Etana Padan

Structure of a Na+/H+ antiporter and insights into mechanism of action and regulation by pH

The control by Na+/H+ antiporters of sodium/proton concentration and cell volume is crucial for the viability of all cells. Adaptation to high salinity and/or extreme pH in plants and bacteria or in human heart muscles requires the action of Na+/H+ antiporters. Their activity is tightly controlled by pH. Here we present the crystal structure of pH-downregulated NhaA, the main antiporter of Escherichia coli and many enterobacteria. A negatively charged ion funnel opens to the cytoplasm and ends in the middle of the membrane at the putative ion-binding site. There, a unique assembly of two pairs of short helices connected by crossed, extended chains creates a balanced electrostatic environment. We propose that the binding of charged substrates causes an electric imbalance, inducing movements, that permit a rapid alternating-access mechanism. This ion-exchange machinery is regulated by a conformational change elicited by a pH signal perceived at the entry to the cytoplasmic funnel.

Molecular aspects of bacterial pH sensing and homeostasis.

Diverse mechanisms for pH sensing and cytoplasmic pH homeostasis enable most bacteria to tolerate or grow at external pH values that are outside the cytoplasmic pH range they must maintain for growth. The most extreme cases are exemplified by the extremophiles that inhabit environments with a pH of below 3 or above 11. Here, we describe how recent insights into the structure and function of key molecules and their regulators reveal novel strategies of bacterial pH homeostasis. These insights may help us to target certain pathogens more accurately and to harness the capacities of environmental bacteria more efficiently.

Na+/H+ antiporters

Na(+)/H(+) antiporters are membrane proteins that play a major role in pH and Na(+) homeostasis of cells throughout the biological kingdom, from bacteria to humans and higher plants. The emerging genomic sequence projects already have started to reveal that the Na(+)/H(+) antiporters cluster in several families. Structure and function studies of a purified antiporter protein have as yet been conducted mainly with NhaA, the key Na(+)/H(+) antiporter of Escherichia coli. This antiporter has been overexpressed, purified and reconstituted in a functional form in proteoliposomes. It has recently been crystallized in both 3D as well as 2D crystals. The NhaA 2D crystals were analyzed by cryoelectron microscopy and a density map at 4 A resolution was obtained and a 3D map was reconstructed. NhaA is shown to exist in the 2D crystals as a dimer of monomers each composed of 12 transmembrane segments with an asymmetric helix packing. This is the first insight into the structure of a polytopic membrane protein. Many Na(+)/H(+) antiporters are characterized by very dramatic sensitivity to pH, a property that corroborates their role in pH homeostasis. The molecular mechanism underlying this pH sensitivity has been studied in NhaA. Amino acid residues involved in the pH response have been identified. Conformational changes transducing the pH change into a change in activity were found in loop VIII-IX and at the N-terminus by probing trypsin digestion or binding of a specific monoclonal antibody respectively. Regulation by pH of the eukaryotic Na(+)/H(+) antiporters involves an intricate signal transduction pathway (recently reviewed by Yun et al., Am. J. Physiol. 269 (1995) G1-G11). The transcription of NhaA has been shown to be regulated by a novel Na(+)-specific regulatory network. It is envisaged that interdisciplinary approaches combining structure, molecular and cell biology as well as genomics should be applied in the future to the study of this important group of transporters.

Projection structure of NhaA, a secondary transporter from Escherichia coli, at 4.0 A resolution.

Electron cryomicroscopy of frozen‐hydrated two‐dimensional crystals of NhaA, a Na+/H+ antiporter from Escherichia coli predicted to have 12 transmembrane α‐helices, has facilitated the calculation of a projection map of NhaA at 4.0 Å resolution. NhaA was homologously expressed in E.coli with a His6 tag, solubilized in dodecyl maltoside and purified in a single step using Ni2+ affinity chromatography. Two‐dimensional crystals were obtained after reconstitution of purified protein with E.coli lipids. The projection map reveals that this secondary transporter has a highly asymmetric structure in projection. NhaA exhibits overall dimensions of ∼38×48 Å with a ring‐shaped density feature probably corresponding to a bundle of tilted helices, adjacent to an elongated region of density containing several peaks indicative of transmembrane helices. Two crystal forms with p22121 symmetry show tightly packed dimers of NhaA which differ in the interactions between adjacent dimers. This work provides the first direct glimpse into the structure of a secondary transporter.

