Integration of Evolutionary Features for the Identification of Functionally Important Residues in Major Facilitator Superfamily Transporters

The identification of functionally important residues is an important challenge for understanding the molecular mechanisms of proteins. Membrane protein transporters operate two-state allosteric conformational changes using functionally important cooperative residues that mediate long-range communication from the substrate binding site to the translocation pathway. In this study, we identified functionally important cooperative residues of membrane protein transporters by integrating sequence conservation and co-evolutionary information. A newly derived evolutionary feature, the co-evolutionary coupling number, was introduced to measure the connectivity of co-evolving residue pairs and was integrated with the sequence conservation score. We tested this method on three Major Facilitator Superfamily (MFS) transporters, LacY, GlpT, and EmrD. MFS transporters are an important family of membrane protein transporters, which utilize diverse substrates, catalyze different modes of transport using unique combinations of functional residues, and have enough characterized functional residues to validate the performance of our method. We found that the conserved cores of evolutionarily coupled residues are involved in specific substrate recognition and translocation of MFS transporters. Furthermore, a subset of the residues forms an interaction network connecting functional sites in the protein structure. We also confirmed that our method is effective on other membrane protein transporters. Our results provide insight into the location of functional residues important for the molecular mechanisms of membrane protein transporters.     

植物寡肽运输与硝酸根运输基因家族的研究进展

氮素是植物生长发育的重要营养元素,也是限制植物生物量尤其是经济产量的关键营养元素之一.植物不仅能从外界获取无机氮素(硝酸根、铵根和尿素等),还能以氨基酸、寡肽等形式获取有机氮素.植物已进化出复杂的运输系统来吸收与运输这些含氮化合物.硝酸根运输基因家族分为低亲和力硝酸根运输基因(low-affmity nitrate t...     

Characterization of Sialyl and Galactosyl Residues on the Body Wall of Different Plant Parasitic Nematodes

The plant parasitic nematodes Helicotylenchus multicinctus, Meloidogyne javanica, Tylenchulus semipenetrans, and Xiphinema index, differing in their host specificity and parasitic habits, were analyzed as to their cuticle surface sialyl, galaclosyl, and/or N-acetylgalactosaminyl residues. The procedure involved the selective oxidation of sialic acid and galactose/N-acetylgal-actosamine residues using periodate and galactose oxidase, respectively, to form reactive aldehyde groups. These functional groups were coupled directly with a new hydrazide-containing compound, the fluorescent reagent lissamine rhodamine-β-alanine hydrazide, or they were utilized to introduce DPN-groups to the nematode cuticle. The distribution of the DNP-tagged glycoconjugates was visualized by treating the nematodes with rabbit anti-DNP antibody and staining with fluorescein isothiocyanate (FITC)-labeled goat antirabbit IgG. Sialo residues were observed along the entire outer body wall of the first three aforementioned nematodes, but there were some differences in reaction among the various life stages within the species. In X. index, sialo residues were sited in the tail and head areas, mainly on the lips, oral opening, amphid apertures and stylet. Galactose oxidase treatments revealed galactose on N-acytylgalactosamine residues on T. sentipenetrans and X. index, but there were no indications that their presence was dependent on the developmental stage. Trypsin, pronase, and neuraminidase pretreatment completely abolished the fluorescence in T. semipenetrans but did not alter the sialo residue binding reaction in H. multicinctus or M. javanica, indicating possible differences in the outer body wall saccharide structure and composition between these nematodes. The existence and nature of sugar residues on the cuticle surface of nematodes could contribute to an understanding of the specific recognition by phytophagous nematodes of their host, and perhaps also of the virus transmission mechanism in those nematodes which serve as vectors.     

