SLC9A3R1 (solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 1)

2010-12-01   Wendy S McDonough , Michael E Berens 

The Translational Genomics Research Institute, 445 N Fifth Street, Phoenix, Arizona 85004, USA

Identity

HGNC
LOCATION
17q25.1
IMAGE
Atlas Image
LEGEND
SLC9A3R1 Physical Map.
LOCUSID
ALIAS
EBP50,NHERF,NHERF-1,NHERF1,NPHLOP2
FUSION GENES

DNA/RNA

Atlas Image
DNA size 20.71 Kb; mRNA size 1978 bp; 6 exons.

Description

The SLC9A3R1 gene is comprised of 6 exons and spans approximately 20.7 kb of genomic DNA.

Transcription

The SLC9A3R1 gene encodes a 1978 bp mRNA transcript.
Reported regulatory transcription factor binding sites upstream of the SLC9A3R1 promoter region include: NF-kappaB1, HNF-4alpha2, COUP-TF1, NF-kappaB, NRSF form 2, NRSF form 1, FOXD1, PPAR-gamma2, PPAR-gamma1, GATA-1.

Proteins

Atlas Image
NHERF (human)-358 aminos acids.

Description

The SLC9A3R1 protein is composed of 353 amino acids (389 kDa).
Post-transcriptional regulation of SLC9A3R1 occurs via Serines S77-p, S162-p, S339-p, S340-p.
SLC9A3R1 is also phosphroylated on T95-p.
SLC9A3R1 has two PDZ (DHR) domains.
SLC9A3R1 can exist as a homodimer or heterodimer with SLC9A3R2.

Expression

SLC9A3R1 is expressed in liver, salivary glands, kidney, pancreas, trachea, small intestine, stomach, prostate and brain.

Localisation

SLC9A3R1 is a cytoplasmic protein. SLC9A3R1 translocates from the cytoplasm to the apical cell membrane in a PODXL-dependent manner. SLC9A3R1 colocalizes with actin in microvilli-rich apical regions of the syncytiotrophoblast. SLC9A3R1 has been found in microvilli, ruffling membrane and filopodia of HeLa cells. SLC9A3R1 is also been discovered in lipid rafts of T-cells.
Subcellular localization is present in cells with apical specialized structure such as micorvili and cilia. SLC9A3R1 also has a membranous expression in cells of non-epithelial origin (astrocytes) and hematopoietic stem cells and has been found in membrane rafts in lymphocytes and at the rear edge of neutrophils.

Function

SLC9A3R1 is a scaffold protein that connects plasma membrane proteins with members of the ezrin/moesin/radixin family and thereby helps to link them to the actin cytoskeleton to regulate their surface expression. SLC9A3R1 has been shown to be necessary for recycling of internalized ADRB2. SLC9A3R1 regulates SLC9A3 as well as its subcellular location. SLC9A3R1 is required for cAMP-mediated phosphorylation and inhibition of SLC9A3R1. SLC9A3R1 interacts with MCC. SLC9A3R1 may participate in HTR4 targeting to microvilli. SLC9A3R1 has been shown to play a role in the WNT signaling pathway.
Induction: SLC9A3R1 can be induced by estrogen.
SLC9A3R1 has been show to have binary interaction with the following proteins: CFTR, CLCN3, MSN, NF2, RDX.

Mutations

Note

SLC9A3R1 has been shown to have three natural variants.
Natural variant 110L --> V in NPHLOP2; the mutant expressed in cultured renal cells increases the generation of cyclic AMP (cAMP) by parathyroid hormone (PTH) and inhibits phosphate transport.
Natural variant 153R --> Q in NPHLOP2; the mutant expressed in cultured renal cells increases the generation of cAMP by PTH and inhibits phosphate transport.
Natural variant 225E --> K in NPHLOP2; the mutant expressed in cultured renal cells increases the generation of cAMP by PTH and inhibits phosphate transport.

