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* This work was supported in part by grants-in-aid from the Ministry of Education, Science, and Culture of Japan. 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.
Four isoforms of the Na+/H+ exchanger (NHE6–NHE9) are distributed to intracellular compartments in human cells. They are localized to Golgi and post-Golgi endocytic compartments as follows: mid- to trans-Golgi, NHE8; trans-Golgi network, NHE7; early recycling endosomes, NHE6; and late recycling endosomes, NHE9. No significant localization of these NHEs was observed in lysosomes. The distribution of these NHEs is not discrete in the cells, and there is partial overlap with other isoforms, suggesting that the intracellular localization of the NHEs is established by the balance of transport in and out of the post-Golgi compartments as the dynamic membrane trafficking. The overexpression of NHE isoforms increased the luminal pH of the compartments in which the protein resided from the mildly acidic pH to the cytosolic pH, suggesting that their in vivo function is to regulate the pH and monovalent cation concentration in these organelles. We propose that the specific NHE isoforms contribute to the maintenance of the unique acidic pH values of the Golgi and post-Golgi compartments in the cell.
The luminal ionic composition of intracellular compartments differs from the cytoplasm, and each compartment is characterized by a unique, organelle-specific ion concentration. This specific ionic composition is thought to be an important determinant for organelle function and is maintained by the concerted action of ion transport carriers on the membrane (
). This progressive acidification is essential for compartmentalizing cellular events, such as post-translational modifications, sorting of newly synthesized proteins into the secretory pathway, and the degradation or recycling of internalized ligand-receptor complexes and fluid-phase solutes in the endocytic pathway (
The differential ionic milieu of the organelles is maintained by a suite of ion carriers on the membrane, including pumps, channels, and transporters. Luminal acidity is primarily generated by the vacuolar-type H+-translocating ATPase (V-ATPase) (
). Because the V-ATPase is electrogenic, the pumping activity could be affected by membrane potential and availability of permeant counterions such as chloride and potassium. In vitro studies using isolated endosomes and Golgi suggested a critical role for Cl- in shunting the inside-positive membrane potential generated by H+ pumping (
). However, although Cl- and K+ serve as counterions for H+ pumping, their conductances on the Golgi complex and the TGN were large compared with the rate of H+ pumping, arguing against modulation of Cl- and K+ conductances as the mechanism for pH regulation and suggesting that the electrical potential across the membrane is not a determinant of steady-state pH in the Golgi and TGN (
). Instead, the steady-state pH is thought to be controlled by the balance between the rate of H+ pumping by V-ATPase and the magnitude of H+ leak from the organelle lumen. The H+ leak mechanism is postulated based on the rapid dissipation of the proton gradient across the membrane after inhibiting the V-ATPase with bafilomycin A1, however the molecular mechanism is still unknown (
). The decreasing pH values of organelles along the secretory pathway is established by gradually increasing the density of active H+-pumps from the ER to the Golgi while concomitantly decreasing the H+ permeability from ER to Golgi to secretory granules (
). Thus, the H+ leak acts as a key determinant of organellar pH. These data emphasize the importance of identifying the molecular components of this system, which could conceivably involve proton channels, proton-coupled cotransporters, or proton-exchanging transporters.
Na+/H+ exchanger (NHE) proteins are integral membrane proteins that mediate electroneutral exchange of H+ for Na+ and K+ across the membrane, down their concentration gradients (
). However, the physiological function of the organellar membrane NHEs is still unknown.
In this study, we characterized organellar alkali-cation/proton exchanger proteins and found that four NHE isoforms are distributed to Golgi and post-Golgi compartments. From these observations we suggest a mechanism regulating the luminal pH and cation composition of the intracellular compartments by NHEs.
Mammalian and Yeast Cell Culture—HEp2, HeLa, and COS7 cells were grown in Dulbecco's modified Eagle's medium containing 10% fetal calf serum. HEK293 and Caco-2 cells were in minimum essential medium containing 10 and 20% fetal calf serum, respectively. All media contained non-essential amino acids, 100 units/ml penicillin, and 100 μg/ml streptomycin. The cells were cultured in a humidified atmosphere of 5% CO2 and 95% air. Transfection of plasmid DNAs was performed as described previously (
) using primers ScNHX1-DFw (5′-ATGCTATCCAAGGTATTGCTGAATATAGCTTTCAAGGTGCGTTGTAAAACG-3′) and ScNHX1-DRv (5′-CTAGTGGTTTTGGGAAGAGAAATCTGCAGGTGATTGCGTACAGGAAACAGCTATGACCAT-3′) to generate a 1-kbp TRP1 fragment, with 5′- and 3′-ends flanked by 40-bp sequences of NHX1 ORF ends. The DNA fragment was introduced into SK5 cells, and the resulting Trp+ transformants were selected on synthetic medium containing 2% glucose (
) but lacking tryptophan. Insertion of the TRP1 gene into NHX1 locus was confirmed by PCR amplification of the genomic DNA using primers corresponding to the DNA sequences 598 bp upstream and 833 bp downstream of the NHX1 ORF.
cDNA Cloning—GenBank™ data bases of expressed sequence tags (EST) and the human cDNA sequencing project were searched by using amino acid sequences of the mammalian NHE isoforms. A human clone KIAA0939 encoding NHE8 (accession number AB023156)
In the course of preparing this manuscript, the human NHE8 cDNA containing the entire ORF was identified at the Kazusa DNA Research Institute (clone hh04825s1). The nucleotide sequence is available at GenBank™, accession number AB023156.
