Rhesus factors and ammonium: a function in efflux?

Completion of fungal, plant and human genomes paved the way to the identification of erythrocytic rhesus proteins and their kidney homologs as ammonium transporters. Ammonium is the preferred nitrogen source of bacteria and fungi, and plants acquire nitrogen from the soil in the form of ammonium [1]. In animals and humans, assimilated forms of nitrogen - amino acids - are much preferred for nutrition, and, in the case of ammonotelic animals, ammonium is used for the excretion of nitrogen instead. In the human kidney, ammonium is produced, reabsorbed and excreted as a means to maintain pH balance and to get rid of surplus inorganic nitrogen. Whether ammonium transport also has a role in the pH regulation of other organs is not known and the molecular mechanisms were not, up to now, understood.

Preferential expression of an ammonium transporter and of two putative nitrate transporters in root hairs of tomato.

Root hairs as specialized epidermal cells represent part of the outermost interface between a plant and its soil environment. They make up to 70% of the root surface and, therefore, are likely to contribute significantly to nutrient uptake. To study uptake systems for mineral nitrogen, three genes homologous to Arabidopsis nitrate and ammonium transporters (AtNrt1 and AtAmt1) were isolated from a root hair-specific tomato cDNA library. Accumulation of LeNrt1-1, LeNrt1-2, and LeAmt1 transcripts was root-specific, with no detectable transcripts in stems or leaves. Expression was root cell type-specific and regulated by nitrogen availability. LeNrt1-2 mRNA accumulation was restricted to root hairs that had been exposed to nitrate. In contrast, LeNrt1-1 transcripts were detected in root hairs as well as other root tissues under all nitrogen treatments applied. Analogous to LeNrt1-1, the gene LeAmt1 was expressed under all nitrogen conditions tested, and root hair-specific mRNA accumulation was highest following exposure to ammonium. Expression of LeAMT1 in an ammonium uptake-deficient yeast strain restored growth on low ammonium medium, confirming its involvement in ammonium transport. Root hair specificity and characteristics of substrate regulation suggest an important role of the three genes in uptake of mineral nitrogen.

Fonction de l'AmtB dans la régulation de la nitrogénase chez Rhodobacter capsulatus

La fixation de l’azote diatomique est un processus très important à la vie, vu sa nécessité dans la biosynthèse de plusieurs molécules de base; acides aminés, acides nucléiques, etc. La réduction de l’azote en ammoniaque est catalysée par la nitrogénase, une enzyme consommatrice de beaucoup d’énergie étant donné qu’elle nécessite 20 à 30 moles d’ATP pour la réduction d’une mole d’azote. De ce fait une régulation rigoureuse est exigée afin de minimiser le gaspillage d’énergie. Plusieurs systèmes de contrôle sont connus, aussi bien au niveau post-traductionnel que traductionnel. Chez la bactérie photosynthétique pourpre non-sulfureuse R. capsulatus, la régulation de l’activité de la nitrogénase nécessite une panoplie de protéines dont la protéine membranaire AmtB, qui est impliquée dans le transport et la perception d’ammonium, et les protéines PII qui jouent plusieurs rôles clés dans la régulation de l’assimilation d’azote. Suite à l’ajout de l’ammonium dans le milieu, une inhibition réversible de l’activité de la nitrogénase est déclenchée via un mécanisme d’ADP-ribosylation de la nitrogénase. La séquestration de GlnK (une protéine PII) par l’AmtB permet à DraT, une ADP-ribosyltransférase, d’ajouter un groupement ADP-ribose sur la protéine-Fe de la nitrogénase l’empêchant ainsi de former un complexe avec la protéine-MoFe. Donc, le transfert d’électrons est bloqué, engendrant ainsi l’inhibition de l’activité de la nitrogénase qui dure aussi long que la concentration d’azote fixé reste élevé, phénomène appelé le « Switch-off/Switch-on » de la nitrogénase. Dans ce mémoire, pour mieux comprendre ce phénomène de régulation, des mutations ponctuelles au niveau de certains résidus conservés de la protéine AmtB, dont D338, G367, H193 et W237, étaient générées par mutagénèse dirigée, afin d’examiner d’avantage leur rôle dans le transport d’ammonium, la formation du complexe AmtB-GlnK, ainsi que dans le « Switch-off » et l’ADP-ribosylation. Les résultats permettent de conclure l’importance et la nécessité de certains résidus telle que le G367 dans la régulation de la nitrogénase et le transport d’ammonium, contrairement au résidu D338 qui ne semble pas être impliqué directement dans la régulation de l’activité de la nitrogénase. Ces résultats suggèrent d’autres hypothèses sur les rôles des acides aminés spécifiques d’AmtB dans ses fonctions comme transporteur et senseur d’ammonium.

