Towards a structural understanding of drug and peptide transport within the proton-dependent oligopeptide transporter (POT) family

Peptide transporter structure reveals binding and action mechanism of a potent PEPT1 and PEPT2 inhibitor

Inhibitors for membrane transporters have been shown to be indispensable as drugs and tool compounds. The proton-dependent oligopeptide transporters PEPT1 and PEPT2 from the SLC15 family play important roles in human and mammalian physiology. With Lys[Z(NO₂)]-Val (LZNV), a modified Lys-Val dipeptide, a potent transport inhibitor for PEPT1 and PEPT2 is available. Here we present the crystal structure of the peptide transporter YePEPT in complex with LZNV. The structure revealed the molecular interactions for inhibitor binding and a previously undescribed mostly hydrophobic pocket, the PZ pocket, involved in interaction with LZNV. Comparison with a here determined ligand-free structure of the transporter unveiled that the initially absent PZ pocket emerges through conformational changes upon inhibitor binding. The provided biochemical and structural information constitutes an important framework for the mechanistic understanding of inhibitor binding and action in proton-dependent oligopeptide transporters.

Cloning, tissue distribution and functional characterization of the donkey (Equus asinus) oligopeptide transporter 2

Oligopeptide transporter 2 (PepT2) is an important transporter of oligopeptides. In the present study, we describe the molecular cloning, tissue distribution and functional characterization of a donkey (Equus asinus) PepT2. The cloned cDNA sequence was 2202 bp at full length, encoding a 733 amino acid peptide with a molecular weight of 81.9 kDa and a theoretical pI of 8.92. Bioinformatics analysis showed that the deduced peptide sequence possessed all the characteristic features of PepT2. The expression of PepT2 in the kidney and lung was significantly higher than that observed in the ileum, duodenum, jejunum, spleen, liver, heart and stomach. Functional characterization by heterologous expression in Chinese hamster ovary cells showed that the uptake of β-Ala-Lys-N-7-amino-4-methylcoumarin-3-acetic acid (β-Ala-Lys-AMCA) by donkey PepT2-Chinese hamster ovary cells was dependent on time, pH and substrate concentration, with a low Km value of 91.51 ± 14.14 μM and a maximum velocity of 41.37 ± 2.193 pmol/min/mg protein. In the present study, for the first time, the expression and functional characteristics of donkey PepT2 were evaluated, the results of which provide new insights and a better understanding of its crucial role in oligopeptide transport in donkeys.

PTR2/POT/NPF transporters: what makes them tick?

PTR2/POT/NPF are a family of primarily proton coupled transporters that belong to the major facilitator super family and are found across most kingdoms of life. They are involved in uptake of nutrients, hormones, ions and several orally administered drug molecules. A wealth of structural and functional data is available for this family; the similarity between the protein structural features have been discussed and investigated in detail on several occasions, however there are no reports on the unification of substrate information. In order to fill this gap, we have collected information about substrates across the entire PTR2/POT/NPF family in order to provide key insights into what makes a molecule a substrate and whether there are common features among confirmed substrates. This review will be of particular interest for researchers in the field trying to probe the mechanisms responsible for the different selectivity of these transporters at a molecular resolution, and to design novel substrates.

Synthesis, bioactivities and phloem uptake of dipeptide-chlorantraniliprole derivatives

Phloem systemicity is a desirable property for insecticides to control sucking insects. However, the development of phloem systemic insecticides is challenging. One possible strategy is to link existed insecticides with endogenous substances so that the resulting conjugates can be transported by specific transporters into the phloem. In this study, novel dipeptide promoieties were introduced into chlorantraniliprole, which is an efficient and broad-spectrum anthranilic diamide insecticide without phloem mobility. Twenty-two new dipeptide-chlorantraniliprole conjugates have been synthesized. Systemic tests showed that all conjugates exhibited phloem mobility in Ricinus communis. In particular, compound 4g with alanyl-alanine dipeptide fragment was able to accumulate in phloem sap (114.49 ± 11.10 μM) in the form of its hydrolysis product 5g. Results of bioassay showed that conjugates 4g and 5g were able to exhibit comparable insecticidal activity against Plutella xylostella L. and Spodoptera exigua compared to its parent compound chlorantraniliprole. This work demonstrated that the dipeptide structures were able to contribute to the improvement of the uptake and phloem mobility of chlorantraniliprole, and two phloem mobile conjugates with satisfactory in vivo insecticidal effect was obtained as new candidates for high-efficient insecticides.