was provided by the Kazusa DNA Research Institute (Kisarazu, Japan). Sequencing analysis of the cDNA suggested that this clone was missing coding information of ∼0.5 kbp at the 5′ region (corresponding to amino acids 1–169 in the mouse homologue). Two mouse EST clones (accession numbers BF782177 and BF787440) encoding NHE8 were obtained from Invitrogen. The nucleotide sequence of BF787440 has been deposited in the DDBJ/GenBank™ (accession number AB089793). A human EST clone (accession number BI600396) encoding NHE9 was obtained from Invitrogen. This EST clone contained the entire NHE9 ORF but carried nonsense (C→A) and frameshift (insertion of C) mutations at positions of 26 and 272 nt from the initiation ATG. We cloned cDNA corresponding to NHE9 ORF by reverse-transcription (RT)-PCR amplification of poly(A)+ RNA isolated from human cultured cell lines, HEp2, HEK293, HeLa, and Caco-2, using the following primers: 5′-CTAAGGAATCCCAAGAAGACTGGGG-3′ and 5′-TGATTACATCTGTACTCTTCATGCC-3′. The nucleotide sequence of the NHE9 cDNA was determined by sequencing three independent PCR products from each cell line and was deposited in the DDBJ/GenBank™ (accession number AB089794). A human NHE6 cDNA clone, KIAA0267, was obtained from the Kazusa DNA Research Institute (Kisarazu, Japan). Human NHE7 cDNA was cloned by PCR amplification as follows. A cDNA fragment of the ORF (160 nt from initiation ATG to the termination codon) was amplified from poly(A)+ RNA isolated from HEK293 cells. The 159-bp DNA fragment corresponding to the 5′-end of ORF was cloned by amplifying a human genome clone, accession number AL050307 (provided by Children's Hospital Oakland Research Institute, Oakland, CA). The full-length NHE7 ORF was reconstituted by PCR, and the integrity of the construct was verified by DNA sequencing.
Northern Blotting and RT-PCR—A human poly(A)+ RNA blot (1 μg/lane, Clontech) was probed with a 1.2-kbp PCR fragment of human NHE8 (the coding region of the KIAA0939 clone) or human NHE9 (263–1535 nt from the initiation codon). The probes were radiolabeled with [32P]dCTP by the random primer method and hybridized at 68 °C for 1 h in the ExpressHyb™ solution (Clontech). The membrane filter was washed extensively under high stringent conditions, and the radioactive signals were then analyzed by using a PhosphorImager (BAS1800, FujiFilm, Tokyo, Japan). For RT-PCR analysis, poly(A)+ RNA was prepared from human cell lines using biotinylated oligo(dT) and streptavidin-conjugated magnetic resin, according to the manufacturer's instructions (Promega, Madison, WI), and reverse-transcribed with BcaBEST reverse transcriptase and random 9-mer primers (Takara, Otsu, Japan). Subsequent PCRs were performed using the following primers: NHE6, 5′-GAAGTGCAGTCAAGTCCAACTACCT-3′ and 5′-CGGAAAAGCCAAGCACTCTCTGCTT-3′ (for first PCR); 5′-AGTGCTGTCCTCCTCAATAGTGGCA-3′ and 5′-TGAACAGTGTCAGCCCCATGTAGGA-3′ (for second PCR); NHE7, 5′-CCCAGTGACTGTGCTGGCGATATTT-3′ and 5′-TCCTGTTTTGTCCGGTTTCCTCTGG-3′; NHE8, 5′-ATTTTACAGGCTGATGTAATCTCTA-3′ and 5′-TCCAAGGAAGGCGTTTTCCTCAAGT-3′; NHE9, 5′-GGGGAATTCATGGAGAGACAGTCAAGGGTTATG-3′ and 5′-GGGGTCGACTTAATTCAACTGGGATTGACC-3′. The PCRs were subjected to agarose gel electrophoresis, stained with ethidium bromide, and photographed according to standard protocols (
). Amplification of the target cDNA fragment was confirmed by DNA sequencing and restriction enzyme digestion.
Plasmid Construction—Mammalian expression plasmids for NHE8 tagged with FLAG tag and ECFP at the C terminus were constructed by introducing an EcoRI-SphI DNA fragment encoding NHE8 and an SphI-SalI DNA fragment encoding the FLAG sequence with the termination codon into pcDNA3.1-mycHisA(-) (Invitrogen), and an EcoRI-BamHI fragment encoding NHE8 lacking the termination codon into pECFP-N1 (Clontech), respectively. The expression plasmid for NHE9 tagged with Myc tag or ECFP was generated by introducing the EcoRI-SalI and NheI-SacI PCR fragments encoding NHE9 lacking the termination codon into pcDNA3.1-mycHisA(-) (Invitrogen) or pECFP-N1 (Invitrogen), respectively. Expression plasmids for human NHE6-HA and NHE7-T7 were constructed by introducing the EcoRI-BamHI PCR fragment encoding NHE6-HA or NHE7-T7 without termination codons into pEGFP-N3 (Clontech). The expression plasmids for human NHE6-ECFP were constructed by introducing the EcoRI-BamHI PCR fragment encoding NHE6-HA lacking a termination codon into pECFP-N1. The linker sequences between NHEs and epitope tags or ECFP are as follows: NHE8-“GMQ”-FLAG, NHE8-“PDPPVAT”-ECFP, NHE9-“VDRSELGTKLGP”-Myc-“NSAVD”-(His)6, NHE9-“VDRSELKLRILQSTVPRARDPPVAT”-ECFP, NHE6-HA-“RDPSPPW”, NHE6-HA-“RDPPVAT”-ECFP, and NHE7-T7-“RDPSSVPSLSLNR.” The expression plasmids for GalT-GFPs and VAMP3-GFPs were constructed by inserting PCR fragments encoding the N-terminal 82 aa of human GalT (β-1,4-galactosyltransferase) and rat VAMP3 into the multiple cloning sites of pEGFP-N3 and pEYFP-N1 (Clontech), respectively. The linker sequences between organelle markers and GFPs are as follows: GalT- “PRSIAT”-EGFP, GalT- “PPVAT”-EYFP, VAMP3-“KLSNSAVDGTAGPGSIAT”-EGFP, and VAMP3-“KLRILQSTVPRARDPPVAT”-EYFP. Yeast expression plasmids for mouse NHE8 and human NHE9 were constructed by introducing the EcoRI-SphI PCR fragment of the NHE8 or NHE9 ORF, and the SphI-SalI DNA fragment encoding His6 or EGFP into the EcoRI-SalI site of yeast expression plasmid pKT10 (
). Amino acid sequences of “GMQ” and “GMP” were added between the NHE coding sequences and the His6 and EGFP, respectively. Escherichia coli expression plasmids for His6-tagged enhanced GFP mutants were constructed as follows. An HincII fragment encoding EGFP (F64L and S65T) from pEGFP-N3 was introduced into the same site of pQE9 to generate an expression plasmid for 6xHis-EGFP (pQE9-EGFP). BamHI-HincII fragments encoding ECFP (F64L, S65T, Y66W, N146I, M153T, and V163A) from pECFP-N1 (Clontech) and EYFP (S65G, V68L, S72A, and T203Y) from pEYFP-N1 (Clontech) were introduced into the BamHI-HincII site of pQE10 to generate expression plasmids for 6xHis-ECFP (pQE10-ECFP) and 6xHis-EYFP (pQE10-EYFP). This places the sequences encoding the GFP mutants downstream of the His6 tag, and the plasmids encode fusion proteins of “MRGSHHHHHHGSVDGTAGPGSIAT”-EGFP (pQE9-EGFP) and “MRGSHHHHHHTDPPVAT”-ECFP/EYFP (pQE10-ECFP/pQE10-EYFP).