The Role of Specific Amino Acids in the Formation of Ternary Complexes in Nitrogenase Regulation in the Photosynthetic Bacterium Rhodobacter capsulatus

L'azote est l'un des éléments les plus essentiels dans le monde pour les êtres vivants, car il est essentiel pour la production des éléments de base de la cellule, les acides aminés, les acides nucléiques et les autres constituants cellulaires. L’atmosphère est composé de 78% d'azote gazeux, une source d'azote inutilisable par la plupart des organismes à l'exception de ceux qui possèdent l’enzyme nitrogénase, tels que les bactéries diazotrophique. Ces micro-organismes sont capables de convertir l'azote atmosphérique en ammoniac (NH3), qui est l'une des sources d'azote les plus préférables. Cette réaction exigeant l’ATP, appelée fixation de l'azote, est catalysée par une enzyme, nitrogénase, qui est l'enzyme la plus importante dans le cycle de l'azote. Certaines protéines sont des régulateurs potentiels de la synthèse de la nitrogénase et de son activité; AmtB, DraT, DraG, les protéines PII, etc.. Dans cette thèse, j'ai effectué diverses expériences afin de mieux comprendre leurs rôles détailés dans Rhodobacter capsulatus. La protéine membranaire AmtB, très répandue chez les archaea, les bactéries et les eucaryotes, est un membre de la famille MEP / Amt / Rh. Les protéines AmtB sont des transporteurs d'ammonium, importateurs d'ammonium externe, et ont également été suggéré d’agir comme des senseurs d'ammonium. Il a été montré que l’AmtB de Rhodobacter capsulatus fonctionne comme un capteur pour détecter la présence d'ammonium externe pour réguler la nitrogénase. La nitrogénase est constituée de deux métalloprotéines nommées MoFe-protéine et Fe-protéine. L'addition d'ammoniaque à une culture R. capsulatus conduit à une série de réactions qui mènent à la désactivation de la nitrogénase, appelé "nitrogénase switch-off". Une réaction critique dans ce processus est l’ajout d’un groupe ADP-ribose à la Fe-protéine par DraT. L'entrée de l'ammoniac dans la cellule à travers le pore AmtB est contrôlée par la séquestration de GlnK. GlnK est une protéine PII et les protéines PII sont des protéines centrales dans la régulation du métabolisme de l'azote. Non seulement la séquestration de GlnK par AmtB est importante dans la régulation nitrogénase, mais la liaison de l'ammonium par AmtB ou de son transport partiel est également nécessaire. Les complexes AmtB-GlnK sont supposés de lier DraG, l’enzyme responsable pour enlever l'ADP-ribose ajouté à la nitrogénase par DraT, ainsi formant un complexe ternaire. Dans cette thèse certains détails du mécanisme de transduction du signal et de transport d'ammonium ont été examinés par la génération et la caractérisation d’un mutant dirigé, RCZC, (D335A). La capacité de ce mutant, ainsi que des mutants construits précédemment, RCIA1 (D338A), RCIA2 (G344C), RCIA3 (H193E) et RCIA4 (W237A), d’effectuer le « switch-off » de la nitrogénase a été mesurée par chromatographie en phase gazeuse. Les résultats ont révélé que tous les résidus d'acides aminés ci-dessus ont un rôle essentiel dans la régulation de la nitrogénase. L’immunobuvardage a également été effectués afin de vérifier la présence de la Fe-protéine l'ADP-ribosylée. D335, D388 et W237 semblent être cruciales pour l’ADP-ribosylation, puisque les mutants RCZC, RCIA1 et RCIA4 n'a pas montré de l’ADP-ribosylation de la Fe-protéine. En outre, même si une légère ADP-ribosylation a été observée pour RCIA2 (G344C), nous le considérons comme un résidu d'acide aminé important dans la régulation de la nitrogénase. D’un autre coté, le mutant RCIA3 (H193E) a montré une ADP-ribosylation de la Fe-protéine après un choc d'ammonium, par conséquent, il ne semble pas jouer un rôle important dans l’ADP-ribosylation. Par ailleurs R. capsulatus possède une deuxième Amt appelé AmtY, qui, contrairement à AmtB, ne semble pas avoir des rôles spécifiques. Afin de découvrir ses fonctionnalités, AmtY a été surexprimée dans une souche d’E. coli manquant l’AmtB (GT1001 pRSG1) (réalisée précédemment par d'autres membres du laboratoire) et la formation des complexes AmtY-GlnK en réponse à l'addition d’ammoniac a été examinée. Il a été montré que même si AmtY est en mesure de transporter l'ammoniac lorsqu'il est exprimé dans E. coli, elle ne peut pass’ associer à GlnK en réponse à NH4 +.

