Nucleotide Excision Repair in Mammalian Cells (1997)

A versatile strategy for repairing damaged DNA, termed nucleotide excision repair (NER), 1The abbreviations used are: NER, nucleotide excision repair; XP, xeroderma pigmentosum; CS, Cockayne syndrome; nt, nucleotide(s). 1The abbreviations used are: NER, nucleotide excision repair; XP, xeroderma pigmentosum; CS, Cockayne syndrome; nt, nucleotide(s). is found throughout the natural world in organisms ranging from mycoplasma to mammals. In humans, NER is a major defense against the carcinogenic effects of ultraviolet light from the sun. This repair pathway acts with varying efficiencies on a wide variety of DNA alterations and is especially important for bulky, helix-distorting lesions. The key event in NER is incision of the damaged strand on each side of a lesion in DNA, releasing the damage in a fragment that is ∼24–32 nucleotides (nt) long in eukaryotes. Nucleotide excision repair defects of various types are found in individuals with the inherited syndromes xeroderma pigmentosum (XP), Cockayne syndrome (CS), and trichothiodystrophy (1Lehmann A.R. Trends Biochem. Sci. 1995; 20: 402-405Abstract Full Text PDF PubMed Scopus (137) Google Scholar). Individuals with XP are sun-sensitive and generally show a greatly increased incidence of UV-induced skin cancers. The disorder has seven genetic complementation groups, designated XP-A through XP-G, and a variant form, XP-V. The recommended nomenclature uses a hyphen to refer to cells of a given complementation group (for example XP-A), distinguishing this from the affected gene XPA and the normal protein product XPA (2Lehmann A.R. Bootsma D. Clarkson S.G. Cleaver J.E. McAlpine P.J. Tanaka K. Thompson L.H. Wood R.D. Mutat. Res. 1994; 315: 41-42Crossref PubMed Scopus (39) Google Scholar). This minireview focuses on the biochemistry of NER in mammalian cells, with an emphasis on recent developments. Many details of the NER reaction mechanism are being elucidated with purified proteins and reconstituted systems. At a minimum, the dual incision reaction of NER requires the factors XPA, RPA, XPC, TFIIH, XPG, and ERCC1-XPF in mammalian cells or the homologous components in yeast (3Wood R.D. Annu. Rev. Biochem. 1996; 65: 135-167Crossref PubMed Scopus (611) Google Scholar, 4Sancar A. Annu. Rev. Biochem. 1996; 65: 43-81Crossref PubMed Scopus (962) Google Scholar). These are summarized in TableI. XPA and the single-stranded binding protein RPA associate with one another and are able to preferentially bind to damaged DNA. TFIIH includes the XPB and XPD DNA helicases among its subunits (5Svejstrup J. Vichi P. Egly J.-M. Trends Biochem. Sci. 1996; 21: 346-350Abstract Full Text PDF PubMed Scopus (196) Google Scholar) and is involved in local opening of DNA around a site of damage. XPC, usually bound to a protein partner hHR23B, may also be involved in damage recognition and opening. The XPG and ERCC1-XPF factors are structure-specific DNA nucleases and are responsible for cleaving on the 3′- and 5′-sides of a lesion, respectively (Fig.1). The excised fragment is replaced in a DNA repair synthesis reaction mediated by DNA polymerase δ or ε holoenzyme (6Wood R. Shivji M. Carcinogenesis. 1997; 18: 605-610Crossref PubMed Scopus (144) Google Scholar), and the process is completed by sealing the repair patch of about 30 nt with a DNA ligase.Table IIdentified proteins participating in the dual incision reaction of mammalian NERHuman proteinNearest S. cerevisiaehomologCommentsXPARad14Preferentially binds damaged and single-stranded DNARPARpa3-subunit single-stranded DNA binding protein; binds to XPAXPCRad4Preferentially binds damaged and single-stranded DNA; not needed for transcription-coupled repair or some DNA lesionshHR23BRad23Binds to XPC and stimulates activityTFIIH XPBSsl2 (Rad25)DNA helicase (3′ to 5′); also known as ERCC3 XPDRad3DNA helicase (5′ to 3′); also known as ERCC2 p62Tfb1TFIIH subunit; also known as GTF2H1 p52Tfb2TFIIH subunit; formerly known as p41 p44Ssl1TFIIH subunit p34Tfb4TFIIH subunitXPGRad2DNA endonuclease for 3′ side of damage; also known as ERCC5ERCC1Rad10Subunit of DNA endonuclease for 5′ side of damageXPFRad1Subunit of DNA endonuclease for 5′ side of damage; also known as ERCC4 Open table in a new tab The cDNA encoding XPF was recently isolated, completing the list of cloned XP core factors (7Sijbers A.M. de Laat W.L. Ariza R.R. Biggerstaff M. Wei Y.