Expansion of the Major Facilitator Superfamily (MFS) to include novel transporters as well as transmembrane-acting enzymes

The Major Facilitator Superfamily (MFS) is currently the largest characterized superfamily of transmembrane secondary transport proteins. Its diverse members are found in essentially all organisms in the biosphere and function by uniport, symport, and/or antiport mechanisms. In 1993 we first named and described the MFS which then consisted of 5 previously known families that had not been known to be related, and by 2012 we had identified a total of 74 families, classified phylogenetically within the MFS, all of which included only transport proteins. This superfamily has since expanded to 89 families, all included under TC# 2.A.1, and a few transporter families outside of TC# 2.A.1 were identified as members of the MFS. In this study, we assign nine previously unclassified protein families in the Transporter Classification Database (TCDB; http://www.tcdb.org) to the MFS based on multiple criteria and bioinformatic methodologies. In addition, we find integral membrane domains distantly related to partial or full-length MFS permeases in Lysyl tRNA Synthases (TC# 9.B.111), Lysylphosphatidyl Glycerol Synthases (TC# 4.H.1), and cytochrome b₅₆₁ transmembrane electron carriers (TC# 5.B.2). Sequence alignments, overlap of hydropathy plots, compatibility of repeat units, similarity of complexity profiles of transmembrane segments, shared protein domains and 3D structural similarities between transport proteins were analyzed to assist in inferring homology. The MFS now includes 105 families.

Genome Mining of Plant NPFs Reveals Varying Conservation of Signature Motifs Associated With the Mechanism of Transport

Nitrogen is essential for all living species and may be taken up from the environment in different forms like nitrate or peptides. In plants, members of a transporter family named NPFs transport nitrate and peptides across biological membranes. NPFs are phylogenetically related to a family of peptide transporters (PTRs) or proton-coupled oligopeptide transporters (POTs) that are evolutionarily conserved in all organisms except in Archaea. POTs are present in low numbers in bacteria, algae and animals. NPFs have expanded in plants and evolved to transport a wide range of substrates including phytohormones and glucosinolates. Functional studies have shown that most NPFs, like POTs, operate as symporters with simultaneous inwardly directed movement of protons. Here we focus on four structural features of NPFs/POTs/PTRs that have been shown by structural and functional studies to be essential to proton-coupled symport transport. The first two features are implicated in proton binding and transport: a conserved motif named ExxER/K, located in the first transmembrane helix (TMH1) and a D/E residue in TMH7 that has been observed in some bacterial and algal transporters. The third and fourth features are two inter-helical salt bridges between residues on TMH1 and TMH7 or TMH4 and TMH10. To understand if the mechanism of transport is conserved in NPFs with the expansion to novel substrates, we collected NPFs sequences from 42 plant genomes. Sequence alignment revealed that the ExxER/K motif is not strictly conserved and its conservation level is different in the NPF subfamilies. The proton binding site on TMH7 is missing in all NPFs with the exception of two NPFs from moss. The two moss NPFs also have a positively charged amino acid on TMH1 that can form the salt bridge with the TMH7 negative residue. None of the other NPFs we examined harbor residues that can form the TMH1-TMH7 salt bridge. In contrast, the amino acids required to form the TMH4-TMH10 salt bridge are highly conserved in NPFs, with some exceptions. These results support the need for further biochemical and structural studies of individual NPFs for a better understanding of the transport mechanism in this family of transporters.

Di- and tripeptide transport in vertebrates: the contribution of teleost fish models

Solute Carrier 15 (SLC15) family, alias H⁺-coupled oligopeptide cotransporter family, is a group of membrane transporters known for their role in the cellular uptake of di- and tripeptides (di/tripeptides) and peptide-like molecules. Of its members, SLC15A1 (PEPT1) chiefly mediates intestinal absorption of luminal di/tripeptides from dietary protein digestion, while SLC15A2 (PEPT2) mainly allows renal tubular reabsorption of di/tripeptides from ultrafiltration, SLC15A3 (PHT2) and SLC15A4 (PHT1) possibly interact with di/tripeptides and histidine in certain immune cells, and SLC15A5 has unknown function. Our understanding of this family in vertebrates has steadily increased, also due to the surge of genomic-to-functional information from 'non-conventional' animal models, livestock, poultry, and aquaculture fish species. Here, we review the literature on the SLC15 transporters in teleost fish with emphasis on SLC15A1 (PEPT1), one of the solute carriers better studied amongst teleost fish because of its relevance in animal nutrition. We report on the operativity of the transporter, the molecular diversity, and multiplicity of structural-functional solutions of the teleost fish orthologs with respect to higher vertebrates, its relevance at the intersection of the alimentary and osmoregulative functions of the gut, its response under various physiological states and dietary solicitations, and its possible involvement in examples of total body plasticity, such as growth and compensatory growth. By a comparative approach, we also review the few studies in teleost fish on SLC15A2 (PEPT2), SLC15A4 (PHT1), and SLC15A3 (PHT2). By representing the contribution of teleost fish to the knowledge of the physiology of di/tripeptide transport and transporters, we aim to fill the gap between higher and lower vertebrates.