Nonmitochondrial ATP/ADP Transporters Accept Phosphate as Third Substrate

Chlamydiales and Rickettsiales as metabolically impaired, intracellular pathogenic bacteria essentially rely on “energy parasitism” by the help of nucleotide transporters (NTTs). Also in plant plastids NTT-type carriers catalyze ATP/ADP exchange to fuel metabolic processes. The uptake of ATP^4-, followed by energy consumption and the release of ADP^3-, would lead to a metabolically disadvantageous accumulation of negative charges in form of inorganic phosphate (P_i) in the bacterium or organelle if no interacting P_i export system exists. We identified that P_i is a third substrate of several NTT-type ATP/ADP transporters. During adenine nucleotide hetero-exchange, P_i is cotransported with ADP in a one-to-one stoichiometry. Additionally, P_i can be transported in exchange with solely P_i. This P_i homo-exchange depends on the presence of ADP and provides a first indication for only one binding center involved in import and export. Furthermore, analyses of mutant proteins revealed that P_i interacts with the same amino acid residue as the γ-phosphate of ATP. Import of ATP in exchange with ADP plus P_i is obviously an efficient way to couple energy provision with the export of the two metabolic products (ADP plus P_i) and to maintain cellular phosphate homeostasis in intracellular living “energy parasites” and plant plastids. The additional P_i transport capacity of NTT-type ATP/ADP transporters makes the existence of an interacting P_i exporter dispensable and might explain why a corresponding protein so far has not been identified.Most organisms possess the capacity to resynthesize the fundamental energy currency ATP by fusion of ADP and P_i. Generally, in eukaryotes the major part of energy is produced in specialized organelles, the mitochondria. Mitochondrial ADP/ATP carriers (AACs)² mediate the export of newly synthesized ATP in strict counter-exchange with cytosolic ADP and therefore provide energy to the cellular metabolism (1). Plants additionally generate high amounts of ATP during photosynthesis in chloroplasts. However, under conditions of limiting or missing photosynthetic activity, plant plastids depend on external energy supply (2–4). Specific nucleotide transporters (NTTs) located in the inner plastid envelope membrane mediate the required energy import (5). These transporters structurally, functionally, and phylogenetically differ from mitochondrial AACs. They catalyze the import of cytosolic ATP in exchange with stromal ADP, are monomers consisting of 12 predicted transmembrane helices, and are related to the functionally heterogeneous group of bacterial NTTs (5).Although most prokaryotic organisms are able to regenerate ATP and therefore are considered as energetically self-sustaining, the obligate intracellular living bacterial orders Chlamydiales and Rickettsiales are impaired in energy and nucleotide synthesis or even completely lost the corresponding pathways (6–8). Therefore, these bacteria, which comprise important human pathogens (9, 10), essentially rely on nucleotide and energy import. Bacterial NTTs catalyze the required import of a broad range of nucleotides and NAD or facilitate the counter-exchange of ATP and ADP (5, 11–15). The latter process has been termed “energy parasitism” and obviously is of high importance for the survival of rickettsial and chlamydial cells (5, 16–18).Although import measurements on intact Escherichia coli cells expressing the corresponding proteins allowed characterization of many bacterial and plastidial NTTs (12–15, 19–24), a very important physiological question is still not clarified. The uptake of ATP^4- in exchange with ADP^3- in absence of a concerted P_i export would result in a charge difference and a phosphate imbalance in the bacterial cell. In mitochondria, phosphate carriers metabolically cooperate with AACs because they provide P_i for ATP synthesis (25). Similarly, it was assumed that NTT-type ATP/ADP transporters cooperate with phosphate exporters to guarantee phosphate homeostasis in the bacterium or plastid. However, a P_i exporter interacting with ATP/ADP transporters is not known in “energy parasites” or plant plastids. Bacterial and plant phosphate transport systems rather facilitate P_i import or the counter-exchange of P_i and phosphorylated compounds and therefore do not allow net P_i export (26–29). Furthermore, the newly identified plastidial (proton-driven) phosphate transporters are not preferentially expressed under conditions or in tissues that require ATP provision to the plastid (30, 31).Recently, we succeeded in the purification of the first recombinant NTT from Protochlamydia amoebophila (PamNTT1), a parachlamydial endosymbiont of the protist Acantamoeba (32). The functional reconstitution of the highly pure PamNTT1 into artificial lipid vesicles for the first time allowed the biochemical characterization of a representative nonmitochondrial ATP/ADP transporter unaffected by the complex metabolic situation of the bacterial cell. We demonstrated that in contrast to mitochondrial AACs, PamNTT1 catalyzes a membrane potential independent, electroneutral adenine nucleotide hetero-exchange (32, 33). The latter could argue for a cotransport of a counterion compensating for the electrogenic ATP^4-/ADP^3- exchange.Here, we investigated possible ions accompanying ATP or ADP transport. Interestingly, we uncovered that PamNTT1 and also rickettsial and plastidial ATP/ADP transporters accept an additional important substrate, which is P_i. We performed a comprehensive characterization of the P_i transport and gained new insights into the transport properties of ATP/ADP transporters.     

