Biology of membrane transport proteins

Enhanced identification of membrane transport proteins: a hybrid approach combining ProtBERT-BFD and convolutional neural networks

Transmembrane transport proteins (transporters) play a crucial role in the fundamental cellular processes of all organisms by facilitating the transport of hydrophilic substrates across hydrophobic membranes. Despite the availability of numerous membrane protein sequences, their structures and functions remain largely elusive. Recently, natural language processing (NLP) techniques have shown promise in the analysis of protein sequences. Bidirectional Encoder Representations from Transformers (BERT) is an NLP technique adapted for proteins to learn contextual embeddings of individual amino acids within a protein sequence. Our previous strategy, TooT-BERT-T, differentiated transporters from non-transporters by employing a logistic regression classifier with fine-tuned representations from ProtBERT-BFD. In this study, we expand upon this approach by utilizing representations from ProtBERT, ProtBERT-BFD, and MembraneBERT in combination with classical classifiers. Additionally, we introduce TooT-BERT-CNN-T, a novel method that fine-tunes ProtBERT-BFD and discriminates transporters using a Convolutional Neural Network (CNN). Our experimental results reveal that CNN surpasses traditional classifiers in discriminating transporters from non-transporters, achieving an MCC of 0.89 and an accuracy of 95.1 % on the independent test set. This represents an improvement of 0.03 and 1.11 percentage points compared to TooT-BERT-T, respectively.

Modulation of antimicrobial efflux pumps of the major facilitator superfamily in Staphylococcus aureus

Variants of the microorganism Staphylococcus aureus which are resistant to antimicrobial agents exist as causative agents of serious infectious disease and constitute a considerable public health concern. One of the main antimicrobial resistance mechanisms harbored by S. aureus pathogens is exemplified by integral membrane transport systems that actively remove antimicrobial agents from bacteria where the cytoplasmic drug targets reside, thus allowing the bacteria to survive and grow. An important class of solute transporter proteins, called the major facilitator superfamily, includes related and homologous passive and secondary active transport systems, many of which are antimicrobial efflux pumps. Transporters of the major facilitator superfamily, which confer antimicrobial efflux and bacterial resistance in S. aureus, are good targets for development of resistance-modifying agents, such as efflux pump inhibition. Such modulatory action upon these antimicrobial efflux systems of the major facilitator superfamily in S. aureus may circumvent resistance and restore the clinical efficacy of therapy towards S. aureus infection.

Transporters in absorption, distribution, and elimination

During the past decades, pharmacokinetics has been defined as the study of drug absorption, distribution, metabolism, and excretion (ADME), when the drug is introduced into a biological system, such as the human body. Pharmacokinetics is now challenged by the growing importance of transporters, a relatively new and potentially major factor in drug ADME. The recent intrusion of drug transporters means that there is no single mechanism by which drugs permeate through membranes. The presence of transporters in membranes modulates the traditional theory of 'diffusional pharmacokinetics' towards 'vectorial pharmacokinetics' in which ADME processes are governed more deterministically. Drug transporters are also clinically important. They can modulate the pharmacological activity of drugs by affecting their intracellular concentrations and causing toxicity in specific organs due to intracellular drug accumulation. Finally, they are key players in drug-drug interactions, where they are as important as the drug metabolizing enzymes.

Membrane transporters and drug development: relevance to pharmacogenomics, nutrigenomics, epigenetics, and systems biology

The study of membrane transporters may result in breakthroughs in the discovery of new drugs and the development of safer drugs. Membrane transporters are essential for fundamental cellular functions and normal physiological processes. These molecules influence drug absorption and distribution and play key roles in drug therapeutic effects. A primary goal of current research in drug discovery and development is to fully understand the interactions between transporters and drugs at both the system levels in the human body and the individual level for personalized therapy. Systematic studies of membrane transporters will help in not only better understanding of diseases from the systems biology point of view but also better drug design and development. The exploration of both pharmacogenomics and systems biology in transporters is necessary to connect individuals' genetic profiles with systematic drug responses in the human body. Understanding of gene-diet interactions and the effects of epigenetic changes on transporter gene expression may help improve clinical drug efficacy. The integration of pharmacogenomics, nutrigenomics, epigenetics, and systems biology may enable us to move from disease treatment to disease prevention and optimal health. The key issues in such integrative understanding include the correlations between structure and function, genotype and phenotype, and systematic interactions among transporters, other proteins, nutrients, drugs, and the environment. The exploration in these key issues may ultimately contribute to personalized medicine with high efficacy but less toxicity.