Implicated in

Entity name
Cancer progression
Note
There is growing evidence SLC9A3R1 plays an important role in cancer progression. SLC9A3R1 functions as an adaptor protein to control cell transformation. In addition, recent evidence suggests that SLC9A3R1 has a dual role either acting as a tumor suppressor when it is localized as the cell membrane or as an oncogenic protein when it is localized in the cytoplasm (Georgescu et al., 2008).
Entity name
Glioblastoma
Note
The invasive nature of glioblastoma multiforme presents a clinical problem rendering tumors incurable by conventional treatment modalities such as surgery, ionizing radiation, and temozolomide.
SLC9A3R1 has been implicated to play a role in sustaining glioma cell migration and invasion. SLC9A3R1 has been shown to be over-expressed in invading glioma cells as compared to the tumor core (Kislin et al., 2009).
Entity name
Breast cancer
Note
Increased cytoplasmic expression of SLC9A3R1 in breast tumors suggests a key role of its localization and compartmentalization in defining cancerogenesis, progression, and invasion. SLC9A3R1 overexpression has been associated with increasing tumor cytohistological grade, aggressive clinical behavior, unfavorable prognosis, and increased tumor hypoxia. Moreover, SLC9A3R1 co-localizes with the oncogenic receptor HER2/neu in HER2/neu-overexpressing carcinoma and in distant metastases (Mangia et al., 2009).
The switch from apical membranous to cytoplasmic expression is compatible with a dual role for NHERF1 as a tumour suppressor or tumour promoter dependent on its subcellular localization (Georgescu et al., 2008).
Entity name
Cystic fibrosis
Note
The inherited disease cystic fibrosis is one of the most common chronic lung diseases in children and young adults and may lead to an early death.
Cystic fibrosis transmembrane regulator (CFTR) functions as a cAMP-regulated chloride channel, and mutations in CFTR are contributory in cystic fibrosis. CFTR contains a C-terminal SLC9A3R1 consensus sequence affording the two proteins to bind with high affinity. Recent experiments have postulated two roles for SLC9A3R1 in CFTR function. Guggino, Stanton, and coworkers have proposed that NHERF functions as a membrane retention signal for CFTR (Moyer et al., 1999).
Raghuram et al. suggest that SLC9A3R1 facilitates the dimerization of CFTR leading to its full expression of chloride channel activity (Raghuram et al., 2001).
Lastly, ss2-adrenoceptors have been shown to physically interact with CFTR Na+/H+ Exchanger Regulatory Factor 1 SLC9A3R1 protein. This function of SLC9A3R1 could be a new therapeutic target in CF patients to facilitate the trafficking of mutated CFTR to plasma membrane (Bossard et al., 2011).
Entity name
Hypophosphatemia and nephrolithiasis
Note
SLC9A3R1 plays an important role in tumor phosphorous transport. Inactivating missense mutations in SLC9AR1 have been identified in patients with hypercalciuria and neprolithiasis (Karim et al., 2008).

