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SLC1A5 (solute carrier family 1 (neutral amino acid transporter), member 5)

Written2014-02Cesare Indiveri, Lorena Pochini, Michele Galluccio, Mariafrancesca Scalise
Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry, Molecular Biotechnology, University of Calabria, 87036 Arcavacata di Rende, Italy

Abstract Review on human SLC1A5, with data on DNA/RNA, on the protein encoded and pathological and physiological implications.

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Identity

Alias_namesRDRC
M7V1
solute carrier family 1 (neutral amino acid transporter)
Alias_symbol (synonym)AAAT
ASCT2
HGNC (Hugo) SLC1A5
LocusID (NCBI) 6510
Atlas_Id 42313
Location 19q13.32  [Link to chromosome band 19q13]
Location_base_pair Starts at 47278140 and ends at 47290545 bp from pter ( according to hg19-Feb_2009)  [Mapping SLC1A5.png]
Local_order Orientation: minus strand.
Fusion genes
(updated 2016)
SLC1A5 (19q13.32) / CNTN4 (3p26.3)SLC1A5 (19q13.32) / P3H2 (3q28)SLC1A5 (19q13.32) / SLC1A5 (19q13.32)
TRBV20-1 () / SLC1A5 (19q13.32)VDR (12q13.11) / SLC1A5 (19q13.32)

DNA/RNA

 
  Figure 1. Isoforms of SLC1A5 gene. The three isoforms are present in the minus strand of the chromosome 19 in position 19q13.3. NM_005628: isoform one, encodes for the longest peptide and is constituted by 8 exons; NM_001145144: isoform two, due to alternative splicing is characterized by only four exons; NM_ 001145145: isoform three presents seven exons. The nucleotide sequence is depicted as black lines. Coding nucleotides and untranslated (UTR) regions are indicated by red and white boxes, respectively. Exons are indicated by roman numbers.
Description The SLC1A5 gene, located at 19q13.3, counts 28692 nucleotides with 8 exons. It has been found in 56 different organisms (NCBI). The gene encodes a protein involved in sodium-dependent neutral amino acid transport (Kekuda et al., 1996; Pingitore et al., 2013).
Transcription Three isoforms (transcripts) are reported either on NCBI and Ensembl databases for SLC1A5 human gene, deriving from different translation start. They differ in length, particularly at 5' extremity. The first variant NM_005628 represents the longest transcript, constituted by 2873 nucleotides and 8 exons. This transcript encodes a peptide of 541 amino acids. The second variant NM_001145144 is constituted by 1737 nucleotides and differs in the 5' UTR from the variant NM_005628. In NM_001145144 the translation starts downstream the third exon generating a shorter peptide of 313 aa. The third isoform NM_ 001145145 has 1927 nucleotides and lacks the first exon. It presents a different translation start at 5', coding a peptide of 339 amino acids. A longer transcript, XM_005259167, is reported only in NCBI database. It has been identified by automated computational analysis. More than 400 SNP(s), both in coding and non-coding regions of the SLC1A5 gene, are reported in dbSNP database (dbSNP). More than 40 are responsible of amino acid substitutions with unknown significance. Only the variant SLC1A5-P17A (rs3027956) is associated with breast cancer (Savas et al., 2006). A region constituted by 907 bp upstream of the ASCT2 gene possesses promoter activity (Bungard and McGivan, 2004). In this region the following putative elements have been identified: an amino acid-regulatory element, a consensus site for binding of the transcription factor activator protein 1 (AP1) and a consensus binding sites for nuclear and hepatocyte nuclear factors.
Pseudogene The gene is virtually present in all vertebrates. The better known orthologous of the human gene are those from rat, mouse and rabbit. Identity between the human and rat, mouse, rabbit are 79%, 82% and 85%, respectively.

