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PRND (Prion Protein 2 (Dublet))

Written2013-12Gabriele Giachin, Giuseppe Legname
Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), via Bonomea 265, Trieste, Italy

(Note : for Links provided by Atlas : click)

Identity

Alias_symbol (synonym)DPL
dJ1068H6.4
DOPPEL
PrPLP
Other alias
HGNC (Hugo) PRND
LocusID (NCBI) 23627
Atlas_Id 44172
Location 20p13  [Link to chromosome band 20p13]
Location_base_pair Starts at 4721854 and ends at 4728462 bp from pter ( according to hg19-Feb_2009)  [Mapping PRND.png]
Local_order PRND lies 27 kb downstream the human prion protein gene (PRNP). PRNP starts at 4702556 and ends at 4709106 bps.
 
  Schematic structural representation of the human PRN locus on chromosome 20p13 containing PRNP, PRND and the putative testis-specific prion protein (PRNT) genes.
Fusion genes
(updated 2016)
LINC00914 () / PRND (20p13)
Note PRND and PRNP genes form the prion gene complex and are regulated by their own promoter. Doppel is an acronym derived from downstream prion protein-like gene (Moore et al., 2001). PRNP and PRND are believed to arise through duplication of a single ancestral gene (Mastrangelo and Westaway, 2001).

DNA/RNA

Note The Prnd gene was originally identified in mice during DNA sequencing of the cosmid clone isolated from the I/LnJ inbred mice strain (Lee et al., 1998). This gene was discovered in transgenic (Tg) mice where the Prnp gene was ablated (Prnp0/0 mice strains) resulting in a diseased phenotype characterized by loss of Purkinje cells in the cerebellum. Interestingly, Prnp deletion in these mouse lines resulted in the formation of a chimeric Prnd transcript under the control of the strong Prnp promoter. Thus, these studies have shown that only the ectopic expression of Dpl, rather than the absence of the Prnp gene, caused neurodegeneration (Li et al., 2000).
 
  Schematic representation of the PRND gene. Exon 1 starts at 4705556 bp and ends at 4702615 bp. Exon 2 containing the Doppel open reading frame (ORF) starts at 4705187 bp and ends at 4709106 bp. The sequence surrounding the splice acceptor site is shown with intronic nucleotides in lower case, exonic nucleotides in capital letters and Met start codon ATG underlined.
Description The PRND gene includes two exons separated by one intron. Exon 2 encodes for the Doppel protein.
Transcription Prnd RNA transcription has been reported in different tissues of adult wild-type (WT) mice including testis, heart, spleen and skeletal muscle (Li et al., 2000). In neonatal mice up to 3 weeks, Prnd RNA has been detected in brain blood vessel endothelial cells (Li et al., 2000).
Pseudogene Prnd pseudogenes have been identified in non-mammalian organisms as Anolis (lizard) and Xenopus (frog) (Harrison et al., 2010).

Protein

Note Doppel tertiary structure has a fold similar to that of the cellular prion protein, PrPC (encoded by PRNP or Prnp genes) although it shares approximately 25% of aminoacidic sequence identity with PrPC.
 