O efeito da complexidade estrutural da fonte de nitrogênio no transporte de amônio em Saccharomyces cerevisiae

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Millennial changes in North American wildfire and soil activity over the last glacial cycle

Climate changes in the North Atlantic region during the last glacial cycle were dominated by the slow waxing and waning of the North American ice sheet as well as by intermittent, millennial-scale Dansgaard–Oeschger climate oscillations. However, prior to the last deglaciation, the responses of North American vegetation and biomass burning to these climate variations are uncertain. Ammonium in Greenland ice cores, a product from North American soil emissions and biomass burning events, can help to fill this gap. Here we use continuous, high-resolution measurements of ammonium concentrations between 110,000 to 10,000 years ago from the Greenland NGRIP and GRIP ice cores to reconstruct North American wildfire activity and soil ammonium emissions. We find that on orbital timescales soil emissions increased under warmer climate conditions when vegetation expanded northwards into previously ice-covered areas. For millennial-scale interstadial warm periods during Marine Isotope Stage 3, the fire recurrence rate increased in parallel to the rapid warmings, whereas soil emissions rose more slowly, reflecting slow ice shrinkage and delayed ecosystem changes. We conclude that sudden warming events had little impact on soil ammonium emissions and ammonium transport to Greenland, but did result in a substantial increase in the frequency of North American wildfires.

Ammonium alters creatine transport and synthesis in a 3D culture of developing brain cells, resulting in secondary cerebral creatine deficiency.

Hyperammonemic disorders in pediatric patients lead to poorly understood irreversible effects on the developing brain that may be life-threatening. We showed previously that some of these NH4+-induced irreversible effects might be due to impairment of axonal growth that can be protected under ammonium exposure by creatine co-treatment. The aim of the present work was thus to analyse how the genes of arginine:glycine amidinotransferase (AGAT) and guanidinoacetate methyltransferase (GAMT), allowing creatine synthesis, as well as of the creatine transporter SLC6A8, allowing creatine uptake into cells, are regulated in rat brain cells under NH4+ exposure. Reaggregated brain cell three-dimensional cultures exposed to NH4Cl were used as an experimental model of hyperammonemia in the developing central nervous system (CNS). We show here that NH4+ exposure differentially alters AGAT, GAMT and SLC6A8 regulation, in terms of both gene expression and protein activity, in a cell type-specific manner. In particular, we demonstrate that NH4+ exposure decreases both creatine and its synthesis intermediate, guanidinoacetate, in brain cells, probably through the inhibition of AGAT enzymatic activity. Our work also suggests that oligodendrocytes are major actors in the brain in terms of creatine synthesis, trafficking and uptake, which might be affected by hyperammonemia. Finally, we show that NH4+ exposure induces SLC6A8 in astrocytes. This suggests that hyperammonemia increases blood-brain barrier permeability for creatine. This is normally limited due to the absence of SLC6A8 from the astrocyte feet lining microcapillary endothelial cells, and thus creatine supplementation may protect the developing CNS of hyperammonemic patients.

Rôle d'AmtB dans la régulation posttraductionnelle de la nitrogénase et le transport de l'ammonium chez Rhodobacter capsulatus

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal.

Ionic Transport and Water Vapor Uptake of Ammonium Exchanged Perfluorosulfonic Acid Membranes

Nafion membranes series N117 doped with ammonium, at different cation fractions (H+/NH4+), were investigated for ionic transport and water vapor uptake, for several water activities and temperatures. Ammonium cations change both properties of the polymer in a similar manner. Membrane ionic conductivity and water vapor uptake (lambda) decrease as the ammonium concentration increases in the polymer. Ionic transport activation energies are calculated and the transport mechanism of ammonium ions in Nafion is discussed. (C) 2012 The Electrochemical Society. [DOI: 10.1149/2.040203jes] All rights reserved.

