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WDR48 (WD repeat domain 48)

Written2017-04Anne Olazabal-Herrero, Godefridus J Peters, Elisa Giovannetti, Jose Antonio Rodriguez
Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain; ane.olazabal@ehu.eus; josean.rodriguez@ehu.eus (AOH, JAR); Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands; gj.peters@vumc.nl; elisa.giovannetti@gmail.com (GJP, EG); Cancer Pharmacology Lab, AIRC Start-Up Unit, University of Pisa, Pisa , Italy (EG).

Abstract WDR48 is a WD40-repeat containing protein that regulates the activity of three human deubiquitinating enzymes: USP1, USP12 and USP46. The best characterized role of WDR48 is regulation of the DNA damage response in complex with USP1. The USP1/WDR48 complex promotes deubiquitination of monoubiquitinated FANCD2 and monoubiquitinated PCNA, which are required in the regulation of translesion synthesis (TLS) and Fanconi anemia (FA) DNA repair pathways, respectively. In addition, in complex with USP12 and USP46, WDR48 regulates other important cellular processes such as synaptic transmission or signalling through the Akt, Notch and T-cell receptor pathways.

Keywords WDR48; USP1; USP12; USP46; DNA damage Fanconi anemia

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Identity

Other aliasP80
UAF1
SPG60
KIAA1449
LocusID (NCBI) 57599
Atlas_Id 53058
Location 3p22.2 (Starts at 39051986 and ends at 39096671 bp from pter (according to hg-38))  [Link to chromosome band 3p22]
Location_base_pair Starts at and ends at bp from pter
Local_order Based on MapViewer, genes flanking WDR48 are:
-SCN10A (sodium voltage-gated channel alpha subunit 10); 3p22.2
-SCN11A (sodium voltage-gated channel alpha subunit 11); 3p22.2
-WDR48 (WD repeat domain 48); 3p22.2
-GORASP1 (golgi reassembly stacking protein 1); 3p22.2
-TTC21A (tetratricopeptide repeat domain 21A); 3p22.2
 
  Figure 1: Localization of WDR48 on chromosome 3p22.2. WDR48 starts from 39051986 and ends at 39096671 bp.

DNA/RNA

Description WDR48 gene is located on chromosome 3 in the region p22.2. WDR48 was first cloned in 2000 (Nagase et al., 2000) as a gene coding for a 607 amino acid protein called KIAA1449. In 2002, Park and co-workers (Park et al., 2002) cloned the full-length cDNA encoding the 677 amino acid WDR48 protein, which they called p80.
Transcription Ten alternatively spliced transcript variants have been identified (WDR48-001, -003, -004, -005, -006, -007, -008, -009, -010 and -011) for this gene. Transcription variants -001 and -008 encode for proteins containing 677 and 162 amino acids, respectively. The remaining variants are not translated into a protein product.
Pseudogene Not reported pseudogenes. Paralogs for WDR48 are STRN4 and STRN3.

Protein

Description The WDR48 gene encodes a 677 amino acid protein (from the -001 splice variant) with a predicted molecular weight of 76,21 kDa. WDR48 belongs to the WD repeat (WDR) domain-containing protein family. This family is characterized by the presence of several copies of an approximately 40 residues-long sequence motif containing Trp-Asp repeats. WDR48 contains eight WD repeats (Figure 2). (Repeats WD1-WD7 adopt a 7-bladed β-propeller structure shaped as a toroid with a narrow central pore (Yin et al., 2015), whereas the WD8 repeat is included into the so-called ancillary domain. On the other hand, the C-terminus of WDR48 contains two SUMO-like domains (SLD1 and SLD2) that adopt a coiled-coil structure.
As further detailed below, WDR48 functions as a cofactor that stimulates the enzymatic activity of deubiquitinating enzymes (DUBs). In this context, the β-propeller domain of WDR48 mediates the binding to the enzymes, whereas the SLD domain contributes to the recruitment of different substrates (Cohn et al., 2007; Yin et al., 2015; Yang et al., 2011).
 
