Xeroderma pigmentosum (XP) patients fail to remove pyrimidine dimers caused by sunlight and, as a consequence, develop multiple cancers in areas exposed to light. The second most common sign, present in 20-30% of XP patients, is a set of neurological abnormalities caused by neuronal death in the central and peripheral nervous systems. Neural tissue is shielded from sunlight-induced DNA damage, so the cause of neurodegeneration in XP patients remains unexplained. In this study, we show that two major oxidative DNA lesions, 8-oxoguanine and thymine glycol, are excised from DNA in vitro by the same enzyme system responsible for removing pyrimidine dimers and other bulky DNA adducts. Our results suggest that XP neurological disease may be caused by defective repair of lesions that are produced in nerve cells by reactive oxygen species generated as by-products of an active oxidative metabolism.

XPF-ERCC1 and XPG proteins are nucleases that are involved in human nucleotide excision repair. In this study, we characterized the structure-specific junctioncutting activities of both nucleases using DNA substrates containing a bubble or loop structure. We found that the junction-cutting activities of XPF-ERCC1 and XPG were greatly stimulated by human replication protein A (RPA), while heterologous single-stranded DNAbinding proteins could not substitute for human RPA. To test for specific interaction between RPA and XPF-ERCC1 as is known to occur between RPA and XPG, we employed a pull-down assay with immobilized "bubble" substrate. We found that the binding of XPF-ERCC1 complex to the bubble substrate was enhanced by RPA, suggesting a possible mechanism for RPA in the excision nuclease system, that is the targeting of the nuclease subunits to their specific sites of action. Furthermore, the RPA-promoted junction cutting by XPF-ERCC1 and XPG nucleases was observed with "loop" substrates as well, raising the possibility that XPF-ERCC1, XPG, and RPA may function in removing loop structures from DNA, independent of the other subunits of the human excinuclease.Nucleotide excision repair is a general repair system that plays an important role in maintaining genetic integrity (1, 2). This repair system removes damaged nucleotides from DNA by dual incisions on both sides of the lesion in the damaged strand (3). Recently, the human and the highly homologous yeast nucleotide excision repair systems have been reconstituted from extensively purified proteins, which demonstrated that 14 -15 polypeptides comprising replication protein A (RPA, 1 also known as HSSB or RF-A) and the general transcription factor, TFIIH, in addition to XP and ERCC proteins were essential for the dual incision step (4 -6).It was found that the two subunits of the excision nuclease had intrinsic endonuclease activities in the absence of the other components of the repair system. XPG was reported to possess a single-stranded DNA endonuclease activity (7,8) and an exonuclease activity with 5Ј to 3Ј directionality (9). Similarly, it was found that XPF-ERCC1 had a single strand-specific endonuclease activity and a weak activity on double-stranded UVirradiated DNA, which was stimulated by RPA (10). Furthermore, it has been reported that the RAD1-RAD10 complex (11), the yeast counterpart of the human XPF-ERCC1 nuclease, and XPG nuclease (12) have structure-specific junction-cutting activities with unique polarities. These results obtained with the model "undamaged" substrates suggested that XPF-ERCC1 and XPG were the 5Ј-and 3Ј-endonucleases of the dual incisions, respectively. A recent study using damaged DNA and specific antibodies supported this model (13).Recently, it has been reported that RPA, which is absolutely required for dual incisions (4), specifically binds to XPA protein and XPG nuclease (14). These findings raised the possibility that RPA may play an important role in recognizing DNA lesions and then targeting the nuclease subunits of hu...