-F. Moggs J.G. Carter K.C. Shell B.K. Evans E. de Jong M.C. Rademakers S. de Rooij J. Jaspers N.G.J. Hoeijmakers J.H.J. Wood R.D. Cell. 1996; 86: 811-822Abstract Full Text Full Text PDF PubMed Scopus (442) Google Scholar, 8Brookman K.W. Lamerdin J.E. Thelen M.P. Hwang M. Reardon J.T. Sancar A. Zhou Z.Q. Walter C.A. Parris C.N. Thompson L.H. Mol. Cell. Biol. 1996; 16: 6553-6562Crossref PubMed Scopus (108) Google Scholar). XPF forms a tight complex with the ERCC1 protein, directly homologous to the similar Rad1-Rad10 complex in the budding yeast Saccharomyces cerevisiae. Both the Rad1-Rad10 and ERCC1-XPF complexes have a structure-specific nuclease activity that cleaves near the border between single-stranded and duplex DNA when the single strand has a polarity 5′ to 3′ moving away from the border. Junctions between duplex and single-stranded DNA are cleaved with the opposite polarity by the XPG protein and itsS. cerevisiae homolog Rad2. The structure-specific cleavage properties of the NER nucleases have strongly suggested that they act on an opened, "bubble" intermediate during repair (Fig. 1 D). Evidence for the existence of such an intermediate has been provided by probing for potassium permanganate sensitivity around a lesion during repairin vitro. ATP-dependent opening of a region of approximately 25 base pairs occurs around the damaged site before dual incision (9Evans E. Fellows J. Coffer A. Wood R.D. EMBO J. 1997; 16: 625-638Crossref PubMed Scopus (204) Google Scholar). Opening does not require the nuclease activity of XPG (9Evans E. Fellows J. Coffer A. Wood R.D. EMBO J. 1997; 16: 625-638Crossref PubMed Scopus (204) Google Scholar) but is dependent on the DNA helicase activity of TFIIH. 2E. Evans and R. D. Wood, unpublished results. XPG and Rad2 are members of a family of enzymes that includes the DNase IV/FEN1 group of structure-specific nucleases which function in DNA replication (10Lieber M.R. Bioessays. 1997; 19: 233-240Crossref PubMed Scopus (396) Google Scholar). Two conserved domains in all of these nucleases are related to sequences in a group of prokaryotic exonucleases, exemplified by the 5′–3′ exonuclease domain of Escherichia coli DNA polymerase I. The solved structures of eubacterial enzymes in this family, such as bacteriophage T5 5′–3′-exo/endonuclease (11Ceska T. Sayers J. Stier G. Suck D. Nature. 1996; 382: 90-93Crossref PubMed Scopus (164) Google Scholar), show that the conserved domains are folded together in the predicted active site and coordinate the binding of two Mg2+ ions. The T5 enzyme has a helical arch with a size and ionic environment appropriate for single-stranded DNA to thread through, starting at a free end. It will be interesting to learn how DNA is bound during repair by XPG or Rad2, which must load onto sites in DNA where there is no free 5′-end. The intervening region between the conserved domains in the various nucleases in this family probably mediates specific protein-protein interactions for replication and repair. The XPG and ERCC1-XPF nucleases require Mg2+ or Mn2+ but not ATP and on some model substrates do not require other protein factors for their structure-specific cleavage activity (7Sijbers A.M. de Laat W.L. Ariza R.R. Biggerstaff M. Wei Y.