Bibliography

Pubmed IDLast YearTitleAuthors
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126518582003The role of the C terminus and Na+/H+ exchanger regulatory factor in the functional expression of cystic fibrosis transmembrane conductance regulator in nonpolarized cells and epithelia.Benharouga M et al
200426042010A conformational switch in the scaffolding protein NHERF1 controls autoinhibition and complex formation.Bhattacharya S et al
158051082005Receptor activity-modifying protein (RAMP) isoform-specific regulation of adrenomedullin receptor trafficking by NHERF-1.Bomberger JM et al
172371492007NHE-RF1 protein rescues DeltaF508-CFTR function.Bossard F et al
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173325062007The NHERF1 PDZ2 domain regulates PKA-RhoA-p38-mediated NHE1 activation and invasion in breast tumor cells.Cardone RA et al
210799872010Estrogens regulate the expression of NHERF1 in normal colon during the reproductive cycle of Wistar rats.Cuello-Carrión FD et al
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200315772009Novel loci, including those related to Crohn disease, psoriasis, and inflammation, identified in a genome-wide association study of fibrinogen in 17 686 women: the Women's Genome Health Study.Danik JS et al
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121453372002Estrogen receptor inducibility of the human Na+/H+ exchanger regulatory factor/ezrin-radixin-moesin binding protein 50 (NHE-RF/EBP50) gene involving multiple half-estrogen response elements.Ediger TR et al
181841092008Beta-oestradiol rescues DeltaF508CFTR functional expression in human cystic fibrosis airway CFBE41o- cells through the up-regulation of NHERF1.Fanelli T et al
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209376952010The scaffolding protein EBP50 regulates microvillar assembly in a phosphorylation-dependent manner.Garbett D et al
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187819532008Roles of NHERF1/EBP50 in cancer.Georgescu MM et al
154893342004The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).Gerhard DS et al
126658012003Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides.Gevaert K et al
145318062003PDZK1: I. a major scaffolder in brush borders of proximal tubular cells.Gisler SM et al
110995002001Interaction of the type IIa Na/Pi cotransporter with PDZ proteins.Gisler SM et al
120800812002Epithelial inducible nitric-oxide synthase is an apical EBP50-binding protein that directs vectorial nitric oxide output.Glynne PA et al
96717061998A C-terminal motif found in the beta2-adrenergic receptor, P2Y1 receptor and cystic fibrosis transmembrane conductance regulator determines binding to the Na+/H+ exchanger regulatory factor family of PDZ proteins.Hall RA et al
95601621998The beta2-adrenergic receptor interacts with the Na+/H+-exchanger regulatory factor to control Na+/H+ exchange.Hall RA et al
104462101999G protein-coupled receptor kinase 6A phosphorylates the Na(+)/H(+) exchanger regulatory factor via a PDZ domain-mediated interaction.Hall RA et al
115330362001Phosphorylation and cell cycle-dependent regulation of Na+/H+ exchanger regulatory factor-1 by Cdc2 kinase.He J et al
126150542003C-terminal phosphorylation of MRP2 modulates its interaction with PDZ proteins.Hegedüs T et al
146083572003A putative RUNX1 binding site variant between SLC9A3R1 and NAT9 is associated with susceptibility to psoriasis.Helms C et al
145079272003GIPC binds to the human lutropin receptor (hLHR) through an unusual PDZ domain binding motif, and it regulates the sorting of the internalized human choriogonadotropin and the density of cell surface hLHR.Hirakawa T et al
190731372009Involvement of NHERF1 in apical membrane localization of MRP4 in polarized kidney cells.Hoque MT et al
190914022009Regulation of protein expression and function of octn2 in forskolin-induced syncytialization in BeWo Cells.Huang FD et al
150709042004kappa Opioid receptor interacts with Na(+)/H(+)-exchanger regulatory factor-1/Ezrin-radixin-moesin-binding phosphoprotein-50 (NHERF-1/EBP50) to stimulate Na(+)/H(+) exchange independent of G(i)/G(o) proteins.Huang P et al
202154042010Sip1, the Drosophila orthologue of EBP50/NHERF1, functions with the sterile 20 family kinase Slik to regulate Moesin activity.Hughes SC et al
118930832002Distinct cell type-specific expression of scaffolding proteins EBP50 and E3KARP: EBP50 is generally expressed with ezrin in specific epithelia, whereas E3KARP is not.Ingraffea J et al
151619432004A NHERF binding site links the betaPDGFR to the cytoskeleton and regulates cell spreading and migration.James MF et al
187841022008NHERF1 mutations and responsiveness of renal parathyroid hormone.Karim Z et al
118826632002Structural determinants of the Na+/H+ exchanger regulatory factor interaction with the beta 2 adrenergic and platelet-derived growth factor receptors.Karthikeyan S et al
155230542005PDZK1 directly regulates the function of organic cation/carnitine transporter OCTN2.Kato Y et al
155532372004Screening of the interaction between xenobiotic transporters and PDZ proteins.Kato Y et al
193082922009NHERF-1: modulator of glioblastoma cell migration and invasion.Kislin KL et al
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195813082009The protein scaffold NHERF-1 controls the amplitude and duration of localized protein kinase D activity.Kunkel MT et al
179822582007Knockdown of NHERF1 enhances degradation of temperature rescued DeltaF508 CFTR from the cell surface of human airway cells.Kwon SH et al
191735792009The scaffold protein PDZK1 undergoes a head-to-tail intramolecular association that negatively regulates its interaction with EBP50.LaLonde DP et al
123698222002The down regulated in adenoma (dra) gene product binds to the second PDZ domain of the NHE3 kinase A regulatory protein (E3KARP), potentially linking intestinal Cl-/HCO3- exchange to Na+/H+ exchange.Lamprecht G et al
129546002003Ca2+-dependent inhibition of NHE3 requires PKC alpha which binds to E3KARP to decrease surface NHE3 containing plasma membrane complexes.Lee-Kwon W et al
195918392009Ezrin induces long-range interdomain allostery in the scaffolding protein NHERF1.Li J et al
161296952005Ezrin controls the macromolecular complexes formed between an adapter protein Na+/H+ exchanger regulatory factor and the cystic fibrosis transmembrane conductance regulator.Li J et al
176135302007Protein kinase C phosphorylation disrupts Na+/H+ exchanger regulatory factor 1 autoinhibition and promotes cystic fibrosis transmembrane conductance regulator macromolecular assembly.Li J et al
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119562112002Protein kinase C epsilon-dependent regulation of cystic fibrosis transmembrane regulator involves binding to a receptor for activated C kinase (RACK1) and RACK1 binding to Na+/H+ exchange regulatory factor.Liedtke CM et al
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110461322000Platelet-derived growth factor receptor association with Na(+)/H(+) exchanger regulatory factor potentiates receptor activity.Maudsley S et al
162368062005Modulation of renal apical organic anion transporter 4 function by two PDZ domain-containing proteins.Miyazaki H et al
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Other Information

