Ammonium transporter gene family

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  • Dominique Loqué (dloque@lbl.gov; Joint BioEnergy Institute, Lawrence Berkeley National laboratory Emeryville, CA 95608, USA)
  • Sylvie Lalonde (slalonde@stanford.edu; Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA)
  • Wolf B. Frommer (wfrommer@stanford.edu; Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA)

Contents

Ammonium transporter

Of all mineral elements required by plants, nitrogen is quantitatively the most important and thus often growth-limiting factor for many plants. Nitrogen is found in many organic compounds such as amino acids, nucleic acid and consequently in proteins, nuclei acids etc. In most soils, nitrogen is heterogeneously distributed and found in various forms such as ammonium, nitrate, urea, amino acids, peptides and water-insoluble fractions (Jackson and Bloom, 1990). Due to the impermeability or poor permeability of the lipid bilayer of the plasma membrane to most of nutrients including nitrogen compounds, uni- and multicellular organisms possess various transporters. In 1979 electrophysiological studies in the unicellular algae Chlara austrialis showed a positive inward currents across the plasma membrane after ammonium supply (Walker et al., 1979). The first ammonium transporter, AtAMT1;1 from Arabidopsis, was consequently cloned only in 1992 by yeast complementation (Ninnemann et al., 1994). Since then, many para- and orthologs were isolated either by yeast complementation or via homology cloning. Homologs were found to be present in bacteria, fungi, plants and animals (Marini et al., 2000). The transport of the charged form of ammonium (NH4+) was further confirmed by electrophysiological characterization of heterologously expressed plant ammonium transporter in Xenopus oocytes (Ludewig et al., 2002, 2003; Wood et al., 2006). Ammonium transporters are divided in three subfamilies, Rhesus, Mep/AMTB and AMT1 and in plant ammonium transporters are distributed in 2 subclasses AMT2 and AMT1 (Sohlenkamp et al., 2002). The AMT2 members are sequence-wise more closely related to fungal and bacterial ammonium transporters (Mep and AMTB) forming the Mep/AMTB subfamily (Ludewig et al., 2001). In 2004, the first ammonium transporter, the bacterial ammonium transporter AMTB, was crystallized as trimeric protein (Khademi et al., 2004). In most of AMTs characterized so far, the first 20-25 amino acid of the cytosolic C-terminus were highly conserved and were shown to be responsible of the allosteric regulation of trimeric complex (Loqué et al., 2007, Severi et al., 2007).

Major findings

  • Analysis of Selaginella moellendorffii genome suggests the presence of 5 ammonium transporters one from the AMT1 family (annotated as AMT1L1 and a putative allele AMT1L2) and 4 from the Mep/AMTB family (annotated as AMT2L1, AMT2L2, AMT2L3-1 and AMT2L4-1; and their putative alleles AMT2L2-2, AMT2L3-2 and AMT2L4-2). The two AMT1 alleles have 7 amino acid changes relative to each other; AMT2L1 relative to AMT2L2, has 10 amino acid changes and both are highly divergent to AMT2L3 and AMT2L4.

Image:AMT_tree.jpg

  • An interesting observation is that Selaginella possesses half of the number of Physcomitrella ammonium transporters and as much ammonium transporter as Arabidopsis but the relative number of AMT1/AMT2 is different. The Arabidopsis genome possesses five AMT1 members and one AMT2, in contrast, the Selaginella genome possesses one AMT1 and four AMT2 types, Physcomitrella has five AMT1 and seven AMT2 types predicted. Due to the higher amount of Mep/AMTB members Selaginella looks closer related to grasses and trees, which have a higher proportion of the AMT2 members. In contrast to the AMT1 members which were shown to be involved in ammonium acquisition from the soil solution (Loqué et al., 2006, Yuan et al., 2007), the physiological role of the AMT2 members in plant is still unclear, thus it is difficult to predict a potential physiological advantage of having more or less Mep/AMTB type transporter in a genome. It is also interesting that the C-terminus of the AMT1 family still highly conserved and the equivalent Thr460 of AtAMT1;1 in the C-terminus involved in allosteric regulation (Loqué et al., 2007) of the AMT complex is also conserved, suggesting a conservation of the regulatory mechanism via phosphorylation. Since the AMT2 ammonium transporter from plants do not have a threonine in that position, AMT1 and AMT2 ammonium transporter types might be differently regulated and thus give to plants an higher adaptability to the fluctuating ammonium availability in the environment and in the cells.