Spectroscopy and pH Titration of EGFP Mutants in Vitro—The recombinant 6xHis-GFP mutants were produced in E. coli BL21(DE3) and purified by Ni2+-affinity chromatography using a linear gradient of 0–1 m imidazole in buffer containing 10 mm Tris-HCl (pH 7.5) and 0.3 m NaCl. Titrations of GFP fluorescence versus pH were performed by cuvette fluorometry. Purified GFPs (10 μg/ml, 134-fold dilution of the purified proteins) were dissolved in either 0.2 m sodium phosphate (pH 8.0 to pH 5.0) or 0.1 m sodium phosphate and 0.1 m sodium acetate (pH 4.5 and pH 4.0). The filters used for excitation were 480 nm ± 10 nm (EGFP), 440 nm ± 10 nm (ECFP), and 505 nm ± 10 nm (EYFP).
Antibodies—The rabbit polyclonal anti-NHE8 antibody was prepared by immunizing a rabbit with the bacterially expressed C-terminal peptides of human NHE8 (105 amino acid residues), followed by affinity purification. Mouse monoclonal antibodies were obtained from commercial sources as follows: anti-Myc (clone 9E10) and anti-HA (clone 12CA5), Roche Diagnostics; anti-FLAG (clone M2), Sigma; anti-T7, Novagen (Madison, WI); anti-GM130 (clone 35), Transduction Laboratories; and anti-CI-M6PR antibody, Affinity Bioreagents, Inc. (Golden, CO). Rabbit polyclonal anti-HA was purchased from Santa Cruz Biotechnology (Santa Cruz, CA). Horseradish peroxidase-conjugated secondary antibodies against rabbit and mouse IgG were purchased from Vector Laboratories (Burlingame, CA). Alexa488- and Alexa-546-conjugated secondary antibodies were purchased from Molecular Probes (Eugene, OR).
Purification of NHE8 Expressed in Yeast—Yeast TYY3 cells expressing NHE8–6xHis or NHE8(E220Q,D225N)-6xHis were cultured in synthetic medium containing 2% glucose, 0.5% casamino acids, and appropriate supplements. The cells (8000 A600 units) were lysed in 70 ml of lysis buffer (50 mm potassium phosphate (pH 7.4), 500 mm NaCl, 0.2 mm phenylmethylsulfonyl fluoride, 1 μg/ml leupeptin, 1 μg/ml pepstatin, 1 μg/ml aprotinin) by two passes through a French press, followed by centrifuging at 500 × g for 5 min. The supernatant (S0.5) was spun at 100,000 × g for 1 h, and the resulting pellet fraction (P100) was resuspended in lysis buffer (5 mg of protein/ml). The solution was mixed with 4 volumes of lysis buffer containing 0.5% n-dodecyl-β-d-maltoside (DDM), 20% glycerol, and 10 mm imidazole and was incubated for 30 min at 4 °C with gentle shaking. Insoluble material was removed by centrifuging at 30,000 × g for 30 min. The supernatant (S30) was applied to a 1-ml column of Hi-Trap Chelating HP charged with Ni2+. The column was washed with lysis buffer containing 0.15% DDM, 20% glycerol, and 10 mm imidazole, followed by elution buffer (50 mm potassium phosphate (pH 7.4), 500 mm NaCl, 0.075% DDM) containing 80 mm imidazole. The protein was eluted with a linear gradient of imidazole (80–400 mm). The protein eluted in the 200–240 mm fractions was concentrated by using a centrifugal concentrator with a 10-kDa cut-off (Ultrafree-MC 10,000 NMWL, Millipore, Billerica, MA).
Reconstitution of NHE8 Proteins into Liposomes—For reconstitution of NHE8 proteins into liposomes, we used the protocol developed previously for reconstitution of the purified His6-tagged H+-ATPase, AHA2, and Na+/H+ exchanger, AtNHX1 (
). NHE8 (50 μg) was mixed with 2.34 mg of soybean phospholipids type II-S (Sigma) in a total volume of 208 μl of reconstitution buffer (20 mm BTP-MES (pH 7.5), 25 mm (NH4)2SO4, 10% glycerol, 2.5 mm pyranine). The sample was solubilized by addition of 12 μl of 1 mn-octyl-β-d-glucoside and loaded onto a 2.5-ml spin column filled with Sephadex G-50 (Amersham Biosciences) preloaded with 2.5 mm pyranine in reconstitution buffer. After centrifugation for 5 min at 180 × g, the eluate was incubated for 30 min at room temperature with 100 mg of wet Bio-Beads (SM-2, Bio-Rad) and again passed over a G-50 spin column.