Identification of Glucose Transporters in Aspergillus nidulans

To characterize the mechanisms involved in glucose transport, in the filamentous fungus Aspergillus nidulans, we have identified four glucose transporter encoding genes hxtB-E. We evaluated the ability of hxtB-E to functionally complement the Saccharomyces cerevisiae EBY.VW4000 strain that is unable to grow on glucose, fructose, mannose or galactose as single carbon source. In S. cerevisiae HxtB-E were targeted to the plasma membrane. The expression of HxtB, HxtC and HxtE was able to restore growth on glucose, fructose, mannose or galactose, indicating that these transporters accept multiple sugars as a substrate through an energy dependent process. A tenfold excess of unlabeled maltose, galactose, fructose, and mannose were able to inhibit glucose uptake to different levels (50 to 80 %) in these s. cerevisiae complemented strains. Moreover, experiments with cyanide-m-chlorophenylhydrazone (CCCP), strongly suggest that hxtB, -C, and –E mediate glucose transport via active proton symport. The A. nidulans ΔhxtB, ΔhxtC or ΔhxtE null mutants showed ~2.5-fold reduction in the affinity for glucose, while ΔhxtB and -C also showed a 2-fold reduction in the capacity for glucose uptake. The ΔhxtD mutant had a 7.8-fold reduction in affinity, but a 3-fold increase in the capacity for glucose uptake. However, only the ΔhxtB mutant strain showed a detectable decreased rate of glucose consumption at low concentrations and an increased resistance to 2-deoxyglucose.     

Amphetamine and Methamphetamine Differentially Affect Dopamine Transporters in Vitro and in Vivo