  A) Primary sequence alignment between human PrPC (GenBank: BAG32277.1) and human Doppel (NCBI Reference Sequence: NP_036541.2). B) Secondary structure motives of human PrPC and Doppel. Highlighted: signal peptides, N-linked glycosylation sites (CHO), disulfide bridges (S-S) and Glycosylphosphatidylinisotol (GPI) anchor. C) Tertiary NMR structures of Doppel (pdb id 1LG4) and PrPC (2LSB).
Description The immature form of human Doppel includes 176 residues with two N- and C-terminal signal peptides cleaved during protein maturation. The mature sequence includes 126 amino acids spanning from residues 27 to 152, with a molecular weight of approximately 14.5 kDa. Tryptic digestion and mass spectroscopy studies have identified two distinct disulfide bridges (Cys109-Cys143 and Cys95-Cys148) which strongly stabilize the Doppel folding (Baillod et al., 2013; Silverman et al., 2000; Whyte et al., 2003). PNGase F digestion and immunoblots have reported two N-linked glycosylation sites at codons 99 and 111. The GPI anchor targets the protein at the extracellular membrane. NMR structures of recombinant human and mouse Dopple have been solved (Luhrs et al., 2003; Mo et al., 2001). The NMR structures of the N-terminal murine and ovine signal peptides (residues 1-30) have also been determined (Papadopoulos et al., 2006). The human Doppel NMR structure features a short flexible N-terminal segment comprising residues 24-51 and a globular domain including four α-helices (α1: residues 72-80; α2a: residues 101-115; α2b: residues 117-121; α3: residues 127-141) and a short two-stranded anti-parallel β-sheet (β1: residues 58-60; β2: residues 88-90) (Luhrs et al., 2003).
Expression Under physiological conditions Doppel is mostly expressed in testis and, in particular, in spermatozoa and Sertoli cells (Behrens et al., 2002; Peoc'h et al., 2002). Additionally, Doppel is expressed with PrPC in spleen cells, notably B lymphocytes, granulocytes and dendritic cells (Cordier-Dirikoc et al., 2008).
Localisation Doppel is attached to the cell membrane through its GPI anchor (Silverman et al., 2000). A study has shown Doppel localization in detergent-resistant membranes or lipid rafts (Caputo et al., 2010).
Function The Doppel expression in spermatozoa and Sertoli cells infers a role in spermatogenesis. Male Tg mice knock-out for Prnd were sterile, clearly indicating that Doppel plays a role in male reproduction as critical regulator of spermatogenesis and sperm-egg interaction (Behrens et al., 2002). Doppel may enhance in vitro ovine spermatozoa fertilizing ability (Pimenta et al., 2012). Doppel has been implicated in early testis differentiation (Kocer et al., 2007). The detection of Prnd mRNA in brain blood vessel endothelial cells might indicate a possible role in the development of brain blood vessels (Li et al., 2000). The observation that Doppel is expressed with PrPC in B lymphocytes, granulocytes and dendritic cells argues for a role in cell-cell interaction in the immunosystem (Cordier-Dirikoc et al., 2008). Several evidence showed that Doppel is able to coordinate in vitro the binding of copper ions with high affinity (Cereghetti et al., 2004; La Mendola et al., 2010; Qin et al., 2003).

Mutations

Note Different polymorphic variants have been identified in PRND. The effect of polymorphisms in Doppel function and their implication in the diseases have not been fully clarified.
Germinal S6I, S22P, T26P, H31R, P56L, F70L, L149S, T174M (Clark et al., 2003; Moore et al., 1999; Peoc'h et al., 2000; Schroder et al., 2001).

Implicated in

Note
  
Entity Ectopic Doppel expression associated with Purkinje cell neurodegeneration in transgenic mouse models.
Note Beside its role in male reproductive system, Doppel has attracted interest for its neurotoxic properties when ectopically expressed in the brain of Tg mice knock-out for the prion protein gene (Prnp0/0 mice). In these mice, denoted as Ngsk PrP-/-, the Doppel-encoding exon was expressed as chimeric mRNA due to the intergenic splicing taking place between Prnp and Prnd. As a result, Prnd became abnormally regulated under the control of Prnp promoter and ectopically expressed in the brain and, in particular, in neurons and glial cells (Li et al., 2000). Similar non-physiological Doppel expression was reported in other Tg mouse lines knock-out for Prnp such as Rcm0 and Zrch mice (Moore et al., 2001; Rossi et al., 2001). Doppel expression in the brain is neurotoxic and causes Purkinje cell degeneration in these mouse models. Doppel neurotoxicity is antagonized by the PrPC N-terminal domain (Atarashi et al., 2003; Yamaguchi et al., 2004). The neuroprotective PrPC role against ectopic Doppel expression has been reported also in human neuronal SH-SY5Y cells (Li et al., 2009) confirming the dominant-negative effects of the PrPC N-terminal region (Yoshikawa et al., 2008). The molecular mechanisms leading to Doppel-induced neurodegeneration in Purkinje and granular cells are still controversial. An earlier study has reported that the chimeric form of Doppel fused to a Fc domain binds specifically granule cells and causes neurodegeneration, raising the possibility that these specific cells expressed a still unidentified protein that mediates the Doppel-induced neurotoxicity (Legname et al., 2002). Oxidative stress may play a role in Doppel-induced neuronal death since NOS activity is induced by Doppel in vitro and in vivo (Cui et al., 2003; Wong et al., 2001). Two independent groups have reported that BAX contributes to Doppel-induced apoptosis (Didonna et al., 2012; Heitz et al., 2007) and that BCL-2 antagonizes Doppel neurotoxicity (Heitz et al., 2008). Another work has observed that ectopic Doppel expression in the brain elicits neurodegeneration through the binding of two metalloproteinase namely the alpha-1-inhibitor-3 (α1I3) and the alpha-2-macroglobin (α2M) (Benvegnu et al., 2009).
  