Measurement of Na+/H+Exchange in Vitro—Pyranine fluorescence was recorded at 463 nm excitation wavelength and 510 nm emission wavelength. Fluorescence of the sample was adjusted to appropriate levels by diluting the sample with reconstitution buffer. The liposomes containing NHE8 were diluted in the reconstitution buffer without (NH4)2SO4 and pyranine in a 2-ml reaction cuvette held at 25 °C. The 40-fold
dilution resulted in acid loading of the vesicles because of outward diffusion of NH3 (
). The resulting pH inside the vesicles determined from the fluorescence of pyranine was 5.73. Thereafter, inward cation gradients were imposed by the addition of NaCl outside the vesicles. Proton efflux coupled to cation influx was monitored by the increase of pyranine fluorescence. The initial rate of fluorescence variation after the addition of cations (ΔF·min-1) was used to determine the affinity for cations and maximum initial rate of vesicle alkalinization by Hanes-Woolf plotting. For radioactive sodium uptake, the liposomes (12.5 μl) were suspended in 0.5 ml of reaction buffer (20 mm BTP-MES (pH 7.5), 10% glycerol, 160 mm22NaCl (0.23 MBq/mmol)). At various times, ice-cold reaction buffer (1.5 ml) without 22Na+ was added to stop the reaction. The sample was applied to a membrane filter (HATF, 0.45-μm pore size, Millipore, Billerica, MA), washed three times with 2 ml of reaction buffer without NaCl, and then dried for quantitation of radioactivity. The background radioactivity was determined by adding 25 mm (NH4)2SO4 to the reaction buffer prior to starting the reaction. Radioactivity was measured with an ACSII liquid scintillation counter (Amersham Biosciences) and a Beckman LS6500 liquid scintillation counter (Beckman Coulter, Inc., Fullerton, CA).
Fluorescence Microscopy—Cells were fixed with 2% formaldehyde and then permeabilized in phosphate-buffered saline containing 1% bovine serum albumin, 0.4% saponin, and 2% normal goat serum (
). The cells were incubated with primary antibodies against NHE proteins, the epitope tags, or organelle marker proteins and then stained with fluorescently labeled secondary antibodies. After washing with phosphate-buffered saline, samples were filled with 10% glycerol and then observed under an Olympus BX51 microscope equipped with differential interference contrast optics (Olympus, Tokyo, Japan). COS7 cells were transfected with pCMV-NHE6-HA or pcDNA3.1-NHE9-mycHis and incubated for 2 days. Cells were serum-starved for 30 min at 37 °C to deplete them of transferrin, chilled on ice, and allowed to bind Alexa 594-Tfn (60 μg/ml in phosphate-buffered saline) for 45 min on ice. Cells were washed briefly in phosphate-buffered saline and placed in Dulbecco's modified Eagle's medium at 37 °C. After incubation for the indicated times, cells were fixed, permeabilized, and stained with anti-HA or anti-Myc antibodies.
Measurement of Organelle pH in Vivo—Between 2 and 4 days after transfection, cells were imaged at 26 °C with an inverted fluorescence microscope (IX70, Olympus, Tokyo, Japan) equipped with a cooled charge-coupled device camera (ORCA-ER, Hamamatsu Photonics, Hamamatsu, Japan). Cells were incubated initially for 5 min with Hanks' balanced salt solution (137 mm NaCl, 5.3 mm KCl, 1.3 mm CaCl2, 0.82 mm MgSO4, 0.34 mm Na2HPO4, 0.44 m KH2PO4, 4.2 mm NaHCO3, 5.6 mm glucose, and 15 mm HEPES-NaOH (pH 7.4)) and observed with a ×40 objective. Data were recorded every 5 s for 300 ms at each of the excitation wavelengths. The medium was then switched to a series of high KCl calibration solutions containing 125 mm KCl, 20 mm NaCl, 0.5 mm CaCl2, 0.5 mm MgCl2, and 25 mm of one of the following buffers: HEPES (pH 8.0 to 7.0), MES (pH 6.5 to 5.5), or acetate (pH 5.0 to 4.0). Nigericin (10 μm) was added to the buffer for in situ titrations in living cells (
). The interference filters (Omega Optical and Chroma Technology, Rockingham, VT) used for excitation and emission were 430–450 and 465–495 nm for ECFP, 470–400 and 515–550 nm for EGFP, and 485–515 and 528–568 nm for EYFP. Image acquisition was controlled by the Aquacosmos software (Hamamatsu Photonics, Hamamatsu, Japan). Regions of interest were selected manually, and pixel intensities were spatially averaged after background subtraction.
Other Materials—22NaCl (37 MBq/ml, 13.2 GBq/mg) was obtained from PerkinElmer Life Sciences. Other chemicals were from Sigma, unless otherwise specified.
Novel Organellar Na+/H+Exchangers, NHE8 and NHE9—Previously, seven isoforms of the NHE protein have been identified using molecular biological approaches (
). Recent progress on the human genome sequencing project provided a powerful tool to identify novel molecules showing characteristic primary structures, and this enabled us to identify all genes encoding organellar NHE members. We searched the human genome sequence, and found that six regions (chromosomes 3q24, 10q11.21, 12q23.1, 20q13.3, 22q11.21, and Xq21.2) contain sequences showing similarity to previously known NHEs, in addition to the seven loci for previously known NHEs and one NHE3 pseudogene (
). Sequence analysis revealed that four of the six chromosome regions (chromosomes 10q11.21, 12q23.1, 22q11.21, and Xq21.2) contain none of the exon-intron boundaries predicted from the genomic structures of the NHE family and carry both nonsense and frameshift mutations. We did not find the corresponding cDNAs in the mammalian EST data bases. Thus, these regions are thought to be pseudogenes.