Ammonia acquisition in enteric bacteria: Physiological role of the ammonium/methylammonium transport B (AmtB) protein

Homologues of the amtB gene of enteric bacteria exist in all three domains of life. Although their products are required for transport of the ammonium analogue methylammonium in washed cells, only in Saccharomyces cerevisiae have they been shown to be necessary for growth at low NH4+ concentrations. We now demonstrate that an amtB strain of Escherichia coli also grows slowly at low NH4+ concentrations in batch culture, but only at pH values below 7. In addition, we find that the growth defect of an S. cerevisiae triple-mutant strain lacking the function of three homologues of the ammonium/methylammonium transport B (AmtB) protein [called methylammonium/ammonium permeases (MEP)] that was observed at pH 6.1 is relieved at pH 7.1. These results provide direct evidence that AmtB participates in acquisition of NH4+/NH3 in bacteria as well as eucarya. Because NH3 is the species limiting at low pH for a given total concentration of NH4+ + NH3, results with both organisms indicate that AmtB/MEP proteins function in acquisition of the uncharged form. We confirmed that accumulation of [14C]methylammonium depends on its conversion to γ-N-methylglutamine, an energy-requiring reaction catalyzed by glutamine synthetase, and found that at pH 7, constitutive expression of AmtB did not relieve the growth defects of a mutant strain of Salmonella typhimurium that appears to require a high internal concentration of NH4+/NH3. Hence, contrary to previous views, we propose that AmtB/MEP proteins increase the rate of equilibration of the uncharged species, NH3, across the cytoplasmic membrane rather than actively transporting—that is, concentrating—the charged species, NH4+.

Ammonium uptake, transport and nitrogen economy in forest trees

AMMONIUM UPTAKE, TRANSPORT AND NITROGEN ECONOMY IN FOREST TREES Francisco M. Cánovas, Concepción Avila, Fernando N. de la Torre, Rafael A. Cañas, Belén Pascual, Vanessa Castro- Rodríguez, Jorge El-Azaz Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Spain. Email: canovas@uma.es Forests ecosystems play a fundamental role in the regulation of global carbon fixation and preservation of biodiversity. Forest trees are also of great economic value because they provide a wide range of products of commercial interest, including wood, pulp, biomass and important secondary metabolites. The productivity of most forest ecosystems is limited by low nitrogen availability and woody perennials have developed adaptation mechanisms, such as ectomycorrhizal associations, to increase the efficiency of N acquisition and metabolic assimilation. The efficient acquisition, assimilation and economy of nitrogen are of special importance in trees that must cope with seasonal periods of growth and dormancy over many years. In fact, the ability to accumulate nitrogen reserves and to recycle N is crucial to determine the growth and production of forest biomass. Ammonium is the predominant form of inorganic nitrogen in the soil of temperate forests and many research efforts are addressed to study the regulation of ammonium acquisition, assimilation and internal recycling for the biosynthesis of amino acids, particularly those relevant for nitrogen storage. In our laboratory, we are interested in studying nitrogen metabolism and its regulation in maritime pine (Pinus pinaster L. Aiton), a conifer species of great ecological and economic importance in Europe and for which whole-transcriptome resources are available. The metabolism of phenylalanine plays a central role in the channeling of carbon from photosynthesis to the biosynthesis of phenylpropanoids and the regulation of this pathway is of broad significance for nitrogen economy of maritime pine. We are currently exploring the molecular properties and regulation of genes involved in the biosynthesis and metabolic fates of phenylalanine in maritime pine. An overview of this research programme will be presented and discussed. Research supported by Spanish Ministry of Economy and Competitiveness and Junta de Andalucía (Grants BIO2015-69285-R, BIO2012-0474 and research group BIO-114).

Ammonia toxicity to the brain: effects on creatine metabolism and transport and protective roles of creatine.