Simulations of the nonlinear dose dependence for substrates of influx and efflux transporters in the human intestine

The purpose of this study was to develop simulation and modeling methods for the evaluation of pharmacokinetics when intestinal influx and efflux transporters are involved in gastrointestinal absorption. The advanced compartmental absorption and transit (ACAT) model as part of the computer program GastroPlus was used to simulate the absorption and pharmacokinetics of valacyclovir, gabapentin, and talinolol. Each of these drugs is a substrate for an influx or efflux transporter and all show nonlinear dose dependence within the normal therapeutic range. These simulations incorporated the experimentally derived gastrointestinal distributions of transporter expression levels for oligopeptide transporters PepT1 and HPT1 (valacyclovir); System L-amino acid transporter LAT2 and organic cation transporter OCTN1 (gabapentin); and organic anion transporter (OATP1A2) and P-glycoprotein (talinolol). By assuming a uniform distribution of oligopeptide transporter and by application of the in vitro K(m) value for valacyclovir, the simulations accurately reproduced the experimental nonlinear dose dependence. For gabapentin, LAT2 distribution produced simulation results that were much more accurate than OCTN1 distributions. For talinolol, an influx transporter distribution for OATP1A2 and the efflux transporter P-glycoprotein distributed with increasing expression in the distal small intestine produced the best results. The physiological characteristics of the small and large intestines used in the ACAT model were able to accurately account for the positional and temporal changes in concentration and carrier-mediated transport of the three drugs included in this study. The ACAT model reproduced the nonlinear dose dependence for each of these drugs.

A nitrite transporter associated with nitrite uptake by higher plant chloroplasts

Chloroplasts take up cytosolic nitrite during nitrate assimilation. In this study we identified a nitrite transporter located in the chloroplasts of higher plants. The transporter, CsNitr1-L, a member of the proton-dependent oligopeptide transporter (POT) family, was detected during light-induced chloroplast development in de-etiolating cucumber seedlings. We detected a CsNitr1-L-green fluorescent protein (GFP) fusion protein in the chloroplasts of leaf cells and found that an immunoreactive 51 kDa protein was present in the isolated inner envelope membrane of chloroplasts. CsNitr1-L has an isoform, CsNitr1-S, with an identical 484 amino acid core sequence; however, in CsNitr1-S the 120 amino acid N-terminal extension is missing. Saccharomyces cerevisiae cells expressing CsNitr1-S absorbed nitrite from an acidic medium at a slower rate than mock-transformed control cells, and accumulated nitrite to only one-sixth the concentration of the control cells, suggesting that CsNitr1-S enhances the efflux of nitrite from the cell. Insertion of T-DNA in a single CsNitr1-L homolog (At1g68570) in Arabidopsis resulted in nitrite accumulation in leaves to more than five times the concentration found in the wild type. These results show that it is possible that both CsNitr1-L and CsNitr1-S encode efflux-type nitrite transporters, but with different subcellular localizations. CsNitr1-L may possibly load cytosolic nitrite into chloroplast stroma in the chloroplast envelope during nitrate assimilation. The presence of genes homologous to CsNitr1-L in the genomes of Arabidopsis and rice indicates that facilitated nitrite transport is of general physiological importance in plant nutrition.