We searched the EST databases for cDNA clones corresponding to the regions at chromosomes 20q13.3 and 3q24, and found KIAA0939 (named NHE8) and BI600394 (named NHE9) for chromosomes 20q13.3 and 3q24, respectively. NHE8/KIAA0939 is the most recently identified NHE homologue reported by Goyal et al. (
), the KIAA0939 clones lacked ∼500 bp in length at the 5′-end of the coding region. We searched mouse cDNA libraries and obtained two cDNA clones (BF782177 and BF787440) carrying the entire length of the ORF from mouse kidney. Sequence analysis of the cDNA (BI600396) corresponding to NHE9 revealed that this clone contained a nonsense (C→A, 26 nt from initiation ATG) and a frameshift (deletion of C at 272 nt from initiation ATG) mutation in the possible coding region when compared with the human genomic sequence. We cloned NHE9 cDNAs from several human cell lines and determined the nucleotide sequence.
Amino acid sequence analysis of NHE8 and NHE9 revealed that both proteins are predicted to have 12 membrane-spanning domains and a large C-terminal domain, characteristic of eukaryotic NHEs (Fig. 1, A and B). The overall similarity of NHE8 to other isoforms is relatively low (23–27% identities to other NHE isoforms), whereas the membrane-spanning regions are more conserved (∼50% identity). NHE9 showed high similarity to NHE6 (55% identity) and NHE7 (57% identity) throughout the entire length. We note that the sequences in four regions, the N terminus (aa 1–29 in NHE9), the second loop (aa 70–127), and two C-terminal hydrophilic domains (aa 495–517 and aa 570–645), are significantly divergent in NHE6, NHE7, and NHE9 isoforms. The charged residues in the membrane-spanning domains (Asp-184, Asp-196, and Asp225; Glu-220, Glu-293, Glu-309,and Glu-354; and Arg-421 in NHE8) are conserved in NHE8 and NHE9 (Fig. 1A).
From these examinations, we concluded that the human NHE family is composed of nine members. Phylogenetic analysis of the amino acid sequences revealed that the nine NHE isoforms are classified into two groups of NHE1–NHE5 and NHE6–NHE9 (Fig. 1C). NHE8 and NHE9 are grouped with NHE6 and NHE7, which are thought to reside on recycling endosomes and the trans-Golgi network (
). These results suggest that NHEs can be classified into two groups, plasma membrane NHEs (NHE1–NHE5) and organelle-specific NHEs (NHE6–NHE9) that include the novel NHE members NHE8 and NHE9.
Tissue and Cellular Distribution of NHE6–NHE9 Isoforms—We examined the distribution of NHE8 and NHE9 transcripts in human tissues by Northern blotting analysis. Previous studies have revealed that plasma membrane NHEs show unique and isoform-specific tissue expression, but NHE6 and NHE7 are ubiquitous (
). Poly(A)+ RNA prepared from various human tissues was hybridized with 32P-labeled DNA probes corresponding to the open reading frames of human NHE8 and NHE9 and then autoradiographed. NHE8 (6.4 and 4.6 kb) and NHE9 (3.7 kb) transcripts were detected in all human tissues tested (Fig. 2A), suggesting that these isoforms are ubiquitously expressed. The highest amounts of NHE8 transcript were found in skeletal muscle and kidney. The NHE9 transcript was detected at similar levels in all the human tissues. We further examined the expression of NHE8 and NHE9 in several human cultured cell lines, HEK293 (embryonic kidney), HeLa (cervix), HEp2 (laryngeal epithelium), and Caco-2 (colon), by RT-PCR. The broad and ubiquitous expression of NHE8 and NHE9 shown by Northern blotting (Fig. 2A) was confirmed at the cellular level. The transcripts of the NHE6 and NHE7 were also detected in all the cell lines by the RT-PCR analysis, suggesting that NHE6NHE9 isoforms each play a role in basic cellular functioning.
Cation/H+Exchange Activity of NHE8—We examined the alkali-cation/H+ exchange activity of the NHE8 gene product. NHE8 protein tagged with His6 was expressed in yeast cells, purified using a nickel-nitrilotriacetic acid column, and subjected to ion-transport assays using artificial liposomes. The NHE8 expressed in yeast cells appeared as a 55-kDa protein on SDS-PAGE (Fig. 3A), which is slightly smaller (∼10 kDa) than the calculated mass, as has been noted for other eukaryotic Na+/H+ exchanger proteins (
). The protein was localized to intracellular compartments, primarily the ER (Fig. 3B).