Protein

 
  Figure 2. Homology structural model of hASCT2. Ribbon diagram viewing of the transporter from the lateral side. The model was built using the glutamate transporter Glpth from Pyrococcus horikoshii crystal structure (1XFH) as the template by Modeller V9.13. The homology model was represented using SpdbViewer 4.01. Asn 163 and 212, predicted as glycosilation sites, are highlighted in blue; Ser 183, 261 and Thr 206, 207, 329, predicted as phosphorilation sites are highlighted in red and orange, respectively. Prediction according to Scan Prosite.
Description 541 amino acids; molecular mass 56598,34 Da.
Human SLC1A5 is a permease (membrane transporter). The 3D structure is not available. Homology modeling highlights a structure similar to that of the glutamate transporter of P. horikoshii (1XFH). N- and C-terminal ends are intracellular. Potential site of N-glycosylation and phosphorilation are predicted. In the structural model, at least one glycosylation site is extracellular and the phosphorilation sites are intracellular (Fig. 2).
Expression Human SLC1A5 has been originally named ASCT2 from AlaSerCysTransporter2 or ATB0. The acronym ASCT2 is the most frequently used to designate this transport system. It is expressed in many tissues, including brain, (Bröer and Brookes, 2001; Deitmer et al., 2003; Gliddon et al., 2009). There is functional evidence of the expression of ASCT2 in kidney and intestine (Bode, 2001). Besides Caco-2 cells, apparently, also the HT-29 intestinal cell line functionally expresses ASCT2 (Kekuda et al., 1996; Kekuda et al., 1997). Poly(A)1 RNA isolated from several tissues of human origin revealed expression in placenta, lung, skeletal muscle, kidney, and pancreas (Kekuda et al., 1996).
Localisation The protein is localized in the plasma membrane.
Function Transport mediated by the human ASCT2 has been originally studied in intact cell systems over-expressing the transport protein (Kekuda et al., 1996; Kekuda et al., 1997). Recently, hASCT2 was over-expressed in the yeast P. pastoris, purified and reconstituted in artificial phospholipid vesicles (proteoliposomes), in absence of other interfering transporters. All experimental systems concur in demonstrating that hASCT2 is an obligate exchanger of neutral amino acid. This antiport requires the presence of extracellular Na+ which cannot be substituted by Li+ or K+. The Na+ ex:amino acidex stoichiometry of the human transporter is likely to be 1:1. Competition studies on 3H-glutamine, 3H-threonine or 3H-alanine transport performed in cells indicated that other potential substrates of hASCT2 are valine, leucine, serine, cysteine, asparagine, methionine, isoleucine, tryptophan, histidine, phenylalanine. While glutamate, lysine, arginine along with MeAIB [α-(methylamino)isobutyric acid] and BCH [2-aminobicyclo-(2,2,1)-heptane-2-carboxylic acid] are neither transported nor inhibit hASCT2. Experiments with radioactive compounds confirmed the competition data (Torres-Zamorano et al., 1998). In proteoliposomes, inhibition has been confirmed for most but not for all of the amino acids. Moreover, proteoliposome studies highlighted an asymmetric specificity for amino acids allowing to distinguish the amino acids inwardly transported (alanine, cysteine, valine, methionine) from those bi-directionally transported (glutamine, serine, asparagine, and threonine). The functional asymmetry was also confirmed by the kinetic analysis of [3H]glutamine/glutamine antiport: different Km values were measured on the external and internal sides of proteoliposomes, 0,097 and 1,8 mM, respectively. The SH reagents HgCl2, mersalyl and pOHMB potently inhibited hASCT2 mediated transport (Pingitore et al., 2013).
The physiological role of hASCT2 consists in providing cells with some neutral amino acids exporting others on the basis of the metabolic need of cells consistently with the intra and extracellular amino acid concentrations. In brain, particularly, hASCT2 contributes to glutamine homeostasis of neurons and astrocytes. On the basis of experiments performed with animal models, it was hypothesized that hASCT2 mediates efflux of glutamine from astrocytes, a process that is critical for the functioning of the glutamate-glutamine cycle to recover synaptically released glutamate in exchange with glutamine efflux (Bröer et al., 1999). The glutamine-glutamate cycle has been shown also in placenta. Glutamine crosses the placenta and enters the fetal liver where it is deamidated to glutamate. About 90% of glutamate generated by the liver is taken up by the placenta and used in the metabolism. The glutamine-glutamate cycle between the placenta and the fetal liver is obligatory for the generation of NADPH in the placenta (Torres-Zamorano et al., 1998). Among other functions reported for hASCT2 there is the regulation of mTOR pathway, translation and autophagy. The transporter regulates an increase in the intracellular concentration of glutamine which is then used by another plasma membrane transporter, named LAT1 (SLC7A5) (Galluccio et al., 2013) as efflux substrate to regulate the uptake of extracellular leucine with subsequent activation of mTORC1 (Nicklin et al., 2009). Moreover, it has been proposed that a group of retroviruses specifically uses the hASCT2 as a common cell surface receptor following a co-evolution phenomenon. The orthologous murine transporter mASCT2 is inactive as a viral receptor (Marin et al., 2003).

