|Introduction to the XP Genes (see our XP Genes duscussion in forums)
Eight genes have been identified among XP patients [Thompson, 1998]: seven are involved in nucleotide excision repair (XPA-XPG) and one, the XP variant, is involved in replication of damaged DNA on the leading strand [Svoboda et al., 1998]. Mutations in any of the genes XPA to XPG result in reductions in the ability of cells to excise cyclobutane pyrimidine dimers,  photoproducts, and other bulky carcinogen adducts from DNA. The functions of most of the gene products in the nucleotide excision repair process have been identified, and mutations located in each of the genes have begun to be correlated with cellular functions and with severity of disease [Thompson, 1998]. Several of the gene products occur in heterodimeric complexes with proteins that are essential for their stability and function: the XPC protein is complexed with HHR23B; the 48 kDa XPE protein (DDB2) is complexed with a larger 127 kDa subunit (DDB1); and the XPF protein is complexed with the ERCC1 protein (ERCC = excision repair cross complementing, to indicate a human gene correcting a rodent cell mutation). Curiously, in each of these examples, mutations associated with XP have only been found in one of the members of the heterodimer. In addition, the XPB and XPD helicases exist as components of TFIIH, which is a basal transcription initiation factor containing at least nine proteins [Hoeijmakers et al., 1996]. Several recent reviews on the UV-sensitive disorders are recommended [Bootsma et al., 1998; Cleaver and Kraemer, 1995; Thompson, 1998].
|XPA [OMIM] [GenBank] [Protein] [Locus] [Mutation Spectrum] [Genomic Structure]
XPA is located on chromosome 9q34.1 and encodes a 273 amino acid Zn2+ finger protein (XPA) that participates in photoproduct recognition and DNA binding [Asahina et al., 1994; Jones and Wood, 1993; Miura et al., 1991; Tanaka et al., 1989]. The earliest reaction step that has been reported involves XPC by itself [Sugasawa et al., 1998]. This binding may be followed by the formation of a quasi-stable complex consisting of XPA, XPC, human single-strand binding protein (RPA/HSSB), and TFIIH, which then acts as a nucleation site for binding of the incision/excision enzymes [Mu et al., 1997]. Of the two major photoproducts,  photoproducts and cyclobutane pyrimidine dimers, XPA alone shows only weak binding to pyrimidine dimers [He et al., 1995; Jones and Wood, 1993; Li et al., 1995a; Miura et al., 1991; Robins et al., 1991]. The XPA-RPA complex appears to bind to damaged sites in DNA once they have been recognized and bound by either XPC/HHR23B in nontranscribed regions of DNA [Sugasawa et al., 1998], or by stalled RNA polymerase II transcription machinery in transcribed regions [Hanawalt, 1994]. XPA is also required for repair of oxidative damage in mitochondrial DNA [Driggers et al., 1996], indicating potential overlap between nucleotide and base excision repair also found with XPG [Cooper et al., 1997]. The gene is encoded in 6 exons distributed over 2225 kb of genomic DNA [Satokata et al., 1993; Topping et al., 1995] and mutations have been found throughout the gene with the exception of exon I. The first exon is essential for nuclear localization but not for DNA repair when the protein is expressed at high levels [Miyamoto et al., 1992]. Exon II encodes a domain for binding to ERCC1, a component of the heterodimeric 5' endonuclease composed of ERCC1 and XPF (ERCC4) [Li et al., 1995b], and deletion of the ERCC1 binding region in vitro generates a dominant negative phenotype [Li et al., 1995b]. Exon III encodes the Zn2+ finger which binds RPA and exons IV and V comprise the DNA binding domain [Kuraoka et al., 1996; Ikegami et al., 1998]. The TFIIH complex interacts with exon VI of XPA [Park et al., 1995]. Two classes of XPA patients are known, those with severe CNS disorders involving sensoneural deafness, reduced nerve conduction, difficulty walking, and occasionally microcephaly, and those with only skin sensitivity and cancer. The more severe cases tend to have both alleles with mutations that occur within the DNA binding region of the protein, often resulting in truncation, and detailed analysis and diagrammatic representation has been published previously [States et al., 1998]. Severe cases in both Japan and Africa have mutations at the same site, the last nucleotide of intron 3. Milder cases generally have at least one allele with a mutation outside of the DNA binding region, such as the exon 6 (R228ter) mutation common in Tunisian patients [Nishigori et al., 1994; Nishigori et al., 1993]. A few other mild cases have mutations close to a splice site such that alternative splicing may allow the production of a low level of normal protein.