Data Mining FAERS to Analyze Molecular Targets of Drugs Highly Associated with Stevens-Johnson Syndrome

Drug features that are associated with Stevens-Johnson syndrome (SJS) have not been fully characterized. A molecular target analysis of the drugs associated with SJS in the FDA Adverse Event Reporting System (FAERS) may contribute to mechanistic insights into SJS pathophysiology. The publicly available version of FAERS was analyzed to identify disproportionality among the molecular targets, metabolizing enzymes, and transporters for drugs associated with SJS. The FAERS in-house version was also analyzed for an internal comparison of the drugs most highly associated with SJS. Cyclooxygenases 1 and 2, carbonic anhydrase 2, and sodium channel 2 alpha were identified as disproportionately associated with SJS. Cytochrome P450 (CYPs) 3A4 and 2C9 are disproportionately represented as metabolizing enzymes of the drugs associated with SJS adverse event reports. Multidrug resistance protein 1 (MRP-1), organic anion transporter 1 (OAT1), and PEPT2 were also identified and are highly associated with the transport of these drugs. A detailed review of the molecular targets identifies important roles for these targets in immune response. The association with CYP metabolizing enzymes suggests that reactive metabolites and oxidative stress may have a contributory role. Drug transporters may enhance intracellular tissue concentrations and also have vital physiologic roles that impact keratinocyte proliferation and survival. Data mining FAERS may be used to hypothesize mechanisms for adverse drug events by identifying molecular targets that are highly associated with drug-induced adverse events. The information gained may contribute to systems biology disease models.

Critical role of PepT1 in promoting colitis-associated cancer and therapeutic benefits of the anti-inflammatory PepT1-mediated tripeptide KPV in a murine model

BACKGROUND AND AIMS

The human intestinal peptide transporter 1, hPepT1, is expressed in the small intestine at low levels in the healthy colon and upregulated during inflammatory bowel disease. hPepT1 plays a role in mouse colitis and human studies have demonstrated that chronic intestinal inflammation leads to colorectal cancer (colitis-associated cancer; CAC). Hence, we assessed here the role of PepT1 in CAC.

METHODS

Mice with hPepT1 overexpression in intestinal epithelial cells (TG) or PepT1 (PepT1-KO) deletion were used and CAC was induced by AOM/DSS.

RESULTS

TG mice had larger tumor sizes, increased tumor burdens, and increased intestinal inflammation compared to WT mice. Conversely, tumor number and size and intestinal inflammation were significantly decreased in PepT1-KO mice. Proliferating crypt cells were increased in TG mice and decreased in PepT1-KO mice. Analysis of human colonic biopsies revealed an increased expression of PepT1 in patients with colorectal cancer, suggesting that PepT1 might be targeted for the treatment of CAC. The use of an anti-inflammatory tripeptide KPV (Lys-Pro-Val) transported by PepT1 was able to prevent carcinogenesis in WT mice. When administered to PepT1-KO mice, KPV did not trigger any of the inhibitory effect on tumorigenesis observed in WT mice.

CONCLUSIONS

The observations that pepT1 was highly expressed in human colorectal tumor and that its overexpression and deletion in mice increased and decreased colitis associated tumorigenesis, respectively, suggest that PepT1 is a potential therapeutic target for the treatment of colitis associated tumorigenesis.

Accurate Prediction of Ligand Affinities for a Proton-Dependent Oligopeptide Transporter

Membrane transporters are critical modulators of drug pharmacokinetics, efficacy, and safety. One example is the proton-dependent oligopeptide transporter PepT1, also known as SLC15A1, which is responsible for the uptake of the β-lactam antibiotics and various peptide-based prodrugs. In this study, we modeled the binding of various peptides to a bacterial homolog, PepT_St, and evaluated a range of computational methods for predicting the free energy of binding. Our results show that a hybrid approach (endpoint methods to classify peptides into good and poor binders and a theoretically exact method for refinement) is able to accurately predict affinities, which we validated using proteoliposome transport assays. Applying the method to a homology model of PepT1 suggests that the approach requires a high-quality structure to be accurate. Our study provides a blueprint for extending these computational methodologies to other pharmaceutically important transporter families.

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A hierarchical computational approach determines ligand affinities to transporters

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Lysine-containing dipeptides proposed to bind vertically like a tripeptide

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Experimental structures are vital for the accurate prediction of affinities

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A model of prodrug interactions to human PepT1 is suggested

Functional Expression of PEPT2 in the Human Distal Lung Epithelial Cell Line NCl-H441

PURPOSE

The peptide transporter PEPT2 is expressed in alveolar type II epithelial cells. So far, however, no appropriate alveolar epithelial cell line for studying PEPT2 function has been known. In this study, we examined the functional expression of PEPT2 in the human distal lung epithelial cell line NCl-H441 (H441).