Locus ID:

NCBI: 9368
MIM: 604990
HGNC: 11075
Ensembl: ENSG00000109062

Variants:

dbSNP: 9368
ClinVar: 9368
TCGA: ENSG00000109062
COSMIC: SLC9A3R1

RNA/Proteins

Gene IDTranscript IDUniprot
ENSG00000109062ENST00000262613O14745
ENSG00000109062ENST00000413388O14745
ENSG00000109062ENST00000581356J3QRA3
ENSG00000109062ENST00000583369J3QRP6

Expression (GTEx)

0
50
100
150
200
250
300
350
400
450
500

Pathways

PathwaySourceExternal ID
Tight junctionKEGGko04530
Tight junctionKEGGhsa04530

Protein levels (Protein atlas)

Not detected
Low
Medium
High

PharmGKB

Entity IDNameTypeEvidenceAssociationPKPDPMIDs
PA27745ELF2GenePathwayassociated

References

Pubmed IDYearTitleCitations
146083572003A putative RUNX1 binding site variant between SLC9A3R1 and NAT9 is associated with susceptibility to psoriasis.71
218045992012PTEN, NHERF1 and PHLPP form a tumor suppressor network that is disabled in glioblastoma.64
128300002003EBP50, a beta-catenin-associating protein, enhances Wnt signaling and is over-expressed in hepatocellular carcinoma.62
173325062007The NHERF1 PDZ2 domain regulates PKA-RhoA-p38-mediated NHE1 activation and invasion in breast tumor cells.61
187841022008NHERF1 mutations and responsiveness of renal parathyroid hormone.60
191655272009Prefrontal cortex shotgun proteome analysis reveals altered calcium homeostasis and immune system imbalance in schizophrenia.56
187546782008The relative binding affinities of PDZ partners for CFTR: a biochemical basis for efficient endocytic recycling.55
129201192003Activation-independent parathyroid hormone receptor internalization is regulated by NHERF1 (EBP50).54
178848162007NHERF1 regulates parathyroid hormone receptor membrane retention without affecting recycling.53
172421912007NHERF1/EBP50 head-to-tail intramolecular interaction masks association with PDZ domain ligands.51

Citation

Wendy S McDonough ; Michael E Berens

SLC9A3R1 (solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 1)

Atlas Genet Cytogenet Oncol Haematol. 2010-12-01

Online version: http://atlasgeneticsoncology.org/gene/46023/slc9a3r1