DNA interstrand cross-links are induced by many carcinogens and anticancer drugs. It was previously shown that mammalian DNA excision repair nuclease makes dual incisions 5 to the cross-linked base of a psoralen cross-link, generating a gap of 22 to 28 nucleotides adjacent to the cross-link. We wished to find the fates of the gap and the cross-link in this complex structure under conditions conducive to repair synthesis, using cell extracts from wild-type and cross-linker-sensitive mutant cell lines. We found that the extracts from both types of strains filled in the gap but were severely defective in ligating the resulting nick and incapable of removing the cross-link. The net result was a futile damage-induced DNA synthesis which converted a gap into a nick without removing the damage. In addition, in this study, we showed that the structure-specific endonuclease, the XPF-ERCC1 heterodimer, acted as a 3-to-5 exonuclease on cross-linked DNA in the presence of RPA. Collectively, these observations shed some light on the cellular processing of DNA cross-links and reveal that cross-links induce a futile DNA synthesis cycle that may constitute a signal for specific cellular responses to cross-linked DNA.Interstrand cross-links are common lesions introduced into DNA by drugs such as psoralen, cisplatin, mitomycin C, and melphalan (17). These lesions are eliminated from DNA by a mechanism involving excision repair and recombination in Escherichia coli (3,5,32) and in yeast (15,20). In mammalian cells, the precise role of excision repair in eliminating crosslinks is not known (35,36). Although mutations in any of the genes required for the dual-incision step of excision repair cause sensitivity to cross-linking chemicals, the XPF and ERCC1 mutant cell lines, in addition to being defective in excision repair, are particularly sensitive to cross-linking agents and hence have been presumed to play a special role in crosslink repair (13). Similarly, mutations in the XRCC2 and XRCC3 genes, encoding proteins with sequence homology to the human RAD51 protein (19), confer sensitivity to crosslinking agents without affecting the excision repair system and hence are thought to play a unique role in processing of crosslinks (35). To understand the mechanism of cross-link repair, it appears that the actions of the excision repair system, the XPF-ERCC1 complex, and XRCC2 and XRCC3 on crosslinks must be investigated.The human nucleotide excision repair system removes base monoadducts and intrastrand diadducts by making a dual incision bracketing the lesion (14). Recently, we reported the surprising finding that with a cross-linked substrate, the human excision nuclease makes both incisions 5Ј to the cross-linked base, excising a damage-free oligomer and generating a gap of 22 to 28 nucleotides (nt) 5Ј to either the furan-side or the pyrone-side adducted thymine of a psoralen cross-link (1). We proposed that the gap generated by this unusual type of dual incision may initiate at least one pathway of cross-link repair. In the present...

The human XPF-ERCC1 protein complex is one of several factors known to be required for general nucleotide excision repair. Genetic data indicate that both proteins of this complex are necessary for the repair of interstrand cross-links, perhaps via recombination. To determine whether XPF-ERCC1 completes a set of six proteins that are sufficient to carry out excision repair, the human XPF and ERCC1 cDNAs were coexpressed in Sf21 insect cells from a baculovirus vector. The purified complex contained the anticipated 5 junction-specific endonuclease activity that is stimulated through a direct interaction between XPF and replication protein A (RPA). The recombinant complex also complemented extracts of XP-F cells and Chinese hamster ovary mutants assigned to complementation groups 1, 4, and 11. Furthermore, reconstitution of the human excision nuclease was observed with a mixture of five repair factors (XPA, XPC, XPG, TFIIH, and RPA) and the recombinant XPF-ERCC1, thus verifying that no additional protein factors are needed for the specific dual incisions characteristic of human excision repair.Nucleotide excision repair in humans consists of dual incisions on both sides of the lesion in the damaged strand, which results in excision of 24 -32-nucleotide-long oligomers followed by repair synthesis and ligation (1-3). The enzyme system responsible for the dual incisions is referred to as excision nuclease (2). Individuals lacking excision nuclease suffer from xeroderma pigmentosum (XP), 1 a disease that is characterized by photodermatoses and in some cases by neurological abnormalities (4,5).Recently, human excision nuclease has been reconstituted from highly purified proteins including those encoded by XPA through XPG (6 -8). These reconstitutions have helped define the minimum essential set of proteins for the dual incision/ excision activity. It was found that all proteins encoded by the XP genes with the exception of the XPE gene product were required for excision. Other proteins necessary for this reaction pathway are replication protein A (RPA, consisting of three subunits), transcription factor TFIIH (composed of 5-8 subunits including XPB and XPD), and ERCC1 (which together with XPF forms a distinct complex). These studies were conducted with proteins purified mostly from human cells; therefore, a requirement for additional proteins that were present in the reconstitution fractions as "contaminants" was a realistic possibility. The need for additional unknown proteins was argued using evidence that a factor (IF7) of one or more proteins that purified through several columns with XPF-ERCC1 and finally separated from this complex by a DEAE resin was essential for incision specificity by the reconstituted human excision nuclease (8). However, a later report with proteins purified to apparent homogeneity failed to confirm the need for an additional factor (7). To clarify the discrepancy raised by these studies, we attempted to use proteins expressed and purified from heterologous systems because the presence of tr...

Most DNA repair mechanisms rely on the redundant information inherent to the duplex to remove damaged nucleotides and replace them with normal ones, using the complementary strand as a template. Interstrand cross-links pose a unique challenge to the DNA repair machinery because both strands are damaged. To study the repair of interstrand cross-links by mammalian cells, we tested the activities of cell extracts of wild-type or excision repair-defective rodent cell lines and of purified human excision nuclease on a duplex with a site-specific cross-link. We found that in contrast to monoadducts, which are removed by dual incisions bracketing the lesion, the cross-link causes dual incisions, both 5' to the cross-link in one of the two strands. The net result is the generation of a 22- to 28-nucleotide-long gap immediately 5' to the cross-link. This gap may act as a recombinogenic signal to initiate cross-link removal.