METHODS

Expression of PEPT2 mRNA and protein was examined in H441 cells. Transport function of PEPT2 was studied using glycylsarcosine (Gly-Sar) as a substrate.

RESULTS

Lamellar bodies were well developed in H441 cells and mRNA expression of type II cell markers and PEPT2 increased during time in culture. PEPT2 protein expression was confirmed in H441 cells, but not in A549 cells, by immunostaining and Western blotting. The uptake of Gly-Sar in H441 cells was inhibited by cefadroxil, and the cefadroxil-sensitive uptake was pH-dependent and peaked at pH 6.5. Gly-Sar uptake in H441 cells showed saturation kinetics with a Km value of 112.5 μM. In addition, apical-to-basal, but not basal-to-apical, transport of cephalexin across H441 cell monolayers was sensitive to cefadroxil.

CONCLUSIONS

PEPT2 is functionally expressed in H441 cells, making the cell line a good in vitro model to study PEPT2 function and its regulation in human distal lung.

USP18 Sensitivity of Peptide Transporters PEPT1 and PEPT2

USP18 (Ubiquitin-like specific protease 18) is an enzyme cleaving ubiquitin from target proteins. USP18 plays a pivotal role in antiviral and antibacterial immune responses. On the other hand, ubiquitination participates in the regulation of several ion channels and transporters. USP18 sensitivity of transporters has, however, never been reported. The present study thus explored, whether USP18 modifies the activity of the peptide transporters PEPT1 and PEPT2, and whether the peptide transporters are sensitive to the ubiquitin ligase Nedd4-2. To this end, cRNA encoding PEPT1 or PEPT2 was injected into Xenopus laevis oocytes without or with additional injection of cRNA encoding USP18. Electrogenic peptide (glycine-glycine) transport was determined by dual electrode voltage clamp. As a result, in Xenopus laevis oocytes injected with cRNA encoding PEPT1 or PEPT2, but not in oocytes injected with water or with USP18 alone, application of the dipeptide gly-gly (2 mM) was followed by the appearance of an inward current (I_gly-gly). Coexpression of USP18 significantly increased I_gly-gly in both PEPT1 and PEPT2 expressing oocytes. Kinetic analysis revealed that coexpression of USP18 increased maximal I_gly-gly. Conversely, overexpression of the ubiquitin ligase Nedd4-2 decreased I_gly-gly. Coexpression of USP30 similarly increased I_gly-gly in PEPT1 expressing oocytes. In conclusion, USP18 sensitive cellular functions include activity of the peptide transporters PEPT1 and PEPT2.

Downregulation of peptide transporters PEPT1 and PEPT2 by oxidative stress responsive kinase OSR1

BACKGROUND/AIMS

OSR1 (oxidative-stress-responsive kinase 1) participates in the regulation of renal tubular ion transport, cell volume and blood pressure. Whether OSR1 contributes to the regulation of organic solute transport remained; however, elusive. The present study thus explored the OSR1 sensitivity of the peptide transporters PEPT1 and PEPT2.

METHODS

cRNA encoding PEPT1 or PEPT2 were injected into Xenopus oocytes without or with additional injection of cRNA encoding wild-type OSR1, WNK1 insensitive inactive (T185A)OSR1, constitutively active (T185E)OSR1, and catalytically inactive (D164A)OSR1. Electrogenic peptide (glycine-glycine) transport was determined by dual electrode voltage clamp, the abundance of hemagglutinin-tagged PEPT2 (PEPT2-HA) by chemiluminescence.

RESULTS

In Xenopus oocytes injected with cRNA encoding PEPT1 or PEPT2, but not in oocytes injected with water, the dipeptide gly-gly (2 mM) generated an appreciable inward current (I(gly-gly)). Coexpression of OSR1 significantly decreased Igly-gly in both PEPT1 and PEPT2 expressing oocytes. The effect of OSR1 coexpression on Igly-gly in PEPT1 expressing oocytes was mimicked by coexpression of (T185E)OSR1, but not of (D164A)OSR1 or (T185A)OSR1. Kinetic analysis revealed that coexpression of OSR1 decreased maximal Igly-gly. OSR1 further decreased the PEPT2-HA protein abundance in the cell membrane.

CONCLUSION

OSR1 has the capacity to downregulate the peptide transporters PEPT1 and PEPT2 by decreasing the carrier protein abundance in the cell membrane.