Implicated in

Note
  
Entity Molecular basis of cancerogenesis
Note Tumor cells acquire altered metabolism. Due to these changes, the expression of membrane transporters involved in providing nutrients is altered. The plasma membrane transporter for glutamine ASCT2 has been clearly associated to cancer development and progression, together with another amino acid membrane transporter, LAT1 specific for glutamine and other neutral amino acids (Fuchs and Bode, 2005). The energetic needs of cancer cells are different from normal ones due to the Warburg effect. According to this phenomenon ATP derives from anaerobic glycolisis bypassing mitochondrial function (Ganapathy et al., 2009). In this scenario glutamine provided by means of ASCT2 and LAT1 transport function sustains tumor growth and signaling through mTOR pathway (Nicklin et al., 2009). The importance of ASCT2 in this network is revealed by induction of apoptosis when silencing its gene in human hepatoma cells (Fuchs et al., 2004).
In the following paragraphs specific examples of human cancers are reported.
  
  
Entity Prostate cancer
Note Tissue microarray technology (TMA) has been used for studying ASCT2 in normal prostatic tissue, in benign prostatic hyperplasia and in prostate adenocarcinoma. In particular, a negative prognosis and a shorter time of recurrence for adenocarcinoma were associated to hASCT2 expression. Moreover, a more aggressive behavior of adenocarcinoma is described (Li et al., 2003).
  
  
Entity Colorectal carcinoma
Note The expression of ASCT2 in colorectal carcinoma is normally associated to a decrease of percentage in patient survival (Witte et al., 2002).
  
  
Entity Neuroblastoma and glioma
Note Neuroblastoma are childhood tumors very often benign. In some cases, however, neuroblastoma became malignant. One of the biological marker of this second category is the increased uptake of glutamine and other neutral aminoacids via ASCT2 (Wasa et al., 2002). Human glioma C6 cells have been demonstrated to mediate uptake of glutamine via ASCT2 (Dolinska et al., 2003).
  
  
Entity Hepatoma
Note Hepatocell carcinoma (HCC) is the most common malignant tumor of liver and one of the main cause of death. A study reported that higher rate of glutamine uptake via ASCT2 is a common feature of six examined hepatoma cell line (Bode et al., 2002; Fuchs et al., 2004).
  
  
Entity Lung cancer
Note ASCT2 has been found over expressed in lung cancer by proteomic approach and then confirmed at molecular level. Pharmacologic and genetic targeting of ASCT2 decreased cell growth and viability in lung cancer cells, an effect mediated in part by mTOR signaling (Hassanein et al., 2013).
  
  
Entity Breast cancer
Note In breast cancer ASCT2 has been found over expressed together with other proteins related to glutamine metabolism like glutamminase and glutamate dehydrogenase (Kim et al., 2012). The study revealed that this metabolism is essential for sustaining breast cancer development and that the protein levels are different according to different subtypes of cancer. The subtype HER2 showed the highest level of glutamine related proteins and that the basal-like breast cancers are more dependent on glutamine compared to luminal-likeones.
  