Identification of a cerulenin resistance gene from Monascus pilosus

Detoxification is essential for the fungal growth in the drug stress environments, and the multidrug transporters play an important role in this process. Here a cerulenin transporter gene (MpMdt, AB206476) was identified from Monascus pilosus. MpMdt mRNA contains 1951 bp and encodes a protein of 559 amino acid residues with 11 trans-membrane domains; and there is no difference in the sequence of MpMdt mRNA between the wild type M. pilosus IFO4520 and its cerulenin resistant mutant MK-1. Up-expression of MpMdt renders the cerulenin resistance of the mutant MK-1. Over-expression of MpMdt could also increase the cerulenin tolerance in the transgenic M. pilosus IFO4520. These results suggested that MpMdt is able to efflux-transport the anti-fungal antibiotic cerulenin and increase the cerulenin resistance of M. pilosus.

Predicting functional sites in proteins: site-specific evolutionary models and their application to neurotransmitter transporters

Currently there exist several computational methods for predicting the functional sites in a set of homologous proteins based on their sequences. Due to difficulties in defining the functional site in a protein, it is not trivial to compare the performance of these methods, evaluate their limitations and quantify improvements by new approaches. Here, we use extensive mutation data from two proteins, Lac repressor and subtilisin, to perform such an analysis. Along with the evaluation of existing approaches, we describe a site class model of evolution as a tool to predict functional sites in proteins. The results indicate that this model, which simulates the evolution process at the amino acid level using site-specific substitution matrices, provides the most accurate information on functional sites in a given protein family. Secondly, we present an application of this model to neurotransmitter transporters, a superfamily of proteins of which we have limited experimental knowledge. Based on this application we present testable hypotheses regarding the mechanism of action of these proteins.

Molecular biology and regulation of nucleoside and nucleobase transporter proteins in eukaryotes and prokaryotes

The molecular cloning of cDNAs encoding nucleoside transporter proteins has greatly advanced understanding of how nucleoside permeants are translocated across cell membranes. The nucleoside transporter proteins identified thus far have been categorized into five distinct superfamilies. Two of these superfamilies, the equilibrative and concentrative nucleoside transporters, have human members and these will be examined in depth in this review. The human equilibrative nucleoside transporters translocate nucleosides and nucleobases bidirectionally down their concentration gradients and are important in the uptake of anticancer and antiviral nucleoside drugs. The human concentrative nucleoside transporters cotranslocate nucleosides and sodium unidirectionally against the nucleoside concentration gradients and play a vital role in certain tissues. The regulation of nucleoside and nucleobase transporters is being studied more intensely now that more tools are available. This review provides an overview of recent advances in the molecular biology and regulation of the nucleoside and nucleobase transporters.

Monitoring intracellular pH changes in response to osmotic stress and membrane transport activity using 5-chloromethylfluorescein

Intracellular free H+ concentration (pHi) responds to numerous extracellular stimuli. The use of fluorescent indicator dyes to measure pHi is strongly influenced by the ability of target cells to retain activated dye within the cytoplasmic compartment. Here, 3 pH-sensitive indicator dye - acetoxymethyl (AM) esters of SNARF-1 and BCECF, and the thiol-reactive 5-chloromethyfluorescein (CMFDA) - were examined for monitoring pHi. The stability of pH measurements was strongly affected by temperature, cell type, indicator dye, and use of transport inhibitors to prevent dye export. Cellular retention of CMFDA, which forms covalent complexes, was sufficient to permit monitoring of transient pHi changes over extended time periods in a multi-well plate assay format. In human embryonic kidney (HEK293) and Chinese hamster ovary (CHO) cells, increasing osmotic pressure caused a significant rise in pHi. In contrast, activation of native or transfected beta-adrenergic, cholinergic, and d and m opioid receptors did not measurably affect pHi in HEK293 cells. Decreases in pHi were observed in CHO cells expressing the human H+/peptide transporter PEPT1 upon addition of dipeptide substrates. The use of CMFDA in multi-well formats should facilitate study of osmotic and transport activity and screening for drugs that affect pHi.