|XPB (ERCC3) [OMIM] [GenBank] [Protein] [Locus] [Mutation Spectrum] [Genomic Structure]
XPB is located on chromosome 2q21 and encodes a 782 amino acid 3'5' helicase, the p89 subunit of TFIIH. The gene is also known as ERCC3. The helicase may be involved in unwinding the DNA 5'-ward of a damaged base. The N terminus of the protein interacts with the XPD and XPG proteins whereas the C terminus is required for the 5' cleavage during excision repair [Evans et al., 1997]. The protein also interacts with the BCR-ABL oncoprotein, although its potential role in hematopoeitic malignancies is unknown [Takeda et al., 1999]. Only a small number of patients are known in this complementation group, and their clinical symptoms are extremely varied with mutations at both extremes of the gene.
|XPC [OMIM] [GenBank] [Protein] [Locus] [Mutation Spectrum] [Genomic Structure]
XPC is located on chromosome 3p25.1 and encodes a 940 amino acid single-stranded DNA binding protein that is essential for repair of the nontranscribed regions of the genome. The protein acts in the initial step of damage recognition in these regions [Sugasawa et al., 1998], but is then released from the pre-incision complex before strand incision occurs [Wakasugi and Sancar, 1998]. XPC exists in vivo in a tight complex with another protein HHR23B, which is encoded by a gene closely linked (within 650 kb) to XPC [Masutani et al., 1994]. Mutations in HHR23B are not known to be associated with any human disorder, although the mutations in the corresponding gene in yeast makes cells UV sensitive. XP-C patients are among the more common form of XP and exhibit predominantly skin cancer without neurological disorders.
|XPD (ERCC2) [OMIM] [GenBank] [Protein] [Locus] [XPD Mutations] [XP-TTD Mutations] [XP-TTD-CS Mutations] [Genomic Structure]
The XPD gene is located on chromosome 19q13.2 and encodes a 760 amino acid 5'3' helicase, a component of transcription factor TFIIH [Bootsma et al., 1998]. The gene, encoded in 23 exons, is also known as ERCC2 . The helicase may be involved in 3'-ward unwinding of the DNA in the vicinity of a damaged base and in the opposite direction to the XPB helicase. The phenotypes of mutations in this gene are among the most complex of all XP groups, being associated with three different clinical disorders: XP group D, trichothiodystrophy (TTD), or a rare combination of XP and Cockayne syndrome. Most TTD patients exhibiting UV sensitivity fall into the XP-D complementation group [Botta et al., 1998; Stefanini et al., 1993]. Since the clinical characteristics of XP and TTD are so different, mutation analysis has sought to explain how two dissimilar disorders are associated with the same gene. The result of such studies is that all mutations thus far reported appear to be specific for the disease, and only missense mutations are important for the disease, although the severity can be influenced by gene dosage [Botta et al., 1998]. As a member of the TFIIH complex, XPD is an essential protein for transcription and cell viability [de Boer et al., 1998a]. Thus, no patient can have two null alleles. The interpretation of XPD mutations is confounded by the fact that in several cases XP-D and TTD patients have an allele in common, suggesting that the second alleles determine the clinical presentation. By examining the phenotype in Schizosaccharomyces pombe of mutations homologous to those present in these shared alleles, the S. pombe mutations were shown to behave as null mutations [Taylor et al., 1997]. Therefore, by extrapolation these common alleles can conveniently be regarded as nonfunctional and playing no direct role in the specific disease. Examination of the distribution of mutations within the XPD protein reveals that essentially all XP-D mutations fall within one of the conserved helicase domains (Koonin, 1993). This pattern indicates that these mutations can be expected to reduce the proteins helicase activity [Coin et al., 1998]. In contrast, the TTD mutations usually fall outside of the helicase domains and show significant clustering at the C-terminus of the protein. TTD-specific mutations may subtly interfere with the ability of XPD to interact with its partner proteins within the TFIIH complex and thereby destabilize the complex ([Coin et al., 1998]. It has been argued that TTD mutations cause subtle deficiencies in transcription because of reduced stability of TFIIH [de Boer et al., 1998b; Hoeijmakers et al., 1996].
