Switching substrate specificity of AMT/MEP/ Rh proteins

In organisms from all kingdoms of life, ammonia and its conjugated ion ammonium are transported across membranes by proteins of the AMT/Rh family. Efficient and successful growth often depends on sufficient ammonium nutrition. The proteins mediating this transport, the so called Ammonium Transporter (AMT) or Rhesus like (Rh) proteins, share a very similar trimeric overall structure and a high sequence similarity even throughout the kingdoms. Even though structural components of the transport mechanism, like an external substrate recruitment site, an essential twin histidine pore motif, a phenylalanine gate and the hydrophobic pore are strongly conserved and have been analyzed in detail by molecular dynamic simulations and mutational studies, the substrate(s), which pass the central pores of the AMT/Rh subunits, NH₄⁺, NH₃ + H⁺, NH₄⁺ + H⁺ or NH₃, are still a matter of debate for most proteins, including the best characterized AmtB protein from Escherichia coli. The lack of a robust expression system for functional analysis has hampered proof of structural and mutational studies, although the NH₃ transport function for Rh-like proteins is rarely disputed. In plant transporters belonging to the subfamily AMT1, transport is associated with electrical currents, while some plant transporters, notably of the AMT2 type, were suggested to transport NH₃ across the membrane, without associated ionic currents. Here we summarize data in favor of each substrate for the distinct AMT/Rh classes, discuss mutants and how they differ in structure and functionality. A common mechanism with deprotonation and subsequent NH₃ transport through the central subunit pore is suggested.     

Switching substrate specificity of AMT/MEP/ Rh proteins

In organisms from all kingdoms of life, ammonia and its conjugated ion ammonium are transported across membranes by proteins of the AMT/Rh family. Efficient and successful growth often depends on sufficient ammonium nutrition. The proteins mediating this transport, the so called Ammonium Transporter (AMT) or Rhesus like (Rh) proteins, share a very similar trimeric overall structure and a high sequence similarity even throughout the kingdoms. Even though structural components of the transport mechanism, like an external substrate recruitment site, an essential twin histidine pore motif, a phenylalanine gate and the hydrophobic pore are strongly conserved and have been analyzed in detail by molecular dynamic simulations and mutational studies, the substrate(s), which pass the central pores of the AMT/Rh subunits, NH₄⁺, NH₃ + H⁺, NH₄⁺ + H⁺ or NH₃, are still a matter of debate for most proteins, including the best characterized AmtB protein from Escherichia coli. The lack of a robust expression system for functional analysis has hampered proof of structural and mutational studies, although the NH₃ transport function for Rh-like proteins is rarely disputed. In plant transporters belonging to the subfamily AMT1, transport is associated with electrical currents, while some plant transporters, notably of the AMT2 type, were suggested to transport NH₃ across the membrane, without associated ionic currents. Here we summarize data in favor of each substrate for the distinct AMT/Rh classes, discuss mutants and how they differ in structure and functionality. A common mechanism with deprotonation and subsequent NH₃ transport through the central subunit pore is suggested.     

Pore Mutations in Ammonium Transporter AMT1 with Increased Electrogenic Ammonium Transport Activity