A mechanistic approach to understanding the factors affecting drug absorption: a review of fundamentals

This article provides an overview of the patient-specific and drug-specific variables that can affect drug absorption following oral product administration. The oral absorption of any chemical entity reflects a complex spectrum of events. Factors influencing product bioavailability include drug solubility, permeability, and the rate of in vivo dissolution. In this regard, the Biopharmaceutics Classification System has proven to be an important tool for predicting compounds likely to be associated with bioavailability problems. It also helps in identifying those factors that may alter the rate and extent of drug absorption. Product bioavailability can also be markedly influenced by patient attributes such as the integrity of the gastrointestinal tract, physiological status, site of drug absorption, membrane transporters, presystemic drug metabolism (intrinsic variables), and extrinsic variables such as the effect of food or concomitant medication. Through an awareness of a drug's physicochemical properties and the physiological processes affecting drug absorption, the skilled pharmaceutical scientist can develop formulations that will maximize product availability. By appreciating the potential impact of patient physiological status, phenotype, age, gender, and lifestyle, dosing regimens can be tailored to better meet the needs of the individual patient.

Multiple interactions of cimetidine and probenecid with valaciclovir and its metabolite acyclovir

The effects of probenecid and cimetidine on the pharmacokinetics of valaciclovir and its metabolite acyclovir have been investigated. Twelve healthy male volunteers participated in this open single-dose study with a four-way-crossover randomized and balanced design. At the first of four administrations, volunteers in four groups received 1 g of valaciclovir alone, valaciclovir with 1 g of probenecid, valaciclovir with 800 mg of cimetidine, or valaciclovir with a combination of probenecid and cimetidine. At three subsequent administrations, drug regimens were alternated among groups so that each group received each regimen. Probenecid and cimetidine increased the mean maximum concentrations in serum (C(max)) of valaciclovir by 23 and 53% and the areas under the concentration-time curves (AUC) for valaciclovir by 22 and 73%, respectively; probenecid and cimetidine also increased the mean acyclovir C(max) by 22 and 8% and its AUC by 48 and 27%, respectively. The combination had a greater effect than either drug alone. Their effects may be due to competitive inhibition of membrane transport of valaciclovir and acyclovir in the liver and kidney. Neither cimetidine nor probenecid affected the absorption of valaciclovir. Both probe drugs reduced the rate of valaciclovir metabolism but not its extent. These pharmacokinetic modifications did not affect the tolerability of valaciclovir.

Predicting the impact of physiological and biochemical processes on oral drug bioavailability

Recent advances in computational methods applied to the fields of drug delivery and biopharmaceutics will be reviewed with a focus on prediction of the impact of physiological and biochemical factors on simulation of gastrointestinal absorption and bioavailability. Our application of a gastrointestinal simulation for the prediction of oral drug absorption and bioavailability will be described. First, we collected literature data or we estimated biopharmaceutical properties by application of statistical methods to a set of 2D and 3D molecular descriptors. Second, we integrated the differential equations for an advanced compartmental absorption and transit (ACAT) model in order to determine the rate, extent, and approximate gastrointestinal location of drug liberation (for controlled release), dissolution, passive and carrier-mediated absorption, and saturable metabolism and efflux. We predict fraction absorbed, bioavailability, and C(p) vs. time profiles for common drugs and compare those estimates to literature data. We illustrate the simulated impact of physiological and biochemical processes on oral drug bioavailability.

Drug inhibition of Gly-Sar uptake and hPepT1 localization using hPepT1-GFP fusion protein