Microsomal membranes were isolated from the yeast cells expressing NHE8–6xHis, and the proteins were solubilized using n-dodecyl-β-d-maltoside. The protein (Fig. 3C) was reconstituted in soybean phospholipid vesicles containing the pH indicator pyranine in the presence of (NH4)2SO4. Dilution of the proteoliposome solution in reconstitution buffer without (NH4)2SO4 resulted in an immediate fluorescence diminution of vesicle-trapped pyranine, reflective of the internal acidification of the vesicles (Fig. 4A, time 30 s). When proteoliposomes were diluted under equilibrium conditions (equal concentrations of ammonium inside and outside the vesicles), the lumen of the liposome was not acidified (data not shown). The internal pH, estimated using standard pH buffers, was 5.73. When vesicles were diluted in the presence of (NH4)2SO4, the internal pH as indicated from pyranine fluorescence was 7.5. The variation of pyranine fluorescence (pKa 7.2) was approximately linear between pH 5.7 and 7.5 (data not shown) and therefore is directly related to intravesicular pH changes. The addition of NaCl (300 mm) increased the pyranine fluorescence, which indicates the alkalization of the liposome lumen to pH 6.4 (Fig. 4A). No significant recovery of pyranine fluorescence was observed upon the addition of organic cation, choline chloride, or addition of NaCl to control liposomes that did not contain the NHE8 protein (Fig. 4A). The addition of (NH4)2SO4 fully collapsed the pH gradient in both liposomes and proteoliposomes. These observations are consistent with NHE8-mediated Na+-dependent proton efflux from the liposomes. The ion exchange reaction showed saturable kinetics with increasing cation concentrations (Fig. 4B). The affinity of NHE8 for Na+ and K+ was relatively low, with apparent Km values of 130 and 75 mm, respectively. The affinities for Li+, Cs+, and Rb+ were much lower, and the Km value was difficult to determine because it is relatively high (>200 mm) (data not shown). The maximum initial rate of vesicle alkalinization (Vmax) obtained from fitting the data was 3.6 and 3.8 ΔF·min-1. We examined Na+ uptake into the proteoliposomes. If the increase in pH in the liposomes is because of proton efflux coupled with Na+ influx through Na+/H+ antiport, then the proteoliposomes should sequester Na+. As expected, 22Na+ uptake was observed with these proteoliposomes (Fig. 4B), whereas 22Na+ uptake was negligible in liposomes without NHE8 and in proteoliposomes carrying NHE8 mutated at the glutamate 220 and asparagine 225 residues (Fig. 4B), which are important for the exchange activity in NHE1 (
). These results indicate that NHE8 is capable of performing alkali-cation/H+ exchange.
Intracellular Distribution of NHE6–NHE9 Isoforms—The similarity of primary structures among NHE6 to NHE9 isoforms suggested that these isoforms act on the intracellular compartments. We examined the subcellular localization of NHE8 and NHE9 by immunofluorescence microscopy, and compared their distributions with those of NHE6 and NHE7. COS7 cells were fixed, permeabilized, and stained with antibodies against either NHE8, NHE9, or epitope tags fused to the C terminus of the NHE proteins. Fluorescence microscopy revealed that NHE8 proteins were found primarily in curvy tubular structures at the region juxtaposed to the nucleus (Fig. 5A). A portion of the signal was detected in punctate structures dispersed throughout the cell. Double staining of NHE8 with organelle-marker proteins suggested that the localization of NHE8 is quite similar to that of GM130, a marker for cis-Golgi compartments (Fig. 5A). However, the signals from NHE8 and GM130 are not overlapping but rather closely adjacent to one another at higher magnifications (Fig. 5A). The same result was obtained by staining NHE8-FLAG transiently expressed in COS7 cells (data not shown). We did not find colocalization with protein markers for other compartments, including ER (calnexin), early endosomes (EEA1), late endosomes and lysosomes (Lamp-2), TGN and late endosomes (cation-independent mannose 6-phosphate receptor) (data not shown). From these observations, we concluded that NHE8 is mainly localized to the mid- to trans-Golgi compartments.
We next investigated the intracellular localization of NHE9 by immunofluorescence microscopy. This protein is also localized to intracellular compartments. The signals were found as punctate structures, highly concentrated around the nucleus and dispersed throughout the cell periphery (Fig. 5B). NHE9 showed a partial colocalization with NHE6 in punctate structures between the cell periphery and the peri-nuclear region (Fig. 5C).
Since the distribution of NHE9-positive compartments is similar to that of endosomes, we performed double staining with EEA1, Lamp-2, and cation-independent mannose 6-phosphate receptors. No significant overlap of NHE9 with Lamp-2 or cation-independent mannose 6-phosphate receptor was observed, and only a small portion of NHE9 was colocalized with EEA1 (Fig. 5D). Signals from NHE9 were found in compartments labeled by rhodamine-conjugated transferrin (Fig. 5E), suggesting the localization of NHE9 to the recycling endosomes rather than EEA1-residing early endosomes. To differentiate among endosomal compartments in the recycling pathway, rhodamine-labeled transferrin was internalized and chased in the presence of nonlabeled transferrin for up to 30 min. After fixation, NHE6 and NHE9 were detected by immunostaining. Early after internalization (2–10 min), the major population of transferrin-labeled structures was found at the cell periphery and labeled with NHE6 (Fig. 6), suggesting that NHE6 is localized to an early stage of recycling pathway. Consistently, most of the NHE6-positive compartments contained EEA1, a marker for early endosomes (data not shown). The colocalization with NHE6 was transient and decreased after longer chase periods. The signals from labeled transferrin were translocated to the juxtanuclear region, and the number of transferrin-labeled endosomes containing NHE9 increased slowly from 10 to 15 to 30 min of chase (Fig. 6). These observations, together with the partial colocalization of NHE6 and NHE9 (see Fig. 5C), suggest that the proteins reside on compartments of the early and late stages of recycling pathway, respectively, with partial overlap, which are possibly early endosome and recycling endosome, respectively.
Overexpression of Na+/H+Exchangers Causes Alkalinization of the Compartment—The isoform-specific distribution of NHE6–NHE9 prompted us to investigate their function in regulation of organellar pH and cation concentration. Some GFP mutants are reported to exhibit pH-sensitive fluorescence (
). We examined the pH sensitivity of EGFP (F64L and S65T), EYFP (S65G, V68L, S72A, and T203Y), and ECFP (F64L, S65T, Y66W, N146I, M153T, and V163A) expressed in E. coli cells. EGFP and EYFP showed an acidification-dependent decrease in the fluorescence emission at 510 and 528 nm, respectively (Fig. 7A). The apparent pKa values of EGFP and EYFP were 5.9 and 5.4 with Hill coefficients (n) of 2.1 and 2.3, respectively. The pH-dependent change in fluorescence of ECFP was smaller than that of EGFP or EYFP (pKa 6.2). The fluorescence change was reversible in the pH range 4–8 for all three proteins (data not shown).