Hyperammonemia can provoke irreversible damage to the developing brain, with the formation of cortical atrophy, ventricular enlargement, demyelination or gray and white matter hypodensities. Among the various pathogenic mechanisms involved, alterations in cerebral energy have been demonstrated. In particular, we could show that ammonia exposure generates a secondary deficiency in creatine in brain cells, by altering the brain expression and activity of the genes allowing creatine synthesis (AGAT and GAMT) and transport (SLC6A8). On the other hand, it is known that creatine administration can exert protective effects in various neurodegenerative processes. We could also show that creatine co-treatment under ammonia exposure can protect developing brain cells from some of the deleterious effects of ammonia, in particular axonal growth impairment. This article focuses on the effects of ammonia exposure on creatine metabolism and transport in developing brain cells, and on the potential neuroprotective properties of creatine in the brain exposed to ammonium.

Desert dust deposition on Mt. Elbrus, Caucasus Mountains, Russia in 2009-2012 as recorded in snow and shallow ice core: high-resolution "provenancing", transport patterns, physical properties and soluble ionic composition

A record of dust deposition events between 2009 and 2012 on Mt. Elbrus, Caucasus Mountains derived from a snow pit and a shallow ice core is presented for the first time for this region. A combination of isotopic analysis, SEVIRI red-green-blue composite imagery, MODIS atmospheric optical depth fields derived using the Deep Blue algorithm, air mass trajectories derived using the HYSPLIT model and analysis of meteorological data enabled identification of dust source regions with high temporal (hours) and spatial (cf. 20–100 km) resolution. Seventeen dust deposition events were detected; fourteen occurred in March–June, one in February and two in October. Four events originated in the Sahara, predominantly in north-eastern Libya and eastern Algeria. Thirteen events originated in the Middle East, in the Syrian Desert and northern Mesopotamia, from a mixture of natural and anthropogenic sources. Dust transportation from Sahara was associated with vigorous Saharan depressions, strong surface winds in the source region and mid-tropospheric south-westerly flow with daily winds speeds of 20–30 m s−1 at 700 hPa level and, although these events were less frequent, they resulted in higher dust concentrations in snow. Dust transportation from the Middle East was associated with weaker depressions forming over the source region, high pressure centered over or extending towards the Caspian Sea and a weaker southerly or south-easterly flow towards the Caucasus Mountains with daily wind speeds of 12–18 m s−1 at 700 hPa level. Higher concentrations of nitrates and ammonium characterise dust from the Middle East deposited on Mt. Elbrus in 2009 indicating contribution of anthropogenic sources. The modal values of particle size distributions ranged between 1.98 μm and 4.16 μm. Most samples were characterised by modal values of 2.0–2.8 μm with an average of 2.6 μm and there was no significant difference between dust from the Sahara and the Middle East.

The Equilibrium Structure of Lithium Salt Solutions in Ether-Functionalized Ammonium Ionic Liquids

Molecular dynamics simulations have been performed for ionic liquids based on a ternary mixture of lithium and ammonium cations and a common anion, bis(trifluoromethylsulfonyl)imide, [Tf2N](-). We address structural changes resulting from adding Li+ in ionic liquids with increasing length of an ether-functionalized chain in the ammonium cation. The calculation of static structure factors reveals the lithium effect on charge ordering and intermediate range order in comparison with the neat ionic liquids. The charge ordering is modified in the lithium solution because the coordination of [Tf2N](-) toward Li+ is much stronger than ammonium cations. Intermediate range order is observed in neat ionic liquids based on ammonium cations with a long chain, but in the lithium solutions, there is also a nonhomogenous distribution of Li+ cations. The presence of Li+ enhances interactions between the ammonium cations due to correlations between the oxygen atom of the ether chain and the nitrogen atom of another ammonium cation.

Identification and characterization of GABA, proline and quaternary ammonium compound transporters from Arabidopsis thaliana

Arabidopsis thaliana grows efficiently on GABA as the sole nitrogen source, thereby providing evidence for the existence of GABA transporters in plants. Heterologous complementation of a GABA uptake-deficient yeast mutant identified two previously known plant amino acid transporters, AAP3 and ProT2, as GABA transporters with Michaelis constants of 12.9±1.7 and 1.7±0.3 mM at pH 4, respectively. The simultaneous transport of [1-14C]GABA and [2,3-3H]proline by ProT2 as a function of pH, provided evidence that the zwitterionic state of GABA is an important parameter in substrate recognition. ProT2-mediated [1-14C]GABA transport was inhibited by proline and quaternary ammonium compounds.