  Figure 2: Structural organization of the WDR48 protein. WDR48 contains eight WD40 repeats. WD1-WD7 adopt a β-propeller structure. WD8 is part of the ancillary domain. The C-terminus contains two tandem SUMO-like domains (SLD1 and SLD2) that adopt a coiled-coil structure.
Expression WDR48 is expressed in a wide variety of tissue types including testis, brain, thyroid, prostate, lung and bone marrow.
Localisation Initially reported as an endosomal protein (Park et al., 2002), WDR48 is also detected in the cytoplasm. The nucleocytoplasmic distribution of WDR48 can be further regulated by interaction with other proteins, such as the human papillomavirus (HPV) E1 helicase or the human deubiquitinating enzyme USP1. These proteins bear active nuclear localization signals (NLSs), and facilitate WDR48 import into the nucleus via a piggyback mechanism (Cotée-Martin et al., 2008; Garcia-Santisteban et al., 2012).
 
  Figure 3: By activating USP1, USP12 and USP46 deubiquitinases, WDR48 regulates the ubiquitination level of several substrate proteins and takes part in a variety of cellular processes.
Function The best-characterized role of WDR48 is as a cofactor of USP1, USP12 and USP46, three deubiquitinating enzymes belonging to the Ubiquitin Specific Protease (USP) family (Cohn et al., 2009). The intrinsic enzymatic activity of these DUBs is relatively low, and is increased by up to 30 fold upon complex formation with WDR48 (Cohn et al., 2007, Faesen et al., 2011, Yin et al., 2015). Through its β-propeller domain, WDR48 binds to the so-called "Fingers" domain of the DUBs (Garcèa-Santisteban et al., 2012; Olazabal-Herrero et al., 2015; Yin et al., 2015). The Fingers domain is far away from the catalytic site of these enzymes, and WDR48-mediated stimulation of DUB activity involves an allosteric mechanism. WDR48 binding induces a structural rearrangement of the DUB active site that increases catalytic turnover. (Villamil et al., 2012; Yin et al., 2015; Li et al., 2016). Of note, binding to WDR48 does not modify the affinity of the DUBs for their substrates.
By activating these three different deubiquitinating enzymes, WDR48 contributes to the regulation of the ubiquitination level of several substrate proteins, and thus plays a role in a variety of cellular processes (summarized in figure 3).
In complex with USP1, WDR48 regulates DNA repair by reverting the monoubiquitination of PCNA in the translesion synthesis pathway (Huang et al., 2006), and of FANCD2 / FANCI in the Fanconi anaemia pathway (Nijman et al., 2005; Cohn et al., 2007, Yang et al., 2011; Van Tweest et al., 2017). Moreover, the USP1/WDR48 complex promotes the repair of DNA damage by homologous recombination (Murai et al., 2011; Park et al., 2013). This has been reported to be, at least in part, mediated by the interaction of WDR48 withRAD51AP1 (Liang et al., 2016; Cukras et al., 2016) in a manner that could be independent from USP1 (Liang et al., 2016) (Figure 4). Besides these DNA repair-related functions, the USP1/WDR48 complex deubiquitinates inhibitors of DNA binding (ID) proteins and thus regulates differentiation in osteosarcoma cells (Williams et al., 2011).
In complex with either USP12 or USP46, WDR48 regulates embryonic development in a Xenopus model by deubiquitinating histones H2A and H2B, (Joo et al. 2011), and negatively regulates the Akt signaling pathway by stabilizing the PHLPP1 phosphatase (Gangula et al., 2013; Li et al., 2013). ).
Besides the Akt pathway, at least three other signalling pathways are regulated by WDR48 in complex with USP12. The USP12/WDR48 complex negatively regulates Notch signaling by stabilizing the nonactivated form of the Notch receptor (NotchR) (Moretti et al., 2012). Conversely, it positively regulates T-cell receptor (TCR) signaling by increasing the stability of the TCR signaling complex (Jahan et al., 2016), and it promotes androgen receptor ( AR) signaling both directly (by deubiquitinating and stabilizing the AR protein) and indirectly (by reducing Akt-mediated AR inactivation) (Burska et al., 2013; McClurgh et al., 2104). ).
Finally, in complex with USP46, WDR48 may contribute to modulate synaptic transmission in the brain by deubiquitinating and regulating the turnover of neuronal glutamate receptors (GluR) and AMPA receptors (AMPAR) (Dalhberg et al., 2014; Huo et al., 2015).
In addition to the cellular functions described above, WDR48 also plays a role in viral pathogenesis. In fact, WDR48 was originally identified as p80, a cellular protein targeted by the herpesvirus saimiri Tip protein during viral infection (Park et al., 2002). WDR48 has been subsequently found to bind other viral proteins, such as the E1 helicase of HPV (Cté-Martin et al., 2008) or the EBNA3C protein of Epstein-Barr virus (EBV) (Ohashi et al., 2015). These interactions, which may also involve the DUBs, appear to promote the replication and maintenance of the viral genome in HPV-infected keratinocytes (Cté-Martin et al., 2008, Lehoux et al., 2014, Gagnon et al., 2015), as well as the growth of EBV-infected lymphoblastoid cells (Ohashi et al., 2015).
 