An hPepT1-GFP fusion construct was made to study drug inhibition of dipeptide uptake and apical, basolateral, or subcellular hPepT1 localization. The hPepT1 stop codon was mutated by polymerase chain reaction and was subsequently cloned into the pEGFP-N1 vector. The hPepT1-GFP fusion construct was then transfected into Caco-2 and HeLa cells, and drug inhibition was studied by inhibiting 3H-Gly-Sar uptake. Western blot analysis was used to determine hPepT1-GFP expression levels and confocal microscopy was used to examine the localization. Both anti-hPepT1 antibody and anti-GFP antibody recognized a 120-kd hPepT1-GFP fusion protein in the transfected cells. The 3H-Gly-Sar uptake in transfected HeLa cells was enhanced more than 20 times compared with the control. Valacyclovir (5 mmol/L) was able to completely inhibit 3H-Gly-Sar uptake in these transfected cells. Confocal microscopy showed that the hPepT1-GFP mainly localized in the Caco-2 cell apical membrane, but was present throughout the entire HeLa cell membranes. The hPepT1-GFP fusion protein was not found in either early endosome or lysosome of Caco-2 cells under normal conditions; however, it was detected in some subsets of lysosomes and early endosomes in phorbol 12-myristate 13-acetate (PMA)-treated Caco-2 cells.

Genomic structure of proton-coupled oligopeptide transporter hPEPT1 and pH-sensing regulatory splice variant

Proton-coupled oligopeptide transporter PEPT1 facilitates the transport of dipeptides and peptoid drugs (including antibiotics) across the cell membranes of endothelial and epithelial cells. Substrate transport by the proton symport is driven by pH gradients, while the profile of pH sensitivity is regulated by a closely related protein, hPEPT1-RF. We investigated the genomic structure of hPEPT1 and hPEPT1-RF. Analysis of the high-throughput genomic sequence (HTGS) database revealed that hPEPT1 and hPEPT1-RF are splice variants encoded by the same gene located in chromosome 13, consisting of 24 exons. hPEPT1 is encoded by 23 exons and hPEPT1-RF by 6 exons. Coding sequences of hPEPT1-RF share 3 exons completely and 2 exons partially with hPEPT1. The genomic organization of hPEPT1 shows high similarity with its mouse orthologue. Exon-intron boundaries occur mostly in the loops connecting transmembrane segments (TMSs), suggesting a modular gene structure reflecting the TMS-loop repeat units in hPEPT1. The putative promoter region of hPEPT1 contains TATA boxes and GC-rich regions and a potential insulin responsive element.

Human membrane transporter database: a Web-accessible relational database for drug transport studies and pharmacogenomics

The human genome contains numerous genes that encode membrane transporters and related proteins. For drug discovery, development, and targeting, one needs to know which transporters play a role in drug disposition and effects. Moreover, genetic polymorphisms in human membrane transporters may contribute to interindividual differences in the response to drugs. Pharmacogenetics, and, on a genome-wide basis, pharmacogenomics, address the effect of genetic variants on an individual's response to drugs and xenobiotics. However, our knowledge of the relevant transporters is limited at present. To facilitate the study of drug transporters on a broad scale, including the use of microarray technology, we have constructed a human membrane transporter database (HMTD). Even though it is still largely incomplete, the database contains information on more than 250 human membrane transporters, such as sequence, gene family, structure, function, substrate, tissue distribution, and genetic disorders associated with transporter polymorphisms. Readers are invited to submit additional data. Implemented as a relational database, HMTD supports complex biological queries. Accessible through a Web browser user interface via Common Gateway Interface (CGI) and Java Database Connection (JDBC), HMTD also provides useful links and references, allowing interactive searching and downloading of data. Taking advantage of the features of an electronic journal, this paper serves as an interactive tutorial for using the database, which we expect to develop into a research tool.

Detection of the membrane protein recognized by the kidney-specific alkylglucoside vector

PURPOSE

Previously, we suggested that alkylglucoside can be an effective vector for renal-specific drug delivery (Suzuki et al., J. Pharmacol. Exp. Ther, 288:57-61, 1999). The purpose of the present study is to characterize the membrane protein which is recognized by this alkylglucoside.

METHODS

The binding of [125I] tyrosine conjugated with a octylthioglucoside (Glc-S-C8-[125I]Tyr) Glc-S-C8-[125I]Tyr to crude membrane fractions of kidney was determined. In addition, the membrane was cross-linked with this alkylglucoside and examined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis.

