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Vol. 59, Issue 2, 339-348, February 2001
Department of Biopharmaceutical Sciences, School of Pharmacy, University of California, San Francisco, San Francisco, California
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Abstract |
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In this study, we describe the cloning and characterization of a proton-dependent, broadly selective nucleoside transporter from Caenorhabditis elegans. Recently, we constructed a broadly selective nucleoside transporter which accepts both purine and pyrimidine nucleosides. Based on these studies, we hypothesized that CNTs with novel substrate selectivities exist in nature and that a CNT homolog in the C. elegans genomic database may function as a broadly selective nucleoside transporter. We cloned the cDNA for this transporter, termed CeCNT3 because of its broad selectivity, using polymerase chain reaction-based methods. CeCNT3 is predicted to have 575 amino acid residues (63.4 kDa) with 11 to 14 putative transmembrane domains and exhibits ~30% identity to members of the mammalian CNT family. This transporter exhibits a novel substrate selectivity, transporting a wide range of purine and pyrimidine nucleosides (inosine, guanosine, adenosine, uridine, and thymidine) but not cytidine. The apparent Km values for inosine and thymidine are 15.2 ± 5.3 µM and 11.0 ± 2.4 µM, respectively. Kinetic studies demonstrate that purine and pyrimidine nucleosides share a common recognition site in the transporter. In contrast to all known members of the mammalian CNT family, CeCNT3-mediated transport of nucleosides is proton-, but not sodium-, dependent. Mutation of tyrosine 332 in CeCNT3 decreased both the maximum uptake rate and apparent Km of thymidine, suggesting that this residue is in the domain of nucleoside recognition and translocation. The broad nucleoside specificity of CeCNT3 may be explained by this and other residues that restrict purine and pyrimidine nucleoside uptake and that discriminate among pyrimidine nucleosides.
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Introduction |
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Membrane transporters play a key role in determining exposure of a cell or organism to a variety of solutes, including nutrients, cellular by-products, environmental toxins, drugs, and other xenobiotics. A major challenge in transporter biology is to understand the structural basis for substrate recognition. Knowledge of the structural basis for substrate recognition is not only important in understanding the initial steps of transport but is also critical in designing and using drugs because membrane transporters are major determinants of drug response.
During evolution, as organisms have increased in complexity,
transporters have increased in number and diversity of function. Although many studies have compared the sequences of transporters among
organisms and highlighted sequence similarities and differences, this
phylogenetic analysis has been used primarily to establish evolutionary
relationships among transporters. Only a few studies on comparative
functional analysis of transporter homologs have identified critical
amino acids and structural domains involved in substrate recognition
(Barker and Blakely, 1996
; Barker et al., 1998
). Functional comparisons
of transporter homologs among organisms may also aid in understanding
structural elements responsible for other processes such as coupling
mechanisms involved in active transport.
Nucleoside transporters are integral membrane proteins that mediate
both the uptake and release of nucleosides and many synthetic nucleoside analogs across plasma membranes. A major class of nucleoside transporters, concentrative nucleoside transporters (CNTs), mediate the
active intracellular influx of nucleosides by coupling to the sodium or
proton gradients across the plasma membrane (Baldwin et al., 1999
).
Based on substrate selectivity, the concentrative nucleoside
transporters can be divided into two major subtypes (Belt et al.,
1993
). One type (N1 or CNT2) is generally purine selective; the other
type (N2 or CNT1) is generally pyrimidine selective. Genes for both
CNT1 and CNT2 (also termed SPNT) have been cloned from rat and human;
their protein products are predicted to be approximately 65% identical
in amino acid sequence (Crawford et al., 1990
; Dagnino et al., 1991
).
Both types accept uridine and adenosine. Mammalian CNT family members
usually transport nucleosides by coupling to sodium (Che et al., 1995
;
Ritzel et al., 1997
) whereas nucleoside transport systems in bacteria
usually transport nucleosides by coupling to protons (Craig et al.,
1994
).