|XPE [Mutation Spectrum] [Genomic Structure]
DDB1 [OMIM] [GenBank] [Protein] [Locus]
DDB2 [OMIM] [GenBank] [Protein] [Locus]
The XPE complementation group includes patients who are mildly to moderately affected and whose cells carry out near normal levels of nucleotide excision repair (Itoh et al. 2000). The XPE group involves defects in a dimeric protein having subunits of 127 kDa (DDB1) and 48 kDa (DDB2) (Chu and Chang 1988; Keeney et al. 1993; Nichols et al. 2001). The DDB1 and DDB2 genes are located on chromosome 11q12-13 and 11p11-12 respectively (Dualan et al. 1995). Mutations diagnostic for XPE are located in the DDB2 subunit and cells without such mutations should be assigned to other groups after further diagnosis (Cleaver et al. 1999; Itoh and Linn 2001; Itoh et al. 2000; Nichols et al. 1996). The DDB1/2 heterodimer is thought to be involved with the recognition of damaged DNA because it has the capacity to bind to UV-damaged DNA with a chemically defined footprint (Reardon et al. 1993) and detectable by an electrophoretic mobility shift assay (EMSA) (Chu and Chang 1988). But a precise biochemical role for DDB1/2 in the pathway of excision repair has proved elusive (Thompson 1998). Reconstitution of excision repair using purified proteins showed no requirement for DDB1/2 for damage removal and repair synthesis from synthetic substrates lacking chromatin structure (Aboussekhra et al. 1995; Bessho et al. 1997; Mu et al. 1995). Excision repair in XPE cell extracts can be stimulated by single-strand binding protein RPA, but this stimulation is not specific for XPE (Kazantsev et al. 1996). Moreover, no mutations have been found in the subunits of RPA (Aboussekhra et al. 1995; Kazantsev et al. 1996; Rapic Otrin et al. 1998). These results suggest that DDB1/2 may not be directly involved in excision repair directly, although it is involved in UV-induced mutagenesis (Tang et al. 2000). DDB2 expression is induced by UV light through p53 transactivation in human, but not mouse, cells (Nichols et al. 2001; Tan and Chu 2002) which provides a partial explanation for observations that excision repair can be low in some mouse cell strains.
Since excision repair is close to normal in XPE cells, a definitive diagnosis of XPE should be done by EMSA and DNA sequencing of DDB2 to identify mutations (Cleaver et al. 1999; Itoh and Linn 2001; Itoh et al. 2000; Nichols et al. 1996).
|XPF (ERCC4) [OMIM] [GenBank] [Protein] [Locus] [Mutation Spectrum] [Genomic Structure]
XPF is located on chromosome 16p13.3 and encodes a structure-specific endonuclease of 916 amino acids, which in association with the ERCC1 protein, incises DNA on the 5' side of the damaged site [Bessho et al., 1997; Sijbers et al., 1996]. XPF is also known as ERCC4. Mutations in ERCC1 are not known to be associated with any human disorder, and knockout mice are neonatal lethals [McWhir et al., 1993]. The XP-F complementation group is rare and the majority of cases have been found in Japan.