Sequences

  • AMT sequences lacking the "soluble" part of N-terminus (sequence before the first TM) and the far end of the "soluble" C-terminus (sequence missing in most of the bacterial AMT such as EcAMTB and AfAMT_1 and corresponding to the sequence after Y467 in AtAMT1;1 (Media:All-AMTs-C-N-Rh.txt).

References

  • Jackson LE, Bloom AJ (1990) Root distribution in relation to soil nitrogen availability in field grown tomatoes. Plant Soil. 128: 115-121.
  • Khademi S, O'Connell J, Remis J, Robles-Colmenares Y, Miercke LJ, and Stroud RM (2004). Mechanism of ammonia transport by Amt/MEP/Rh: structure of AmtB at 1.35 A. Science 305: 1587-1594.
  • Loqué D, Yuan L, Kojima S, Gojon A, Wirth J, Gazzarrini S, Ishiyama K, Takahashi H, and von Wirén N (2006) Additive contribution of AMT1;1 and AMT1;3 to high-affinity ammonium uptake across the plasma membrane of nitrogen-deficient Arabidopsis roots. Plant J. 48: 522-534.
  • Loqué D, Lalonde S, Looger LL, von Wirén N, and Frommer WB (2007) A cytosolic trans-activation domain essential for ammonium uptake. Nature 446:195-198.
  • Ludewig U, von Wirén N, Frommer WB (2002) Uniport of NH4+ by the root hair plasma membrane ammonium transporter LeAMT1;1. J Biol Chem. 277: 13548-13555.
  • Ludewig U, von Wirén N, Rentsch D, Frommer WB (2001) Rhesus factors and ammonium: a function in efflux? Genome Biol. 2: 1010.1–1010.5
  • Ludewig U, Wilken S, Wu B, Jost W, Obrdlik P, El Bakkoury M, Marini AM, Andre B, Hamacher T, Boles E, von Wirén N, Frommer WB (2003) Homo- and hetero-oligomerization of ammonium transporter-1 NH4+ uniporters. J Biol Chem. 278: 45603-45610
  • Ninnemann O, Jauniaux JC, Frommer WB (1994) Identification of a high affinity NH4+ transporter from plants. EMBO J. 13: 3464-3471
  • Marini AM, Andre B (2000) In vivo N-glycosylation of the Mep2 high-affinity ammonium transporter of Saccharomyces cerevisiae reveals an extracytosolic N-terminus. Mol microbiol. 38: 552-564.
  • Severi E, Javelle A, Merrick M (2007) The conserved carboxy-terminal region of the ammonia channel AmtB plays a critical role in channel function. Mol Membr Biol. 24:161-171.
  • Sohlenkamp C, Wood CC, Roeb GW, Udvardi M (2002) Characterization of Arabidopsis AtAMT2, a high-affinity ammonium transporter of the plasma membrane. Plant Physiol. 130: 1788-1796.
  • Walker NA, Beilby MJ, Smith FA (1979a) Amine uniport at the plasmalemma of charophyte cells: I. Current-voltage curves, saturation kinetics, and effects of unstirred layers. J Membrane Biology. 49: 21-25.
  • Walker NA, Beilby MJ, Smith FA (1979b) Amine uniport at the plasmalemma of charophyte cells: II. Ratio of matter to charge transported and permeability to free base. J Membrane Biology. 49: 286-296.
  • Wood CC, Porée F, Dreyer I, Koehler GJ, Udvardi MK. (2006) Mechanisms of ammonium transport, accumulation, and retention in ooyctes and yeast cells expressing Arabidopsis AtAMT1;1. FEBS Lett. 580: 3931-3936.
  • Yuan L, Loqué D, Kojima S, Rauch S, Ishiyama K, Inoue E, Takahashi H, von Wirén N (2007) The Organization of high-affinity ammonium uptake in Arabidopsis roots relies on the isoform-specific localization and biochemical properties of AMT1-type transporters. Plant Cell 19: 2636-2652.

Table of gene numbers


Gene functions Gene Gene used as a query The number of putative orthologs
Arabidopsis thaliana Lycopersicon esculentum Oryza sativa Selaginalla moellendorffii Physcomitrella patens Chlamydomonas reinhardtii
Ammonium Transport AMT1 AtAMT1;1 (AT4G13510) 5 3 3 2 5 8
Ammonium Transport AMT2 AtAMT2 (At2g38290) 1 1pseudo 7 + 1pseudo 4 (6) 7 0
Ammonium Transport Rh RhAG (CAA45883) 0 0 0 0 0 2
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