Amino acid transporter gene family

From Purdue Genomics Database Facility

Amino acid transporter gene family

Daniel Wipf (daniel.wipf@dijon.inra.fr; UMR INRA 1088/CNRS 5184/ Université de Bourgogne Plante-Microbe-Environnement, BP 86510, 21065 DIJON Cedex - France)

Amino acid transporters

Amino acids play fundamental roles in a multitude of functions including protein synthesis, hormone metabolism, nerve transmission, cell growth, production of metabolic energy, nucleobase synthesis, nitrogen metabolism and urea biosynthesis. In multicellular organisms, many of the nitrogenous compounds are transported between cells. Long distance transport of organic nitrogen in the plant is at least as complex as sugar transport. The transported substrates are highly diverse, including the 20 proteogenic amino acids, GABA and a variety of amino acid analogs and even oligopeptides, but also many other N-containing compounds found in phloem sap. Furthermore, amino acids are not only transported in the phloem but also in xylem, and they exchange between phloem and xylem in a complex manner (Atkins, 2000). If we take also into account that nitrogen metabolism is highly compartmentalized; we must expect a large number of transporter genes. Amino acid transporters for cellular import were initially identified by suppression cloning in yeast, and they comprise primarily two major families. One may speculate that transporters for the efflux of amino acids and for transport across the vacuolar membrane are part of these families. So far, amino acid transporters have been identified as members of at least five gene families (Rentsch et al., 2007) and these transport proteins display different substrate selectivities and affinities as well as distinct subcellular localizationdemonstrated (Wipf et al., 2002).

Amino acid transporter superfamily 1 (ATF1)

In contrast to the other families, ATF1 members were first described in plants. ATF1 members contain 9-11 putative membrane spanning domains with cytosolic N- and extracellular C-termini (Chang et al., 1997). The Arabidopsis AAPs (amino acid permeases), which mediate Na+-independent, H+-coupled uptake of a wide spectrum of amino acids, are the best characterized members of the superfamily (Fischer et al., 2002). Slight differences in substrate specificity exist among the different members requiring novel approaches for an exact assessment of the in vivo function. Imaging tools need to be devised to determine amino acid concentrations at the sites of transport and to correlate dynamic analysis of amino acid concentration changes in subcellular compartments with transporter characteristics and localization. Plants take up amino acids as a nitrogen source and, more importantly amino acids are the principal long distance transport forms of organic nitrogen. In accordance, plant amino acid transporter genes are preferentially expressed in vascular tissue.

Amino acid-Polyamine-Choline transporter superfamily (APC)

In the absence of structural data, computer-aided predictions of secondary structures were used to categorize plant APC transporters into two subgroups (http://crombec.botanik.uni-koeln.de/index.html). Members of the cationic amino acid transporters (CATs) contain 14 putative transmembrane domains and are also found in animals (Wipf et al., 2002). The second subfamily comprises proteins with 12 putative transmembrane domains (Wipf et al., 2002). In short, amino acid transport mediated by members of the APC family from different organisms is diverse, uses Na+ or H+ coupling by sym- or antiport serving functions in uptake and nutrition. So far, only one plant member has been characterized in more detail, and knock-out mutants have not yet been studied.

Amino acid transporters in other gene families.

Several other gene families contain plant amino acid transporters, which are localized at organellar membranes. Transporters have been identified that facilitate amino acid transport from the cytosol across the plastid envelopes. In the outer envelope, OEP16 from pea forms a cation selective high-conductance channel with a strong bias for amino acids and amines (Pohlmeyer et al., 1997). So far, the only amino acid transporter identified to operate at the inner plastid envelope is DiT2.1 (dicarboxylate transport), belonging to the DASS (divalent anion:Na+ symporter) family. DiT2.1 functions in glutamate/malate exchange essential in thephotorespiratory pathway (Renné et al., 2003). Mitochondrial amino acid transporters have been found in plants that, like the yeast and animal mitochondrial transport systems, are members of the MCF (mitochondrial carrier family (Catoni et al., 2003). In Arabidopsis, two AtmBACs (mitochondrial basic amino acid carriers) have been functionally characterized, and their substrate selectivities resemble those of the corresponding human proteins.