SPAK dependent regulation of peptide transporters PEPT1 and PEPT2

BACKGROUND/AIMS

SPAK (STE20-related proline/alanine-rich kinase) is a powerful regulator of renal tubular ion transport and blood pressure. Moreover, SPAK contributes to the regulation of cell volume. Little is known, however, about a role of SPAK in the regulation or organic solutes. The present study thus addressed the influence of SPAK on the peptide transporters PEPT1 and PEPT2.

METHODS

To this end, cRNA encoding PEPT1 or PEPT2 were injected into Xenopus laevis oocytes without or with additional injection of cRNA encoding wild-type, SPAK, WNK1 insensitive inactive (T233A)SPAK, constitutively active (T233E)SPAK, and catalytically inactive (D212A)SPAK. Electrogenic peptide (glycine-glycine) transport was determined by dual electrode voltage clamp and PEPT2 protein abundance in the cell membrane by chemiluminescence. Intestinal electrogenic peptide transport was estimated from peptide induced current in Ussing chamber experiments of jejunal segments isolated from gene targeted mice expressing SPAK resistant to WNK-dependent activation (spak(tg/tg)) and respective wild-type mice (spak(+/+)).

RESULTS

In PEPT1 and in PEPT2 expressing oocytes, but not in oocytes injected with water, the dipeptide gly-gly (2 mM) generated an inward current, which was significantly decreased following coexpression of SPAK. The effect of SPAK on PEPT1 was mimicked by (T233E)SPAK, but not by (D212A)SPAK or (T233A)SPAK. SPAK decreased maximal peptide induced current of PEPT1. Moreover, SPAK decreased carrier protein abundance in the cell membrane of PEPT2 expressing oocytes. In intestinal segments gly-gly generated a current, which was significantly higher in spak(tg/tg) than in spak(+/+) mice.

CONCLUSION

SPAK is a powerful regulator of peptide transporters PEPT1 and PEPT2.

Functional implications and ubiquitin-dependent degradation of the peptide transporter Ptr2 in Saccharomyces cerevisiae

The peptide transporter Ptr2 plays a central role in di- or tripeptide import in Saccharomyces cerevisiae. Although PTR2 transcription has been extensively analyzed in terms of upregulation by the Ubr1-Cup9 circuit, the structural and functional information for this transporter is limited. Here we identified 14 amino acid residues required for peptide import through Ptr2 based on the crystallographic information of Streptococcus thermophilus peptide transporter PepTst and based on the conservation of primary sequences among the proton-dependent oligopeptide transporters (POTs). Expression of Ptr2 carrying one of the 14 mutations of which the corresponding residues of PepTst are involved in peptide recognition, salt bridge interaction, or peptide translocation failed to enable ptr2Δtrp1 cell growth in alanyl-tryptophan (Ala-Trp) medium. We observed that Ptr2 underwent rapid degradation after cycloheximide treatment (half-life, approximately 1 h), and this degradation depended on Rsp5 ubiquitin ligase. The ubiquitination of Ptr2 most likely occurs at the N-terminal lysines 16, 27, and 34. Simultaneous substitution of arginine for the three lysines fully prevented Ptr2 degradation. Ptr2 mutants of the presumed peptide-binding site (E92Q, R93K, K205R, W362L, and E480D) exhibited severe defects in peptide import and were subjected to Rsp5-dependent degradation when cells were moved to Ala-Trp medium, whereas, similar to what occurs in the wild-type Ptr2, mutant proteins of the intracellular gate were upregulated. These results suggest that Ptr2 undergoes quality control and the defects in peptide binding and the concomitant conformational change render Ptr2 subject to efficient ubiquitination and subsequent degradation.

Fluorescent sensors for activity and regulation of the nitrate transceptor CHL1/NRT1.1 and oligopeptide transporters

To monitor nitrate and peptide transport activity in vivo, we converted the dual-affinity nitrate transceptor CHL1/NRT1.1/NPF6.3 and four related oligopeptide transporters PTR1, 2, 4, and 5 into fluorescence activity sensors (NiTrac1, PepTrac). Substrate addition to yeast expressing transporter fusions with yellow fluorescent protein and mCerulean triggered substrate-dependent donor quenching or resonance energy transfer. Fluorescence changes were nitrate/peptide-specific, respectively. Like CHL1, NiTrac1 had biphasic kinetics. Mutation of T101A eliminated high-affinity transport and blocked the fluorescence response to low nitrate. NiTrac was used for characterizing side chains considered important for substrate interaction, proton coupling, and regulation. We observed a striking correlation between transport activity and sensor output. Coexpression of NiTrac with known calcineurin-like proteins (CBL1, 9; CIPK23) and candidates identified in an interactome screen (CBL1, KT2, WNKinase 8) blocked NiTrac1 responses, demonstrating the suitability for in vivo analysis of activity and regulation. The new technology is applicable in plant and medical research.