The psychostimulants d-amphetamine (AMPH) and methamphetamine (METH) release excess dopamine (DA) into the synaptic clefts of dopaminergic neurons. Abnormal DA release is thought to occur by reverse transport through the DA transporter (DAT), and it is believed to underlie the severe behavioral effects of these drugs. Here we compare structurally similar AMPH and METH on DAT function in a heterologous expression system and in an animal model. In the in vitro expression system, DAT-mediated whole-cell currents were greater for METH stimulation than for AMPH. At the same voltage and concentration, METH released five times more DA than AMPH and did so at physiological membrane potentials. At maximally effective concentrations, METH released twice as much [Ca²⁺]_i from internal stores compared with AMPH. [Ca²⁺]_i responses to both drugs were independent of membrane voltage but inhibited by DAT antagonists. Intact phosphorylation sites in the N-terminal domain of DAT were required for the AMPH- and METH-induced increase in [Ca²⁺]_i and for the enhanced effects of METH on [Ca²⁺]_i elevation. Calmodulin-dependent protein kinase II and protein kinase C inhibitors alone or in combination also blocked AMPH- or METH-induced Ca²⁺ responses. Finally, in the rat nucleus accumbens, in vivo voltammetry showed that systemic application of METH inhibited DAT-mediated DA clearance more efficiently than AMPH, resulting in excess external DA. Together these data demonstrate that METH has a stronger effect on DAT-mediated cell physiology than AMPH, which may contribute to the euphoric and addictive properties of METH compared with AMPH.The dopamine transporter (DAT)³ is a main target for psychostimulants, such as d-amphetamine (AMPH), methamphetamine (METH), cocaine (COC), and methylphenidate (Ritalin®). DAT is the major clearance mechanism for synaptic dopamine (DA) (1) and thereby regulates the strength and duration of dopaminergic signaling. AMPH and METH are substrates for DAT and competitively inhibit DA uptake (2, 3) and release DA through reverse transport (4–9). AMPH- and METH-induced elevations in extracellular DA result in complex neurochemical changes and profound psychiatric effects (2, 10–16). Despite their structural and pharmacokinetic similarities, a recent National Institute on Drug Abuse report describes METH as a more potent stimulant than AMPH with longer lasting effects at comparable doses (17). Although the route of METH administration and its availability must contribute to the almost four times higher lifetime nonmedical use of METH compared with AMPH (18), there may also be differences in the mechanisms that underlie the actions of these two drugs on the dopamine transporter.Recent studies by Joyce et al. (19) have shown that compared with d-AMPH alone, the combination of d- and l-AMPH in Adderall® significantly prolonged the time course of extracellular DA in vivo. These experiments demonstrate that subtle structural features of AMPH, such as chirality, can affect its action on dopamine transporters. Here we investigate whether METH, a more lipophilic analog of AMPH, affects DAT differently than AMPH, particularly in regard to stimulated DA efflux.METH and AMPH have been reported as equally effective in increasing extracellular DA levels in rodent dorsal striatum (dSTR), nucleus accumbens (NAc) (10, 14, 20), striatal synaptosomes, and DAT-expressing cells in vitro (3, 6). John and Jones (21), however, have recently shown in mouse striatal and substantia nigra slices, that AMPH is a more potent inhibitor of DA uptake than METH. On the other hand, in synaptosomes METH inhibits DA uptake three times more effectively than AMPH (14), and in DAT-expressing COS-7 cells, METH releases DA more potently than AMPH (EC₅₀ = 0.2 μm for METH versus EC₅₀ = 1.7 μm for AMPH) (5). However, these differences do not hold up under all conditions. For example, in a study utilizing C6 cells, the disparity between AMPH and METH was not found (12).The variations in AMPH and METH data extend to animal models. AMPH- and METH-mediated behavior has been reported as similar (22), lower (20), or higher (23) for AMPH compared with METH. Furthermore, although the maximal locomotor activation response was less for METH than for AMPH at a lower dose (2 mg/kg, intraperitoneal), both drugs decreased locomotor activity at a higher dose (4 mg/kg) (20). In contrast, in the presence of a salient stimuli, METH is more potent in increasing the overall magnitude of locomotor activity in rats yet is equipotent with AMPH in the absence of these stimuli (23).The simultaneous regulation of DA uptake and efflux by DAT substrates such as AMPH and METH, as well as the voltage dependence of DAT (24), may confound the interpretation of existing data describing the action of these drugs. Our biophysical approaches allowed us to significantly decrease the contribution of DA uptake and more accurately determine DAT-mediated DA efflux with millisecond time resolution. We have thus exploited time-resolved, whole-cell voltage clamp in combination with in vitro and in vivo microamperometry and Ca²⁺ imaging to compare the impact of METH and AMPH on DAT function and determine the consequence of these interactions on cell physiology.We find that near the resting potential, METH is more effective than AMPH in stimulating DAT to release DA. In addition, at efficacious concentrations METH generates more current, greater DA efflux, and higher Ca²⁺ release from internal stores than AMPH. Both METH-induced or the lesser AMPH-induced increase in intracellular Ca²⁺ are independent of membrane potential. The additional Ca²⁺ response induced by METH requires intact phosphorylation sites in the N-terminal domain of DAT. Finally, our in vivo voltammetry data indicate that METH inhibits clearance of locally applied DA more effectively than AMPH in the rat nucleus accumbens, which plays an important role in reward and addiction, but not in the dorsal striatum, which is involved in a variety of cognitive functions. Taken together these data imply that AMPH and METH have distinguishable effects on DAT that can be shown both at the molecular level and in vivo, and are likely to be implicated in the relative euphoric and addictive properties of these two psychostimulants.     