AMT/Mep ammonium transporters mediate high affinity ammonium/ammonia uptake in bacteria, fungi, and plants. The Arabidopsis AMT1 proteins mediate uptake of the ionic form of ammonium. AMT transport activity is controlled allosterically via a highly conserved cytosolic C terminus that interacts with neighboring subunits in a trimer. The C terminus is thus capable of modulating the conductivity of the pore. To gain insight into the underlying mechanism, pore mutants suppressing the inhibitory effect of mutations in the C-terminal trans-activation domain were characterized. AMT1;1 carrying the mutation Q57H in transmembrane helix I (TMH I) showed increased ammonium uptake but reduced capacity to take up methylammonium. To explore whether the transport mechanism was altered, the AMT1;1-Q57H mutant was expressed in Xenopus oocytes and analyzed electrophysiologically. AMT1;1-Q57H was characterized by increased ammonium-induced and reduced methylammonium-induced currents. AMT1;1-Q57H possesses a 100× lower affinity for ammonium (K_m) and a 10-fold higher V_max as compared with the wild type form. To test whether the trans-regulatory mechanism is conserved in archaeal homologs, AfAmt-2 from Archaeoglobus fulgidus was expressed in yeast. The transport function of AfAmt-2 also depends on trans-activation by the C terminus, and mutations in pore-residues corresponding to Q57H of AMT1;1 suppress nonfunctional AfAmt-2 mutants lacking the activating C terminus. Altogether, our data suggest that bacterial and plant AMTs use a conserved allosteric mechanism to control ammonium flux, potentially using a gating mechanism that limits flux to protect against ammonium toxicity.All organisms depend on an adequate supply of nutrients, especially nitrogen. For microorganisms and plants, which are able to assimilate ammonium, NH₄⁺ represents the sole bioavailable nitrogen form. (Nitrate use requires enzymatic conversion to ammonia.) Plants preferentially take up ammonium; however, overaccumulation of NH₄⁺ is toxic to microorganisms and plants (1, 2.) Levels above 50 μm become toxic for the central nervous system of most mammals (3, 4). A precise homeostasis of the cellular levels of ammonium is therefore critical.Plant ammonium uptake is mediated by low affinity/high capacity and high affinity/low capacity transporters (5). Nonselective cation channels (2), potassium channels (6), and members of the aquaporin family appear to be able to mediate NH₃/NH₄⁺ low affinity uptake (7–9). High affinity uptake by transporters of the AMT/Mep superfamily is essential at supply levels in the micromolar to low millimolar range (10–12). AMT/Mep ammonium transporter genes were originally identified in yeast and plants by complementation of a yeast mutant deficient in ammonium uptake (13, 14). In contrast to potassium channels, which do not effectively differentiate between potassium and ammonium, AMTs are highly selective for ammonium and its methylated form, methylammonium (MeA).⁶ Plant AMT1 ammonium transporters were shown to be electrogenic when expressed in Xenopus oocytes, suggesting transport of charged NH₄⁺ or co-transport of NH₃ with a proton (15). Quantitation of charge movement and tracer uptake demonstrated that AMT1 transports exclusively the ionic form, i.e. each transported ¹⁴C-MeA molecule corresponded to the transfer of a single positive elementary charge across the membrane (16). The high affinity and low capacity of AMT1, which is too slow to be classified as a channel, suggests that it rather functions as a transporter, with significant conformational changes limiting its turnover numbers. Interestingly, it has been suggested that the bacterial homologs use a different mechanism, in that they mediate transport of uncharged NH₃ (17), although this hypothesis has been disputed (18, 19).Biochemical as well as structural analyses of bacterial and archaeal AMTs revealed a highly stable and conserved trimeric complex (15). Each monomer is composed of 11 transmembrane helices (TMHs) that form a noncontinuous channel through which the substrate can pass. Highly conserved residues are observed in positions that are likely crucial for function: a tryptophan located in a central extracellular surface cleft is thought to be part of a selectivity filter, discriminating K⁺ ions and water molecules from NH₄⁺ via a cation-π interaction and H-bonds via neighboring residues. Below this cleft, a pair of phenylalanines is assumed to function as a gate that blocks the entrance of the channel, which, after that point, appears open to the cytoplasmic side. Two histidines on helices V and VI are in H-bonding distance and line the central part of the channel pathway.Similar to the bacterial Na⁺/leucine and the Na⁺/arabinose transporters (20, 21), AMT monomers are built from an ancient duplication of a subunit of five TMHs, organized as a pseudo-2-fold axis in the membrane plane; in the case of the AMT/Meps, an additional 11th segment M11 (5 + 5 + 1), a 50-Å α-helix, belts the surface of the monomer at an angle of ∼50° relative to the normal vector of the membrane plane and connects to the cytosolic C terminus (17, 23, 24). Recent findings demonstrate that AMTs can exist in active and inactive states, probably controlled by phosphorylation of residues in the conserved C terminus (25).⁷ In the Arabidopsis thaliana AMT1, an allosteric trans-activation is mediated through the interaction of the C termini with cytosolic loops of the neighboring subunits in a trimer (25). This finding is consistent with a novel regulatory mechanism that can provide for rapid shut-off of transport. This feedback loop may potentially be important for protection against ammonium toxicity by limiting peak output, namely ammonium uptake capacity at high external supply. Analysis of >900 AMT homologs shows that the C terminus is highly conserved from cyanobacteria to fungi and plants, indicating that the regulatory mechanism may be conserved (25).A suppressor screen using inactive mutants carrying a mutation in the cytosolic C terminus of AMT1;1 identified mutants that had lost their strict dependence on allosteric trans-activation (25). Here, we show that, when expressed in yeast, some of these mutants show increased ammonium transport capacity. Electrophysiological analysis of one of the pore mutants, AMT1;1-Q57H, demonstrates that transport is still electrogenic and that the increased ammonium sensitivity is due to a conversion from a saturable high affinity kinetic profile to low affinity and high capacity uptake kinetics. Mutation of the corresponding glutamine residue (Q53H) also suppresses an inactive mutant of the archaeal Archaeoglobus fulgidus AfAmt-2, demonstrating the conservation of these mechanisms from archaea to higher plants.     