DOI:http://dx.doi.org/10.7554/eLife.01917.001

About 1% of global energy output is used to produce nitrogen-enriched fertiliser to improve crop yields, but much of this energy is wasted because plants absorb only a fraction of the nitrogen that is applied as fertiliser. Even worse, the excess nitrogen leaches into water sources, poisoning the environment and causing health problems. However, to date, most efforts to increase the efficiency of nitrogen uptake in plants have been unsuccessful.

The key to improving the uptake efficiency of a nutrient is to identify obstacles in its journey from the soil to cells inside the plant. The first obstacle that nitrate ions encounter is the membrane of the cells on the surface of the roots of the plant. Many researchers believe that it would be possible to increase the amount of nitrogen absorbed by the plant if more was known about the ways that plants control how nitrate ions and other chemicals enter cells.

The cell membrane contains gated pores called transporters that allow particular molecules to pass through it. Although the transporters responsible for the uptake of nitrate ions, peptides, and ammonium ions (the main nitrogen compounds that plants acquire) have been identified, current experimental techniques cannot determine when and where a specific transporter is active within a living plant. This makes it difficult to know where to target modifications and to determine how effective they have been at each step. The nitrate transporter also acts as an antenna that measures nitrate concentration to ensure it is used optimally in the plant, but current techniques cannot show how this actually works.

Now, Ho and Frommer have exploited the fact that a transporter changes shape as it does its job to create sensors that can track the movement of nitrate and peptides through the cell membrane. By using fluorescent proteins to monitor how the shape of the transporter changes, Ho and Frommer were able to measure how structural mutations and regulatory proteins influenced the movement of nitrate and peptides through the membrane.

For efficiency, all of this work was performed in yeast cells. The next goal is to use the technique in plants to uncover how they adjust to changes in nutrient levels in the soil.

DOI:http://dx.doi.org/10.7554/eLife.01917.002

Peptide transporter isoforms are discriminated by the fluorophore-conjugated dipeptides β-Ala- and d-Ala-Lys-N-7-amino-4-methylcoumarin-3-acetic acid

Peptide transporters of the SLC15 family are classified by structure and function into PEPT1 (low‐affinity/high‐capacity) and PEPT2 (high‐affinity/low‐capacity) isoforms. Despite the differences in kinetics, both transporter isoforms are reckoned to transport essentially all possible di‐ and tripeptides. We here report that the fluorophore‐conjugated dipeptide derivatives β‐Ala‐Lys‐N‐7‐amino‐4‐methylcoumarin‐3‐acetic acid (β‐AK‐AMCA) and d‐Ala‐Lys‐N‐7‐amino‐4‐methylcoumarin‐3‐acetic acid (d‐AK‐AMCA) are transported by distinct PEPT isoforms in a species‐specific manner. Transport of the fluorophore peptides was studied (1) in vitro after heterologous expression in Xenopus oocytes of PEPT1 and PEPT2 isoforms from different vertebrate species and of PEPT1 and PEPT2 transporters from Caenorhabditis elegans by using electrophysiological and fluorescence methods and (2) in vivo in C. elegans by using fluorescence methods. Our results indicate that both substrates are transported by the vertebrate “renal‐type” and the C. elegans “intestinal‐type” peptide transporter only. A systematic analysis among species finds four predicted amino acid residues along the sequence that may account for the substrate uptake differences observed between the vertebrate PEPT1/nematode PEPT2 and the vertebrate PEPT2/nematode PEPT1 subtype. This selectivity on basis of isoforms and species may be helpful in better defining the structure–function determinants of the proteins of the SLC15 family.

Peptide transporters of the SLC15 family can be classified by structure and function into the PEPT1 (low‐affinity/high‐capacity) and PEPT2 (high‐affinity/low‐capacity) phenotype. We found that the fluorophore‐conjugated dipeptide derivatives β‐Ala‐Lys‐N‐7‐amino‐4‐methylcoumarin‐3‐acetic acid (β‐AK‐AMCA) and d‐Ala‐Lys‐N‐7‐amino‐4‐methylcoumarin‐3‐acetic acid (d‐AK‐AMCA) are transported only by distinct PEPT isoforms in a species‐specific manner. This selectivity on basis of isoforms and species should be helpful in further defining the substrate‐binding domain of peptide transporters.