Energy Coupling Factor-Type ABC Transporters for Vitamin Uptake in Prokaryotes

Energy coupling factor (ECF) transporters are a subgroup of ATP-binding cassette (ABC) transporters involved in the uptake of vitamins and micronutrients in prokaryotes. In contrast to classical ABC importers, ECF transporters do not make use of water-soluble substrate binding proteins or domains but instead employ integral membrane proteins for substrate binding (named S-components). S-components form active translocation complexes with the ECF module, an assembly of two nucleotide-binding domains (NBDs, or EcfA) and a second transmembrane protein. In some cases, the ECF module is dedicated to a single S-component, but in many cases, the ECF module can interact with several different S-components that are unrelated in sequence and bind diverse substrates. The modular organization with exchangeable S-components on a single ECF module allows the transport of chemically different substrates via a common route. The recent determination of the crystal structures of the S-components that recognize thiamin and riboflavin has provided a first clue about the mechanism of S-component exchange. This review describes recent advances and the current views of the mechanism of transport by ECF transporters.     

ATP Binding to the C Terminus of the Arabidopsis thaliana Nitrate/Proton Antiporter, AtCLCa, Regulates Nitrate Transport into Plant Vacuoles

Nitrate, one of the major nitrogen sources for plants, is stored in the vacuole. Nitrate accumulation within the vacuole is primarily mediated by the NO₃⁻/H⁺ exchanger AtCLCa, which belongs to the chloride channel (CLC) family. Crystallography analysis of hCLC5 suggested that the C-terminal domain, composed by two cystathionine β-synthetase motifs in all eukaryotic members of the CLC family is able to interact with ATP. However, interaction of nucleotides with a functional CLC protein has not been unambiguously demonstrated. Here we show that ATP reversibly inhibits AtCLCa by interacting with the C-terminal domain. Applying the patch clamp technique to isolated Arabidopsis thaliana vacuoles, we demonstrate that ATP reduces AtCLCa activity with a maximum inhibition of 60%. ATP inhibition of nitrate influx into the vacuole at cytosolic physiological nitrate concentrations suggests that ATP modulation is physiologically relevant. ADP and AMP do not decrease the AtCLCa transport activity; nonetheless, AMP (but not ADP) competes with ATP, preventing inhibition. A molecular model of the C terminus of AtCLCa was built by homology to hCLC5 C terminus. The model predicted the effects of mutations of the ATP binding site on the interaction energy between ATP and AtCLCa that were further confirmed by functional expression of site-directed mutated AtCLCa.Nitrate is among the major nitrogen sources for plants in aerobic soils. It is taken up by root cells through plasma membrane transporters of nitrate-nitrite transporter and peptide transporter families. Once in the cytoplasm it can enter the amino acid biosynthesis pathway (1) or be accumulated in the vacuolar lumen via tonoplast transporters (2).The vacuolar nitrate transporter of the model plant Arabidopsis thaliana, AtCLCa, has been shown to work as an anion/proton antiporter (3, 4), similarly to the bacterial CLCec-1 (5) and human hCLC-4 (6) as well as hCLC-5 (7). However, whereas bacterial and animal CLCs² transport chloride ions, the AtCLCa antiporter is more selective for nitrate, and therefore, it is able to mediate the accumulation of nitrate into the plant vacuole.Little is known on the modulation of CLC-proteins by nucleotides. The effects of ATP on the ion channel hCLC-1 are a matter of debate (8). Indeed, some reports have shown that ATP inhibits hCLC-1 currents, probably interacting with the C terminus of the protein (9–11). Conversely, other reports indicate that ATP does not modify the properties of hCLC-1 current (12). This discrepancy has been attributed to the oxidation state of the channel, as ATP would be effective only in the presence of reducing agents (13).The C terminus domain of all eukaryotic CLC proteins has two cystathionine β-synthetase motifs (CBS (14, 15)), each one characterized by a βαββα topology (16, 17). A structural and biochemical study of the hCLC-5 C-terminal part demonstrates that this region binds nucleotides (14). However, the effect of ATP binding on the transport activity of hCLC-5 is still unknown.The presence of analogous CBS domains in the C terminus of the AtCLCa antiporter suggested the hypothesis that ATP binds to this plant transporter and modulates its transport activity. Hence, we undertook a functional analysis of the effect of adenosine nucleotides on AtCLCa and found that ATP inhibits the AtCLCa-mediated transport. Based on a homology model of the C terminus of the channel, we identified two residues that would be putatively involved in the protein-nucleotide interaction.     