There is growing evidence to show that nucleoside transporters with
broader substrate selectivities exist in nature. First, in isolated
tissues from several mammalian species, a broadly selective nucleoside
transporter, N3, which accepts both purine and pyrimidine nucleosides,
and N4 and N5, transporters with distinct substrate selectivities, have
been characterized (Wu et al., 1992
, 1994
; Huang et al., 1993
). Second,
by construction of chimeras, we engineered a broadly selective N3-type
nucleoside transporter from rCNT1 and rCNT2 (Wang and Giacomini, 1997
,
1999a
). An N3-like transporter was also created by changing a single
amino acid at position 318 of rCNT1 (Wang and Giacomini, 1999b
).
Recently, a nucleoside transporter with broad selectivity has been
cloned from hagfish (GenBank accession number AF132298).
The free-living nematode Caenorhabditis elegans is a simple
model system to study a variety of complex biological problems. Based
on its genome sequence (Anonymous, 1998
), many transporters in C. elegans have been cloned and characterized, including transporters for dopamine (Jayanthi et al., 1998
), glutamate (Kawano et al., 1996
),
phosphate (Lee et al., 1999
), organic anions and cations (George et
al., 1999
; Wu et al., 1999
), monoamines (Duerr et al., 1999
) and
oligopeptides (Fei et al., 1998
). Functional studies of these
transporters show that, in C. elegans, some transporters are
sodium-dependent (Jayanthi et al., 1998
; Lee et al., 1999
) whereas some
others are proton-dependent (Fei et al., 1998
; Duerr et al., 1999
; Wu
et al., 1999
).
Based on the gene F27E11, two CNT transporters were predicted to exist in C. elegans. After multiple sequence alignments and examination of critical amino acids involved in substrate recognition, we hypothesized that one of CNT homologs encoded by gene F27E11 may function as a broadly selective nucleoside transporter. We cloned the cDNA for this transporter, termed CeCNT3, and determined its functional characteristics. CeCNT3 exhibited novel characteristics in terms of both its driving force and selectivity. Namely, unlike CNT transporters in mammals, CeCNT3 was sensitive to proton gradients but not to sodium gradients. The transporter was selective for both naturally occurring purine and pyrimidine nucleosides except for cytidine. These unique functional characteristics permit us to pursue a better understanding of the amino acid residues involved in both substrate recognition and driving forces of the transporters in the CNT family and shed light on the evolution of functional domains in this major family of transporters.
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Materials and Methods |
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RNA Isolation and cDNA Preparation. Total RNA was isolated from C. elegans (strain N2) with Trizol reagent (Life Technologies) according to the manufacturer's protocol, then was taken as the template to synthesize cDNA by reverse transcribed polymerase chain reaction (reverse transcription-PCR) using oligo(dT) primer (Life Technologies). CeCNT3 was then amplified by nested PCR technique using the cDNA as template. These primers were designed specially to amplify the potential nucleoside transporter coded by the genomic sequence in the F27E11.2 locus (GenBank accession number AF016413). The first pair of primers were 5'-ttagaggatccgcggtgccgaccaatca-3' (sense), 5'-aatttttatacaatagaataatatatgtac-3' (antisense). The second pair of primers were 5'-cgaccaatcagcgatgcgc aatgggcgtgg-3' (sense), 5'-aaaaactttgaatttatccgctaggaatccgg-3' (antisense). PCR was performed with the following conditions: 94°C for 5 min; 30 cycles of 94°C for 1 min, 62°C for 2 min, and 72°C for 2 min. The reaction was then extended by incubation at 72°C for an additional 15 min. A PCR product of 1.8 kilobases (encoding CeCNT3) was obtained, subcloned into the pGEM-T vector (Promega, Madison, WI) and sequenced at the Biomolecular Resource Center at the University of California, San Francisco.
Sequence Analysis. Multiple alignment and motif prediction were carried out using the Genetics Computer Group (GCG) software package (Wisconsin Package, Version 9, Madison, WI). Hydropathy analysis was performed using DNA Strider (Version 1.2). BLAST network at the National Center for Biotechnology Information was used in database searching.