RESULTS

Glc-S-C8-[125I]Tyr was shown to have a specific binding site on the kidney membrane (Kd = 931 nM and Bmax = 987 pmol/mg protein). Cross-linking of the membrane with Glc-S-C8-[125I]Tyr resulted in the detection of a protein (Mr = 62,000), which was unaffected by reducing agents. The results of this cross-linking study were consistent with previous information on its localization and binding characteristics.

CONCLUSIONS

The kidney membrane protein, to which alkylglucoside binds in a specific manner, has a molecular weight of 62,000. Crosslinking is a useful tool for detecting this novel membrane protein in kidney.

Caco-2 versus Caco-2/HT29-MTX co-cultured cell lines: permeabilities via diffusion, inside- and outside-directed carrier-mediated transport

PURPOSE

The objective of this study was a systematic characterization and evaluation of cell culture models based on mixtures of Caco-2/HT29-MTX co-cultures for their use in screening for drug absorption and intestinal permeability in comparison to the properties of the respective mono-cultures.

METHODS

Co-cultures of Caco-2 cells (absorptive-type) and HT29-MTX cells (goblet-type) were set up. Three different co-cultures (initial seeding ratios Caco-2/HT29-MTX: 90/10, 70/30, and 50/50) were grown on permeable filter supports, and monolayers were used for permeability studies with model compounds for paracellular absorption (atenolol, furosemide, H334/75, mannitol, terbutaline), transcellular absorption (antipyrine, ketoprofen, metoprolol, piroxicam), carrier-mediated absorption (D-glucose, Gly-Pro, and L-phenylalanine) as well as substrates for carrier-mediated secretion via P-glycoprotein (cimetidine and talinolol). Electrophysiological and microscopic controls were performed to characterize the cell cultures.

RESULTS

For compounds undergoing passive intestinal absorption permeabilities were generally higher in co-cultures than in Caco-2 monolayers, yielding highest values in pure HT29-MTX monolayers. This difference was most obvious for compounds transported via the paracellular pathway, where HT29-MTX cells may be up to 30 times more permeable than Caco-2 cells, whereas for lipophilic and highly permeable compounds, the difference in permeability values was less obvious. For drugs undergoing intestinal secretion mediated by P-glycoprotein, co-cultivation of Caco-2 cells with HT29-MTX cells led to increased apical to basolateral permeability which was decreased in the opposite direction, consistent with the fact that HT29-MTX cells do not express P-glycoprotein. When a carrier-mediated absorption mechanism is involved, the permeabilities observed were lower than the values reported for human small intestine and co-cultivation of HT29-MTX cells with Caco-2 cells resulted in even lower values as compared to the plain Caco-2 cultures.

CONCLUSIONS

Co-cultures of HT29-MTX and Caco-2 cells offer the opportunity of modifying the permeability barrier of the cell monolayers both with respect to paracellular resistance and secretory transport via P-gp. Thus, in special cases, they allow more flexibility in adapting the in vitro system to the in vivo situation as compared to the monocultures. Another advantage is the obvious robustness of the method with respect to the reproducibility of the results. A problem remaining, however, is the quantitative expression of carriers involved in intestinal uptake of many nutrients and drugs.

Cloning of a bovine orphan transporter and its short splicing variant

We have isolated a cDNA (bv7-3) encoding a member of the Na+,Cl(-)-dependent transporter family and its short splicing variant (bv7-3s) by screening a bovine retina cDNA library. Sequence analysis revealed that bv7-3 encodes a protein of 729 amino acids and is a bovine homologue of the rat orphan transporter v7-3-2. bv7-3s contains 265 amino acids, sharing 252 N-terminal amino acids with bv7-3. Both mRNAs for bv7-3 and bv7-3s were detected in nervous system by Northern blot analysis. In immunofluorescence analysis in transfected HEK 293T cells, myc-tagged bv7-3 was mainly detected on the plasma membrane, whereas myc-tagged bv7-3s showed a pattern of intracellular membrane staining.