Uniport of NH4+ by the root hair plasma membrane ammonium transporter LeAMT1;1

The transport of ammonium/ammonia is a key process for the acquisition and metabolism of nitrogen. Ammonium transport is mediated by the AMT/MEP/Rh family of membrane proteins which are found in microorganisms, plants, and animals, including the Rhesus blood group antigens in humans. Although ammonium transporters from all kingdoms have been functionally expressed and partially characterized, the transport mechanism, as well as the identity of the true substrate (NH(4+) or NH(3)) remains unclear. Here we describe the functional expression and characterization of LeAMT1;1, a root hair ammonium transporter from tomato (Lycopersicon esculentum) in Xenopus oocytes. Micromolar concentrations of external ammonium were found to induce concentration- and voltage-dependent inward currents in oocytes injected with LeAMT1;1 cRNA, but not in water-injected control oocytes. The NH(4+)-induced currents were more than 3-fold larger than methylammonium currents and were not subject to inhibition by Na(+) or K(+). The voltage dependence of the affinity of LeAMT1;1 toward its substrate strongly suggests that charged NH(4+), rather than NH(3), is the true transport substrate. Furthermore, ammonium transport was independent of the external proton concentration between pH 5.5 and pH 8.5. LeAMT1;1 is concluded to mediate potential-driven NH(4+) uptake and retrieval depending on root membrane potential and NH(4+) concentration gradient.     

N-terminal cysteines affect oligomer stability of the allosterically regulated ammonium transporter LeAMT1;1

AMMONIUM TRANSPORTER (AMT) proteins are conserved in all domains of life and mediate the transport of ammonium or ammonia across cell membranes. AMTs form trimers and use intermolecular interaction between subunits to regulate activity. So far, binding forces that stabilize AMT protein complexes are not well characterized. High temperature or reducing agents released mono- and dimeric forms from trimeric complexes formed by AMT1;1 from Arabidopsis and tomato. However, in the paralogue LeAMT1;3, trimeric complexes were not detected. LeAMT1;3 differs from the other AMTs by an unusually short N-terminus, suggesting a role for the N-terminus in oligomer stability. Truncation of the N-terminus in LeAMT1;1 destabilized the trimer and led to loss of functionality when expressed in yeast. Swapping of the N-terminus between LeAMT1;1 and LeAMT1;3 showed that sequences in the N-terminus of LeAMT1;1 are necessary and sufficient for stabilization of the interaction among the subunits. Two N-terminal cysteine residues are highly conserved among AMT1 transporters in plants but are lacking in LeAMT1;3. C3S or C27S variants of LeAMT1;1 showed reduced complex stability, which coincided with lower transport capacity for the substrate analogue methylammonium. Both cysteine-substituted LeAMT1;1 variants showed weaker interactions with the wildtype as determined by a quantitative analysis of the complex stability using the mating-based split-ubiquitin assay. These data indicate that the binding affinity of AMT1 subunits is stabilized by cysteines in the N-terminus and suggest a role for disulphide bridge formation via apoplastic N-terminal cysteine residues.     

Ammonium (methylammonium) transport by Klebsiella pneumoniae

Klebsiella pneumoniae can accumulate methylammonium up to 80-fold by means of a transport system as indicated by the energy requirement, saturation kinetics and a narrow pH profile around pH 6.8. Methylammonium transport (apparent $\text{K}{}_{\mathrm{<mtext>m</mtext>}}\text{= 100 μ}\text{M}$, $\text{V = 40 μ}\text{mol/min}$ per g dry weight at 15°C) is competitively inhibited by ammonium (apparent $\text{K}{}_{\mathrm{<mtext>i</mtext>}}\text{= 7 μ}\text{M}$). The low $\text{K}{}_{\mathrm{<mtext>i</mtext>}}$ value and the finding that methylammonium cannot serve as a nitrogen source indicate that ammonium rather than methylammonium is the natural substrate. Uphill transport is driven by a component of the protonmotive force, probably the membrane potential. The transport system is under genetic control; it is partially repressed by amino acids and completely by ammonium. Analysis of mutants suggest that the synthesis of the ammonium transport system is subject to the same ‘nitrogen control’ as nitrogenase and glutamine synthetase.     