  Figure 4: Summary of the roles of the USP1/WDR48 complex in the DNA damage response. USP1/WDR48 regulates DNA repair by reverting the monoubiquitination of PCNA in the translesion synthesis pathway and of FANCD2/FANCI in the Fanconi anaemia pathway. In addition, the USP1/WDR48 complex promotes the repair of DNA damage by homologous recombination by the interaction of WDR48 with RAD51AP1.
Homology The WDR48 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, fruit fly, mosquito, C.elegans, A.thaliana, rice and frog.

Mutations

Somatic A survey in the COSMIC mutation database (accession date: 17 November 2016) revealed a total of 71 mutations that lead to different modification in different human tumors. Most of the modifications are missense mutations whose functional consequences need to be addressed (Table 1).
Table 1: Cancer-associated mutations in WDR48. The table shows a detailed list of WDR48 cancer-associated mutations reported to date (November 2016) in the COSMIC mutation database, including the DNA modification (CDS Mutation), protein modification (AA mutation) and affected tissue. Missense amino acid substitutions are indicated in black, nonsense amino acid substitution in red and frameshift insertion/deletions in blue. Synonymous amino acid substitutions have been omitted.
CDS MutationAA mutationTissue
c.8C>Tp.A3VSkin
c.35 36GG>>AAp.R12QSkin
c.43G>Tp.V15LUrinary tract
c.53C>Tp.S18FSkin
c.56A>Gp.Y19CHaematopoietic and lymphoid
c.64C>Tp.R22*Endometrium
c.83A>Gp.Y28CLarge intestine
c.88C>Tp.R30*Large intestine
c.113C>Tp.L45FNS
c.148C>Tp.R50*Large intestine
c.175G>Ap.V59INS
c.189G>Tp.K63NUpper aerodigestive tract
c.206C>Tp.A69VStomach
c.221A>Gp.H74RStomach
c. 277G>Tp.A93SAutonomic ganglia
c.284C>Tp.S95FProstate
c.290C>Tp.T97MOesophagus
c. 304T>Cp.W102RBreast
c.317A>Gp.K106ROesophagus
c.330G>Tp.M110ISkin
c.374_375insTp.A126fs*4Oesophagus
c.403G>Tp.A135SLiver
c.504A>Cp.K168NLarge intestine
c.565G>Ap.E189KBreast
c.585G>Tp.W195CStomach
c.610A>Gp.M204VHaematopoietic and lymphoid
c.659G>Cp.R220TOesophagus
c.668C>Tp.T223MLarge intestine
c.682G>Tp.G228CSmall intestine
c.703C>Tp.R235CLarge intestine
c.745C>Tp.R249*Large intestine
c.746G>Tp.R249LLiver
c.770C>Tp.A257VProstate
c.784G>Ap.D262NCervix
c.859C>Tp.R287WSkin
c.871T>Gp.C291GEndometrium
c.916G>Tp.A306SEndometrium
c.934A>Gp.I312VBreast
c.1001C>Tp.A334VStomach
c.1006G>Tp.G336*Liver
c.1007G>Cp.G33AUrinary tract
c.1024T>Ap.C342SCentral nervous system
c.1036A>Gp.I346VUpper aerodigestive tract
c.1102A>Gp.I368VHaematopoietic and lymphoid
c.1210G>Ap.E404KCervix
c.1326G>Tp.W442CLarge intestine
c.1343C>Ap.A448DEndometrium
c.1343C>Tp.A448VProstate
c.1345G>Ap.G449SPancreas