-F. Moggs J.G. Carter K.C. Shell B.K. Evans E. de Jong M.C. Rademakers S. de Rooij J. Jaspers N.G.J. Hoeijmakers J.H.J. Wood R.D. Cell. 1996; 86: 811-822Abstract Full Text Full Text PDF PubMed Scopus (442) Google Scholar, 9Evans E. Fellows J. Coffer A. Wood R.D. EMBO J. 1997; 16: 625-638Crossref PubMed Scopus (204) Google Scholar). With other substrates, RPA protein can dramatically stimulate nuclease activity (12Bessho T. Sancar A. Thompson L.H. Thelen M.P. J. Biol. Chem. 1997; 272: 3833-3837Abstract Full Text Full Text PDF PubMed Scopus (161) Google Scholar). Although the 3′- and 5′-incisions are nearly simultaneous, the 3′-incision mediated by XPG is normally first (13O' Donovan A. Davies A.A. Moggs J.G. West S.C. Wood R.D. Nature. 1994; 371: 432-435Crossref PubMed Scopus (395) Google Scholar, 14Mu D. Hsu D.S. Sancar A. J. Biol. Chem. 1996; 271: 8285-8294Abstract Full Text Full Text PDF PubMed Scopus (339) Google Scholar). For some lesions, the 3′-incision can be carried out by purified core incision factors in the absence of ERCC1-XPF (14Mu D. Hsu D.S. Sancar A. J. Biol. Chem. 1996; 271: 8285-8294Abstract Full Text Full Text PDF PubMed Scopus (339) Google Scholar), although repair of a 1,3-intrastrand d(GpTpG)-cisplatin cross-link in DNA required all components to be present to form either incision (15Moggs J.G. Yarema K.J. Essigmann J.M. Wood R.D. J. Biol. Chem. 1996; 271: 7177-7186Abstract Full Text Full Text PDF PubMed Scopus (182) Google Scholar). After the 5′-incision, mediated by ERCC1-XPF nuclease (7Sijbers A.M. de Laat W.L. Ariza R.R. Biggerstaff M. Wei Y.-F. Moggs J.G. Carter K.C. Shell B.K. Evans E. de Jong M.C. Rademakers S. de Rooij J. Jaspers N.G.J. Hoeijmakers J.H.J. Wood R.D. Cell. 1996; 86: 811-822Abstract Full Text Full Text PDF PubMed Scopus (442) Google Scholar, 14Mu D. Hsu D.S. Sancar A. J. Biol. Chem. 1996; 271: 8285-8294Abstract Full Text Full Text PDF PubMed Scopus (339) Google Scholar), the damaged oligonucleotide is excised and seems to be bound to one or more components of the repair complex (14Mu D. Hsu D.S. Sancar A. J. Biol. Chem. 1996; 271: 8285-8294Abstract Full Text Full Text PDF PubMed Scopus (339) Google Scholar). In repair-proficient cell extracts some uncoupled 3′- or 5′-incisions can occur, indicating that the order of incisions is not always strict, although uncoupled 3′-incisions are more frequent than uncoupled 5′-incisions (7Sijbers A.M. de Laat W.L. Ariza R.R. Biggerstaff M. Wei Y.-F. Moggs J.G. Carter K.C. Shell B.K. Evans E. de Jong M.C. Rademakers S. de Rooij J. Jaspers N.G.J. Hoeijmakers J.H.J. Wood R.D. Cell. 1996; 86: 811-822Abstract Full Text Full Text PDF PubMed Scopus (442) Google Scholar, 14Mu D. Hsu D.S. Sancar A. J. Biol. Chem. 1996; 271: 8285-8294Abstract Full Text Full Text PDF PubMed Scopus (339) Google Scholar). The precise positions of incisions for several different lesions have been mapped in the human system. Depending on the adduct, incisions are introduced 2–9 phosphodiester bonds away from the 3′-side of a lesion and 16–25 phosphodiester bonds away from the 5′-side. A unifying feature is that the modal length of incision products is 26–27 nt in each case (15Moggs J.G. Yarema K.J. Essigmann J.M. Wood R.D. J. Biol. Chem. 1996; 271: 7177-7186Abstract Full Text Full Text PDF PubMed Scopus (182) Google Scholar). The XPC protein plays a role in NER that is just beginning to be revealed. This 106-kDa human protein copurifies with a tightly bound 43-kDa partner, hHR23B. XPC binds DNA with a preference for single-stranded (16Reardon J.T. Mu D. Sancar A. J. Biol. Chem. 1996; 271: 19451-19456Abstract Full Text Full Text PDF PubMed Scopus (105) Google Scholar, 17Sugasawa K. Masutani C. Uchida A. Maekawa T. van der Spek P.J. Bootsma D. Hoeijmakers J.H.J. Hanaoka F. Mol. Cell. Biol. 1996; 16: 4852-4861Crossref PubMed Scopus (143) Google Scholar) or damaged DNA (16Reardon J.T. Mu D. Sancar A. J. Biol. Chem. 1996; 271: 19451-19456Abstract Full Text Full Text PDF PubMed Scopus (105) Google Scholar). In some reconstituted repair systems, recombinant XPC protein alone is sufficient, and adding hHR23B does