Expression and Transport Assay in Xenopus Laevis
Oocytes.
To obtain higher expression, CeCNT3 was subcloned into
vector pOX (a gift from Andrew T. Gray, University of California, San Francisco), which contains the 5' and 3' untranslated regions of the
X. laevis
-globin gene flanking the insert (Jegla and Salkoff, 1997
; Chavez et al., 1999
). CeCNT3 cRNA was synthesized using
T3 polymerase (Stratagene, La Jolla, CA) following the manufacturer's protocol. Oocytes were harvested and treated as described previously (Wang et al., 1997
). The cRNA (50 nl; ~0.4 ng/nl) or water was injected individually into defolliculated oocytes. Oocytes were incubated at 18°C for 30 to 40 h and then the uptake assays were performed in 100 µl of transport buffer [2 mM KCl, 1 mM
CaCl2, 10 mM HEPES, or 10 mM
2-(N-morpholino)ethanesulfonic acid (MES)] containing
different concentrations of 3H-labeled
nucleosides (Moravek Biochemicals, Brea, CA). To test the effect of
sodium-gradient on the activity of CeCNT3, uptake assays were carried
out in transport buffer containing 0 to 100 mM NaCl with choline
chloride to maintain the iso-osmolality. In experiments testing the
effect of proton-gradient on the activity of CeCNT3, oocytes were
preincubated in choline buffer at pH 7.4 and then transferred to
transport buffers with pH ranging from 5.0 to 8.0. To study the effects
of FCCP, a proton ionophore, on the activity of CeCNT3, oocytes were
preincubated in choline buffer (pH 8.0, no FCCP) for 3 h. Oocytes
were then incubated in choline buffer (pH 5.5 or 8.0, with or without 5 µM FCCP) for 0, 30, and 60 min, and the uptake of thymidine or
inosine was measured in sodium buffer at pH 5.5 and pH 8.0. In the pH
range of 5.0 to 6.5, 10 mM MES was used in the uptake buffer; 10 mM HEPES was used in the pH range of 7.0 to 8.0. In inhibition studies, chemicals at tested concentrations were added to the uptake buffer individually. After 30 min of incubation at 25°C, oocytes were washed
five times in 3 ml of ice-cold choline buffer and lysed individually in
10% SDS. The amount of radiolabeled nucleoside transported into each
oocyte was determined by liquid scintillation counting. Most studies
were carried out in transport buffer containing 100 mM NaCl, pH 6.5. A
pH of 6.5 was selected because preliminary studies suggest that uptake
of nucleosides was high at pH 6.5 and that this pH did not destroy the
viability of the oocytes.
Site-Directed Mutagenesis. Single (tyrosine 332 to phenylalanine, Y332F) and double (threonine 327 to serine and valine 328 to leucine, T327S/V328L) mutations were constructed with QuickChange Site-directed Mutagenesis Kit (Stratagene), using wild-type CeCNT3 cDNA as the template. The sequences of Y332F and T327S/V328L mutants were confirmed by DNA sequencing at the Biomolecular Resource Center at the University of California, San Francisco. Expression and transport assays of Y332F and T327S/V328L mutants were the same as described above for wild-type CeCNT3.
Statistics and Data Analysis. Groups of 8 to 10 cRNA-injected or water-injected oocytes were used for each experiment. Uptake values are expressed as mean ± S.E. For kinetic studies of CeCNT3, uptake rates (V) determined at different substrate concentrations (S) were fit to the Michaelis-Menten equation: V = Vmax × S/(Km + S) + Kd × S, where Vmax is the maximal uptake rate, Km is the Michaelis-Menten constant (the substrate concentration at Vmax/2), and Kd is the nonsaturable first-order rate constant. Fits were carried out using a nonlinear least-squares regression-fitting program (Kaleidagraph v. 3.0; Abelbeck/Synergy Software, Reading, PA). Kinetic experiments were repeated several times in different batches of oocytes; data for one representative experiment are presented in this study. For inhibition study, statistical analysis was carried out by comparing the uptakes from tested compounds with the uptake from controls in the same experiments using a two-tailed, two-sample equal variance t test. Results with the probability of p < 0.05 were considered significantly different.