Major findings

Amino acid-Polyamine-Choline transporter superfamily (APC)

Analysis of Selaginella moellendorffii genome suggests the presence of 9 amino acid transporters belonging to the Amino acid-Polyamine-Choline transporter superfamily. Four belonging to the L-type Amino acid Transporter clade (respectively annotated as LAT1-1 ( and a putative allele LAT1-2), LAT2-1 ( and a putative allele LAT2-2), LAT3-1 ( and a putative allele LAT3-2) and LAT4-1 ( and a putative allele LAT4-2) ; five belonging to the Cationic Amino acid Transporter clade (respectively annotated as CAT1-1 ( and a putative allele CAT1-2), CAT2-1 ( and a putative allele CAT2-2), CAT3-1 ( and a putative allele CAT3-2), CAT 4-1 ( and a putative allele 4AT4-2) and CAT5-1 ( and a putative allele CAT5-2). An interesting observation is that Selaginella possesses the same number of LAT transporters than rice (4), number which is close to the arabidopsis one (5). In Physcomitrella patens only three LAT homologs were found whereas no one was found in the Chlamydomonas reinhardtii genome. Concerning the second clade of amino acid transporters from the APC super-family the situation is different. Less CAT type transporters were found in mosses (Sm : 5, Pp : 6, Cr : 3) compared to rice (8) and arabidopsis (10). As so far les sis known concerning plants CATs and that furthermore no biochemical data are available on LAT transporters in plants, it is difficult to develop any hypothesis concerning these differences.

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Amino acid transporters in other gene families

AtDIT2 homologs

Analysis of Selaginella moellendorffii genome suggests the presence of 3 putative amino acid transporters ( DIT2L2-1 (putative allèle DIT2L2-2) ; DIT2L2-2 and DIT2L3-1 (putative allèle DIT2L3-2) homologous to AtDIT2. DIT2L2 is closely related to DIT2L3-1 and 3-2, and could constitute a supplementary allele. It is interesting to note that at least the same numbers of DIT2 putative amino transporters were found in mosses (Sm : 3, Pp : 4, Cr : 2) as in arabidopsis (2) and rice (2). So far, the only amino acid transporter identified to operate at the inner plastid envelope is AtDiT2.1 (dicarboxylate transport), belonging to the DASS (divalent anion:Na+ symporter) family. DiT2.1 functions in glutamate/malate exchange essential in the photorespiratory pathway; transport activity for its closest homolog, AtDiT2.2, has not been demonstrated yet.

AtmBAC1 homologs

Mitochondrial amino acid transporters have been found in plants that, like the yeast and animal mitochondrial transport systems, are members of the MCF (mitochondrial carrier family). In Arabidopsis, two AtmBACs (mitochondrial basic amino acid carriers) have been functionally characterized, and their substrate selectivities ressemble those of the corresponding human proteins. Up to 10 genes homologous to AtmBAC1 could be found in the Selaginella moellendorffii. In the current state of the art it is impossible to determine which of these 10 members of the MCF (mitochondrial carrier family) are transporting amino acids. The same comment can be applied to the 8 homologs found in the Physcomitrella patens genome. Nevertheless it is interesting to note that quit two times more mBAC1 homologs were found in the Sm genome as in the Cr one.

AtOEP16-1 homologs

A major part of amino acid assimilation and biosynthesis of plants occurs in plastids. Amino acids pass the outer envelope via OEP proteins forming cation-selective high conductance channels permeable to amines and amino acids. A single AtOEP16 homolog was found in the Selaginella moellendorffiii and in the Physcomitrella patens genomes. Furthermore no homolog was found in the Chlamydomonas reinhardtii genome. These facts could reflect an evolution in the physiology of amino acids from mosses to higher plants. Even if it is difficult to conclude if a higher number of transporters corresponds to a physiological advantage.

References

• Atkins CA. 2000. Biochemical aspects of assimilate transfers along the phloem path: N-solutes in lupins. Aust. J. Plant Physiol. 27: 531-37

• Catoni E, Desimone M, Hilpert M, Wipf D, Kunze R, Schneider A, Flügge UI, Schumacher K and Frommer WB. 2003 Expression pattern of a nuclear encoded mitochondrial arginine–ornithine translocator gene from Arabidopsis. BMC Plant Biol. 3, 1

• Chang HC and Bush DR. 1997. Topology of NAT2, a prototypical example of a new family of amino acid transporters. J. Biol. Chem. 272: 30552-57

• Fischer WN, Loo DDF, Koch W, Ludewig U, Boorer KJ and Frommer WB. 2002. Low and high affinity amino acid H+-cotransporters for cellular import of neutral and charged amino acids. Plant J. 29: 717-31

• Pohlmeyer K, Soll J, Steinkamp T, Hinnah S and Wagner R. 1997. Isolation and characterization of an amino acid selective channel protein present in the chloroplastic outer envelope membrane. Proc. Natl. Acad. Sci. USA 94, 9504–09

• Renné P, Dressen U, Hebbeker U, Hille D, Flügge UI, Westhoff P and Weber APM. 2003. The Arabidopsis mutant dct is deficient in the plastidic glutamate/malate translocator DiT2. Plant J. 35, 316–31

• Rentsch D, Schmidt S and Tegeder M. 2007. Transporters for uptake and allocation of organic nitrogen compounds in plants. FEBS Lett. 581(12):2281-89

• Wipf D, Ludewig U, Tegeder M, Rentsch D, Koch W and Frommer WB. 2002. Conservation of amino acid transporters in fungi, plants and animals. Trends Biochem. Sci. 27: 139-47