c.1434_1435insTGp.V479fs*2Biliary tract
c.1141C>Tp.P481SSkin
c.1451A>Gp.E484GPancreas
c.1486C>Ap.Q496KHaematopoietic and lymphoid
c.1495C>Tp.R499*Endometrium
c.1508_1524del17p.N504fs*10Ovary
c.1522C>Tp.Q508*Skin
c.1543G>Tp.V515LUrinary tract
c.1567C>Tp.R523CSkin
c.1682A>Gp.K561RLarge intestine and Pancreas
c.1705C>Tp.L569FSkin
c.1743A>Cp.K581NLung
c.1740delAp.D583fs*75Biliary tract
c.1812T>Gp.I604MLarge intestine
c.1858G>Ap.E620KUrinary tract
c.1870G>Ap.E624KLarge intestine and Urinary tract
c.1895C>Tp.A632VEndometrium
c.1963C>Tp.R655*Stomach
c.1969G>Ap.V657MSkin
c.1989G>Cp.K663NLung
c.1999G>Ap.D667NSkin
c.2017C>Tp.R673CBreast

Implicated in

  
Entity Fanconi anaemia
Note In mice, knockout of WDR48 results is a phenotype that resembles the phenotype of human patients with Fanconi anemia (FA) (Park et al., 2013), a rare genetic disease characterized by congenital malformations, progressive bone marrow failure, genomic instability, hypersensitivity to DNA cross-linking agents and increased susceptibility to cancer (Kee and DAndrea 2012).
  
  
Entity Autosomal recessive spastic paraplegia type 60 (SPG60)
Note Hereditary spastic paraplegias (HSP) are rare neurodegenerative disorders. The main pathological characteristic is the degeneration of the corticospinal tracts. Novarino and co-workers (Novarino et al., 2014) identified homozygosity for a WDR48 deletion mutant (c.1879_1881delAAG), resulting in a deletion of glutamic acid at position 628 (E628del), in a single individual from a consanguineous family that leads to spastic paraplegia type 60. The contribution of this variant to SPG60 has not been confirmed.
  

To be noted

This work was supported by grants from the Spanish Government MICINN (Ministerio de Ciencia e Innovación) (grant number BFU2009-13,245) and the University of the Basque Country (UFI11/20) to JAR, and a fellowship from the University of the Basque Country (to AOH). We also acknowledge support from the European Cooperation in Science and Technology through COST Action PROTEOSTASIS BM1307. This work was partially supported by grants from the Cancer Center Amsterdam (CCA) Foundation (GJP and EG) and Italian Association for Cancer Research (AIRC) to EG.

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Citation

This paper should be referenced as such :
Olazabal-Herrero A, Peters GJ, Giovannetti El, Antonio Rodriguez J
WDR48 (WD repeat domain 48);
Atlas Genet Cytogenet Oncol Haematol. in press
On line version : http://AtlasGeneticsOncology.org/Genes/WDR48ID53058ch3p22.html


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BioGPS (Tissue expression)57599
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