Ammonium ion transport by the Na+K+2Cl--cotransporter induces apoptosis in hybridoma cells

Ammonium ions induced significant apoptosis in hybridoma cells that were suspended in PBS containing glucose and glutamine; 40% of the cells became apoptotic within 200 min. In the presence of bumetanide, an inhibitor of the Na+K+2Cl--cotransporter, the ammonium ion induced apoptotic response was completely abolished. This result shows that the inward transport of ammonium ions by the Na+K+2Cl--cotransporter was the sole cause of apoptosis in the ammonium (and ammonia) exposed hybridoma cells.     

Additive contribution of AMT1;1 and AMT1;3 to high-affinity ammonium uptake across the plasma membrane of nitrogen-deficient Arabidopsis roots

In Arabidopsis four root-expressed AMT genes encode functional ammonium transporters, which raises the question of their role in primary ammonium uptake. After pre-culturing under nitrogen-deficiency conditions, we quantified the influx of (15)N-labeled ammonium in T-DNA insertion lines and observed that the loss of either AMT1;1 or AMT1;3 led to a decrease in the high-affinity ammonium influx of approximately 30%. Under nitrogen-sufficient conditions the ammonium influx was lower in Columbia glabra compared with Wassilewskija (WS), and AMT1;1 did not contribute significantly to the ammonium influx in Col-gl. Ectopic expression of AMT1;3 under the control of a 35S promoter in either of the insertion lines amt1;3-1 or amt1;1-1 increased the ammonium influx above the level of their corresponding wild types. In transgenic lines carrying AMT-promoter-GFP constructs, the promoter activities of AMT1;1 and AMT1;3 were both upregulated under nitrogen-deficiency conditions and were localized to the rhizodermis, including root hairs. AMT gene-GFP fusions that were stably expressed under the control of their own promoters were localized to the plasma membrane. The double insertion line amt1;1-1amt1;3-1 showed a decreased sensitivity to the toxic ammonium analog methylammonium and a decrease in the ammonium influx of up to 70% relative to wild-type plants. These results suggest an additive contribution of AMT1;1 and AMT1;3 to the overall ammonium uptake capacity in Arabidopsis roots under nitrogen-deficiency conditions.     

Different transport mechanisms in plant and human AMT/Rh-type ammonium transporters

The conserved family of AMT/Rh proteins facilitates ammonium transport across animal, plant, and microbial membranes. A bacterial homologue, AmtB, forms a channel-like structure and appears to function as an NH₃ gas channel. To evaluate the function of eukaryotic homologues, the human RhCG glycoprotein and the tomato plant ammonium transporter LeAMT1;2 were expressed and compared in Xenopus oocytes and yeast. RhCG mediated the electroneutral transport of methylammonium (MeA), which saturated with K_m = 3.8 mM at pH_o 7.5. Uptake was strongly favored by increasing the pH_o and was inhibited by ammonium. Ammonium induced rapid cytosolic alkalinization in RhCG-expressing oocytes. Additionally, RhCG expression was associated with an alkali-cation conductance, which was not significantly permeable to NH₄⁺ and was apparently uncoupled from the ammonium transport. In contrast, expression of the homologous LeAMT1;2 induced pH_o-independent MeA⁺ uptake and specific NH₄⁺ and MeA⁺ currents that were distinct from endogenous currents. The different mechanisms of transport, including the RhCG-associated alkali-cation conductance, were verified by heterologous expression in appropriate yeast strains. Thus, homologous AMT/Rh-type proteins function in a distinct manner; while LeAMT1;2 carries specifically NH₄⁺, or cotransports NH₃/H⁺, RhCG mediates electroneutral NH₃ transport.     

The Amt/Mep/Rh family of ammonium transport proteins

The Amt/Mep/Rh family of integral membrane proteins comprises ammonium transporters of bacteria, archaea and eukarya, as well as the Rhesus proteins found in animals. They play a central role in the uptake of reduced nitrogen for biosynthetic purposes, in energy metabolism, or in renal excretion. Recent structural information on two prokaryotic Amt proteins has significantly contributed to our understanding of this class, but basic questions concerning the transport mechanism and the nature of the transported substrate, NH3 or [NH4(+)], remain to be answered. Here we review functional and structural studies on Amt proteins and discuss the bioenergetic issues raised by the various mechanistic proposals present in the literature.     

Ammonium and methylammonium transport by the nitrogen-fixing bacterium Azotobacter vinelandii.