Structure, function, and molecular modeling approaches to the study of the intestinal dipeptide transporter PepT1

The proton-coupled intestinal dipeptide transporter, PepT1, has 707 amino acids, 12 putative transmembrane domains (TMD), and is of importance in the transport of nutritional di- and tripeptides and structurally related drugs, such as penicillins and cephalosporins. By using a combination of molecular modeling and site-directed mutagenesis, we have identified several key amino acid residues that effect catalytic transport properties of PepT1. Our molecular model of the transporter was examined by dividing it into four sections, parallel to the membrane, starting from the extracellular side. The molecular model revealed a putative transport channel and the approximate locations of several aromatic and charged amino acid residues that were selected as targets for mutagenesis. Wild type or mutagenized human PepT1 cDNA was transfected into human embryonic kidney (HEK293) cells, and the uptake of tritiated glycylsarcosine [3H]-(Gly-Sar) was measured. Michaelis-Menton analysis of the wild-type and mutated transporters revealed the following results for site-directed mutagenesis. Mutation of Tyr-12 or Arg-282 into alanine has only a very modest effect on Gly-Sar uptake. By contrast, mutation of Trp-294 or Glu-595 into alanine reduced Gly-Sar uptake by 80 and 95%, respectively, and mutation of Tyr-167 reduced Gly-Sar uptake to the level of mock-transfected cells. In addition, preliminary data from fluorescence microscopy following the expression of N-terminal-GFP-labeled PepT1Y167A in HEK cells indicates that the Y167A mutation was properly inserted into the plasma membrane but has a greatly reduced Vmax.

Chimeric purine transporters of Aspergillus nidulans define a domain critical for function and specificity conserved in bacterial, plant and metazoan homologues

In Aspergillus nidulans, purine uptake is mediated by three transporter proteins: UapA, UapC and AzgA. UapA and UapC have partially overlapping functions, are 62% identical and have nearly identical predicted topologies. Their structural similarity is associated with overlapping substrate specificities; UapA is a high-affinity, high-capacity specific xanthine/uric acid transporter. UapC is a low/moderate-capacity general purine transporter. We constructed and characterized UapA/UapC, UapC/UapA and UapA/UapC/UapA chimeric proteins and UapA point mutations. The region including residues 378-446 in UapA (336-404 in UapC) has been shown to be critical for purine recognition and transport. Within this region, we identified: (i) one amino acid residue (A404) important for transporter function but probably not for specificity and two residues (E412 and R414) important for UapA function and specificity; and (ii) a sequence, (F/Y/S)X(Q/E/P) NXGXXXXT(K/R/G), which is highly conserved in all homologues of nucleobase transporters from bacteria to man. The UapC/UapA series of chimeras behaves in a linear pattern and leads to an univocal assignment of functional domains while the analysis of the reciprocal and 'sandwich' chimeras revealed unexpected inter-domain interactions. cDNAs coding for transporters including the specificity region defined by these studies have been identified for the first time in the human and Caenorhabditis elegans databases.

Molecular determinants of substrate selectivity in Na+-dependent nucleoside transporters

In mammalian cells, the salvage of purine and pyrimidine nucleosides is mediated by both facilitated and Na+-dependent nucleoside transporters. These transporters also play important roles in the transmembrane flux of therapeutic nucleoside analogs, which are widely used in the treatment of cancer and viral infections. The N1, N2, and N3 Na+-dependent nucleoside transporters differ in terms of their transport selectivity for purine and pyrimidine nucleosides. N1 is purine-selective, N2 is pyrimidine-selective, and N3 is broadly selective. To identify structural domains involved in substrate binding and molecular determinants responsible for distinct transport selectivity, chimeric transporters were made from the cloned rat N1 and N2 transporters. Of the 14 transmembrane domains (TM) of N1 and N2, transplanting TM8-9 of N1 into N2 converted N2 from a pyrimidine- to a purine-selective transporter. Transplanting only TM8 generated a chimera with characteristics similar to the N3 transporter that has yet to be cloned. These data suggest that TM8-9 confer substrate selectivity and may form at least part of a substrate-binding site in Na+-dependent nucleoside transporters.