not increase repair (16Reardon J.T. Mu D. Sancar A. J. Biol. Chem. 1996; 271: 19451-19456Abstract Full Text Full Text PDF PubMed Scopus (105) Google Scholar). In other fractionated and purified systems, only weak repair occurs with XPC alone, and repair is significantly stimulated by adding hHR23B (17Sugasawa K. Masutani C. Uchida A. Maekawa T. van der Spek P.J. Bootsma D. Hoeijmakers J.H.J. Hanaoka F. Mol. Cell. Biol. 1996; 16: 4852-4861Crossref PubMed Scopus (143) Google Scholar). Intriguingly, the XPC subunit is dispensable for the repair of two different types of DNA structures in vitro, an observation that has implications for the mechanism of transcription-coupled repair in human cells. Transcription-coupled nucleotide excision repair is a specialized mode of NER that removes DNA adducts significantly faster from the transcribed strand of genes than from the non-transcribed strand or the bulk of DNA. In mammalian cells, transcription-coupled repair of pyrimidine dimers can take place in the absence of XPC (while requiring the other NER subunits including XPA and TFIIH) and is believed to be initiated when RNA polymerase is stalled at a lesion in DNA (18Hanawalt P.C. Science. 1994; 266: 1957-1958Crossref PubMed Scopus (452) Google Scholar). A particular cholesterol moiety incorporated synthetically into a DNA backbone is thought to cause an unusual degree of helix distortion, and NER of this moiety does not require XPC (14Mu D. Hsu D.S. Sancar A. J. Biol. Chem. 1996; 271: 8285-8294Abstract Full Text Full Text PDF PubMed Scopus (339) Google Scholar). Similarly, a model substrate consisting of a pyrimidine dimer flanked on the 3′-side by a 10-nt unpaired region is repaired independently of XPC, while still requiring the other NER subunits (19Mu D. Sancar A. J. Biol. Chem. 1997; 272: 7570-7573Abstract Full Text Full Text PDF PubMed Scopus (87) Google Scholar). Perhaps XPC is involved in forming or stabilizing the damage recognition-incision complex at the 3′-side of a lesion and is not needed when the DNA structure is already sufficiently altered on this side by a DNA adduct or by a stalled RNA polymerase (Fig. 1 B). An XP group that remains to be fully explained at the molecular level is XP-E. XP-E patients are generally mildly affected and show 50% or more residual repair capacity. Cells from some but not all XP-E individuals are missing an activity that binds damaged DNA, as measured in electrophoretic mobility shift experiments. This activity is associated with two polypeptides of 127 and 48 kDa. Sequence changes in the 48-kDa subunit are present in cell lines that are missing the DNA damage-binding activity (20Nichols A.F. Ong P. Linn S. J. Biol. Chem. 1996; 271: 24317-24320Abstract Full Text Full Text PDF PubMed Scopus (142) Google Scholar). This XP-E-associated complex is not required for the core NER system but may well play an accessory role. Further accessory proteins that modulate NER activity are being uncovered. A factor designated IF7 was found to be needed for appreciable repair of UV-irradiated plasmid DNA (21Aboussekhra A. Biggerstaff M. Shivji M.K.K. Vilpo J.A. Moncollin V. Podust V.N. Protić M. Hübscher U. Egly J.-M. Wood R.D. Cell. 1995; 80: 859-868Abstract Full Text PDF PubMed Scopus (750) Google Scholar) and stimulates incision at a cisplatin lesion in DNA by about 6-fold, 3J. G. Moggs and R. D. Wood, unpublished results. but a gene encoding this stimulatory protein component has not been identified. The p53 protein or some of the downstream target genes controlled by p53 may also be accessory factors for NER. A study with human fibroblasts showed that cells homozygous for p53 mutations have about 50–60% of the normal rate of excision of pyrimidine dimers from the overall genome (22Ford J.M. Hanawalt P.C. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: 8876-8880Crossref PubMed Scopus (326) Google Scholar). Although p53 can bind to some components of the NER apparatus, including TFIIH (reviewed in Ref. 23Leveillard T. Andera L. Bissonnette N. Schaeffer L. Bracco L. Egly J.M. Wasylyk B. EMBO J. 1996; 15: 1615-1624Crossref PubMed Scopus (138) Google Scholar), this binding may not have a direct effect on repair efficiency. Instead, protein products of genes that are transcriptionally regulated by p53, such as Gadd45 and p21 cip1/waf1, may enhance NER. There is good evidence that in human cells, less repair of UV damage to DNA occurs in the absence of Gadd45 or p21 cip1/waf1 induction (24McDonald E.-I. Wu G. Waldman T. El-Deiry W. Cancer Res. 1996; 56: 2250-2255PubMed Google Scholar, 25Smith M.L. Kontny H.U. Zhan Q.M. Sreenath A. O' Connor P.M. Fornace A.J. Oncogene. 1996; 13: 2255-2263PubMed Google Scholar, 26Savio M. Stivala L.A. Scovassi A.I. Bianchi L. Prosperi E. Oncogene. 1996; 13: 1591-1598PubMed Google Scholar). Post-translational modifications are also likely to regulate the activity of core factors. For example, the proper phosphorylation state of one or more components is necessary to observe significant NER in a cell-free system (27Ariza R.R. Keyse S.M. Moggs J.G. Wood R.D. Nucleic Acids Res. 1996; 24: 433-440Crossref PubMed Google Scholar). NER in eukaryotes might work either by sequential assembly of individual factors or by the action of a preformed "repairosome" or by the interaction of intermediate subassemblies. Many interactions that would be consistent with any of these possibilities have been documented between NER proteins. An extreme view is that all the required repair factors can preassemble in the cell, and evidence has been provided for such assemblies in yeast (28Svejstrup J.Q. Wang Z. Feaver W.J. Wu X. Bushnell D.A. Donahue T.F. Friedberg E.C. Kornberg R.D. Cell. 1995; 80: 21-28Abstract Full Text PDF PubMed Scopus (239) Google Scholar) and mammalian cells (29He Z.G. Ingles C.J. Nucleic Acids Res. 1997; 25: 1136-1141Crossref PubMed Scopus (25) Google Scholar). An intermediate hypothesis is that several subassemblies (for example Rad1-Rad10-Rad14 and TFIIH-Rad2 in yeast) exist in the cell, which are then sequentially recruited to a repair site (30Habraken Y. Sung P. Prakash S. Prakash L. Proc. Natl. Acad. Sci. U. S. A. 1996; 93: 10718-10722Crossref PubMed Scopus (45) Google Scholar). The details of observed interactions vary and depend on the exact purification and analysis procedures. In particular, moderate salt conditions disrupt some interactions that may be significant. A line of study that could help clarify this subject is a systematic and quantitative measurement of the binding constants between different NER proteins. The densely packed chromosome structure in the nucleus introduces an additional level of complexity, in that chromatin disassembly and reassembly need to be coupled with DNA repair. A recent study analyzed nucleotide excision repair of DNA in a cell-free system capable of chromatin assembly (31Gaillard P.H.L. Martini E.M.D. Kaufman P.D. Stillman B. Moustacchi E. Almouzni G. Cell. 1996; 86: 887-896Abstract Full Text Full Text PDF PubMed Scopus (272) Google Scholar). Chromatin formation occurred concomitantly with repair DNA synthesis and required the chromatin assembly factor CAF-1. Yeast lacking CAF-1 are viable but UV-sensitive (32Kaufman P.D. Kobayashi R. Stillman B. Genes 1997; PubMed Scopus Google Scholar). DNA replication and NER might be preferentially at a of in the the XPG protein was observed to in the nucleus UV of cells, that NER may at specific sites J.A. Proc. Natl. Acad. Sci. U. S. A. 1996; 93: PubMed Scopus Google Scholar). Cockayne syndrome is an disorder of particular XP individuals with are also sun-sensitive but show a of and is by mutations in or The also occurs with XP in patients to XP and G. of can be by particular mutations in at genes (1Lehmann A.R. Trends Biochem. Sci. 1995; 20: 402-405Abstract Full Text PDF PubMed Scopus (137) Google Scholar). 