Saccharomyces cerevisiae-based platform for rapid production and evaluation of eukaryotic nutrient transporters and transceptors for biochemical studies and crystallography

To produce large quantities of high quality eukaryotic membrane proteins in Saccharomyces cerevisiae, we modified a high-copy vector to express membrane proteins C-terminally-fused to a Tobacco Etch Virus (TEV) protease detachable Green Fluorescent Protein (GFP)-8His tag, which facilitates localization, quantification, quality control, and purification. Using this expression system we examined the production of a human glucose transceptor and 11 nutrient transporters and transceptors from S. cerevisiae that have not previously been overexpressed in S. cerevisiae and purified. Whole-cell GFP-fluorescence showed that induction of GFP-fusion synthesis from a galactose-inducible promoter at 15°C resulted in stable accumulation of the fusions in the plasma membrane and in intracellular membranes. Expression levels of the 12 fusions estimated by GFP-fluorescence were in the range of 0.4 mg to 1.7 mg transporter pr. liter cell culture. A detergent screen showed that n-dodecyl-ß-D-maltopyranoside (DDM) is acceptable for solubilization of the membrane-integrated fusions. Extracts of solubilized membranes were prepared with this detergent and used for purifications by Ni-NTA affinity chromatography, which yielded partially purified full-length fusions. Most of the fusions were readily cleaved at a TEV protease site between the membrane protein and the GFP-8His tag. Using the yeast oligopeptide transporter Ptr2 as an example, we further demonstrate that almost pure transporters, free of the GFP-8His tag, can be achieved by TEV protease cleavage followed by reverse immobilized metal-affinity chromatography. The quality of the GFP-fusions was analysed by fluorescence size-exclusion chromatography. Membranes solubilized in DDM resulted in preparations containing aggregated fusions. However, 9 of the fusions solubilized in DDM in presence of cholesteryl hemisuccinate and specific substrates, yielded monodisperse preparations with only minor amounts of aggregated membrane proteins. In conclusion, we developed a new effective S. cerevisiae expression system that may be used for production of high-quality eukaryotic membrane proteins for functional and structural analysis.

Teleost fish models in membrane transport research: the PEPT1(SLC15A1) H+-oligopeptide transporter as a case study

Human genes for passive, ion-coupled transporters and exchangers are included in the so-called solute carrier (SLC) gene series, to date consisting of 52 families and 398 genes. Teleost fish genes for SLC proteins have also been described in the last two decades, and catalogued in preliminary SLC-like form in 50 families and at least 338 genes after systematic GenBank database mining (December 2010-March 2011). When the kinetic properties of the expressed proteins are studied in detail, teleost fish SLC transporters always reveal extraordinary 'molecular diversity' with respect to the mammalian counterparts, which reflects peculiar adaptation of the protein to the physiology of the species and/or to the environment where the species lives. In the case of the H+ -oligopeptide transporter PEPT1(SLC15A1), comparative analysis of diverse teleost fish orthologs has shown that the protein may exhibit very eccentric properties in terms of pH dependence (e.g., the adaptation of zebrafish PEPT1 to alkaline pH), temperature dependence (e.g., the adaptation of icefish PEPT1 to sub-zero temperatures) and/or substrate specificity (e.g., the species-specificity of PEPT1 for the uptake of l-lysine-containing peptides). The revelation of such peculiarities is providing new contributions to the discussion on PEPT1 in both basic (e.g., molecular structure-function analyses) and applied research (e.g., optimizing diets to enhance growth of commercially valuable fish).

ABA transport and transporters

Abscisic acid (ABA) metabolism, perception, and transport form a triptych allowing higher plants to use ABA as a signaling molecule. The molecular bases of ABA metabolism are now well described and, over the past few years, several ABA receptors have been discovered. Although ABA transport has long been demonstrated in planta, the first breakthroughs in identifying plasma membrane-localized ABA transporters came in 2010, with the identification of two ATP-binding cassette (ABC) proteins. More recently, two ABA transporters in the nitrate transporter 1/peptide transporter (NRT1/PTR) family have been identified. In this review, we discuss the role of these different ABA transporters and examine the scientific impact of their identification. Given that the NRT1/PTR family is involved in the transport of nitrogen (N) compounds, further work should determine whether an interaction between ABA and N signaling or nutrition occurs.

Identification of molecular hinge points mediating alternating access in the vesicular monoamine transporter VMAT2

Vesicular monoamine transporter 2 (VMAT2) catalyzes transport of monoamines into storage vesicles in a process that involves exchange of the charged monoamine with two protons. VMAT2 is a member of the DHA12 family of multidrug transporters that belongs to the major facilitator superfamily (MFS) of secondary transporters. Here we present a homology model of VMAT2, which has the standard MFS fold, that is, with two domains of six transmembrane helices each which are related by twofold pseudosymmetry and whose axis runs normal to the membrane and between the two halves. Demonstration of the essential role of a membrane-embedded glutamate and confirmation of the existence of a hydrogen bond probably involved in proton transport provide experimental evidence that validates some of the predictions inherent to the model. Moreover, we show the essential role of residues at two anchor points between the two bundles. These residues appear to function as molecular hinge points about which the two six transmembrane-helix bundles flex and straighten to open and close the pathways on either side of the membrane as required for transport. Polar residues that create a hydrogen bond cluster form one of the anchor points of VMAT2. The other results from hydrophobic interactions. Residues at the anchor points are strongly conserved in other MFS transporters in one way or another, suggesting that interactions at these locations will be critical in most, if not all, MFS transporters.