Azotobacter vinelandii, grown with NH4+ as nitrogen source, was shown to possess an active transport system which can take up NH4+ against a concentration gradient of 58-fold. The properties of the NH4+ uptake system were investigated with the NH4+ analog CH3NH3+. The use of this analog was justified on the basis of the conclusion that the uptake of NH4+ and CH3NH3 involves a common binding site, as shown by the competitive inhibition of CH3NH3+ uptake by NH4+ (Ki approximately 3 microM). A Lineweaver-Burk plot for CH3NH3+ uptake revealed a biphasic curve, suggesting the existence of two CH3NH3+ (NH4+) uptake systems with apparent Km's for CH3NH3+ equal to 61 microM and 661 microM. The uptake of CH3NH3+ was inhibited by arsenate, as well as by cyanide or carbonyl cyanide-m-chlorophenyl hydrazone, indicating that phosphate bond energy is required.     

Phosphoregulation of the budding yeast EB1 homologue Bim1p by Aurora/Ipl1p

EB1 (end binding 1) proteins have emerged as central regulators of microtubule (MT) plus ends in all eukaryotes, but molecular mechanisms controlling the activity of these proteins are poorly understood. In this study, we show that the budding yeast EB1 protein Bim1p is regulated by Aurora B/Ipl1p-mediated multisite phosphorylation. Bim1p forms a stable complex with Ipl1p and is phosphorylated on a cluster of six Ser residues in the flexible linker connecting the calponin homology (CH) and EB1 domains. Using reconstitution of plus end tracking in vitro and total internal reflection fluorescence microscopy, we show that dimerization of Bim1p and the presence of the linker domain are both required for efficient tip tracking and that linker phosphorylation removes Bim1p from static and dynamic MTs. Bim1 phosphorylation occurs during anaphase in vivo, and it is required for normal spindle elongation kinetics and an efficient disassembly of the spindle midzone. Our results define a mechanism for the use and regulation of CH domains in an EB1 protein.     

Ammonium transport and CitAMT1 expression are regulated by light and sucrose in Citrus plants

Here the isolation and characterization of CitAMT1 cDNA from citrange Troyer (Citrus sinensis L. OsbeckxPoncirus trifoliata Blanco) is reported, suggesting that this belongs to the AMT gene family, which is involved in the high-affinity transport system (HATS). Results show that in Citrus plants, the HATS is much more dependent on the light conditions and C status of the roots than the low-affinity transport system. Most importantly, a strong correlation was found between the regulation of both HATS activity and CitAMT1 expression. CitAMT1 expression is sucrose-stimulated and may account for the regulation of NH(4)(+) HATS. Furthermore, a similar link was also recorded with photosynthetic activity in the shoots, suggesting that the variations in production and transport of photosynthates to the roots are responsible for the diurnal changes of both CitAMT1 expression and NH(4)(+) HATS activity. On the other hand, results indicate that the effect of stimulating light on CitAMT1 expression and NH(4)(+) HATS activity is independent of the circadian rhythm. Finally, CitAMT1 expression seems to be specifically stimulated by sucrose, suggesting that sucrose is a pivotal signal governing both assimilate partitioning from source organs and assimilate utilization in sink organs.     

Distinct transport mechanisms in yeast ammonium transport/sensor proteins of the Mep/Amt/Rh family and impact on filamentation

Ammonium transport proteins of the Mep/Amt/Rh family include microbial and plant Mep/Amt members, crucial for ammonium scavenging, and animal Rhesus factors likely involved in ammonium disposal. Recent structural information on two bacterial Mep/Amt proteins has revealed the presence, in the hydrophobic conducting pore, of a pair of preserved histidines proposed to play an important role in substrate conductance, by participating either in NH(4)(+) deprotonation or in shaping the pore. Here we highlight the existence of two functional Mep/Amt subfamilies distinguishable according to whether the first of these histidines is conserved, as in yeast ScMep2, or replaced by glutamate, as in ScMep1. Replacement of the native histidine of ScMep2 with glutamate leads to conversion from ScMep2 to ScMep1-like properties. This includes a two-unit upshift of the optimal pH for transport and an increase of the transport rate, consistent with alleviation of an energy-limiting step. Similar effects are observed when the same substitution is introduced into the Escherichia coli AmtB protein. In contrast to ScMep1, ScMep2 is proposed to play an additional signaling role in the induction of filamentous growth, a dimorphic change often associated with virulence in pathogenic fungi. We show here that the histidine to glutamate substitution in ScMep2 leads to uncoupling of the transport and sensor functions, suggesting that a ScMep2-specific transport mechanism might be responsible for filamentation. Our overall data suggest the existence of two functional groups of Mep/Amt-type proteins with different transport mechanisms and distinct impacts on cell physiology and signaling.