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Results |
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Nucleotide and the Deduced Amino Acid Sequences of CeCNT3.
A
BLAST search of the C. elegans genome database with the cDNA
sequence of rCNT1 revealed only two homologs of the CNT family. These
two transporters are encoded by the genes, F27E11.1 and F27E11.2. We
cloned the full-length cDNA of both homologs, using primers designed to
anneal to the 5' and 3' ends of the predicted exons (GenBank accession
number AF016413). Because the activity of the transporter encoded by
F27E11.1 was low and we could not make any conclusions about its
selectivity, we focused on the other transporter, CeCNT3 (encoded by
gene F27E11.2) in this study. The nucleotide sequence and deduced amino
acid sequences of CeCNT3 were deposited in GenBank with accession no.
AF162674. As shown in Fig. 1A, the cDNA
is 1826 bp long with an open reading frame of 1728 bp (including the
termination codon). Because there is an in-frame stop codon upstream of
the ATG and because the cloned transporter was functional, we concluded
that the entire open reading frame was obtained. The sequence predicts
a protein of 575 amino acid residues with a molecular mass of
63.4 kDa. Two fragments (158 bp and 48 bp) in the 5' region of the cDNA
(GenBank accession number AF016413) predicted from the genomic sequence are absent from our cloned CeCNT3 cDNA, suggesting that either these
two fragments were mistakenly predicted as exons or that there is
alternative splicing. The initiation codon of CeCNT3 is preceded by a
consensus Kozak sequence (A/GXXATG) (Kozak, 1986
). Using Kyte-Doolittle
(1982)
hydropathy analysis, CeCNT3 is predicted to have 11 to 14 transmembrane domains (TMD) (Fig. 1B). The 14 putative TMDs are
highlighted (Fig. 1A). Multiple alignments show that, at the amino acid
sequence level, this transporter is related to mammalian CNTs (~30%
identity) (Fig. 2A) (Huang et al., 1994
; Che et al., 1995
; Ritzel et al., 1997
; Wang et al., 1997
) and bacterial
CNTs (~14-24% identity) (data not shown) (Craig et al., 1994
;
Fleischmann et al., 1995
; Kunst et al., 1997
; Tomb et al., 1997
), but
is not related to the equilibrative nucleoside transporter family (data
not shown). We also compared the identity of the amino acid residues in
the regions that have been found to be important in determining the
purine and pyrimidine selectivity of hCNT and rCNT (Wang and Giacomini,
1997
, 1999b
; Loewen et al., 1999
). In this particular region, CeCNT3
shows ~44% identity to hCNT2 and rCNT2 and ~33% identity to hCNT1
and rCNT1 (Fig. 2B). The most divergent regions between CeCNT3 and
mammalian CNT are in the N-terminal and C-terminal domains. There are
three putative N-linked glycosylation sites (Asn-171, Asn-506, and
Asn-546) and five potential protein kinase C phosphorylation sites
(Thr-25, Thr-98, Ser-123, Ser-523, and Ser-563). The presence of
presumptive protein kinase C sites suggests that CeCNT3 may be
regulated by phosphorylation.
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Substrate Selectivity of CeCNT3.
Functional studies of CeCNT3
were carried out using naturally occurring nucleosides. Oocytes
injected with CeCNT3 cRNA were incubated in transport buffer containing
10 µM 3H-labeled nucleosides for 30 min.
Initial studies established that the uptake of both thymidine and
inosine was linear with time up to 3 h (Fig.
3). A 30-min time point was selected for further kinetic studies. Compared with control oocytes
(water-injected), the uptake of inosine, thymidine, uridine, guanosine,
and adenosine was significantly increased (20 to 30 fold) (Fig.
4). In contrast, the uptake of cytidine
was not increased significantly. These data indicate that CeCNT3
exhibits a unique substrate selectivity, transporting inosine,
thymidine, uridine, adenosine and guanosine, but not cytidine.