Because these pH-dependent changes span the pH range of most subcellular compartments, we reasoned that these GFP mutants could be used as physiological pH indicators for Golgi and endosomes. EYFP was fused with integral membrane protein markers for the mid- to trans-Golgi, GalT (
). COS7 cells expressing GalT-GFP and either NHE8-FLAG or NHE8-ECFP were observed under the fluorescence microscope. NHE8-FLAG and NHE8-ECFP were colocalized with GalT-GFP and GalT-EYFP, respectively (Fig. 8). This confirms the mid- and trans-Golgi localization of NHE8 protein. Steady-state Golgi pH in COS7 cells was 6.50 ± 0.05, which is consistent with values measured in HeLa and Vero cells (Fig. 9A) (
). Overexpression of NHE8 dissipated the acidic pH of the Golgi complex and increased the pH by about 0.78 pH unit to pH 7.28 ± 0.15 (Fig. 9A), indicating that NHE8 mediates proton efflux from the Golgi lumen.
We examined the pH in recycling endosomes using VAMP3-GFP. VAMP3 is a type II integral membrane protein on the recycling endosome (
). The VAMP3-EYFP was localized to punctate structures in the peri-nuclear region and cell periphery of COS7 cells (Fig. 8). Most interestingly, NHE9-ECFP was partially colocalized with VAMP3-EYFP in the peri-nuclear region (Fig. 8), but NHE6-ECFP was not significantly colocalized with VAMP3-EYFP (data not shown). The resting pH in recycling endosomes of COS7 cells was 6.73 ± 0.03, slightly higher than that reported previously (pH 6.2; Refs.
). When NHE9-ECFP was overexpressed in cells, the pH in the recycling endosomes increased 0.41 pH unit to 7.14 ± 0.07 (Fig. 9B). Most interestingly, overexpression of NHE6 did not cause the alkalinization of VAMP3 compartments (pH 6.73 ± 0.01, Fig. 9B), consistent with the differential localization of NHE9 and NHE6 in cells.
In this study, we showed that four types of Na+/H+ exchanger proteins, including the two novel isoforms NHE8 and NHE9, were distributed to intracellular compartments, Golgi complex, and post-Golgi endosomal compartments in human cells. The distribution of these NHEs was isoform-specific, but there was partial overlap among the distributions. This suggests that different NHEs function in particular organelles and regulate the specific compositions of monovalent alkali cations and protons in the Golgi and post-Golgi compartments.
Four Organellar NHE Isoforms in the Human NHE Family—By searching the human genome sequence, we found that the NHE family is composed of nine members that are classified into two groups, NHE1–NHE5 and NHE6–NHE9. The sequence analysis of the entire human genome and EST data base enabled us to identify all members of this protein family; indeed, all NHE isoforms reported previously were found in the data base. Although the overall similarity of amino acid sequences among the NHE isoforms is relatively low (17–67% identity), all the NHE isoforms possess a characteristic secondary structure composed of multiple transmembrane domains at the N terminus and a large hydrophilic domain at the C terminus. Charged amino acid residues in the predicted transmembrane segments are conserved in all members of this family. Although little is known about the specific amino acids involved in the exchanging transport and about the mechanism of operation in mammalian NHEs, mutations in the conserved residues, glutamine 262, glutamine 391, and asparagine-267 (in NHE1), greatly reduced the exchange activity (Fig. 4) (
). These data suggest the importance of the charged residues in ion transport across the membrane and essentially the same molecular mechanism of ion transport mediated by the NHE isoforms. We showed that NHE8 mediates the exchange of H+ for Na+ using the recombinant protein reconstituted in liposomes. Most interestingly, the luminal acidity of the liposome was not fully collapsed by the exchange reaction but appeared to reach an equilibrium at the mildly acidic pH of 6.4 (Fig. 4). These results indicate that NHE8 acts as an ion exchanger on the membrane and also suggest that this protein modulates the acidic pH of the lumen. Further investigations of the pH sensitivity and ion selectivity are now in progress using the in vitro assay and will provide insight into the molecular mechanism of transport and the in vivo function of this protein.
In contrast to the NHE1–NHE5 isoforms, which are known to act on the plasma membrane and which exhibit distinctive patterns of tissue and cell expression in order to fulfill their tissue- and cell-specific functions, NHE6–NHE9 isoforms are ubiquitously and concurrently expressed in single cells. In addition, the yeast endosomal NHE homologue, Nhx1p (
) falls into the NHE6–NHE9 group by phylogenetic analysis (data not shown). From these observations, we hypothesized that NHE6–NHE9 are members of organellar NHEs concurrently acting in the cell and involved in fundamental cellular events. Of the four isoforms, NHE8 is phylogenetically distinct from other organelle NHE isoforms, whereas NHE6, NHE7, and NHE9 show more closely related primary and secondary structures across their entire length. Noteworthy, the C-terminal hydrophilic domain of NHE8 (∼100 amino acid residues) is shorter than those of other NHE isoforms (150–190 amino acid residues) and shows no significant amino acid similarity, suggesting that the function and the regulation of NHE8 are different from other organellar NHE isoforms. The transcript of NHE8 was relatively high in skeletal muscle and kidney, where it is abundant in proximal tubules in the outer medulla and cortex of the kidney, as reported by Goyal et al. (
). This may suggest a specialized function of NHE8 in Golgi apparatus and these tissues.