  
Entity Abnormal Doppel expression levels in human astrocytomas and other non-glial brain tumor specimens
Note Doppel is aberrantly expressed in astrocytic tumors where it displays cytoplasmic, nuclear and lysosomal localization and molecular properties (i.e. altered glycosilation pattern) different from Doppel as normally expressed in testis (Azzalin et al., 2006; Azzalin et al., 2008; Comincini et al., 2006; Comincini et al., 2004; Comincini et al., 2007; Rognoni et al., 2010; Sbalchiero et al., 2008).
  

Bibliography

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PMID 18604867
 
Analysis of doppel protein toxicity.
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PMID 12799144
 
The role of Bax and caspase-3 in doppel-induced apoptosis of cerebellar granule cells.
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PMID 20206252
 
BCL-2 counteracts Doppel-induced apoptosis of prion-protein-deficient Purkinje cells in the Ngsk Prnp(0/0) mouse.
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PMID 18085563
 
BAX contributes to Doppel-induced apoptosis of prion-protein-deficient Purkinje cells.
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PMID 17443816
 
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PMID 17226816
 
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PMID 20411530
 
Complete genomic sequence and analysis of the prion protein gene region from three mammalian species.
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PMID 12446843
 
Identification of a novel gene encoding a PrP-like protein expressed as chimeric transcripts fused to PrP exon 1/2 in ataxic mouse line with a disrupted PrP gene.
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Doppel-induced cytotoxicity in human neuronal SH-SY5Y cells is antagonized by the prion protein.
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Two different neurodegenerative diseases caused by proteins with similar structures.
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The human "prion-like" protein Doppel is expressed in both Sertoli cells and spermatozoa.
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The prion-like protein Doppel enhances ovine spermatozoa fertilizing ability.
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PMID 21806689
 
The PrP-like protein Doppel binds copper.
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Doppel is an N-glycosylated, glycosylphosphatidylinositol-anchored protein. Expression in testis and ectopic production in the brains of Prnp(0/0) mice predisposed to Purkinje cell loss.
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Stability and conformational properties of doppel, a prion-like protein, and its single-disulphide mutant.
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PMID 12665426
 
Induction of HO-1 and NOS in doppel-expressing mice devoid of PrP: implications for doppel function.
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Mol Cell Neurosci. 2001 Apr;17(4):768-75.
PMID 11312611
 
Doppel-induced Purkinje cell death is stoichiometrically abrogated by prion protein.
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PMID 15194501
 
Dominant-negative effects of the N-terminal half of prion protein on neurotoxicity of prion protein-like protein/doppel in mice.
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J Biol Chem. 2008 Aug 29;283(35):24202-11. doi: 10.1074/jbc.M804212200. Epub 2008 Jun 18.
PMID 18562311
 

Citation

This paper should be referenced as such :
Giachin, G ; Legname, G
PRND (Prion Protein 2 (Dublet))
Atlas Genet Cytogenet Oncol Haematol. 2014;18(8):576-580.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/PRNDID44172ch20p13.html