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Inhibition Profile of Nucleoside Transport.
To further
determine the characteristics of CeCNT3, we examined the inhibitory
effects of naturally occurring nucleosides (inosine, thymidine,
uridine, guanosine, adenosine, and cytidine), nucleobases
(hypoxanthine, thymine), ribose, thymidine monophosphate (5'TMP) and
nitrobenzylthioinosine (NBMPR) on CeCNT3-mediated transport of inosine
and thymidine. We observed that all of the naturally occurring
nucleosides, except cytidine, significantly inhibited the transport of
both inosine and thymidine (Fig. 5A, 5B).
Although cytidine significantly inhibited the transport of thymidine
(p < 0.05), the inhibitory effect was much lower than that of other naturally occurring nucleosides.
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Kinetic Studies of CeCNT3.
CeCNT3-mediated transport of
inosine and thymidine was saturable, with apparent
Km values of 15.2 ± 5.3 µM and
11.0 ± 2.4 µM, respectively. The apparent
Vmax values of inosine and thymidine were
3.20 ± 0.50 pmol/oocyte/30 min and 3.85 ± 2.88 pmol/oocyte/30 min, respectively (Table
1). Although differences in the kinetics of inosine and thymidine transport were observed between batches of
oocytes, within the same batch of oocytes, the apparent
Km value of thymidine was always lower than
that of inosine; at the same (nonsaturating) concentration, thymidine
was always transported at greater rate than inosine.
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Effects of Sodium-Gradient and Proton-Gradient on the Activity of
CeCNT3.
In initial studies, we observed that CeCNT3-mediated
transport of inosine into oocytes functioned well in media at pH 7.4 containing either 100 mM NaCl or 100 mM choline chloride, with uptake
rates of 6.74 ± 0.56 and 6.33 ± 0.69 pmol/oocyte/30 min, respectively, indicating that transport was not dependent on sodium. No
stimulatory effect of sodium up to concentrations of 100 mM on the
activity of CeCNT3 was observed (Fig.
7A).
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Site-Directed Mutagenesis.
Multiple alignments of the amino
acid sequence of CeCNT3 with hCNT and rCNT in the region (between amino
acids 275 and 335 of CeCNT3) shown previously to be critical in
substrate recognition and binding (Wang and Giacomini, 1997
, 1999b
;
Loewen et al., 1999
) were performed. These alignments show that, of the
nine conserved residues in this particular region, CeCNT3 has seven
residues identical with those of hCNT2 and rCNT2 (except the tyrosine
at 332, which is identical with hCNT1 and rCNT1) (Fig. 2B). Because CeCNT3 transports not only purine nucleosides but also thymidine, we
hypothesized that the tyrosine at position 332 of CeCNT3 may facilitate
the recognition and subsequent transport of thymidine as well as other
nucleosides. We mutated this residue to the equivalent residue,
phenylalanine, in CNT2. Compared with that of the wild-type transporter, the uptake of thymidine mediated by Y332F mutant was
decreased (Fig. 9A). At equivalent
concentrations, thymidine is the nucleoside transported most rapidly by
the wild-type transporter (Fig. 4); however, it is the nucleoside
transported most slowly by the Y332F mutant. Kinetic studies revealed
that the Km value of thymidine is increased
from 11.4 ± 2.1 µM to 31.7 ± 5.5 µM (Fig. 9B). Further
studies demonstrated that the Km value of
inosine was also increased (Table 2), suggesting that the tyrosine in this position is indeed involved in nucleoside recognition.
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Discussion |
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We report here the cloning of a cDNA from C. elegans coding for a novel member, CeCNT3, of the concentrative nucleoside transporter family. We demonstrate that CeCNT3 has unique functional characteristics.
CeCNT3 has a unique substrate selectivity compared with other concentrative nucleoside transporters. In particular, in contrast to the cloned purine (CNT2 or SPNT) and pyrimidine (CNT1) selective transporters, CeCNT3 transports all naturally occurring nucleosides tested with the exception of cytidine (Fig. 4). Based upon the competitive interaction between thymidine and inosine (Fig. 6), our data suggest that there is a single recognition site in CeCNT3 for both purine and pyrimidine nucleosides. Thus, the molecular basis for broad selectivity resides in a single permeation pathway rather than multiple pathways.