  
Entity Other diseases
Note Due to importance of glutamine in cell metabolism and the chromosomal localization of SLC1A5 gene, several association studies have been conducted to ascertain the involvement of hASCT2 in pathologies like cystinuria, cystic fibrosis, schizophrenia, Hartnup disorder and pre-eclampsia. However, no genetic associations have been revealed.
  

To be noted

Aknowledgements: This work was supported by funds from: Programma Operativo Nazionale [PON 01_00937] "Modelli sperimentali Biotecnologici integrati per lo sviluppo e la selezione di molecole di interesse per la salute dell'uomo", Ministero Istruzione Università e Ricerca (MIUR).

Bibliography

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PMID 14563674
 
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Citation

This paper should be referenced as such :
C Indiveri, L Pochini, M Galluccio, M Scalise
SLC1A5 (solute carrier family 1 (neutral amino acid transporter), member 5)
Atlas Genet Cytogenet Oncol Haematol. 2014;18(9):673-677.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/SLC1A5ID42313ch19q13.html


External links

Nomenclature
HGNC (Hugo)SLC1A5   10943
Cards
AtlasSLC1A5ID42313ch19q13
Entrez_Gene (NCBI)SLC1A5  6510  solute carrier family 1 member 5
AliasesAAAT; ASCT2; ATBO; M7V1; 
M7VS1; R16; RDRC
GeneCards (Weizmann)SLC1A5
Ensembl hg19 (Hinxton)ENSG00000105281 [Gene_View]  chr19:47278140-47290545 [Contig_View]  SLC1A5 [Vega]
Ensembl hg38 (Hinxton)ENSG00000105281 [Gene_View]  chr19:47278140-47290545 [Contig_View]  SLC1A5 [Vega]
ICGC DataPortalENSG00000105281
TCGA cBioPortalSLC1A5
AceView (NCBI)SLC1A5
Genatlas (Paris)SLC1A5
WikiGenes6510
SOURCE (Princeton)SLC1A5
Genetics Home Reference (NIH)SLC1A5
Genomic and cartography
GoldenPath hg19 (UCSC)SLC1A5  -     chr19:47278140-47290545 -  19q13.32   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)SLC1A5  -     19q13.32   [Description]    (hg38-Dec_2013)
EnsemblSLC1A5 - 19q13.32 [CytoView hg19]  SLC1A5 - 19q13.32 [CytoView hg38]
Mapping of homologs : NCBISLC1A5 [Mapview hg19]  SLC1A5 [Mapview hg38]
OMIM109190   
Gene and transcription
Genbank (Entrez)AB209738 AF102826 AF105230 AF105423 AF334818
RefSeq transcript (Entrez)NM_001145144 NM_001145145 NM_005628
RefSeq genomic (Entrez)NC_000019 NC_018930 NT_011109 NW_004929415
Consensus coding sequences : CCDS (NCBI)SLC1A5
Cluster EST : UnigeneHs.631582 [ NCBI ]
CGAP (NCI)Hs.631582
Alternative Splicing GalleryENSG00000105281
Gene ExpressionSLC1A5 [ NCBI-GEO ]   SLC1A5 [ EBI - ARRAY_EXPRESS ]   SLC1A5 [ SEEK ]   SLC1A5 [ MEM ]
Gene Expression Viewer (FireBrowse)SLC1A5 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6510
GTEX Portal (Tissue expression)SLC1A5
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ15758   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ15758  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ15758
Splice isoforms : SwissVarQ15758
PhosPhoSitePlusQ15758
Domaine pattern : Prosite (Expaxy)NA_DICARBOXYL_SYMP_1 (PS00713)    NA_DICARBOXYL_SYMP_2 (PS00714)   
Domains : Interpro (EBI)Na-dicarboxylate_symporter    Na-dicarboxylate_symporter_CS   
Domain families : Pfam (Sanger)SDF (PF00375)   
Domain families : Pfam (NCBI)pfam00375   
Conserved Domain (NCBI)SLC1A5
DMDM Disease mutations6510
Blocks (Seattle)SLC1A5
SuperfamilyQ15758
Human Protein AtlasENSG00000105281
Peptide AtlasQ15758
HPRD00173