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Science. 1997; PubMed Scopus Google Scholar). lesions in DNA by active such as are subject to from the transcribed strand of active pyrimidine dimer this repair of damage is of XPA, and the nuclease function of XPG but on and The repair in cells with mutations T. Clarkson S.G. Science. 1997; PubMed Scopus Google Scholar). This that XPG may have a function in to its role in NER, the transcription-coupled repair of some forms of damage. It for example, with a complex at a and base excision repair at such a It has been suggested that some lesions in DNA and are not well by normal NER but may only be with by a and repair The and proteins might also help RNA polymerase to damaged sites on a repair or play a role in releasing complexes at damage A.J. van der E. Hoeijmakers J.H.J. EMBO J. 1997; 16: PubMed Scopus (105) Google Scholar, A. R. van A.A. Mol. Cell. Biol. 1996; 16: PubMed Scopus (87) Google Scholar). lesions (for example, types of with these adducts could components on the DNA and in cells A.J. van der E. Hoeijmakers J.H.J. EMBO J. 1997; 16: PubMed Scopus (105) Google Scholar). This might help for the and of human do the and proteins function in transcription-coupled is that they are an interaction between a stalled RNA polymerase and the repair proteins and to DNA repair to a damaged site on a transcribed a mechanism to during transcription-coupled repair of pyrimidine dimers in E. where the protein acts as a factor that the interaction of RNA polymerase with the NER factor Sancar A. J. Biol. Chem. 1995; Full Text Full Text PDF PubMed Scopus Google Scholar). An that the proteins do directly or with RNA polymerase is the observation that UV light of the subunit of human RNA polymerase by and that this is in and cells R. van A.J. Friedberg E.C. Proc. Natl. Acad. Sci. U. S. A. 1996; 93: PubMed Scopus Google Scholar). It is not known the activity or the to repair damaged and unpaired can during DNA human cells a of of the E. coli repair proteins and to and of P. R. Annu. Rev. Biochem. 1996; 65: PubMed Scopus Google Scholar). of the DNA repair and found to transcription-coupled NER of the in E. I. Proc. Natl. Acad. Sci. U. S. A. 1996; 93: PubMed Scopus Google Scholar), and human cells with mutations in particular repair genes found to have a in transcription-coupled repair of UV-induced pyrimidine dimers I. M. Science. 1996; 272: PubMed Scopus Google Scholar). S. in the homologous repair genes are in transcription-coupled repair of UV-induced DNA damage J. Hanawalt P.C. 1996; PubMed Google Scholar). The mechanism of any of repair proteins on NER is but has been observed that the binding protein and a complex of and can bind to DNA base damage to some This has been for pyrimidine dimers and for a cross-link J.T. Reardon J.T. Sancar A. P. Proc. Natl. Acad. Sci. U. S. A. 1996; 93: PubMed Scopus Google Scholar, J.A. S. R. Essigmann J.M. Chem. Biol. 1996; Full Text PDF PubMed Scopus Google Scholar). The binding of can be when the adducts are to D. M. J.T. P. Sancar A. Mol. Cell. Biol. 1997; PubMed Scopus Google Scholar, M. O' E. R. P. Nucleic Acids Res. 1997; 25: PubMed Scopus Google Scholar). in have to any appreciable effect of such binding on NER. Nucleotide excision repair is in more when an adduct has in the opposite but this to repair NER of such adducts occurs well with extracts from cells either or in D. M. J.T. P. Sancar A. Mol. Cell. Biol. 1997; PubMed Scopus Google Scholar, J.G. M. P. Wood R.D. Nucleic Acids Res. 1997; 25: PubMed Scopus Google Scholar). Similarly, of purified to in NER does not or enhance NER D. M. J.T. P. Sancar A. Mol. Cell. Biol. 1997; PubMed Scopus Google Scholar). Further of transcription-coupled repair defects in cells is required to a in mammalian cells. of interactions between repair proteins and NER proteins be in this the members of and and van for and provided in the