosomes usually reside.
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The knocked out Rac1 gene is lethal (50). Conditionally knocked out Rac1 was done by using the cre-LoxP system with either interferon-inducible (51) or with cell line-specific cre expression (with lysozyme promoter-cre) (52). The analysis of macrophages and leukocytes in these papers showed anomalies in cell-dependent immunity. It may well have been that some of these defects were caused by the absence of functional Rab7·Rac1 complex that was needed for normal endocytosis. In a Chlamydia-induced arthritis model, it was found that the clearance of pathogen in Rac1-deficient animal was defective (53). All these findings point in the direction of Rac1 being an integral component of the endocytic/recycling pathway.
| FOOTNOTES |
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* The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. ![]()
1 To whom correspondence should be addressed. Tel.: 358-2-3337232; Fax: 358-2-3337352; E-mail: kalervo.vaananen{at}utu.fi.
2 The abbreviations used are: RILP, Rab-interacting lysosomal protein; GST, glutathione S-transferase; PBS, phosphate-buffered saline; Pipes, 1,4-piperazinediethanesulfonic acid; X-gal, 5-bromo-4-chloro-3-indolyl
-D-galactopyranoside; TRITC, tetramethylrhodamine isothiocyanate. ![]()
3 Y. Sun, K. G. Büki, O. Ettala, J. P. Vääräniemi, and H. K. Väänänen, unpublished data. ![]()
| ACKNOWLEDGMENTS |
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| REFERENCES |
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