Interaction of oligonucleotide-conjugates with the dipeptide transporter system in Caco-2 cells

Oligonucleotide-based therapies represent novel strategies for manipulating the expression and function of target proteins and are undergoing clinical evaluation for the treatment of viral diseases and malignancies. However, poor biological stability and cellular delivery represent potential limitations to the therapeutic development of oligonucleotides. Conjugation of oligonucleotides to lipophilic groups can improve delivery to cells but the enhanced cellular binding may also facilitate nonspecific interactions. In this report, we show that phosphorothioate oligonucleotides conjugated to lipophilic groups, either tocopherol (Vitamin E) or 2-Di-O-hexadecyl-3-glycerol, can significantly inhibit the functioning of the dipeptide transporter system (DTS) in cultured Caco-2 intestinal cells. Because the DTS mediates the binding and absorption of nutrient peptides and important drugs, such as the cephalosporin and penicillin antibiotics, this finding has important implications in relation to the potential toxicity of lipophilic conjugates in vivo. It also suggests a potential drug interaction with lipophilic oligonucleotide-conjugates if they were to be delivered orally.

Sequence alignments of the H(+)-dependent oligopeptide transporter family PTR: inferences on structure and function of the intestinal PET1 transporter

PURPOSE

To study the structure and function of the intestinal H+/ peptide transporter PET1, we compared its amino acid sequence with those of related transporters belonging to the oligopeptide transporter family PTR, and with more distant transporter families.

METHODS

We have developed a new approach to the sequence analysis of proteins with multiple transmembrane domains (TMDs) which takes into account the repeated TMD-loop topology. In addition to conventional analyses of the entire sequence, each TMD and its adjacent loop residues (= TMD segments) were analyzed separately as independent structural units. In combination with hydropathy analysis, this approach reveals any changes in the order of the TMD segments in the primary structure and permits TMD alignments among divergent structures even if rearrangements of the order of TMD segments have occurred in the course of evolution.

RESULTS

Alignments of TMD segments indicate that the TMD order in PTR transporters may have changed in the process of evolution. Consideration of such changes permits the alignment of homologous TMD segments from PTR transporters belonging to distant akaryotic and eukaryotic phyla. Multiple alignments of TMDs reveal several highly conserved regions that may play a role in transporter function. In comparing the PTR transporters with other transporter gene families, alignment scores using the entire primary structure are too low to support a finding of probable homology. However, statistically significant alignments were observed among individual TMD segments if one disregards the order in which they occur in the primary structure.

CONCLUSIONS

Our results support the hypothesis that the PTR transporters may have evolved by rearrangement, duplication, or insertions and deletions of TMD segments as independent modules. This modular structure suggests new alignment strategies for determining functional domains and testing relationship among distant transporter families.

Human dipeptide transporter, hPEPT1, stably transfected into Chinese hamster ovary cells

PURPOSE

A cDNA encoding the H(+)-coupled peptide transporter, hPEPT1, has previously been cloned from human ileum (8). The objective of this study was to establish a stably transfected cell line expressing hPEPT1 in mammalian cell culture.

METHODS

The hPEPT1 cDNA was subcloned into an expression vector carrying the CMV promoter and a neomycin resistance gene. This vector, pCDNA3-PEPT1, was transiently transfected into several cell lines to identify those capable of expressing PEPT1 transport function. CHO cells were selected and stably transfected with PEPT1 (CHO-PEPT1). Dipeptide transport activity was measured with 3H-Gly-Sar, in the presence and absence of inhibitors.

RESULTS

The clonal cell line, CHO-PEPT1, displayed high transport activity. Dipeptide transport was sensitive to pH and specific for dipeptides and other small peptides. Peptidomimetic antibiotics, such as cephalexin, were competitors for peptide transport.

CONCLUSIONS

The stably transfected cell line, CHO-PEPT1 exhibits enhanced transport over that of cell lines with native expression of PEPT1, and therefore, represents a useful tool for rapid screening of drugs that utilize the peptide transporter in the human intestine for absorption.