Molecular Determinants of Substrate Discrimination. CeCNT3 is ~30% identical with mammalian CNTs (hCNT and rCNT) (Fig. 2A). Like hCNT and rCNT, it also has 11 to 14 putative transmembrane domains (Fig. 1). CeCNT3 thus has the overall structural features of a concentrative nucleoside transporter.
To understand the structural basis for the unique substrate selectivity of CeCNT3, it is of interest to compare its amino acid sequence with that of the CNT1 (pyrimidine-selective) and CNT2 (purine-selective) transporters. Of particular interest are residues that differ between the CNT1 and CNT2 transporters, which may therefore be responsible for substrate selectivity. Twenty-two amino acid residues of CeCNT3 are identical with the two purine-selective transporters, rCNT2 and hCNT2, but not with the two pyrimidine-selective transporters, rCNT1 and hCNT1. Similarly, 23 amino acid residues of CeCNT3 are identical with the pyrimidine-selective transporters but not the purine-selective transporters. Thus, CeCNT3 is not strikingly more similar to either type of transporter. A bias toward CNT2 is seen in one region (positions 275-335; see below). Previously, we and others identified amino acid residues of the concentrative nucleoside transporters that are involved in substrate discrimination (Wang and Giacomini, 1997Proton Dependence.
Another unique characteristic of CeCNT3 is
that in contrast to mammalian transporters in the CNT family,
nucleoside transport is dependent on the proton gradient, but not on
the sodium gradient (Figs. 7 and 8). Concentrative transporters use
ion-coupled electrochemical energy stored in a transmembrane gradient
to actively transport substrates into or out of cells. In bacteria as
well as in plants, a proton is the preferred coupling ion and the
proton gradient is maintained by
H+/K+-ATPase. In
vertebrates, sodium is the preferred coupling ion of many coupled
transporters because of the evolutionary substitution of
H+/K+-ATPase by
Na+/K+-ATPase in animal
cells (Hediger, 1994
; Nelson, 1994
). To date, only a few mammalian
plasma membrane transporters (e.g., the oligopeptide transporters,
PepT1 and PepT2) have been described that use protons as the coupling
ion (Fei et al., 1994
; Leibach and Ganapathy, 1996
). In the case of
ion-coupled (also known as concentrative) nucleoside transporters, the
NupC family, in bacteria such as Escherichia coli, Bacillus
subtilis, and Helicobacter pylori, consists of
several proton-coupled nucleoside transporters (Craig et al., 1994
). In
contrast, all documented concentrative nucleoside transporters in
vertebrates are sodium-dependent (Crawford et al., 1990
; Dagnino et
al., 1991
; Wu et al., 1992
, 1994
; Huang et al., 1993
, 1994
; Che et al.,
1995
; Wang et al., 1997
).
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Acknowledgments |
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We thank Dr. David Byrd for providing C. elegans, Dr. Ira Herskowitz for reviewing this manuscript, and Mark Dresser for his helpful suggestions and discussions.
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Footnotes |
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Received May 11, 2000; Accepted October 18, 2000
This study was supported by National Institutes of Health Grant GM42230.
Send reprint requests to: Kathleen M. Giacomini, Ph.D., Department of Biopharmaceutical Sciences, Box 0446, University of California, San Francisco, California. E-mail: kmg{at}itsa.ucsf.edu
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Abbreviations |
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CNT, concentrative nucleoside transporter; rCNT, rat concentrative nucleoside transporter; PCR, polymerase chain reaction; MES, 2-(N-morpholino)-ethanesulfonic acid; bp, base pair(s); TMD, transmembrane domain; hCNT, human concentrative nucleoside transporter; 5'TMP, thymidine monophosphate; NBMPR, nitrobenzylthioinosine; FCCP, carbonyl cyanide p-trifluoromethoxyphenylhydrazone.
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