|XPG (ERCC5) [OMIM] [GenBank] [Protein] [Locus] [Mutation Spectrum] [Genomic Structure]
XPG is located on chromosome 13q32-33 and encodes an 1186 amino acid nuclease, which incises DNA 3' to the damaged site [ODonovan et al., 1994]. The XPG protein also plays a role in transcription-coupled repair of base damage such as thymine glycols [Cooper et al., 1997]. The gene is also known as ERCC5. The XP-G complementation group is rare, and most cases are known from Europe. Patients are severely affected and often exhibit combined symptoms of XP and CS. These combined symptoms have been used to reveal a second function for XPG in repair of oxidative damage [Nouspikel et al., 1997]. Some mutations specifically affect nucleotide excision repair and not oxidative-damage repair [Cooper et al., 1997; Nouspikel et al., 1997].
|XP-Variant [OMIM] [GenBank] [Protein] [Locus] [Mutation Spectrum] [Genomic Structure]
XPV is located on chromosome 6p21 and encodes a protein of 713 amino acids (Johnson et al. 1999; Masutani et al. 1999). The protein is a low-fidelity class Y DNA polymerase, variously known as hRad30A, pol h or Pol H (Ohmori et al. 2001). The complete human genomic sequence spans about 40kb containing 10 coding exons and a cDNA of 2.14kb; exon I is untranslated and is 6kb upstream from the first coding exon. Pol H can replicate UV-induced pyrimidine dimers in vivo with the insertion of the correct bases in the daughter strand; in vitro it is very error-prone and inserts mutagenic bases at about 1% frequency (Johnson et al. 2000; Matsuda et al. 2000; Ohashi et al. 2000; Tissier et al. 2000).
|CSA (ERCC8) [OMIM] [GenBank] [Protein] [Locus] [Mutation Spectrum] [Genomic Structure]
CSA is located on chromosome 5 and encodes a 396 amino acid WD repeat protein that is involved in the coupling between transcription and repair [Henning et al., 1995]. The gene is also known as ERCC8. Cells with mutations in CSA fail to ubiquitinate RNA polymerase II after UV exposure [Bregman et al. 1996] and cannot remove and degrade the transcription complex stalled at a damaged site in DNA. CSA may participate in a CSB/RNA polII complex stalled at damaged sites in transcriptionally active DNA [Sugasawa et al., 1998].
|CSB (ERCC6) [OMIM] [GenBank] [Protein] [Locus] [Mutation Spectrum] [Genomic Structure]
CSB is located on chromosome 10q11-21 and encodes a 1493 amino acid protein with helicase motifs and is also involved in the coupling between repair and transcription. The gene is also known as ERCC6. Cells with mutations in CSB fail to ubiquitinate RNA polymerase II and cannot remove and degrade the transcription complex stalled at a damaged site in DNA [Bregman et al., 1996]. The protein has a nucleotide binding site and acts as a DNA-dependent ATPase, but despite the helicase motifs at the sequence level the protein does not appear to possess helicase activity in vitro [Citterio et al., 1998; Selby and Sancar, 1997].
Some UV-sensitive patients have provided cell lines that are UV sensitive and show normal excision repair and a failure of RNA synthesis to recover from UV damage. These have been defined as the UVs syndrome and their molecular characterization remains to be defined [Fujiwara et al., 1981]. Although the properties of these cell lines resemble those of CS cells, the patients show highly varied symptoms [Cleaver et al., 1992; Fujiwara et al., 1981]. Complementation assays and DNA sequencing have shown that some of these represent unusual manifestations of mutations in the known XP or CS genes, but others appear to genuinely different [Itoh et al., 1995; Itoh et al., 1994]. One case of TTD, TTDA, is defective in excision repair but complements all the other groups. This group may correspond to one of the members of the TFIIH transcription factor or an associated protein or a factor that regulates TFIIH levels [Vermeulen et al., 1994b;; Itin, et al., 2001].
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