Primary production in a desert-enclosed sea— the Gulf of Elat (Aqaba), Red Sea

Abstract Chlorophyll a , primary production, nutrient levels, and microphytoplankton abundances were determined during 1976 and 1977 in the northern basin of the Gulf of Elat (Aqaba). During most of the year (April–November) the photic zone extends to great depth (170 m) and is oligotrophic (chl. a 16 to 54 mg m −2 , primary production 200 to 900 mg C m −2 day −1 ). During winter (mainly December to March) the upper waters are much more productive (chl. a 33 to 70 mg m −2 , primary production 690 to 1,120 mg C m −2 day −1 ). The seasonal pattern is also expressed in the depth-distribution of these parameters. Overall the gulf is moderately productive, averaging 160 g C m −2 year −1 . The biological characteristics are closely related to nutrient distribution in the water column. Nutrient distribution is determined by the circulation regime in the gulf, which is stratified in summer and mixed in winter. Phytoplankton blooms following peaks of the NO 2 + NO 3 − N and of N/P ratios suggest that nitrogen is the major limiting factor. There is also an increase in productivity from the open waters towards the coral reef, as well as from the northern to the southern basin at the approaches to the more productive Red Sea proper.

Histidine 225, a Residue of the NhaA-Na+/H+ Antiporter of Escherichia coli Is Exposed and Faces the Cell Exterior

Cysteine residues were found nonessential in the mechanism of the NhaA antiporter activity of Escherichia coli. The functional C-less NhaA has provided the groundwork to study further histidine 225 of NhaA which has previously been suggested to play an important role in the activation of NhaA at alkaline pH (Rimon, A., Gerchman, Y., Olami, Y., Schuldiner, S. and Padan, E. (1995) J. Biol. Chem. 270, 26813-26817). C-less H225C was constructed and shown to possess an antiporter activity 60% of that of C-less antiporter and a pH profile similar to that of both the C-less or wild-type antiporters. Remarkably, whereas neither the wild-type nor the C-less antiporters were affected by N-ethylmaleimide, C-less H225C was inhibited by this reagent. To determine the degree of alkylation of the antiporter protein by N-ethylmaleimide, antiporter derivatives tagged at their C termini with six histidines residues were constructed. Alkylation of C-less H225C was measured by labeling of everted membrane vesicles with [14C]N-ethylmaleimide, affinity purification of the His-tagged antiporter, and determination of the radioactivity of the purified protein. This assay showed that H225C is alkylated to a much higher level than any of the native cysteinyl residues of NhaA reaching saturation at alkyl/NhaA stoichiometry of 1. The wild-type derivative showed at least 10-fold less alkylation even at higher concentrations, suggesting that H225C resides in a domain that is much more exposed to N-ethylmaleimide than the native cysteinyl residues of NhaA. Since H225C residues both in right-side out and inside-out membrane vesicles were quantitatively alkylated by N-ethylmaleimide, this assay was used to determine the accessibility of H225C to other SH reagents by titrating the H225C left free to react with N-ethylmaleimide, following exposure of the membranes to the reagents. Furthermore, since membrane-impermeant probes can react with residues in membrane-embedded protein only if accessible to the medium containing the reagent, the assay was used to determine the membrane topology of H225C. As expected for a membrane-permeant probe, p-chloromercuribenzoate reacted with H225C as efficiently as N-ethylmaleimide in both membrane orientations. Similar results were obtained with methanethiosulfonate ethylammonium supporting the recent observations that this probe is membrane-permeant. On the other hand, both membrane-impermeant reagents p-chloromercuribenzosulfonate and methanethiosulfonate ethyl-trimethyl ammonium bromide reacted with H225C 10-fold more in right-side out than in inside-out vesicles, and p-chloromercuribenzosulfonate also blocked completely the H225C in intact cells. These results strongly suggest that H225C is exposed at the periplasmic face of the membrane.