External links

Nomenclature
HGNC (Hugo)PRND   15748
Cards
AtlasPRNDID44172ch20p13
Entrez_Gene (NCBI)PRND  23627  prion like protein doppel
AliasesDOPPEL; DPL; PrPLP; dJ1068H6.4
GeneCards (Weizmann)PRND
Ensembl hg19 (Hinxton)ENSG00000171864 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000171864 [Gene_View]  chr20:4721854-4728462 [Contig_View]  PRND [Vega]
ICGC DataPortalENSG00000171864
TCGA cBioPortalPRND
AceView (NCBI)PRND
Genatlas (Paris)PRND
WikiGenes23627
SOURCE (Princeton)PRND
Genetics Home Reference (NIH)PRND
Genomic and cartography
GoldenPath hg38 (UCSC)PRND  -     chr20:4721854-4728462 +  20p13   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PRND  -     20p13   [Description]    (hg19-Feb_2009)
EnsemblPRND - 20p13 [CytoView hg19]  PRND - 20p13 [CytoView hg38]
Mapping of homologs : NCBIPRND [Mapview hg19]  PRND [Mapview hg38]
OMIM604263   
Gene and transcription
Genbank (Entrez)AF086354 AF187843 AF187844 AK313404 AY358985
RefSeq transcript (Entrez)NM_012409
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)PRND
Cluster EST : UnigeneHs.406696 [ NCBI ]
CGAP (NCI)Hs.406696
Alternative Splicing GalleryENSG00000171864
Gene ExpressionPRND [ NCBI-GEO ]   PRND [ EBI - ARRAY_EXPRESS ]   PRND [ SEEK ]   PRND [ MEM ]
Gene Expression Viewer (FireBrowse)PRND [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)23627
GTEX Portal (Tissue expression)PRND
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9UKY0   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9UKY0  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9UKY0
Splice isoforms : SwissVarQ9UKY0
PhosPhoSitePlusQ9UKY0
Domains : Interpro (EBI)Doppel    Prion/Doppel_prot_b-ribbon_dom   
Domain families : Pfam (Sanger)Doppel (PF11466)    Prion (PF00377)   
Domain families : Pfam (NCBI)pfam11466    pfam00377   
Conserved Domain (NCBI)PRND
DMDM Disease mutations23627
Blocks (Seattle)PRND
PDB (SRS)1LG4   
PDB (PDBSum)1LG4   
PDB (IMB)1LG4   
PDB (RSDB)1LG4   
Structural Biology KnowledgeBase1LG4   
SCOP (Structural Classification of Proteins)1LG4   
CATH (Classification of proteins structures)1LG4   
SuperfamilyQ9UKY0
Human Protein AtlasENSG00000171864
Peptide AtlasQ9UKY0
HPRD05039
IPIIPI00018275   
Protein Interaction databases
DIP (DOE-UCLA)Q9UKY0
IntAct (EBI)Q9UKY0
FunCoupENSG00000171864
BioGRIDPRND
STRING (EMBL)PRND
ZODIACPRND
Ontologies - Pathways
QuickGOQ9UKY0
Ontology : AmiGOcopper ion binding  extracellular region  plasma membrane  C-terminal protein lipidation  cellular copper ion homeostasis  anchored component of membrane  protein homooligomerization  
Ontology : EGO-EBIcopper ion binding  extracellular region  plasma membrane  C-terminal protein lipidation  cellular copper ion homeostasis  anchored component of membrane  protein homooligomerization  
REACTOMEQ9UKY0 [protein]
REACTOME PathwaysR-HSA-163125 [pathway]   
NDEx NetworkPRND
Atlas of Cancer Signalling NetworkPRND
Wikipedia pathwaysPRND
Orthology - Evolution
OrthoDB23627
GeneTree (enSembl)ENSG00000171864
Phylogenetic Trees/Animal Genes : TreeFamPRND
HOVERGENQ9UKY0
HOGENOMQ9UKY0
Homologs : HomoloGenePRND
Homology/Alignments : Family Browser (UCSC)PRND
Gene fusions - Rearrangements
Fusion: TCGARAGE PRND 20p13 HNSC
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPRND [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PRND
dbVarPRND
ClinVarPRND
1000_GenomesPRND 
Exome Variant ServerPRND
ExAC (Exome Aggregation Consortium)PRND (select the gene name)
Genetic variants : HAPMAP23627
Genomic Variants (DGV)PRND [DGVbeta]
DECIPHERPRND [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPRND 
Mutations
ICGC Data PortalPRND 
TCGA Data PortalPRND 
Broad Tumor PortalPRND
OASIS PortalPRND [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPRND  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDPRND
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 PRND
DgiDB (Drug Gene Interaction Database)PRND
DoCM (Curated mutations)PRND (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PRND (select a term)
intoGenPRND
NCG5 (London)PRND
Cancer3DPRND(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM604263   
Orphanet
MedgenPRND
Genetic Testing Registry PRND
NextProtQ9UKY0 [Medical]
TSGene23627
GENETestsPRND
Target ValidationPRND
Huge Navigator PRND [HugePedia]
snp3D : Map Gene to Disease23627
BioCentury BCIQPRND
ClinGenPRND
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD23627
Chemical/Pharm GKB GenePA33795
Clinical trialPRND
Miscellaneous
canSAR (ICR)PRND (select the gene name)
Probes
Litterature
PubMed37 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePRND
EVEXPRND
GoPubMedPRND
iHOPPRND
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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