Isoform-specific Localization of NHEs—Microscopic observations revealed that NHE6–NHE9 isoforms were localized to distinct intracellular compartments. NHE6 was found in early recycling endosomes, NHE7 in the trans-Golgi network, NHE8 in the mid- and trans-Golgi, and NHE9 localized to late recycling endosomes. Most interestingly, the distributions of these isoforms are not discrete in these compartments but partially overlap one another. Post-Golgi compartments are connected by dynamic membrane flow of exocytic and endocytic membrane trafficking (
). The overlapping distribution of the NHE isoforms suggests that they are circulating in the post-Golgi membrane traffic, and the distribution of the isoforms would be maintained by the balance of export from and retention in each compartment. Most interestingly, the amino acid sequence of four regions, the N terminus (aa 1–29 in NHE9), second loop (aa 70–127), and two segments in the C-terminal hydrophilic domain (aa 495–517 and 570–645), are diverged in the NHE6, NHE7, and NHE9 isoforms. Recent topological analyses of plant vacuolar and yeast endosomal Na+/H+ exchangers suggested that the N termini and second loop are exposed to the cytoplasm and that the C-terminal domain resides in the organelle lumen (
). This topological feature implies that the N terminus and the second loop are involved in the localization of the NHEs through recognition by cytoplasmic machinery for vesicular membrane trafficking and that the C-terminal region may act as a regulatory domain for ion transport by sensing the intra-compartment ionic concentration. Further examination will uncover how these isoforms are distinguished and localized to specific compartments.
Role of NHE6–NHE9 Isoforms in Maintaining Organelle Ion Homeostasis and Their Unique Acidity—Previous studies revealed that intracellular compartments are mildly acidified to specific pH values and exhibit a gradient of decreasing pH from ER (pH ∼7.1) to Golgi (pH ∼6.2–7.0), trans-Golgi network (pH ∼6.0), and secretory granules (pH ∼5.0) and from early and late endosomes (pH ∼6.5) to lysosomes (pH ∼4.5) (
). Steady-state pH values of ER, Golgi, and secretory vesicles appeared to be controlled by rates of H+ pumping and by the gradual decrease in organelle H+ permeability from ER to Golgi to secretory vesicles in the secretory pathway, whereas the membrane potential in Golgi and secretory vesicles is small and not perturbed by large changes in Cl- and K+ conductances, indicating that membrane potential is not a determinant of steady-state pH values (
Based on these findings, we hypothesized the role of NHEs in controlling luminal pH through the cation/H+ exchange activity, and examined the organellar pH using pH-dependent GFP mutants. Overexpression of NHE8 and NHE9 caused luminal alkalinization to near cytosolic pH of the compartments in which they reside. This observation suggests that these NHEs effuse luminal H+ in exchange for cytosolic cations. Electroneutral one for one ion exchange driven by the concentration gradients across the membrane equalizes the ratios of inside and outside ion concentrations, i.e. [A+]i/[A+]o = [B+]i/[B+]o. The Golgi luminal [K+] is ∼107 mm, which is only slightly lower than the cytosolic concentration (
). Because of the much higher concentration of K+ than H+, the electroneutral exchange by overexpressed NHEs would dissipate the transmembrane ΔpH of ∼ 0.7 without changing both Golgi and cytosolic k+ concentrations and neutralize the compartment to near the cytosolic pH. This assumption is validated by incubating cells in the presence of nigericin, a K+/H+ ionophore, which caused rapid neutralization of the Golgi pH (data not shown). The protein levels of NHE8 and NHE9 proteins in overexpressing cells were increased by 51 ± 33-fold (55 overexpressing cells, total 150 cells) and 99 ± 83-fold (67 overexpressing cells, total 138 cells), respectively, compared with the endogenous levels under the fluorescence microscope. Further examination such as knock-down experiments would be required to confirm that endogenous NHE8 and NHE9 are involved in the organellar pH regulation. A detailed analysis of the relation between protein levels and luminal pH is currently in progress to provide further insight into the action of NHEs to control the organellar pH.
Recently, a plant vacuolar Na+/H+ exchanger has been suggested to play a role in the regulation of vacuolar pH (
). Vacuolar pH is known to be a main determinant for flower coloration, and a shift from reddish purple buds to blue open flowers correlates with an increase in the vacuolar pH. The vacuolar Na+/H+ exchanger proteins utilize the proton electrochemical gradient generated by the V-ATPase and H+-translocating pyrophosphatase to couple the movement of H+ down its concentration gradient in exchange for cytosolic alkali cation (
). Mutations in the gene encoding the vacuolar Na+/H+ exchanger protein NHX1 causes excessive acidification of vacuolar lumen and, consequently, empurpling of flowers of the Japanese morning glory. The fact that NHX1 confers salt tolerance to plants by sequestrating excess Na+ in the vacuole (
) is consistent with the idea that the vacuolar Na+/H+ exchanger transports luminal H+ out of the vacuole, exchanging it for cytosolic Na+. These observations support our idea that K+/H+ exchange mediates the H+ leak that has been proposed to regulate the luminal pH of intracellular compartments and that specific NHE isoforms present on Golgi and post-Golgi compartments are involved in controlling the unique acidic pH of these compartments. We found no apparent localization of NHE isoforms to lysosomes, which is consistent with the previous observation that rat liver lysosomes have no detectable Na+/H+ exchange activity (
). Lysosomes are the most acidic compartment of the cell, pH ∼4.5, and it may be that the H+ leak mechanism is omitted to accomplish such high acidification, or an alternative mechanism may exist in the lysosomal system.
Further analyses of the organelle NHE isoforms by examining the ion transporting activity, including the ion selectivity and pH dependence in vitro and by interchanging isoforms residing on the compartments in vivo, will uncover the role of NHEs in organelle ion homeostasis and the mechanism of organelle pH regulation in the cell.
Glasgow J. Littlejohn T. Major F. Lathrop R. Sankoff D. Sensen C. Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology. AAAI Press,
Menlo Park, CA1998: 175-182 (June 28–July 1, 1998)