Lipo-Chitin Oligosaccharides,Plant Symbiosis Signalling Molecules That Modulate Mammalian Angiogenesis In Vitro

Lipochitin oligosaccharides (LCOs) are signaling molecules required by ecologically and agronomically important bacteria and fungi to establish symbioses with diverse land plants. In plants, oligo-chitins and LCOs can differentially interact with different lysin motif (LysM) receptors and affect innate immunity responses or symbiosis-related pathways. In animals, oligo-chitins also induce innate immunity and other physiological responses but LCO recognition has not been demonstrated. Here LCO and LCO-like compounds are shown to be biologically active in mammals in a structure dependent way through the modulation of angiogenesis, a tightly-regulated process involving the induction and growth of new blood vessels from existing vessels. The testing of 24 LCO, LCO-like or oligo-chitin compounds resulted in structure-dependent effects on angiogenesis in vitro leading to promotion, or inhibition or nil effects. Like plants, the mammalian LCO biological activity depended upon the presence and type of terminal substitutions. Un-substituted oligo-chitins of similar chain lengths were unable to modulate angiogenesis indicating that mammalian cells, like plant cells, can distinguish between LCOs and un-substituted oligo-chitins. The cellular mode-of-action of the biologically active LCOs in mammals was determined. The stimulation or inhibition of endothelial cell adhesion to vitronectin or fibronectin correlated with their pro- or anti-angiogenic activity. Importantly, novel and more easily synthesised LCO-like disaccharide molecules were also biologically active and de-acetylated chitobiose was shown to be the primary structural basis of recognition. Given this, simpler chitin disaccharides derivatives based on the structure of biologically active LCOs were synthesised and purified and these showed biological activity in mammalian cells. Since important chronic disease states are linked to either insufficient or excessive angiogenesis, LCO and LCO-like molecules may have the potential to be a new, carbohydrate-based class of therapeutics for modulating angiogenesis.     

Importance of a Small N-Terminal Region in Mammalian Peptide Transporters for Substrate Affinity and Function

The two closely related, proton-coupled, electrogenic mammalian peptide transporters PEPT1 and PEPT2 differ substantially in substrate affinity and mode of function. The intestinal carrier PEPT1 has a lower affinity for most substrates than the isoform PEPT2 that is expressed in kidney, lung, brain and other tissues. A previous analysis of PEPT1-PEPT2 chimeras has suggested that the N-terminal half of the carrier proteins is important for substrate affinity. We constructed and analyzed new PEPT1-PEPT2 chimeras for identifying smaller segments within the N-terminal region of the transporter proteins that contribute to the kinetic properties. The first 59 or 91 amino-acid residues of PEPT1 were used to replace the corresponding region in PEPT2 leading to the chimeras CH3 and CH4, which could be analyzed when expressed in Xenopus laevis oocytes. Substrate affinities of both chimeras for the zwitterionic substrate D-Phe-Ala ranged between those that are characteristic for either PEPT1 or PEPT2, but when charged dipeptide substrates were employed, both chimeras possessed PEPT1-like affinities. The chimera CH3 carrying the N-terminal 59 amino-acid residues of PEPT1 exhibited a PEPT2-like phenotype with respect to pHout-dependency as well as to the current-voltage relationship of inward currents. In the chimera CH4 possessing the 91 amino-terminal residues of PEPT1, a pronounced alteration in the pHout-dependence was observed, with highest transport rates occurring at pH values as low as pH 4.0. Based on this analysis, we propose that the two identified aminoterminal regions in mammalian peptide carriers play an important role in determining the substrate affinity and also other characteristic features of the two transporter subtypes.