IPIIPI00019472   IPI01010276   IPI00922487   IPI00922776   
Protein Interaction databases
DIP (DOE-UCLA)Q15758
IntAct (EBI)Q15758
FunCoupENSG00000105281
BioGRIDSLC1A5
STRING (EMBL)SLC1A5
ZODIACSLC1A5
Ontologies - Pathways
QuickGOQ15758
Ontology : AmiGOvirus receptor activity  amino acid transmembrane transport  receptor activity  protein binding  Golgi apparatus  plasma membrane  plasma membrane  integral component of plasma membrane  dicarboxylic acid transport  amino acid transport  glutamine transport  amino acid transmembrane transporter activity  neutral amino acid transmembrane transporter activity  L-glutamine transmembrane transporter activity  neutral amino acid transport  membrane  sodium:dicarboxylate symporter activity  melanosome  viral entry into host cell  extracellular exosome  
Ontology : EGO-EBIvirus receptor activity  amino acid transmembrane transport  receptor activity  protein binding  Golgi apparatus  plasma membrane  plasma membrane  integral component of plasma membrane  dicarboxylic acid transport  amino acid transport  glutamine transport  amino acid transmembrane transporter activity  neutral amino acid transmembrane transporter activity  L-glutamine transmembrane transporter activity  neutral amino acid transport  membrane  sodium:dicarboxylate symporter activity  melanosome  viral entry into host cell  extracellular exosome  
Pathways : KEGGProtein digestion and absorption   
REACTOMEQ15758 [protein]
REACTOME Pathways352230 [pathway]   
NDEx NetworkSLC1A5
Atlas of Cancer Signalling NetworkSLC1A5
Wikipedia pathwaysSLC1A5
Orthology - Evolution
OrthoDB6510
GeneTree (enSembl)ENSG00000105281
Phylogenetic Trees/Animal Genes : TreeFamSLC1A5
HOVERGENQ15758
HOGENOMQ15758
Homologs : HomoloGeneSLC1A5
Homology/Alignments : Family Browser (UCSC)SLC1A5
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSLC1A5 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SLC1A5
dbVarSLC1A5
ClinVarSLC1A5
1000_GenomesSLC1A5 
Exome Variant ServerSLC1A5
ExAC (Exome Aggregation Consortium)SLC1A5 (select the gene name)
Genetic variants : HAPMAP6510
Genomic Variants (DGV)SLC1A5 [DGVbeta]
DECIPHER (Syndromes)19:47278140-47290545  ENSG00000105281
CONAN: Copy Number AnalysisSLC1A5 
Mutations
ICGC Data PortalSLC1A5 
TCGA Data PortalSLC1A5 
Broad Tumor PortalSLC1A5
OASIS PortalSLC1A5 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSLC1A5  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSLC1A5
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch SLC1A5
DgiDB (Drug Gene Interaction Database)SLC1A5
DoCM (Curated mutations)SLC1A5 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SLC1A5 (select a term)
intoGenSLC1A5
NCG5 (London)SLC1A5
Cancer3DSLC1A5(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM109190   
Orphanet
MedgenSLC1A5
Genetic Testing Registry SLC1A5
NextProtQ15758 [Medical]
TSGene6510
GENETestsSLC1A5
Huge Navigator SLC1A5 [HugePedia]
snp3D : Map Gene to Disease6510
BioCentury BCIQSLC1A5
ClinGenSLC1A5
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6510
Chemical/Pharm GKB GenePA35830
Clinical trialSLC1A5
Miscellaneous
canSAR (ICR)SLC1A5 (select the gene name)
Probes
Litterature
PubMed70 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSLC1A5
EVEXSLC1A5
GoPubMedSLC1A5
iHOPSLC1A5
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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