Do physiological roles foster persistence of drug/multidrug-efflux transporters? A case study

Drug and multidrug resistance have greatly compromised the compounds that were once the mainstays of antibiotic therapy. This resistance often persists despite reductions in the use of antibiotics, indicating that the proteins encoded by antibiotic-resistance genes have alternative physiological roles that can foster such persistence in the absence of selective pressure by antibiotics. The recent observations that Tet(L), a tetracycline-efflux transporter, and MdfA, a multidrug-efflux transporter, both confer alkali tolerance offer a striking case study in support of this hypothesis.

Model Structure of the Na+/H+ Exchanger 1 (NHE1) FUNCTIONAL AND CLINICAL IMPLICATIONS

Eukaryotic Na+/H+ exchangers are transmembrane proteins that are vital for cellular homeostasis and play key roles in pathological conditions such as cancer and heart diseases. Using the crystal structure of the Na+/H+ antiporter from Escherichia coli (EcNhaA) as a template, we predicted the three-dimensional structure of human Na+/H+ exchanger 1 (NHE1). Modeling was particularly challenging because of the extremely low sequence identity between these proteins, but the model structure is supported by evolutionary conservation analysis and empirical data. It also revealed the location of the binding site of NHE inhibitors; which we validated by conducting mutagenesis studies with EcNhaA and its specific inhibitor 2-aminoperimidine. The model structure features a cluster of titratable residues that are evolutionarily conserved and are located in a conserved region in the center of the membrane; we suggest that they are involved in the cation binding and translocation. We also suggest a hypothetical alternating-access mechanism that involves conformational changes.

The enlightening encounter between structure and function in the NhaA Na+–H+ antiporter

Na(+)-H(+) antiporters are integral membrane proteins that exchange Na(+) for H(+) across the cytoplasmic membrane and many intracellular membranes. They are essential for Na(+), pH, and volume homeostasis, which are processes crucial for cell viability. Accordingly, antiporters are important drug targets in humans and underlie salt resistance in plants. Many Na(+)-H(+) antiporters are tightly regulated by pH. Escherichia coli NhaA, a prototype pH-regulated antiporter, exchanges 2H(+) for 1Na(+) (or Li(+)). The NhaA crystal structure has provided insight into the pH-regulated mechanism of antiporter action and revealed transmembrane segments, which are interrupted by extended mid-membrane chains that have since been found with variations in other ion-transport proteins. This novel structural fold creates a delicately balanced electrostatic environment in the middle of the membrane, which might be essential for ion binding and translocation.

Mechanisms for the uptake of inorganic carbon by two species of symbiont-bearing foraminifera

The mechanisms for uptake of inorganic carbon (Ci) for photosynthesis and calcification of a perforate foraminifer, Amphistegina lobifera Larsen, and an imperforate species, Amphisorus hemprichii Ehrenberg, from the Gulf of Eilat, Red Sea were studied in 1986–1987 using 14C tracer techniques. Total Ci uptake of A. lobifera and photosynthetic carbon uptake of A. hemprichii fit the Hill-Whittingham equation that describes the overall rate of enzymatic reactions that are provided with their substrate through a diffusion barrier. This suggests that diffusion is the rate limiting step for total Ci uptake in A. lobifera. Photosynthesis by the isolated symbionts and uptake of CO32- for calcification obey Michaelis-Menten kinetics indicating that enzymatic reactions determine the rate of the separate processes. Both photosynthesis and calcification can be inhibited without affecting each other. Calcification rates in A. lobifera were optimal at Ca levels around normal seawater concentration and were sensitive to inhibitors of respiratory adenosine triphosphate (ATP) generation and Ca-ATP-ase. This indicates that Ca uptake is also active. Calcification rates of A. hemprichii increased linearly as a function of external Ci concentration over the entire experimental range (0 to 4 mM Ci). In contrast, photosynthetic rates showed Hill-Whittingham type kinetics. The dependence of calcification on the CO32- concentration was also linear, suggesting that its diffusion is the rate limiting step for calcification in A. hemprichii. Increasing Ca concentrations yielded higher calcification rates over the entire range measured (0 to 40 mM Ca). Calcification in A. hemprichii was less sensitive to inhibitors of ATP generation than in A. lobifera, suggesting that in A. hemprichii energy supply is less important for this process.