Characterization of the transport of lysine-containing dipeptides by PepT1 orthologs expressed in Xenopus laevis oocytes

During digestion, dietary proteins cleaved in di and tri-peptides are translocated from the intestinal lumen into the enterocytes via PepT1 (SLC15A1) using an inwardly directed proton electrochemical gradient. The kinetic properties in various PepT1 orthologs (Dicentrarchus labrax, Oryctolagus cuniculus, Danio rerio) have been explored to determine the transport efficiency of different combinations of lysine, methionine, and glycine. Species-specific differences were observed. Lys-Met resulted the best substrate at all tested potentials in sea bass and rabbit PepT1, whereas in the zebrafish transporter all tested dipeptides (except Gly-Lys) elicited similar currents independently on the charge position or amino acid composition. For the sea bass and rabbit PepT1, kinetic parameters, K(0.5) and I(max) and their ratio, show the importance of the position of the charged lysine in the peptide. The PepT1 transporter of these species has very low affinity for Lys-Lys and Gly-Lys; this reduces the transport efficiency which is instead higher for Lys-Met and Lys-Gly. PepT1 from zebrafish showed relatively high affinity and excellent transport efficiency for Met-Lys and Lys-Met. These data led us to speculate about the structural determinants involved in substrate interaction according to the model proposed for this transporter.

Transforming dietary peptides in promising lead compounds: the case of bioavailable carnosine analogs

The ability of carnosine to prevent advanced glycoxidation end products (AGEs) and advanced lipoxidation end products (ALEs) formation, on the one hand, and the convincing evidence that these compounds act as pathogenetic factors, on the other hand, strongly support carnosine as a promising therapeutic agent for oxidative-based diseases. The mechanism/s by which carnosine inhibits AGEs and ALEs is still under investigation but an emerging hypothesis is that carnosine acts by deactivating the AGEs and ALEs precursors and in particular the reactive carbonyl species (RCS) generated by both lipid and sugar oxidation. The ability of carnosine to inhibit AGEs and ALEs formation and the corresponding biological effects has been demonstrated in several in vitro studies and in some animal models. However, such effects are in line of principle, limited in humans, due to the effect of serum carnosinase (absent in rodents), which catalyzes the carnosine hydrolysis to its constitutive amino acids. Such a limitation has prompted a great interest in the design of carnosine derivatives, which maintaining (or improving) the reactivity with RCS, are more resistant to carnosinase. The present paper intends to critically review the most recent studies oriented to obtaining carnosine derivatives, optimized in terms of reactivity with RCS, selectivity (no reaction with physiological aldehydes) and the pharmacokinetic profile (mainly through an enhanced resistance to carnosinase hydrolysis). The review also includes a brief description of AGEs and ALEs as drug targets and the evidence so far reported regarding the ability of carnosine as inhibitor of AGEs and ALEs formation and the proposed reaction mechanisms.

Alternating access mechanism in the POT family of oligopeptide transporters

Proton-dependent oligopeptide transporters are required for the uptake of diet-derived peptides in all kingdoms of life. The crystal structure of a bacterial transporter in the inward open conformation, together with a published structure in an occluded conformation, reveals the peptide transport mechanism.

Short chain peptides are actively transported across membranes as an efficient route for dietary protein absorption and for maintaining cellular homeostasis. In mammals, peptide transport occurs via PepT1 and PepT2, which belong to the proton-dependent oligopeptide transporter, or POT family. The recent crystal structure of a bacterial POT transporter confirmed that they belong to the major facilitator superfamily of secondary active transporters. Despite the functional characterization of POT family members in bacteria, fungi and mammals, a detailed model for peptide recognition and transport remains unavailable. In this study, we report the 3.3-Å resolution crystal structure and functional characterization of a POT family transporter from the bacterium Streptococcus thermophilus. Crystallized in an inward open conformation the structure identifies a hinge-like movement within the C-terminal half of the transporter that facilitates opening of an intracellular gate controlling access to a central peptide-binding site. Our associated functional data support a model for peptide transport that highlights the importance of salt bridge interactions in orchestrating alternating access within the POT family.